R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] BiocManager_1.30.4 loaded via a namespace (and not attached): [1] compiler_3.6.1 tools_3.6.1 CAGEr_1.27.0.tar.gz ./CAGEr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CAGEr.Rcheck’ ./CAGEr.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./CAGEr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CAGEr.Rcheck/00check.log:* using session charset: UTF-8 ./CAGEr.Rcheck/00check.log:* checking for file ‘CAGEr/DESCRIPTION’ ... OK ./CAGEr.Rcheck/00check.log:* this is package ‘CAGEr’ version ‘1.27.0’ ./CAGEr.Rcheck/00check.log:* package encoding: UTF-8 ./CAGEr.Rcheck/00check.log:* checking package namespace information ... OK ./CAGEr.Rcheck/00check.log:* checking package dependencies ... OK ./CAGEr.Rcheck/00check.log:* checking if this is a source package ... OK ./CAGEr.Rcheck/00check.log:* checking if there is a namespace ... OK ./CAGEr.Rcheck/00check.log:* checking for executable files ... OK ./CAGEr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./CAGEr.Rcheck/00check.log:* checking for portable file names ... OK ./CAGEr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CAGEr.Rcheck/00check.log:* checking whether package ‘CAGEr’ can be installed ... OK ./CAGEr.Rcheck/00check.log:* checking installed package size ... NOTE ./CAGEr.Rcheck/00check.log: installed size is 7.1Mb ./CAGEr.Rcheck/00check.log: sub-directories of 1Mb or more: ./CAGEr.Rcheck/00check.log: R 1.5Mb ./CAGEr.Rcheck/00check.log: doc 3.8Mb ./CAGEr.Rcheck/00check.log:* checking package directory ... OK ./CAGEr.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CAGEr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./CAGEr.Rcheck/00check.log:* checking top-level files ... OK ./CAGEr.Rcheck/00check.log:* checking for left-over files ... OK ./CAGEr.Rcheck/00check.log:* checking index information ... OK ./CAGEr.Rcheck/00check.log:* checking package subdirectories ... OK ./CAGEr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CAGEr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CAGEr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CAGEr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CAGEr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CAGEr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CAGEr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CAGEr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CAGEr.Rcheck/00check.log:* checking dependencies in R code ... OK ./CAGEr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CAGEr.Rcheck/00check.log:* checking replacement functions ... OK ./CAGEr.Rcheck/00check.log:* checking foreign function calls ... OK ./CAGEr.Rcheck/00check.log:* checking R code for possible problems ... OK ./CAGEr.Rcheck/00check.log:* checking Rd files ... OK ./CAGEr.Rcheck/00check.log:* checking Rd metadata ... OK ./CAGEr.Rcheck/00check.log:* checking Rd cross-references ... OK ./CAGEr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./CAGEr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CAGEr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./CAGEr.Rcheck/00check.log:* checking Rd contents ... OK ./CAGEr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CAGEr.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./CAGEr.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./CAGEr.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./CAGEr.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./CAGEr.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CAGEr.Rcheck/00check.log:* checking examples ... ERROR ./CAGEr.Rcheck/00check.log:Running examples in ‘CAGEr-Ex.R’ failed ./CAGEr.Rcheck/00check.log:The error most likely occurred in: ./CAGEr.Rcheck/00check.log:> ### Name: CAGEexp-class ./CAGEr.Rcheck/00check.log:> ### Title: CAGEr class to hold all data and metadata about one CAGE ./CAGEr.Rcheck/00check.log:> ### experiment. ./CAGEr.Rcheck/00check.log:> ### Aliases: CAGEexp-class CAGEexp coerce,data.frame,CAGEexp-method ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> ### ** Examples ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> library("MultiAssayExperiment") ./CAGEr.Rcheck/00check.log:Loading required package: SummarizedExperiment ./CAGEr.Rcheck/00check.log:Loading required package: GenomicRanges ./CAGEr.Rcheck/00check.log:Loading required package: stats4 ./CAGEr.Rcheck/00check.log:Loading required package: BiocGenerics ./CAGEr.Rcheck/00check.log:Loading required package: parallel ./CAGEr.Rcheck/00check.log:Attaching package: ‘BiocGenerics’ ./CAGEr.Rcheck/00check.log:The following objects are masked from ‘package:parallel’: ./CAGEr.Rcheck/00check.log: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, ./CAGEr.Rcheck/00check.log: clusterExport, clusterMap, parApply, parCapply, parLapply, ./CAGEr.Rcheck/00check.log: parLapplyLB, parRapply, parSapply, parSapplyLB ./CAGEr.Rcheck/00check.log:The following objects are masked from ‘package:stats’: ./CAGEr.Rcheck/00check.log: IQR, mad, sd, var, xtabs ./CAGEr.Rcheck/00check.log:The following objects are masked from ‘package:base’: ./CAGEr.Rcheck/00check.log: Filter, Find, Map, Position, Reduce, anyDuplicated, append, ./CAGEr.Rcheck/00check.log: as.data.frame, basename, cbind, colnames, dirname, do.call, ./CAGEr.Rcheck/00check.log: duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, ./CAGEr.Rcheck/00check.log: lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, ./CAGEr.Rcheck/00check.log: pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, ./CAGEr.Rcheck/00check.log: tapply, union, unique, unsplit, which, which.max, which.min ./CAGEr.Rcheck/00check.log:Loading required package: S4Vectors ./CAGEr.Rcheck/00check.log:Attaching package: ‘S4Vectors’ ./CAGEr.Rcheck/00check.log:The following object is masked from ‘package:base’: ./CAGEr.Rcheck/00check.log: expand.grid ./CAGEr.Rcheck/00check.log:Loading required package: IRanges ./CAGEr.Rcheck/00check.log:Loading required package: GenomeInfoDb ./CAGEr.Rcheck/00check.log:Loading required package: Biobase ./CAGEr.Rcheck/00check.log:Welcome to Bioconductor ./CAGEr.Rcheck/00check.log: Vignettes contain introductory material; view with ./CAGEr.Rcheck/00check.log: 'browseVignettes()'. To cite Bioconductor, see ./CAGEr.Rcheck/00check.log: 'citation("Biobase")', and for packages 'citation("pkgname")'. ./CAGEr.Rcheck/00check.log:Loading required package: DelayedArray ./CAGEr.Rcheck/00check.log:Loading required package: matrixStats ./CAGEr.Rcheck/00check.log:Attaching package: ‘matrixStats’ ./CAGEr.Rcheck/00check.log:The following objects are masked from ‘package:Biobase’: ./CAGEr.Rcheck/00check.log: anyMissing, rowMedians ./CAGEr.Rcheck/00check.log:Loading required package: BiocParallel ./CAGEr.Rcheck/00check.log:Attaching package: ‘DelayedArray’ ./CAGEr.Rcheck/00check.log:The following objects are masked from ‘package:matrixStats’: ./CAGEr.Rcheck/00check.log: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges ./CAGEr.Rcheck/00check.log:The following objects are masked from ‘package:base’: ./CAGEr.Rcheck/00check.log: aperm, apply, rowsum ./CAGEr.Rcheck/00check.log:> library("SummarizedExperiment") ./CAGEr.Rcheck/00check.log:> pathsToInputFiles <- list.files( system.file("extdata", package = "CAGEr") ./CAGEr.Rcheck/00check.log:+ , "ctss$" ./CAGEr.Rcheck/00check.log:+ , full.names = TRUE) ./CAGEr.Rcheck/00check.log:> sampleLabels <- sub( ".chr17.ctss", "", basename(pathsToInputFiles)) ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> # The CAGEexp object can be created using specific constructor commands ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> exampleCAGEexp <- ./CAGEr.Rcheck/00check.log:+ CAGEexp( genomeName = "BSgenome.Drerio.UCSC.danRer7" ./CAGEr.Rcheck/00check.log:+ , inputFiles = pathsToInputFiles ./CAGEr.Rcheck/00check.log:+ , inputFilesType = "ctss" ./CAGEr.Rcheck/00check.log:+ , sampleLabels = sub( ".chr17.ctss", "", basename(pathsToInputFiles))) ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> # Alternatively, it can be created just like another MultiAssayExperiment. ./CAGEr.Rcheck/00check.log:> # This is useful when providing pre-existing colData with many columns. ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> exampleCAGEexp <- ./CAGEr.Rcheck/00check.log:+ CAGEexp( metadata = list(genomeName = "BSgenome.Drerio.UCSC.danRer7") ./CAGEr.Rcheck/00check.log:+ , colData = DataFrame( inputFiles = pathsToInputFiles ./CAGEr.Rcheck/00check.log:+ , sampleLabels = sampleLabels ./CAGEr.Rcheck/00check.log:+ , inputFilesType = "ctss" ./CAGEr.Rcheck/00check.log:+ , row.names = sampleLabels)) ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> # Expression data is loaded by the getCTSS() function, that also calculates ./CAGEr.Rcheck/00check.log:> # library sizes and store them in the object's column data. ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> getCTSS(exampleCAGEexp) ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.30p.dome.chr17.ctss... ./CAGEr.Rcheck/00check.log:Loading required namespace: BSgenome.Drerio.UCSC.danRer7 ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.high.chr17.ctss... ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.prim6.rep1.chr17.ctss... ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.prim6.rep2.chr17.ctss... ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.unfertilized.egg.chr17.ctss... ./CAGEr.Rcheck/00check.log:Error in initialize(value, ...) : ./CAGEr.Rcheck/00check.log: 'initialize' method returned an object of class “StitchedGPos” instead of the required class “CTSS” ./CAGEr.Rcheck/00check.log:Calls: getCTSS -> getCTSS -> .CTSS -> new -> initialize ./CAGEr.Rcheck/00check.log:Execution halted ./CAGEr.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CAGEr.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CAGEr.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./CAGEr.Rcheck/00check.log: ‘CAGE_Resources.Rmd’using ‘UTF-8’... OK ./CAGEr.Rcheck/00check.log: ‘CAGEexp.Rmd’using ‘UTF-8’... OK ./CAGEr.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./CAGEr.Rcheck/00check.log:Error(s) in re-building vignettes: ./CAGEr.Rcheck/00check.log:--- re-building ‘CAGE_Resources.Rmd’ using rmarkdown ./CAGEr.Rcheck/00check.log:--- finished re-building ‘CAGE_Resources.Rmd’ ./CAGEr.Rcheck/00check.log:--- re-building ‘CAGEexp.Rmd’ using rmarkdown ./CAGEr.Rcheck/00check.log:Loading required package: SummarizedExperiment ./CAGEr.Rcheck/00check.log:Loading required package: GenomicRanges ./CAGEr.Rcheck/00check.log:Loading required package: stats4 ./CAGEr.Rcheck/00check.log:Loading required package: BiocGenerics ./CAGEr.Rcheck/00check.log:Loading required package: parallel ./CAGEr.Rcheck/00check.log:Attaching package: 'BiocGenerics' ./CAGEr.Rcheck/00check.log:The following objects are masked from 'package:parallel': ./CAGEr.Rcheck/00check.log: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, ./CAGEr.Rcheck/00check.log: clusterExport, clusterMap, parApply, parCapply, parLapply, ./CAGEr.Rcheck/00check.log: parLapplyLB, parRapply, parSapply, parSapplyLB ./CAGEr.Rcheck/00check.log:The following objects are masked from 'package:stats': ./CAGEr.Rcheck/00check.log: IQR, mad, sd, var, xtabs ./CAGEr.Rcheck/00check.log:The following objects are masked from 'package:base': ./CAGEr.Rcheck/00check.log: Filter, Find, Map, Position, Reduce, anyDuplicated, append, ./CAGEr.Rcheck/00check.log: as.data.frame, basename, cbind, colnames, dirname, do.call, ./CAGEr.Rcheck/00check.log: duplicated, eval, evalq, get, grep, grepl, intersect, ./CAGEr.Rcheck/00check.log: is.unsorted, lapply, mapply, match, mget, order, paste, pmax, ./CAGEr.Rcheck/00check.log: pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, ./CAGEr.Rcheck/00check.log: setdiff, sort, table, tapply, union, unique, unsplit, which, ./CAGEr.Rcheck/00check.log: which.max, which.min ./CAGEr.Rcheck/00check.log:Loading required package: S4Vectors ./CAGEr.Rcheck/00check.log:Attaching package: 'S4Vectors' ./CAGEr.Rcheck/00check.log:The following object is masked from 'package:base': ./CAGEr.Rcheck/00check.log: expand.grid ./CAGEr.Rcheck/00check.log:Loading required package: IRanges ./CAGEr.Rcheck/00check.log:Loading required package: GenomeInfoDb ./CAGEr.Rcheck/00check.log:Loading required package: Biobase ./CAGEr.Rcheck/00check.log:Welcome to Bioconductor ./CAGEr.Rcheck/00check.log: Vignettes contain introductory material; view with ./CAGEr.Rcheck/00check.log: 'browseVignettes()'. To cite Bioconductor, see ./CAGEr.Rcheck/00check.log: 'citation("Biobase")', and for packages 'citation("pkgname")'. ./CAGEr.Rcheck/00check.log:Loading required package: DelayedArray ./CAGEr.Rcheck/00check.log:Loading required package: matrixStats ./CAGEr.Rcheck/00check.log:Attaching package: 'matrixStats' ./CAGEr.Rcheck/00check.log:The following objects are masked from 'package:Biobase': ./CAGEr.Rcheck/00check.log: anyMissing, rowMedians ./CAGEr.Rcheck/00check.log:Loading required package: BiocParallel ./CAGEr.Rcheck/00check.log:Attaching package: 'DelayedArray' ./CAGEr.Rcheck/00check.log:The following objects are masked from 'package:matrixStats': ./CAGEr.Rcheck/00check.log: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges ./CAGEr.Rcheck/00check.log:The following objects are masked from 'package:base': ./CAGEr.Rcheck/00check.log: aperm, apply, rowsum ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.30p.dome.chr17.ctss... ./CAGEr.Rcheck/00check.log:Loading required namespace: BSgenome.Drerio.UCSC.danRer7 ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.high.chr17.ctss... ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.prim6.rep1.chr17.ctss... ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.prim6.rep2.chr17.ctss... ./CAGEr.Rcheck/00check.log:Reading in file: /home/mdowle/build/revdeplib/CAGEr.Rcheck/CAGEr/extdata/Zf.unfertilized.egg.chr17.ctss... ./CAGEr.Rcheck/00check.log:Quitting from lines 240-242 (CAGEexp.Rmd) ./CAGEr.Rcheck/00check.log:Error: processing vignette 'CAGEexp.Rmd' failed with diagnostics: ./CAGEr.Rcheck/00check.log:'initialize' method returned an object of class "StitchedGPos" instead of the required class "CTSS" ./CAGEr.Rcheck/00check.log:--- failed re-building ‘CAGEexp.Rmd’ ./CAGEr.Rcheck/00check.log:SUMMARY: processing the following file failed: ./CAGEr.Rcheck/00check.log: ‘CAGEexp.Rmd’ ./CAGEr.Rcheck/00check.log:Error: Vignette re-building failed. ./CAGEr.Rcheck/00check.log:Execution halted ./CAGEr.Rcheck/00check.log:* checking PDF version of manual ... OK ./CAGEr.Rcheck/00check.log:* DONE ./CAGEr.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 1 NOTE cellbaseR_1.9.0.tar.gz ./cellbaseR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/cellbaseR.Rcheck’ ./cellbaseR.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./cellbaseR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./cellbaseR.Rcheck/00check.log:* using session charset: UTF-8 ./cellbaseR.Rcheck/00check.log:* checking for file ‘cellbaseR/DESCRIPTION’ ... OK ./cellbaseR.Rcheck/00check.log:* checking extension type ... Package ./cellbaseR.Rcheck/00check.log:* this is package ‘cellbaseR’ version ‘1.9.0’ ./cellbaseR.Rcheck/00check.log:* checking package namespace information ... OK ./cellbaseR.Rcheck/00check.log:* checking package dependencies ... OK ./cellbaseR.Rcheck/00check.log:* checking if this is a source package ... OK ./cellbaseR.Rcheck/00check.log:* checking if there is a namespace ... OK ./cellbaseR.Rcheck/00check.log:* checking for executable files ... OK ./cellbaseR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./cellbaseR.Rcheck/00check.log:* checking for portable file names ... OK ./cellbaseR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./cellbaseR.Rcheck/00check.log:* checking whether package ‘cellbaseR’ can be installed ... OK ./cellbaseR.Rcheck/00check.log:* checking installed package size ... OK ./cellbaseR.Rcheck/00check.log:* checking package directory ... OK ./cellbaseR.Rcheck/00check.log:* checking ‘build’ directory ... OK ./cellbaseR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./cellbaseR.Rcheck/00check.log:* checking top-level files ... OK ./cellbaseR.Rcheck/00check.log:* checking for left-over files ... OK ./cellbaseR.Rcheck/00check.log:* checking index information ... OK ./cellbaseR.Rcheck/00check.log:* checking package subdirectories ... OK ./cellbaseR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./cellbaseR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./cellbaseR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./cellbaseR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./cellbaseR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./cellbaseR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./cellbaseR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./cellbaseR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./cellbaseR.Rcheck/00check.log:* checking dependencies in R code ... OK ./cellbaseR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./cellbaseR.Rcheck/00check.log:* checking replacement functions ... OK ./cellbaseR.Rcheck/00check.log:* checking foreign function calls ... OK ./cellbaseR.Rcheck/00check.log:* checking R code for possible problems ... OK ./cellbaseR.Rcheck/00check.log:* checking Rd files ... OK ./cellbaseR.Rcheck/00check.log:* checking Rd metadata ... OK ./cellbaseR.Rcheck/00check.log:* checking Rd cross-references ... OK ./cellbaseR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./cellbaseR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./cellbaseR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./cellbaseR.Rcheck/00check.log:* checking Rd contents ... OK ./cellbaseR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./cellbaseR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./cellbaseR.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./cellbaseR.Rcheck/00check.log:* checking examples ... ERROR ./cellbaseR.Rcheck/00check.log:Running examples in ‘cellbaseR-Ex.R’ failed ./cellbaseR.Rcheck/00check.log:The error most likely occurred in: ./cellbaseR.Rcheck/00check.log:> ### Name: createGeneModel ./cellbaseR.Rcheck/00check.log:> ### Title: createGeneModel ./cellbaseR.Rcheck/00check.log:> ### Aliases: createGeneModel ./cellbaseR.Rcheck/00check.log:> ./cellbaseR.Rcheck/00check.log:> ### ** Examples ./cellbaseR.Rcheck/00check.log:> ./cellbaseR.Rcheck/00check.log:> cb <- CellBaseR() ./cellbaseR.Rcheck/00check.log:> test <- createGeneModel(object = cb, region = "17:1500000-1550000") ./cellbaseR.Rcheck/00check.log:Error in `[.tbl_df`(hope, , c("gene", "symbol", "transcript", "exons"), : ./cellbaseR.Rcheck/00check.log: unused argument (with = FALSE) ./cellbaseR.Rcheck/00check.log:Calls: createGeneModel -> [ ./cellbaseR.Rcheck/00check.log:Execution halted ./cellbaseR.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./cellbaseR.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./cellbaseR.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./cellbaseR.Rcheck/00check.log: ‘cellbaseR.Rmd’using ‘UTF-8’... OK ./cellbaseR.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./cellbaseR.Rcheck/00check.log:Error(s) in re-building vignettes: ./cellbaseR.Rcheck/00check.log: ... ./cellbaseR.Rcheck/00check.log:--- re-building ‘cellbaseR.Rmd’ using rmarkdown ./cellbaseR.Rcheck/00check.log:Quitting from lines 136-144 (cellbaseR.Rmd) ./cellbaseR.Rcheck/00check.log:Error: processing vignette 'cellbaseR.Rmd' failed with diagnostics: ./cellbaseR.Rcheck/00check.log:unused argument (with = FALSE) ./cellbaseR.Rcheck/00check.log:--- failed re-building ‘cellbaseR.Rmd’ ./cellbaseR.Rcheck/00check.log:SUMMARY: processing the following file failed: ./cellbaseR.Rcheck/00check.log: ‘cellbaseR.Rmd’ ./cellbaseR.Rcheck/00check.log:Error: Vignette re-building failed. ./cellbaseR.Rcheck/00check.log:Execution halted ./cellbaseR.Rcheck/00check.log:* checking PDF version of manual ... OK ./cellbaseR.Rcheck/00check.log:* DONE ./cellbaseR.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING ENCODExplorerData_0.99.1.tar.gz ./ENCODExplorerData.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ENCODExplorerData.Rcheck’ ./ENCODExplorerData.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./ENCODExplorerData.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ENCODExplorerData.Rcheck/00check.log:* using session charset: UTF-8 ./ENCODExplorerData.Rcheck/00check.log:* checking for file ‘ENCODExplorerData/DESCRIPTION’ ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking extension type ... Package ./ENCODExplorerData.Rcheck/00check.log:* this is package ‘ENCODExplorerData’ version ‘0.99.1’ ./ENCODExplorerData.Rcheck/00check.log:* checking package namespace information ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking package dependencies ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking if this is a source package ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking if there is a namespace ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for executable files ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for hidden files and directories ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for portable file names ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking whether package ‘ENCODExplorerData’ can be installed ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking installed package size ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking package directory ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking ‘build’ directory ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking top-level files ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for left-over files ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking index information ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking package subdirectories ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking dependencies in R code ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking replacement functions ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking foreign function calls ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking R code for possible problems ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking Rd files ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking Rd metadata ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking Rd cross-references ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for missing documentation entries ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking Rd \usage sections ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking Rd contents ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking include directives in Makefiles ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking examples ... ERROR ./ENCODExplorerData.Rcheck/00check.log:Running examples in ‘ENCODExplorerData-Ex.R’ failed ./ENCODExplorerData.Rcheck/00check.log:The error most likely occurred in: ./ENCODExplorerData.Rcheck/00check.log:> ### Name: get_schemas ./ENCODExplorerData.Rcheck/00check.log:> ### Title: Extract the schemas from ENCODE's github ./ENCODExplorerData.Rcheck/00check.log:> ### Aliases: get_schemas ./ENCODExplorerData.Rcheck/00check.log:> ./ENCODExplorerData.Rcheck/00check.log:> ### ** Examples ./ENCODExplorerData.Rcheck/00check.log:> ./ENCODExplorerData.Rcheck/00check.log:> ENCODExplorerData:::get_schemas() ./ENCODExplorerData.Rcheck/00check.log:Error in open.connection(con, "rb") : HTTP error 404. ./ENCODExplorerData.Rcheck/00check.log:Calls: ./ENCODExplorerData.Rcheck/00check.log:Execution halted ./ENCODExplorerData.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking tests ... OK ./ENCODExplorerData.Rcheck/00check.log: Running ‘runTests.R’ ./ENCODExplorerData.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./ENCODExplorerData.Rcheck/00check.log: ‘DataUpdate.Rmd’using ‘UTF-8’... OK ./ENCODExplorerData.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./ENCODExplorerData.Rcheck/00check.log:* checking PDF version of manual ... OK ./ENCODExplorerData.Rcheck/00check.log:* DONE ./ENCODExplorerData.Rcheck/00check.log:Status: 1 ERROR GENESIS_2.15.5.tar.gz ./GENESIS.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/GENESIS.Rcheck’ ./GENESIS.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./GENESIS.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./GENESIS.Rcheck/00check.log:* using session charset: UTF-8 ./GENESIS.Rcheck/00check.log:* checking for file ‘GENESIS/DESCRIPTION’ ... OK ./GENESIS.Rcheck/00check.log:* checking extension type ... Package ./GENESIS.Rcheck/00check.log:* this is package ‘GENESIS’ version ‘2.15.5’ ./GENESIS.Rcheck/00check.log:* checking package namespace information ... OK ./GENESIS.Rcheck/00check.log:* checking package dependencies ... OK ./GENESIS.Rcheck/00check.log:* checking if this is a source package ... OK ./GENESIS.Rcheck/00check.log:* checking if there is a namespace ... OK ./GENESIS.Rcheck/00check.log:* checking for executable files ... OK ./GENESIS.Rcheck/00check.log:* checking for hidden files and directories ... OK ./GENESIS.Rcheck/00check.log:* checking for portable file names ... OK ./GENESIS.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./GENESIS.Rcheck/00check.log:* checking whether package ‘GENESIS’ can be installed ... OK ./GENESIS.Rcheck/00check.log:* checking installed package size ... NOTE ./GENESIS.Rcheck/00check.log: installed size is 6.9Mb ./GENESIS.Rcheck/00check.log: sub-directories of 1Mb or more: ./GENESIS.Rcheck/00check.log: doc 3.2Mb ./GENESIS.Rcheck/00check.log: extdata 3.1Mb ./GENESIS.Rcheck/00check.log:* checking package directory ... OK ./GENESIS.Rcheck/00check.log:* checking ‘build’ directory ... OK ./GENESIS.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./GENESIS.Rcheck/00check.log:* checking top-level files ... OK ./GENESIS.Rcheck/00check.log:* checking for left-over files ... OK ./GENESIS.Rcheck/00check.log:* checking index information ... OK ./GENESIS.Rcheck/00check.log:* checking package subdirectories ... OK ./GENESIS.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./GENESIS.Rcheck/00check.log:* checking R files for syntax errors ... OK ./GENESIS.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./GENESIS.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./GENESIS.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./GENESIS.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./GENESIS.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./GENESIS.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./GENESIS.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./GENESIS.Rcheck/00check.log:Unexported object imported by a ':::' call: ‘survey:::saddle’ ./GENESIS.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./GENESIS.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./GENESIS.Rcheck/00check.log:* checking replacement functions ... OK ./GENESIS.Rcheck/00check.log:* checking foreign function calls ... OK ./GENESIS.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./GENESIS.Rcheck/00check.log:.pcrelate: no visible binding for global variable ‘k’ ./GENESIS.Rcheck/00check.log:calcISAFBeta: no visible binding for global variable ‘k’ ./GENESIS.Rcheck/00check.log:pcrelateSampBlock: no visible binding for global variable ‘k’ ./GENESIS.Rcheck/00check.log:Undefined global functions or variables: ./GENESIS.Rcheck/00check.log: k ./GENESIS.Rcheck/00check.log:* checking Rd files ... OK ./GENESIS.Rcheck/00check.log:* checking Rd metadata ... OK ./GENESIS.Rcheck/00check.log:* checking Rd cross-references ... OK ./GENESIS.Rcheck/00check.log:* checking for missing documentation entries ... OK ./GENESIS.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./GENESIS.Rcheck/00check.log:* checking Rd \usage sections ... OK ./GENESIS.Rcheck/00check.log:* checking Rd contents ... OK ./GENESIS.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./GENESIS.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./GENESIS.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./GENESIS.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./GENESIS.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./GENESIS.Rcheck/00check.log:* checking compiled code ... OK ./GENESIS.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./GENESIS.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./GENESIS.Rcheck/00check.log:* checking examples ... OK ./GENESIS.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./GENESIS.Rcheck/00check.log:* checking tests ... ERROR ./GENESIS.Rcheck/00check.log: Running ‘testthat.R’ ./GENESIS.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./GENESIS.Rcheck/00check.log:Complete output: ./GENESIS.Rcheck/00check.log: > library(testthat) ./GENESIS.Rcheck/00check.log: > library(GENESIS) ./GENESIS.Rcheck/00check.log: > ./GENESIS.Rcheck/00check.log: > test_check("GENESIS") ./GENESIS.Rcheck/00check.log: ── 1. Failure: logistic (@test_null_model_logistic_regression.R#15) ─────────── ./GENESIS.Rcheck/00check.log: all(nullmod$fixef == summary(glm.mod)$coef) isn't true. ./GENESIS.Rcheck/00check.log: ./GENESIS.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./GENESIS.Rcheck/00check.log: [ OK: 418 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ] ./GENESIS.Rcheck/00check.log: 1. Failure: logistic (@test_null_model_logistic_regression.R#15) ./GENESIS.Rcheck/00check.log: ./GENESIS.Rcheck/00check.log: Error: testthat unit tests failed ./GENESIS.Rcheck/00check.log: Execution halted ./GENESIS.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./GENESIS.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./GENESIS.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./GENESIS.Rcheck/00check.log: ‘assoc_test.Rmd’using ‘UTF-8’... OK ./GENESIS.Rcheck/00check.log: ‘assoc_test_seq.Rmd’using ‘UTF-8’... OK ./GENESIS.Rcheck/00check.log: ‘pcair.Rmd’using ‘UTF-8’... OK ./GENESIS.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./GENESIS.Rcheck/00check.log:* checking PDF version of manual ... OK ./GENESIS.Rcheck/00check.log:* DONE ./GENESIS.Rcheck/00check.log:Status: 1 ERROR, 3 NOTEs ImmuneSpaceR_1.13.2.tar.gz ./ImmuneSpaceR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ImmuneSpaceR.Rcheck’ ./ImmuneSpaceR.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./ImmuneSpaceR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ImmuneSpaceR.Rcheck/00check.log:* using session charset: UTF-8 ./ImmuneSpaceR.Rcheck/00check.log:* checking for file ‘ImmuneSpaceR/DESCRIPTION’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking extension type ... Package ./ImmuneSpaceR.Rcheck/00check.log:* this is package ‘ImmuneSpaceR’ version ‘1.13.2’ ./ImmuneSpaceR.Rcheck/00check.log:* checking package namespace information ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking package dependencies ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking if this is a source package ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking if there is a namespace ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for executable files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for portable file names ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether package ‘ImmuneSpaceR’ can be installed ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking installed package size ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking package directory ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking ‘build’ directory ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking top-level files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for left-over files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking index information ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking package subdirectories ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./ImmuneSpaceR.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./ImmuneSpaceR.Rcheck/00check.log: ‘Rlabkey:::.lkdefaults’ ‘Rlabkey:::labkey.getRequestOptions’ ./ImmuneSpaceR.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./ImmuneSpaceR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking replacement functions ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking foreign function calls ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./ImmuneSpaceR.Rcheck/00check.log:.getDataToPlot: no visible binding for global variable ‘value_reported’ ./ImmuneSpaceR.Rcheck/00check.log:Undefined global functions or variables: ./ImmuneSpaceR.Rcheck/00check.log: value_reported ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd metadata ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd cross-references ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd contents ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking examples ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking tests ... ERROR ./ImmuneSpaceR.Rcheck/00check.log: Running ‘testthat.R’ ./ImmuneSpaceR.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./ImmuneSpaceR.Rcheck/00check.log:Last 13 lines of output: ./ImmuneSpaceR.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./ImmuneSpaceR.Rcheck/00check.log: [ OK: 2 | SKIPPED: 14 | WARNINGS: 0 | FAILED: 46 ] ./ImmuneSpaceR.Rcheck/00check.log: 1. Failure: all studies can loaded with empty string (@test-CreateConnection.R#26) ./ImmuneSpaceR.Rcheck/00check.log: 2. Failure: Nonexistent study fails to load (@test-CreateConnection.R#32) ./ImmuneSpaceR.Rcheck/00check.log: 3. Failure: Existing study can be loaded (@test-CreateConnection.R#37) ./ImmuneSpaceR.Rcheck/00check.log: 4. Failure: ImmuneSignatures study can be loaded (@test-CreateConnection.R#42) ./ImmuneSpaceR.Rcheck/00check.log: 5. Failure: ImmuneSignatures study can be loaded (@test-CreateConnection.R#43) ./ImmuneSpaceR.Rcheck/00check.log: 6. Failure: Lyoplate study cannot be loaded (@test-CreateConnection.R#49) ./ImmuneSpaceR.Rcheck/00check.log: 7. Error: Connection loads with cohort-type in GE_matrices (@test-CreateConnection.R#53) ./ImmuneSpaceR.Rcheck/00check.log: 8. Error: (unknown) (@test-cytometry.R#4) ./ImmuneSpaceR.Rcheck/00check.log: 9. Error: (unknown) (@test-dataIntegration.R#4) ./ImmuneSpaceR.Rcheck/00check.log: 1. ... ./ImmuneSpaceR.Rcheck/00check.log: ./ImmuneSpaceR.Rcheck/00check.log: Error: testthat unit tests failed ./ImmuneSpaceR.Rcheck/00check.log: Execution halted ./ImmuneSpaceR.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./ImmuneSpaceR.Rcheck/00check.log: ‘Intro_to_ImmuneSpaceR.Rmd’... OK ./ImmuneSpaceR.Rcheck/00check.log: ‘getDataset.Rmd’... OK ./ImmuneSpaceR.Rcheck/00check.log: ‘getGEMatrix.Rmd’... OK ./ImmuneSpaceR.Rcheck/00check.log: ‘interactiveNetrc.Rmd’... OK ./ImmuneSpaceR.Rcheck/00check.log: ‘report_SDY144.Rmd’... OK ./ImmuneSpaceR.Rcheck/00check.log: ‘report_SDY180.Rmd’... OK ./ImmuneSpaceR.Rcheck/00check.log: ‘report_SDY269.Rmd’... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./ImmuneSpaceR.Rcheck/00check.log:Error(s) in re-building vignettes: ./ImmuneSpaceR.Rcheck/00check.log:--- re-building ‘Intro_to_ImmuneSpaceR.Rmd’ using rmarkdown ./ImmuneSpaceR.Rcheck/00check.log:Quitting from lines 68-71 (Intro_to_ImmuneSpaceR.Rmd) ./ImmuneSpaceR.Rcheck/00check.log:Error: processing vignette 'Intro_to_ImmuneSpaceR.Rmd' failed with diagnostics: ./ImmuneSpaceR.Rcheck/00check.log:Invalid credential or deactivated account. Check your account in the portal. ./ImmuneSpaceR.Rcheck/00check.log:--- failed re-building ‘Intro_to_ImmuneSpaceR.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:--- re-building ‘getDataset.Rmd’ using rmarkdown ./ImmuneSpaceR.Rcheck/00check.log:Quitting from lines 37-40 (getDataset.Rmd) ./ImmuneSpaceR.Rcheck/00check.log:Error: processing vignette 'getDataset.Rmd' failed with diagnostics: ./ImmuneSpaceR.Rcheck/00check.log:Invalid credential or deactivated account. Check your account in the portal. ./ImmuneSpaceR.Rcheck/00check.log:--- failed re-building ‘getDataset.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:--- re-building ‘getGEMatrix.Rmd’ using rmarkdown ./ImmuneSpaceR.Rcheck/00check.log:Quitting from lines 38-41 (getGEMatrix.Rmd) ./ImmuneSpaceR.Rcheck/00check.log:Error: processing vignette 'getGEMatrix.Rmd' failed with diagnostics: ./ImmuneSpaceR.Rcheck/00check.log:Invalid credential or deactivated account. Check your account in the portal. ./ImmuneSpaceR.Rcheck/00check.log:--- failed re-building ‘getGEMatrix.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:--- re-building ‘interactiveNetrc.Rmd’ using rmarkdown ./ImmuneSpaceR.Rcheck/00check.log:--- finished re-building ‘interactiveNetrc.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:--- re-building ‘report_SDY144.Rmd’ using rmarkdown ./ImmuneSpaceR.Rcheck/00check.log:Quitting from lines 40-45 (report_SDY144.Rmd) ./ImmuneSpaceR.Rcheck/00check.log:Error: processing vignette 'report_SDY144.Rmd' failed with diagnostics: ./ImmuneSpaceR.Rcheck/00check.log:Invalid credential or deactivated account. Check your account in the portal. ./ImmuneSpaceR.Rcheck/00check.log:--- failed re-building ‘report_SDY144.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:--- re-building ‘report_SDY180.Rmd’ using rmarkdown ./ImmuneSpaceR.Rcheck/00check.log:Quitting from lines 57-59 (report_SDY180.Rmd) ./ImmuneSpaceR.Rcheck/00check.log:Error: processing vignette 'report_SDY180.Rmd' failed with diagnostics: ./ImmuneSpaceR.Rcheck/00check.log:Invalid credential or deactivated account. Check your account in the portal. ./ImmuneSpaceR.Rcheck/00check.log:--- failed re-building ‘report_SDY180.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:--- re-building ‘report_SDY269.Rmd’ using rmarkdown ./ImmuneSpaceR.Rcheck/00check.log:Quitting from lines 53-57 (report_SDY269.Rmd) ./ImmuneSpaceR.Rcheck/00check.log:Error: processing vignette 'report_SDY269.Rmd' failed with diagnostics: ./ImmuneSpaceR.Rcheck/00check.log:Invalid credential or deactivated account. Check your account in the portal. ./ImmuneSpaceR.Rcheck/00check.log:--- failed re-building ‘report_SDY269.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:SUMMARY: processing the following files failed: ./ImmuneSpaceR.Rcheck/00check.log: ‘Intro_to_ImmuneSpaceR.Rmd’ ‘getDataset.Rmd’ ‘getGEMatrix.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log: ‘report_SDY144.Rmd’ ‘report_SDY180.Rmd’ ‘report_SDY269.Rmd’ ./ImmuneSpaceR.Rcheck/00check.log:Error: Vignette re-building failed. ./ImmuneSpaceR.Rcheck/00check.log:Execution halted ./ImmuneSpaceR.Rcheck/00check.log:* checking PDF version of manual ... OK ./ImmuneSpaceR.Rcheck/00check.log:* DONE ./ImmuneSpaceR.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 2 NOTEs qckitfastq_1.1.0.tar.gz ./qckitfastq.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/qckitfastq.Rcheck’ ./qckitfastq.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./qckitfastq.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./qckitfastq.Rcheck/00check.log:* using session charset: UTF-8 ./qckitfastq.Rcheck/00check.log:* checking for file ‘qckitfastq/DESCRIPTION’ ... OK ./qckitfastq.Rcheck/00check.log:* checking extension type ... Package ./qckitfastq.Rcheck/00check.log:* this is package ‘qckitfastq’ version ‘1.1.0’ ./qckitfastq.Rcheck/00check.log:* package encoding: UTF-8 ./qckitfastq.Rcheck/00check.log:* checking package namespace information ... OK ./qckitfastq.Rcheck/00check.log:* checking package dependencies ... OK ./qckitfastq.Rcheck/00check.log:* checking if this is a source package ... OK ./qckitfastq.Rcheck/00check.log:* checking if there is a namespace ... OK ./qckitfastq.Rcheck/00check.log:* checking for executable files ... OK ./qckitfastq.Rcheck/00check.log:* checking for hidden files and directories ... OK ./qckitfastq.Rcheck/00check.log:* checking for portable file names ... OK ./qckitfastq.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./qckitfastq.Rcheck/00check.log:* checking whether package ‘qckitfastq’ can be installed ... OK ./qckitfastq.Rcheck/00check.log:* checking installed package size ... OK ./qckitfastq.Rcheck/00check.log:* checking package directory ... OK ./qckitfastq.Rcheck/00check.log:* checking ‘build’ directory ... OK ./qckitfastq.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./qckitfastq.Rcheck/00check.log:* checking top-level files ... OK ./qckitfastq.Rcheck/00check.log:* checking for left-over files ... OK ./qckitfastq.Rcheck/00check.log:* checking index information ... OK ./qckitfastq.Rcheck/00check.log:* checking package subdirectories ... OK ./qckitfastq.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./qckitfastq.Rcheck/00check.log:* checking R files for syntax errors ... OK ./qckitfastq.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./qckitfastq.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./qckitfastq.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./qckitfastq.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./qckitfastq.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./qckitfastq.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./qckitfastq.Rcheck/00check.log:* checking dependencies in R code ... OK ./qckitfastq.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./qckitfastq.Rcheck/00check.log:* checking replacement functions ... OK ./qckitfastq.Rcheck/00check.log:* checking foreign function calls ... OK ./qckitfastq.Rcheck/00check.log:* checking R code for possible problems ... OK ./qckitfastq.Rcheck/00check.log:* checking Rd files ... OK ./qckitfastq.Rcheck/00check.log:* checking Rd metadata ... OK ./qckitfastq.Rcheck/00check.log:* checking Rd cross-references ... OK ./qckitfastq.Rcheck/00check.log:* checking for missing documentation entries ... OK ./qckitfastq.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./qckitfastq.Rcheck/00check.log:* checking Rd \usage sections ... OK ./qckitfastq.Rcheck/00check.log:* checking Rd contents ... OK ./qckitfastq.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./qckitfastq.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./qckitfastq.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./qckitfastq.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./qckitfastq.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./qckitfastq.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./qckitfastq.Rcheck/00check.log:* checking compiled code ... OK ./qckitfastq.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./qckitfastq.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./qckitfastq.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./qckitfastq.Rcheck/00check.log:* checking examples ... ERROR ./qckitfastq.Rcheck/00check.log:Running examples in ‘qckitfastq-Ex.R’ failed ./qckitfastq.Rcheck/00check.log:The error most likely occurred in: ./qckitfastq.Rcheck/00check.log:> ### Name: plot_per_base_quality ./qckitfastq.Rcheck/00check.log:> ### Title: Generate a boxplot of the per position quality score. ./qckitfastq.Rcheck/00check.log:> ### Aliases: plot_per_base_quality ./qckitfastq.Rcheck/00check.log:> ./qckitfastq.Rcheck/00check.log:> ### ** Examples ./qckitfastq.Rcheck/00check.log:> ./qckitfastq.Rcheck/00check.log:> ./qckitfastq.Rcheck/00check.log:> pbq <- per_base_quality(system.file("extdata", "10^5_reads_test.fq.gz", package = "qckitfastq")) ./qckitfastq.Rcheck/00check.log:> plot_per_base_quality(pbq) ./qckitfastq.Rcheck/00check.log:Error: Can't draw more than one boxplot per group. Did you forget aes(group = ...)? ./qckitfastq.Rcheck/00check.log:Execution halted ./qckitfastq.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./qckitfastq.Rcheck/00check.log:* checking tests ... ERROR ./qckitfastq.Rcheck/00check.log: Running ‘testthat.R’ ./qckitfastq.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./qckitfastq.Rcheck/00check.log:Last 13 lines of output: ./qckitfastq.Rcheck/00check.log: 22: lapply(groups, function(group) { ./qckitfastq.Rcheck/00check.log: self$draw_group(group, panel_params, coord, ...) ./qckitfastq.Rcheck/00check.log: }) ./qckitfastq.Rcheck/00check.log: 23: FUN(X[[i]], ...) ./qckitfastq.Rcheck/00check.log: 24: self$draw_group(group, panel_params, coord, ...) ./qckitfastq.Rcheck/00check.log: 25: f(...) ./qckitfastq.Rcheck/00check.log: 26: stop("Can't draw more than one boxplot per group. Did you forget aes(group = ...)?", ./qckitfastq.Rcheck/00check.log: call. = FALSE) ./qckitfastq.Rcheck/00check.log: ./qckitfastq.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./qckitfastq.Rcheck/00check.log: [ OK: 35 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ] ./qckitfastq.Rcheck/00check.log: 1. Error: Testing run_all (@test_run_all.R#5) ./qckitfastq.Rcheck/00check.log: ./qckitfastq.Rcheck/00check.log: Error: testthat unit tests failed ./qckitfastq.Rcheck/00check.log: Execution halted ./qckitfastq.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./qckitfastq.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./qckitfastq.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./qckitfastq.Rcheck/00check.log: ‘vignette-qckitfastq.Rmd’using ‘UTF-8’... OK ./qckitfastq.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./qckitfastq.Rcheck/00check.log:Error(s) in re-building vignettes: ./qckitfastq.Rcheck/00check.log: ... ./qckitfastq.Rcheck/00check.log:--- re-building ‘vignette-qckitfastq.Rmd’ using rmarkdown ./qckitfastq.Rcheck/00check.log:Quitting from lines 90-93 (vignette-qckitfastq.Rmd) ./qckitfastq.Rcheck/00check.log:Error: processing vignette 'vignette-qckitfastq.Rmd' failed with diagnostics: ./qckitfastq.Rcheck/00check.log:Can't draw more than one boxplot per group. Did you forget aes(group = ...)? ./qckitfastq.Rcheck/00check.log:--- failed re-building ‘vignette-qckitfastq.Rmd’ ./qckitfastq.Rcheck/00check.log:SUMMARY: processing the following file failed: ./qckitfastq.Rcheck/00check.log: ‘vignette-qckitfastq.Rmd’ ./qckitfastq.Rcheck/00check.log:Error: Vignette re-building failed. ./qckitfastq.Rcheck/00check.log:Execution halted ./qckitfastq.Rcheck/00check.log:* checking PDF version of manual ... OK ./qckitfastq.Rcheck/00check.log:* DONE ./qckitfastq.Rcheck/00check.log:Status: 2 ERRORs, 1 WARNING singleCellTK_1.5.5.tar.gz ./singleCellTK.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/singleCellTK.Rcheck’ ./singleCellTK.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./singleCellTK.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./singleCellTK.Rcheck/00check.log:* using session charset: UTF-8 ./singleCellTK.Rcheck/00check.log:* checking for file ‘singleCellTK/DESCRIPTION’ ... OK ./singleCellTK.Rcheck/00check.log:* checking extension type ... Package ./singleCellTK.Rcheck/00check.log:* this is package ‘singleCellTK’ version ‘1.5.5’ ./singleCellTK.Rcheck/00check.log:* package encoding: UTF-8 ./singleCellTK.Rcheck/00check.log:* checking package namespace information ... OK ./singleCellTK.Rcheck/00check.log:* checking package dependencies ... OK ./singleCellTK.Rcheck/00check.log:* checking if this is a source package ... OK ./singleCellTK.Rcheck/00check.log:* checking if there is a namespace ... OK ./singleCellTK.Rcheck/00check.log:* checking for executable files ... OK ./singleCellTK.Rcheck/00check.log:* checking for hidden files and directories ... NOTE ./singleCellTK.Rcheck/00check.log:Found the following hidden files and directories: ./singleCellTK.Rcheck/00check.log: .BBSoptions ./singleCellTK.Rcheck/00check.log:These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ./singleCellTK.Rcheck/00check.log:* checking for portable file names ... OK ./singleCellTK.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./singleCellTK.Rcheck/00check.log:* checking whether package ‘singleCellTK’ can be installed ... OK ./singleCellTK.Rcheck/00check.log:* checking installed package size ... NOTE ./singleCellTK.Rcheck/00check.log: installed size is 5.6Mb ./singleCellTK.Rcheck/00check.log: sub-directories of 1Mb or more: ./singleCellTK.Rcheck/00check.log: data 1.0Mb ./singleCellTK.Rcheck/00check.log: doc 3.8Mb ./singleCellTK.Rcheck/00check.log:* checking package directory ... OK ./singleCellTK.Rcheck/00check.log:* checking ‘build’ directory ... OK ./singleCellTK.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./singleCellTK.Rcheck/00check.log:* checking top-level files ... OK ./singleCellTK.Rcheck/00check.log:* checking for left-over files ... OK ./singleCellTK.Rcheck/00check.log:* checking index information ... OK ./singleCellTK.Rcheck/00check.log:* checking package subdirectories ... OK ./singleCellTK.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./singleCellTK.Rcheck/00check.log:* checking R files for syntax errors ... OK ./singleCellTK.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./singleCellTK.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./singleCellTK.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./singleCellTK.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./singleCellTK.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./singleCellTK.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./singleCellTK.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./singleCellTK.Rcheck/00check.log:Namespaces in Imports field not imported from: ./singleCellTK.Rcheck/00check.log: ‘celda’ ‘shinyBS’ ‘shinythemes’ ./singleCellTK.Rcheck/00check.log: All declared Imports should be used. ./singleCellTK.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./singleCellTK.Rcheck/00check.log:* checking replacement functions ... OK ./singleCellTK.Rcheck/00check.log:* checking foreign function calls ... OK ./singleCellTK.Rcheck/00check.log:* checking R code for possible problems ... OK ./singleCellTK.Rcheck/00check.log:* checking Rd files ... OK ./singleCellTK.Rcheck/00check.log:* checking Rd metadata ... OK ./singleCellTK.Rcheck/00check.log:* checking Rd cross-references ... OK ./singleCellTK.Rcheck/00check.log:* checking for missing documentation entries ... OK ./singleCellTK.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./singleCellTK.Rcheck/00check.log:* checking Rd \usage sections ... OK ./singleCellTK.Rcheck/00check.log:* checking Rd contents ... OK ./singleCellTK.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./singleCellTK.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./singleCellTK.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./singleCellTK.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./singleCellTK.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./singleCellTK.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./singleCellTK.Rcheck/00check.log:* checking examples ... ERROR ./singleCellTK.Rcheck/00check.log:Running examples in ‘singleCellTK-Ex.R’ failed ./singleCellTK.Rcheck/00check.log:The error most likely occurred in: ./singleCellTK.Rcheck/00check.log:> ### Name: enrichRSCE ./singleCellTK.Rcheck/00check.log:> ### Title: enrichR Given a list of genes this function runs the enrichR() ./singleCellTK.Rcheck/00check.log:> ### to perform Gene enrichment ./singleCellTK.Rcheck/00check.log:> ### Aliases: enrichRSCE ./singleCellTK.Rcheck/00check.log:> ./singleCellTK.Rcheck/00check.log:> ### ** Examples ./singleCellTK.Rcheck/00check.log:> ./singleCellTK.Rcheck/00check.log:> enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017") ./singleCellTK.Rcheck/00check.log:EnrichR website not responding ./singleCellTK.Rcheck/00check.log:Error in enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017") : ./singleCellTK.Rcheck/00check.log: database 'GO_Cellular_Component_2017' does not exist. ./singleCellTK.Rcheck/00check.log:Execution halted ./singleCellTK.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./singleCellTK.Rcheck/00check.log:* checking tests ... ERROR ./singleCellTK.Rcheck/00check.log: Running ‘spelling.R’ ./singleCellTK.Rcheck/00check.log: Running ‘testthat.R’ ./singleCellTK.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./singleCellTK.Rcheck/00check.log:Last 13 lines of output: ./singleCellTK.Rcheck/00check.log: `enrichRSCE(mouseBrainSubsetSCE, NULL, "GO_Cellular_Component_2017")` threw an error with unexpected message. ./singleCellTK.Rcheck/00check.log: Expected match: "Please provide a gene list." ./singleCellTK.Rcheck/00check.log: Actual message: "database 'GO_Cellular_Component_2017' does not exist." ./singleCellTK.Rcheck/00check.log: ./singleCellTK.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./singleCellTK.Rcheck/00check.log: [ OK: 74 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 6 ] ./singleCellTK.Rcheck/00check.log: 1. Failure: plotPCA (@test-dims.R#20) ./singleCellTK.Rcheck/00check.log: 2. Error: plotPCA (@test-dims.R#23) ./singleCellTK.Rcheck/00check.log: 3. Failure: plotTSNE (@test-dims.R#51) ./singleCellTK.Rcheck/00check.log: 4. Error: plotTSNE (@test-dims.R#54) ./singleCellTK.Rcheck/00check.log: 5. Failure: plotBiomarker (@test-dims.R#72) ./singleCellTK.Rcheck/00check.log: 6. Failure: Should fail when the gene list is empty (@test-enrichRSCE.R#21) ./singleCellTK.Rcheck/00check.log: ./singleCellTK.Rcheck/00check.log: Error: testthat unit tests failed ./singleCellTK.Rcheck/00check.log: Execution halted ./singleCellTK.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./singleCellTK.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./singleCellTK.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./singleCellTK.Rcheck/00check.log: ‘v01-Introduction_to_singleCellTK.Rmd’using ‘UTF-8’... OK ./singleCellTK.Rcheck/00check.log: ‘v02-Processing_and_Visualizing_Data_in_the_SingleCellTK.Rmd’using ‘UTF-8’... OK ./singleCellTK.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./singleCellTK.Rcheck/00check.log:* checking PDF version of manual ... OK ./singleCellTK.Rcheck/00check.log:* DONE ./singleCellTK.Rcheck/00check.log:Status: 2 ERRORs, 3 NOTEs AUCell_1.7.2.tar.gz ./AUCell.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/AUCell.Rcheck’ ./AUCell.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./AUCell.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./AUCell.Rcheck/00check.log:* using session charset: UTF-8 ./AUCell.Rcheck/00check.log:* checking for file ‘AUCell/DESCRIPTION’ ... OK ./AUCell.Rcheck/00check.log:* checking extension type ... Package ./AUCell.Rcheck/00check.log:* this is package ‘AUCell’ version ‘1.7.2’ ./AUCell.Rcheck/00check.log:* checking package namespace information ... OK ./AUCell.Rcheck/00check.log:* checking package dependencies ... OK ./AUCell.Rcheck/00check.log:* checking if this is a source package ... OK ./AUCell.Rcheck/00check.log:* checking if there is a namespace ... OK ./AUCell.Rcheck/00check.log:* checking for executable files ... OK ./AUCell.Rcheck/00check.log:* checking for hidden files and directories ... OK ./AUCell.Rcheck/00check.log:* checking for portable file names ... OK ./AUCell.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./AUCell.Rcheck/00check.log:* checking whether package ‘AUCell’ can be installed ... OK ./AUCell.Rcheck/00check.log:* checking installed package size ... OK ./AUCell.Rcheck/00check.log:* checking package directory ... OK ./AUCell.Rcheck/00check.log:* checking ‘build’ directory ... OK ./AUCell.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./AUCell.Rcheck/00check.log:* checking top-level files ... OK ./AUCell.Rcheck/00check.log:* checking for left-over files ... OK ./AUCell.Rcheck/00check.log:* checking index information ... OK ./AUCell.Rcheck/00check.log:* checking package subdirectories ... OK ./AUCell.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./AUCell.Rcheck/00check.log:* checking R files for syntax errors ... OK ./AUCell.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./AUCell.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./AUCell.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./AUCell.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./AUCell.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./AUCell.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./AUCell.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./AUCell.Rcheck/00check.log:'library' or 'require' call to ‘rbokeh’ in package code. ./AUCell.Rcheck/00check.log: Please use :: or requireNamespace() instead. ./AUCell.Rcheck/00check.log: See section 'Suggested packages' in the 'Writing R Extensions' manual. ./AUCell.Rcheck/00check.log:Namespace in Imports field not imported from: ‘BiocGenerics’ ./AUCell.Rcheck/00check.log: All declared Imports should be used. ./AUCell.Rcheck/00check.log:Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’ ./AUCell.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./AUCell.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./AUCell.Rcheck/00check.log:* checking replacement functions ... OK ./AUCell.Rcheck/00check.log:* checking foreign function calls ... OK ./AUCell.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./AUCell.Rcheck/00check.log:AUCell_createViewerApp : : no visible global function ./AUCell.Rcheck/00check.log: definition for ‘%>%’ ./AUCell.Rcheck/00check.log:AUCell_createViewerApp : : no visible binding for global ./AUCell.Rcheck/00check.log: variable ‘tsne1’ ./AUCell.Rcheck/00check.log:AUCell_createViewerApp : : no visible binding for global ./AUCell.Rcheck/00check.log: variable ‘tsne2’ ./AUCell.Rcheck/00check.log:AUCell_createViewerApp : : no visible binding for global ./AUCell.Rcheck/00check.log: variable ‘cell’ ./AUCell.Rcheck/00check.log:Undefined global functions or variables: ./AUCell.Rcheck/00check.log: %>% cell tsne1 tsne2 ./AUCell.Rcheck/00check.log:* checking Rd files ... OK ./AUCell.Rcheck/00check.log:* checking Rd metadata ... OK ./AUCell.Rcheck/00check.log:* checking Rd cross-references ... OK ./AUCell.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./AUCell.Rcheck/00check.log:Undocumented S4 methods: ./AUCell.Rcheck/00check.log: generic 'cbind' and siglist 'aucellResults' ./AUCell.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./AUCell.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./AUCell.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./AUCell.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./AUCell.Rcheck/00check.log:Objects in \usage without \alias in documentation object 'aucellResults-class': ./AUCell.Rcheck/00check.log: ‘\S4method{cbind}{aucellResults}’ ./AUCell.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./AUCell.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./AUCell.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./AUCell.Rcheck/00check.log:* checking Rd contents ... OK ./AUCell.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./AUCell.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./AUCell.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./AUCell.Rcheck/00check.log:* checking examples ... OK ./AUCell.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./AUCell.Rcheck/00check.log:* checking tests ... OK ./AUCell.Rcheck/00check.log: Running ‘testthat.R’ ./AUCell.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... NOTE ./AUCell.Rcheck/00check.log:'::' or ':::' import not declared from: ‘reshape2’ ./AUCell.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./AUCell.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./AUCell.Rcheck/00check.log: ‘AUCell.Rmd’using ‘UTF-8’... OK ./AUCell.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./AUCell.Rcheck/00check.log:* checking PDF version of manual ... OK ./AUCell.Rcheck/00check.log:* DONE ./AUCell.Rcheck/00check.log:Status: 2 WARNINGs, 3 NOTEs BASiCS_1.7.10.tar.gz ./BASiCS.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/BASiCS.Rcheck’ ./BASiCS.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./BASiCS.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./BASiCS.Rcheck/00check.log:* using session charset: UTF-8 ./BASiCS.Rcheck/00check.log:* checking for file ‘BASiCS/DESCRIPTION’ ... OK ./BASiCS.Rcheck/00check.log:* checking extension type ... Package ./BASiCS.Rcheck/00check.log:* this is package ‘BASiCS’ version ‘1.7.10’ ./BASiCS.Rcheck/00check.log:* checking package namespace information ... OK ./BASiCS.Rcheck/00check.log:* checking package dependencies ... OK ./BASiCS.Rcheck/00check.log:* checking if this is a source package ... OK ./BASiCS.Rcheck/00check.log:* checking if there is a namespace ... OK ./BASiCS.Rcheck/00check.log:* checking for executable files ... OK ./BASiCS.Rcheck/00check.log:* checking for hidden files and directories ... OK ./BASiCS.Rcheck/00check.log:* checking for portable file names ... OK ./BASiCS.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./BASiCS.Rcheck/00check.log:* checking whether package ‘BASiCS’ can be installed ... OK ./BASiCS.Rcheck/00check.log:* checking installed package size ... NOTE ./BASiCS.Rcheck/00check.log: installed size is 15.0Mb ./BASiCS.Rcheck/00check.log: sub-directories of 1Mb or more: ./BASiCS.Rcheck/00check.log: data 2.0Mb ./BASiCS.Rcheck/00check.log: doc 1.4Mb ./BASiCS.Rcheck/00check.log: libs 11.0Mb ./BASiCS.Rcheck/00check.log:* checking package directory ... OK ./BASiCS.Rcheck/00check.log:* checking ‘build’ directory ... OK ./BASiCS.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./BASiCS.Rcheck/00check.log:* checking top-level files ... OK ./BASiCS.Rcheck/00check.log:* checking for left-over files ... OK ./BASiCS.Rcheck/00check.log:* checking index information ... OK ./BASiCS.Rcheck/00check.log:* checking package subdirectories ... OK ./BASiCS.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./BASiCS.Rcheck/00check.log:* checking R files for syntax errors ... OK ./BASiCS.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./BASiCS.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./BASiCS.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./BASiCS.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./BASiCS.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./BASiCS.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./BASiCS.Rcheck/00check.log:* checking dependencies in R code ... OK ./BASiCS.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./BASiCS.Rcheck/00check.log:* checking replacement functions ... OK ./BASiCS.Rcheck/00check.log:* checking foreign function calls ... OK ./BASiCS.Rcheck/00check.log:* checking R code for possible problems ... OK ./BASiCS.Rcheck/00check.log:* checking Rd files ... OK ./BASiCS.Rcheck/00check.log:* checking Rd metadata ... OK ./BASiCS.Rcheck/00check.log:* checking Rd cross-references ... OK ./BASiCS.Rcheck/00check.log:* checking for missing documentation entries ... OK ./BASiCS.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./BASiCS.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./BASiCS.Rcheck/00check.log:Undocumented arguments in documentation object 'BASiCS_TestDE' ./BASiCS.Rcheck/00check.log: ‘Chain’ ‘ChainRef’ ./BASiCS.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./BASiCS.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./BASiCS.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./BASiCS.Rcheck/00check.log:* checking Rd contents ... OK ./BASiCS.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./BASiCS.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./BASiCS.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./BASiCS.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./BASiCS.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./BASiCS.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./BASiCS.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./BASiCS.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./BASiCS.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./BASiCS.Rcheck/00check.log:* checking compiled code ... OK ./BASiCS.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./BASiCS.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./BASiCS.Rcheck/00check.log:* checking examples ... WARNING ./BASiCS.Rcheck/00check.log:Found the following significant warnings: ./BASiCS.Rcheck/00check.log: Warning: 'isSpike' is deprecated. ./BASiCS.Rcheck/00check.log:Deprecated functions may be defunct as soon as of the next release of R. ./BASiCS.Rcheck/00check.log:See ?Deprecated. ./BASiCS.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./BASiCS.Rcheck/00check.log:* checking tests ... OK ./BASiCS.Rcheck/00check.log: Running ‘testthat.R’ ./BASiCS.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./BASiCS.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./BASiCS.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./BASiCS.Rcheck/00check.log: ‘BASiCS.Rmd’using ‘UTF-8’... OK ./BASiCS.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./BASiCS.Rcheck/00check.log:* checking PDF version of manual ... OK ./BASiCS.Rcheck/00check.log:* DONE ./BASiCS.Rcheck/00check.log:Status: 2 WARNINGs, 1 NOTE BEARscc_1.5.0.tar.gz ./BEARscc.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/BEARscc.Rcheck’ ./BEARscc.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./BEARscc.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./BEARscc.Rcheck/00check.log:* using session charset: UTF-8 ./BEARscc.Rcheck/00check.log:* checking for file ‘BEARscc/DESCRIPTION’ ... OK ./BEARscc.Rcheck/00check.log:* checking extension type ... Package ./BEARscc.Rcheck/00check.log:* this is package ‘BEARscc’ version ‘1.5.0’ ./BEARscc.Rcheck/00check.log:* checking package namespace information ... OK ./BEARscc.Rcheck/00check.log:* checking package dependencies ... OK ./BEARscc.Rcheck/00check.log:* checking if this is a source package ... OK ./BEARscc.Rcheck/00check.log:* checking if there is a namespace ... OK ./BEARscc.Rcheck/00check.log:* checking for executable files ... OK ./BEARscc.Rcheck/00check.log:* checking for hidden files and directories ... OK ./BEARscc.Rcheck/00check.log:* checking for portable file names ... OK ./BEARscc.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./BEARscc.Rcheck/00check.log:* checking whether package ‘BEARscc’ can be installed ... OK ./BEARscc.Rcheck/00check.log:* checking installed package size ... OK ./BEARscc.Rcheck/00check.log:* checking package directory ... OK ./BEARscc.Rcheck/00check.log:* checking ‘build’ directory ... OK ./BEARscc.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./BEARscc.Rcheck/00check.log:* checking top-level files ... OK ./BEARscc.Rcheck/00check.log:* checking for left-over files ... OK ./BEARscc.Rcheck/00check.log:* checking index information ... OK ./BEARscc.Rcheck/00check.log:* checking package subdirectories ... OK ./BEARscc.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./BEARscc.Rcheck/00check.log:* checking R files for syntax errors ... OK ./BEARscc.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./BEARscc.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./BEARscc.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./BEARscc.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./BEARscc.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./BEARscc.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./BEARscc.Rcheck/00check.log:* checking dependencies in R code ... OK ./BEARscc.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./BEARscc.Rcheck/00check.log:* checking replacement functions ... OK ./BEARscc.Rcheck/00check.log:* checking foreign function calls ... OK ./BEARscc.Rcheck/00check.log:* checking R code for possible problems ... OK ./BEARscc.Rcheck/00check.log:* checking Rd files ... OK ./BEARscc.Rcheck/00check.log:* checking Rd metadata ... OK ./BEARscc.Rcheck/00check.log:* checking Rd cross-references ... OK ./BEARscc.Rcheck/00check.log:* checking for missing documentation entries ... OK ./BEARscc.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./BEARscc.Rcheck/00check.log:* checking Rd \usage sections ... OK ./BEARscc.Rcheck/00check.log:* checking Rd contents ... OK ./BEARscc.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./BEARscc.Rcheck/00check.log:* checking contents of ‘data’ directory ... WARNING ./BEARscc.Rcheck/00check.log:Object named ‘.Random.seed’ found in datasets: ./BEARscc.Rcheck/00check.log: ‘BEARscc_examples’ ‘analysis_examples’ ./BEARscc.Rcheck/00check.log:Please remove it. ./BEARscc.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./BEARscc.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./BEARscc.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./BEARscc.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./BEARscc.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./BEARscc.Rcheck/00check.log:* checking examples ... WARNING ./BEARscc.Rcheck/00check.log:Found the following significant warnings: ./BEARscc.Rcheck/00check.log: Warning: 'isSpike' is deprecated. ./BEARscc.Rcheck/00check.log: Warning: 'isSpike' is deprecated. ./BEARscc.Rcheck/00check.log:Deprecated functions may be defunct as soon as of the next release of R. ./BEARscc.Rcheck/00check.log:See ?Deprecated. ./BEARscc.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./BEARscc.Rcheck/00check.log:* checking tests ... OK ./BEARscc.Rcheck/00check.log: Running ‘testthat.R’ ./BEARscc.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./BEARscc.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./BEARscc.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./BEARscc.Rcheck/00check.log: ‘BEARscc.Rmd’using ‘UTF-8’... OK ./BEARscc.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./BEARscc.Rcheck/00check.log:* checking PDF version of manual ... OK ./BEARscc.Rcheck/00check.log:* DONE ./BEARscc.Rcheck/00check.log:Status: 2 WARNINGs BiocParallel_1.19.2.tar.gz ./BiocParallel.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/BiocParallel.Rcheck’ ./BiocParallel.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./BiocParallel.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./BiocParallel.Rcheck/00check.log:* using session charset: UTF-8 ./BiocParallel.Rcheck/00check.log:* checking for file ‘BiocParallel/DESCRIPTION’ ... OK ./BiocParallel.Rcheck/00check.log:* checking extension type ... Package ./BiocParallel.Rcheck/00check.log:* this is package ‘BiocParallel’ version ‘1.19.2’ ./BiocParallel.Rcheck/00check.log:* checking package namespace information ... OK ./BiocParallel.Rcheck/00check.log:* checking package dependencies ... OK ./BiocParallel.Rcheck/00check.log:* checking if this is a source package ... OK ./BiocParallel.Rcheck/00check.log:* checking if there is a namespace ... OK ./BiocParallel.Rcheck/00check.log:* checking for executable files ... OK ./BiocParallel.Rcheck/00check.log:* checking for hidden files and directories ... OK ./BiocParallel.Rcheck/00check.log:* checking for portable file names ... OK ./BiocParallel.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./BiocParallel.Rcheck/00check.log:* checking whether package ‘BiocParallel’ can be installed ... OK ./BiocParallel.Rcheck/00check.log:* checking installed package size ... OK ./BiocParallel.Rcheck/00check.log:* checking package directory ... OK ./BiocParallel.Rcheck/00check.log:* checking ‘build’ directory ... OK ./BiocParallel.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./BiocParallel.Rcheck/00check.log:* checking top-level files ... OK ./BiocParallel.Rcheck/00check.log:* checking for left-over files ... OK ./BiocParallel.Rcheck/00check.log:* checking index information ... OK ./BiocParallel.Rcheck/00check.log:* checking package subdirectories ... OK ./BiocParallel.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./BiocParallel.Rcheck/00check.log:* checking R files for syntax errors ... OK ./BiocParallel.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./BiocParallel.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./BiocParallel.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./BiocParallel.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./BiocParallel.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./BiocParallel.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./BiocParallel.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./BiocParallel.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./BiocParallel.Rcheck/00check.log: ‘parallel:::closeNode’ ‘parallel:::recvData’ ‘parallel:::recvOneData’ ./BiocParallel.Rcheck/00check.log: ‘parallel:::sendData’ ./BiocParallel.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./BiocParallel.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./BiocParallel.Rcheck/00check.log:* checking replacement functions ... OK ./BiocParallel.Rcheck/00check.log:* checking foreign function calls ... OK ./BiocParallel.Rcheck/00check.log:* checking R code for possible problems ... OK ./BiocParallel.Rcheck/00check.log:* checking Rd files ... OK ./BiocParallel.Rcheck/00check.log:* checking Rd metadata ... OK ./BiocParallel.Rcheck/00check.log:* checking Rd cross-references ... OK ./BiocParallel.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./BiocParallel.Rcheck/00check.log:Undocumented S4 methods: ./BiocParallel.Rcheck/00check.log: generic '.close' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic '.recv' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic '.recv_all' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic '.recv_any' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic '.send' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic '.send_to' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic 'bpbackend' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic 'bpstart' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic 'bpstop' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log: generic 'length' and siglist 'TransientMulticoreParam' ./BiocParallel.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./BiocParallel.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./BiocParallel.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./BiocParallel.Rcheck/00check.log:* checking Rd \usage sections ... OK ./BiocParallel.Rcheck/00check.log:* checking Rd contents ... OK ./BiocParallel.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./BiocParallel.Rcheck/00check.log:* checking line endings in shell scripts ... OK ./BiocParallel.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./BiocParallel.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./BiocParallel.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./BiocParallel.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./BiocParallel.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./BiocParallel.Rcheck/00check.log:* checking compiled code ... OK ./BiocParallel.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./BiocParallel.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./BiocParallel.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./BiocParallel.Rcheck/00check.log:* checking examples ... OK ./BiocParallel.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./BiocParallel.Rcheck/00check.log:* checking tests ... OK ./BiocParallel.Rcheck/00check.log: Running ‘test.R’ ./BiocParallel.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./BiocParallel.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./BiocParallel.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./BiocParallel.Rcheck/00check.log: ‘BiocParallel_BatchtoolsParam.Rnw’... OK ./BiocParallel.Rcheck/00check.log: ‘Errors_Logs_And_Debugging.Rnw’... OK ./BiocParallel.Rcheck/00check.log: ‘Introduction_To_BiocParallel.Rnw’... OK ./BiocParallel.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./BiocParallel.Rcheck/00check.log:* checking PDF version of manual ... OK ./BiocParallel.Rcheck/00check.log:* DONE ./BiocParallel.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE CellNOptR_1.31.0.tar.gz ./CellNOptR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CellNOptR.Rcheck’ ./CellNOptR.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./CellNOptR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CellNOptR.Rcheck/00check.log:* using session charset: UTF-8 ./CellNOptR.Rcheck/00check.log:* checking for file ‘CellNOptR/DESCRIPTION’ ... OK ./CellNOptR.Rcheck/00check.log:* checking extension type ... Package ./CellNOptR.Rcheck/00check.log:* this is package ‘CellNOptR’ version ‘1.31.0’ ./CellNOptR.Rcheck/00check.log:* checking package namespace information ... OK ./CellNOptR.Rcheck/00check.log:* checking package dependencies ... NOTE ./CellNOptR.Rcheck/00check.log:Depends: includes the non-default packages: ./CellNOptR.Rcheck/00check.log: 'RBGL', 'graph', 'hash', 'RCurl', 'Rgraphviz', 'XML', 'ggplot2' ./CellNOptR.Rcheck/00check.log:Adding so many packages to the search path is excessive and importing selectively is preferable. ./CellNOptR.Rcheck/00check.log:* checking if this is a source package ... OK ./CellNOptR.Rcheck/00check.log:* checking if there is a namespace ... OK ./CellNOptR.Rcheck/00check.log:* checking for executable files ... OK ./CellNOptR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./CellNOptR.Rcheck/00check.log:* checking for portable file names ... OK ./CellNOptR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CellNOptR.Rcheck/00check.log:* checking whether package ‘CellNOptR’ can be installed ... OK ./CellNOptR.Rcheck/00check.log:* checking installed package size ... OK ./CellNOptR.Rcheck/00check.log:* checking package directory ... OK ./CellNOptR.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CellNOptR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./CellNOptR.Rcheck/00check.log:* checking top-level files ... OK ./CellNOptR.Rcheck/00check.log:* checking for left-over files ... OK ./CellNOptR.Rcheck/00check.log:* checking index information ... OK ./CellNOptR.Rcheck/00check.log:* checking package subdirectories ... OK ./CellNOptR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CellNOptR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CellNOptR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CellNOptR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CellNOptR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CellNOptR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CellNOptR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CellNOptR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CellNOptR.Rcheck/00check.log:* checking dependencies in R code ... OK ./CellNOptR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CellNOptR.Rcheck/00check.log:* checking replacement functions ... OK ./CellNOptR.Rcheck/00check.log:* checking foreign function calls ... OK ./CellNOptR.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : rename_gates: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘%>%’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : rename_gates: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘mutate_if’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : rename_gates: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘mutate’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : rename_gates: no visible binding for global ./CellNOptR.Rcheck/00check.log: variable ‘node_in’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : rename_gates: no visible binding for global ./CellNOptR.Rcheck/00check.log: variable ‘node_out’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : simplify_gates: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘%>%’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : simplify_gates: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘filter’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : simplify_gates: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘mutate’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : simplify_gates: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘node_in’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : simplify_gates: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘node_out’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘setNames’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘%>%’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘mutate_if’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘filter’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘mutate’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘num_or’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘node_out’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘new_node_out’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘unnest’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘node_in’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘new_node_in’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘distinct’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘group_by’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘summarise’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘select’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible binding for ./CellNOptR.Rcheck/00check.log: global variable ‘or_members’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : interpret_sif_list: no visible global ./CellNOptR.Rcheck/00check.log: function definition for ‘ungroup’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : write_sif: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘%>%’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : write_sif: no visible global function ./CellNOptR.Rcheck/00check.log: definition for ‘mutate’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : write_sif: no visible binding for global ./CellNOptR.Rcheck/00check.log: variable ‘node_in’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : write_sif: no visible binding for global ./CellNOptR.Rcheck/00check.log: variable ‘node_out’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : write_sif: no visible binding for global ./CellNOptR.Rcheck/00check.log: variable ‘sign1’ ./CellNOptR.Rcheck/00check.log:build_sif_table_from_rule : write_sif: no visible binding for global ./CellNOptR.Rcheck/00check.log: variable ‘sign2’ ./CellNOptR.Rcheck/00check.log:readBND: no visible global function definition for ‘read_file’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible global function definition for ‘%>%’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible global function definition for ‘rowwise’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible global function definition for ‘mutate’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible binding for global variable ‘factors’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible binding for global variable ‘i_and_gates’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible global function definition for ‘do’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible binding for global variable ‘.’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible global function definition for ‘unnest’ ./CellNOptR.Rcheck/00check.log:readBNET: no visible global function definition for ‘ungroup’ ./CellNOptR.Rcheck/00check.log:Undefined global functions or variables: ./CellNOptR.Rcheck/00check.log: %>% . distinct do factors filter group_by i_and_gates mutate ./CellNOptR.Rcheck/00check.log: mutate_if new_node_in new_node_out node_in node_out num_or or_members ./CellNOptR.Rcheck/00check.log: read_file rowwise select setNames sign1 sign2 summarise ungroup ./CellNOptR.Rcheck/00check.log: unnest ./CellNOptR.Rcheck/00check.log:Consider adding ./CellNOptR.Rcheck/00check.log: importFrom("stats", "filter", "setNames") ./CellNOptR.Rcheck/00check.log:to your NAMESPACE file. ./CellNOptR.Rcheck/00check.log:* checking Rd files ... OK ./CellNOptR.Rcheck/00check.log:* checking Rd metadata ... OK ./CellNOptR.Rcheck/00check.log:* checking Rd cross-references ... OK ./CellNOptR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./CellNOptR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CellNOptR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./CellNOptR.Rcheck/00check.log:* checking Rd contents ... OK ./CellNOptR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CellNOptR.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./CellNOptR.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./CellNOptR.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./CellNOptR.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./CellNOptR.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./CellNOptR.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./CellNOptR.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./CellNOptR.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./CellNOptR.Rcheck/00check.log:* checking compiled code ... OK ./CellNOptR.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./CellNOptR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... NOTE ./CellNOptR.Rcheck/00check.log:The following files should probably not be installed: ./CellNOptR.Rcheck/00check.log: ‘Fig1.png’, ‘Fig5.png’ ./CellNOptR.Rcheck/00check.log:Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, ./CellNOptR.Rcheck/00check.log:or move the vignette sources from ‘inst/doc’ to ‘vignettes’. ./CellNOptR.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CellNOptR.Rcheck/00check.log:* checking examples ... WARNING ./CellNOptR.Rcheck/00check.log:Found the following significant warnings: ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log: Warning: working directory was changed to ‘/tmp/RtmpYw5Zgn’, resetting ./CellNOptR.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./CellNOptR.Rcheck/00check.log:* checking tests ... OK ./CellNOptR.Rcheck/00check.log: Running ‘test_gaBinaryT1.R’ ./CellNOptR.Rcheck/00check.log: Running ‘test_gaBinaryT2.R’ ./CellNOptR.Rcheck/00check.log: Running ‘test_gaBinaryT3.R’ ./CellNOptR.Rcheck/00check.log: Running ‘test_import_rules.R’ ./CellNOptR.Rcheck/00check.log: Running ‘test_manySteadyStates.R’ ./CellNOptR.Rcheck/00check.log: Running ‘test_priorBitString.R’ ./CellNOptR.Rcheck/00check.log: Running ‘test_simulateTN.R’ ./CellNOptR.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CellNOptR.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CellNOptR.Rcheck/00check.log:* checking running R code from vignettes ... OK ./CellNOptR.Rcheck/00check.log: ‘CellNOptR-vignette.Rnw’... OK ./CellNOptR.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./CellNOptR.Rcheck/00check.log:* checking PDF version of manual ... OK ./CellNOptR.Rcheck/00check.log:* DONE ./CellNOptR.Rcheck/00check.log:Status: 1 WARNING, 3 NOTEs CONFESS_1.13.0.tar.gz ./CONFESS.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CONFESS.Rcheck’ ./CONFESS.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./CONFESS.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CONFESS.Rcheck/00check.log:* using session charset: UTF-8 ./CONFESS.Rcheck/00check.log:* checking for file ‘CONFESS/DESCRIPTION’ ... OK ./CONFESS.Rcheck/00check.log:* checking extension type ... Package ./CONFESS.Rcheck/00check.log:* this is package ‘CONFESS’ version ‘1.13.0’ ./CONFESS.Rcheck/00check.log:* package encoding: UTF-8 ./CONFESS.Rcheck/00check.log:* checking package namespace information ... OK ./CONFESS.Rcheck/00check.log:* checking package dependencies ... OK ./CONFESS.Rcheck/00check.log:* checking if this is a source package ... OK ./CONFESS.Rcheck/00check.log:* checking if there is a namespace ... OK ./CONFESS.Rcheck/00check.log:* checking for executable files ... OK ./CONFESS.Rcheck/00check.log:* checking for hidden files and directories ... OK ./CONFESS.Rcheck/00check.log:* checking for portable file names ... OK ./CONFESS.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CONFESS.Rcheck/00check.log:* checking whether package ‘CONFESS’ can be installed ... WARNING ./CONFESS.Rcheck/00check.log:Found the following significant warnings: ./CONFESS.Rcheck/00check.log: Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’ ./CONFESS.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/CONFESS.Rcheck/00install.out’ for details. ./CONFESS.Rcheck/00check.log:* checking installed package size ... OK ./CONFESS.Rcheck/00check.log:* checking package directory ... OK ./CONFESS.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CONFESS.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./CONFESS.Rcheck/00check.log:* checking top-level files ... OK ./CONFESS.Rcheck/00check.log:* checking for left-over files ... OK ./CONFESS.Rcheck/00check.log:* checking index information ... OK ./CONFESS.Rcheck/00check.log:* checking package subdirectories ... OK ./CONFESS.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CONFESS.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CONFESS.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CONFESS.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CONFESS.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CONFESS.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CONFESS.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CONFESS.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CONFESS.Rcheck/00check.log:* checking dependencies in R code ... OK ./CONFESS.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CONFESS.Rcheck/00check.log:* checking replacement functions ... OK ./CONFESS.Rcheck/00check.log:* checking foreign function calls ... OK ./CONFESS.Rcheck/00check.log:* checking R code for possible problems ... OK ./CONFESS.Rcheck/00check.log:* checking Rd files ... OK ./CONFESS.Rcheck/00check.log:* checking Rd metadata ... OK ./CONFESS.Rcheck/00check.log:* checking Rd cross-references ... OK ./CONFESS.Rcheck/00check.log:* checking for missing documentation entries ... OK ./CONFESS.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CONFESS.Rcheck/00check.log:* checking Rd \usage sections ... OK ./CONFESS.Rcheck/00check.log:* checking Rd contents ... OK ./CONFESS.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CONFESS.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./CONFESS.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./CONFESS.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./CONFESS.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./CONFESS.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./CONFESS.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CONFESS.Rcheck/00check.log:* checking examples ... OK ./CONFESS.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CONFESS.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CONFESS.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./CONFESS.Rcheck/00check.log: ‘vignette.Rmd’using ‘UTF-8’... OK ./CONFESS.Rcheck/00check.log: ‘vignette_tex.Rnw’using ‘UTF-8’... OK ./CONFESS.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./CONFESS.Rcheck/00check.log:* checking PDF version of manual ... OK ./CONFESS.Rcheck/00check.log:* DONE ./CONFESS.Rcheck/00check.log:Status: 1 WARNING CytoML_1.11.8.tar.gz ./CytoML.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CytoML.Rcheck’ ./CytoML.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./CytoML.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CytoML.Rcheck/00check.log:* using session charset: UTF-8 ./CytoML.Rcheck/00check.log:* checking for file ‘CytoML/DESCRIPTION’ ... OK ./CytoML.Rcheck/00check.log:* checking extension type ... Package ./CytoML.Rcheck/00check.log:* this is package ‘CytoML’ version ‘1.11.8’ ./CytoML.Rcheck/00check.log:* package encoding: UTF-8 ./CytoML.Rcheck/00check.log:* checking package namespace information ... OK ./CytoML.Rcheck/00check.log:* checking package dependencies ... OK ./CytoML.Rcheck/00check.log:* checking if this is a source package ... OK ./CytoML.Rcheck/00check.log:* checking if there is a namespace ... OK ./CytoML.Rcheck/00check.log:* checking for executable files ... OK ./CytoML.Rcheck/00check.log:* checking for hidden files and directories ... OK ./CytoML.Rcheck/00check.log:* checking for portable file names ... OK ./CytoML.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CytoML.Rcheck/00check.log:* checking whether package ‘CytoML’ can be installed ... OK ./CytoML.Rcheck/00check.log:* checking installed package size ... NOTE ./CytoML.Rcheck/00check.log: installed size is 34.4Mb ./CytoML.Rcheck/00check.log: sub-directories of 1Mb or more: ./CytoML.Rcheck/00check.log: doc 2.4Mb ./CytoML.Rcheck/00check.log: extdata 4.8Mb ./CytoML.Rcheck/00check.log: lib 15.2Mb ./CytoML.Rcheck/00check.log: libs 10.9Mb ./CytoML.Rcheck/00check.log:* checking package directory ... OK ./CytoML.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CytoML.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./CytoML.Rcheck/00check.log:Package listed in more than one of Depends, Imports, Suggests, Enhances: ./CytoML.Rcheck/00check.log: ‘methods’ ./CytoML.Rcheck/00check.log:A package should be listed in only one of these fields. ./CytoML.Rcheck/00check.log:Versioned 'LinkingTo' values for ./CytoML.Rcheck/00check.log: ‘BH’ ‘RProtoBufLib’ ‘cytolib’ ./CytoML.Rcheck/00check.log:are only usable in R >= 3.0.2 ./CytoML.Rcheck/00check.log:* checking top-level files ... OK ./CytoML.Rcheck/00check.log:* checking for left-over files ... OK ./CytoML.Rcheck/00check.log:* checking index information ... OK ./CytoML.Rcheck/00check.log:* checking package subdirectories ... OK ./CytoML.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CytoML.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CytoML.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CytoML.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CytoML.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CytoML.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CytoML.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CytoML.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CytoML.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./CytoML.Rcheck/00check.log:Namespaces in Imports field not imported from: ./CytoML.Rcheck/00check.log: ‘RUnit’ ‘corpcor’ ./CytoML.Rcheck/00check.log: All declared Imports should be used. ./CytoML.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./CytoML.Rcheck/00check.log: ‘flowWorkspace:::.addGatingHierarchies’ ‘lattice:::updateList’ ./CytoML.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./CytoML.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CytoML.Rcheck/00check.log:* checking replacement functions ... OK ./CytoML.Rcheck/00check.log:* checking foreign function calls ... OK ./CytoML.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./CytoML.Rcheck/00check.log:.parse.pData: no visible binding for global variable ‘.’ ./CytoML.Rcheck/00check.log:.parseDivaWorkspace_old: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘pop_add’ ./CytoML.Rcheck/00check.log:DerivedParameterNode: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘write.csv’ ./CytoML.Rcheck/00check.log:DerivedParametersNode: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gs_get_pop_paths’ ./CytoML.Rcheck/00check.log:addCustomInfo: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_get_transformations’ ./CytoML.Rcheck/00check.log:addGate: no visible binding for global variable ‘id’ ./CytoML.Rcheck/00check.log:addGate: no visible binding for global variable ‘gate_id’ ./CytoML.Rcheck/00check.log:addGate: no visible binding for global variable ‘fcs’ ./CytoML.Rcheck/00check.log:addGate: no visible binding for global variable ‘gate_def’ ./CytoML.Rcheck/00check.log:addGate: no visible binding for global variable ‘name’ ./CytoML.Rcheck/00check.log:booleanNode: no visible global function definition for ‘filter_to_list’ ./CytoML.Rcheck/00check.log:constructPopNode: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_pop_get_gate’ ./CytoML.Rcheck/00check.log:constructPopNode : : no visible global function definition ./CytoML.Rcheck/00check.log: for ‘gh_pop_get_gate’ ./CytoML.Rcheck/00check.log:constructTree: no visible binding for global variable ‘id’ ./CytoML.Rcheck/00check.log:constructTree: no visible binding for global variable ‘name’ ./CytoML.Rcheck/00check.log:createTransformIdentifier: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘slotNames’ ./CytoML.Rcheck/00check.log:cytobank_to_gatingset.cytobank_experiment: no visible binding for ./CytoML.Rcheck/00check.log: global variable ‘desc’ ./CytoML.Rcheck/00check.log:diva_to_gatingset: no visible binding for global variable ‘specimen’ ./CytoML.Rcheck/00check.log:diva_to_gatingset: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘sampleSelected’ ./CytoML.Rcheck/00check.log:export_comp_trans: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_get_compensations’ ./CytoML.Rcheck/00check.log:export_comp_trans: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_get_transformations’ ./CytoML.Rcheck/00check.log:export_gates_cytobank: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gs_get_pop_paths’ ./CytoML.Rcheck/00check.log:export_gates_cytobank: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gs_pop_get_gate’ ./CytoML.Rcheck/00check.log:extend.polygonGate: no visible binding for global variable ‘..dim’ ./CytoML.Rcheck/00check.log:extend.polygonGate : : no visible binding for global ./CytoML.Rcheck/00check.log: variable ‘y’ ./CytoML.Rcheck/00check.log:extend.polygonGate : : no visible binding for global ./CytoML.Rcheck/00check.log: variable ‘x’ ./CytoML.Rcheck/00check.log:extend.polygonGate: no visible binding for global variable ‘id’ ./CytoML.Rcheck/00check.log:extend.polygonGate: no visible binding for global variable ‘x’ ./CytoML.Rcheck/00check.log:extend.polygonGate: no visible binding for global variable ‘y’ ./CytoML.Rcheck/00check.log:extend.polygonGate: no visible binding for global variable ‘is.smaller’ ./CytoML.Rcheck/00check.log:flinTr: no visible global function definition for ‘lintGml2’ ./CytoML.Rcheck/00check.log:flowjo_to_gatingset: no visible binding for global variable ‘groupName’ ./CytoML.Rcheck/00check.log:fratioTr: no visible global function definition for ‘ratiotGml2’ ./CytoML.Rcheck/00check.log:getSpilloverMat: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_get_compensations’ ./CytoML.Rcheck/00check.log:gs_compare_cytobank_counts: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘population’ ./CytoML.Rcheck/00check.log:gs_compare_cytobank_counts: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘parent’ ./CytoML.Rcheck/00check.log:gs_compare_cytobank_counts: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘count’ ./CytoML.Rcheck/00check.log:gs_compare_cytobank_counts: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘parent_count’ ./CytoML.Rcheck/00check.log:gs_compare_cytobank_counts: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘.’ ./CytoML.Rcheck/00check.log:gs_compare_cytobank_counts: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘fcs_filename’ ./CytoML.Rcheck/00check.log:hyperlogTr: no visible global function definition for ‘hyperlogtGml2’ ./CytoML.Rcheck/00check.log:open_cytobank_experiment: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘unzip’ ./CytoML.Rcheck/00check.log:range.GatingHierarchy: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_get_transformations’ ./CytoML.Rcheck/00check.log:read.gatingML.cytobank: no visible binding for global variable ‘id’ ./CytoML.Rcheck/00check.log:read.gatingML.cytobank: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘comp_ref’ ./CytoML.Rcheck/00check.log:sampleNode: no visible global function definition for ‘gh_pop_get_gate’ ./CytoML.Rcheck/00check.log:sampleNode: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_get_transformations’ ./CytoML.Rcheck/00check.log:transDg1polynomial: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘dg1polynomial’ ./CytoML.Rcheck/00check.log:transEH: no visible global function definition for ‘EHtrans’ ./CytoML.Rcheck/00check.log:transExponential: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘exponential’ ./CytoML.Rcheck/00check.log:transHyperLog: no visible global function definition for ‘hyperlog’ ./CytoML.Rcheck/00check.log:transHyperbolicSin: no visible global function definition for ‘sinht’ ./CytoML.Rcheck/00check.log:transInvSplitScale: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘invsplitscale’ ./CytoML.Rcheck/00check.log:transInverseHyperbolicSin: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘asinht’ ./CytoML.Rcheck/00check.log:transLogarithm: no visible global function definition for ‘logarithm’ ./CytoML.Rcheck/00check.log:transQuadratic: no visible global function definition for ‘quadratic’ ./CytoML.Rcheck/00check.log:transRatio: no visible global function definition for ‘ratio’ ./CytoML.Rcheck/00check.log:transSplitScale: no visible global function definition for ‘splitscale’ ./CytoML.Rcheck/00check.log:transSquareroot: no visible global function definition for ‘squareroot’ ./CytoML.Rcheck/00check.log:transformationNode: no visible global function definition for ./CytoML.Rcheck/00check.log: ‘gh_get_transformations’ ./CytoML.Rcheck/00check.log:write.gatingML: no visible global function definition for ‘sessionInfo’ ./CytoML.Rcheck/00check.log:identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate: ./CytoML.Rcheck/00check.log: no visible binding for global variable ‘expressionFilter’ ./CytoML.Rcheck/00check.log:identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate: ./CytoML.Rcheck/00check.log: no visible global function definition for ‘polytopeGate’ ./CytoML.Rcheck/00check.log:identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix: ./CytoML.Rcheck/00check.log: no visible global function definition for ‘pseudoinverse’ ./CytoML.Rcheck/00check.log:show,flowjo_workspace: no visible global function definition for ‘.’ ./CytoML.Rcheck/00check.log:show,flowjo_workspace: no visible binding for global variable ./CytoML.Rcheck/00check.log: ‘groupName’ ./CytoML.Rcheck/00check.log:Undefined global functions or variables: ./CytoML.Rcheck/00check.log: . ..dim EHtrans asinht comp_ref count desc dg1polynomial exponential ./CytoML.Rcheck/00check.log: expressionFilter fcs fcs_filename filter_to_list gate_def gate_id ./CytoML.Rcheck/00check.log: gh_get_compensations gh_get_transformations gh_pop_get_gate groupName ./CytoML.Rcheck/00check.log: gs_get_pop_paths gs_pop_get_gate hyperlog hyperlogtGml2 id ./CytoML.Rcheck/00check.log: invsplitscale is.smaller lintGml2 logarithm name parent parent_count ./CytoML.Rcheck/00check.log: polytopeGate pop_add population pseudoinverse quadratic ratio ./CytoML.Rcheck/00check.log: ratiotGml2 sampleSelected sessionInfo sinht slotNames specimen ./CytoML.Rcheck/00check.log: splitscale squareroot unzip write.csv x y ./CytoML.Rcheck/00check.log:Consider adding ./CytoML.Rcheck/00check.log: importFrom("methods", "slotNames") ./CytoML.Rcheck/00check.log: importFrom("utils", "sessionInfo", "unzip", "write.csv") ./CytoML.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./CytoML.Rcheck/00check.log:* checking Rd files ... OK ./CytoML.Rcheck/00check.log:* checking Rd metadata ... OK ./CytoML.Rcheck/00check.log:* checking Rd cross-references ... OK ./CytoML.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./CytoML.Rcheck/00check.log:Undocumented code objects: ./CytoML.Rcheck/00check.log: ‘ce_get_cmpensations’ ‘ce_get_transformations’ ‘parseWorkspace’ ./CytoML.Rcheck/00check.log:Undocumented S4 methods: ./CytoML.Rcheck/00check.log: generic 'colnames' and siglist 'cytobank_experiment' ./CytoML.Rcheck/00check.log: generic 'markernames' and siglist 'cytobank_experiment' ./CytoML.Rcheck/00check.log: generic 'pData' and siglist 'cytobank_experiment' ./CytoML.Rcheck/00check.log: generic 'sampleNames' and siglist 'cytobank_experiment' ./CytoML.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./CytoML.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./CytoML.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CytoML.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./CytoML.Rcheck/00check.log:Undocumented arguments in documentation object 'diva_workspace-class' ./CytoML.Rcheck/00check.log: ‘name’ ‘subset’ ‘path’ ‘fast’ ‘worksheet’ ‘swap_cols’ ‘verbose’ ./CytoML.Rcheck/00check.log:Undocumented arguments in documentation object 'getSampleGroups' ./CytoML.Rcheck/00check.log: ‘...’ ./CytoML.Rcheck/00check.log:Undocumented arguments in documentation object 'parseWorkspace,flowjo_workspace-method' ./CytoML.Rcheck/00check.log: ‘name’ ‘subset’ ‘requiregates’ ‘sampNloc’ ‘additional.keys’ ./CytoML.Rcheck/00check.log: ‘additional.sampleID’ ‘keywords’ ‘keywords.source’ ‘execute’ ‘path’ ./CytoML.Rcheck/00check.log: ‘keyword.ignore.case’ ./CytoML.Rcheck/00check.log:Undocumented arguments in documentation object 'getSamples' ./CytoML.Rcheck/00check.log: ‘...’ ./CytoML.Rcheck/00check.log:Undocumented arguments in documentation object 'cytobankExperiment' ./CytoML.Rcheck/00check.log: ‘...’ ./CytoML.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./CytoML.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./CytoML.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./CytoML.Rcheck/00check.log:* checking Rd contents ... OK ./CytoML.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CytoML.Rcheck/00check.log:* checking line endings in shell scripts ... OK ./CytoML.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./CytoML.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./CytoML.Rcheck/00check.log:* checking compilation flags in Makevars ... NOTE ./CytoML.Rcheck/00check.log:Package has both ‘src/Makevars.in’ and ‘src/Makevars’. ./CytoML.Rcheck/00check.log:Installation with --no-configure' is unlikely to work. If you intended ./CytoML.Rcheck/00check.log:‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ ./CytoML.Rcheck/00check.log:otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ./CytoML.Rcheck/00check.log:‘cleanup’ script. ./CytoML.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... NOTE ./CytoML.Rcheck/00check.log:GNU make is a SystemRequirements. ./CytoML.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./CytoML.Rcheck/00check.log:* checking compiled code ... NOTE ./CytoML.Rcheck/00check.log:File ‘CytoML/libs/CytoML.so’: ./CytoML.Rcheck/00check.log: Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) ./CytoML.Rcheck/00check.log: Object: ‘parseFlowJoWorkspace.o’ ./CytoML.Rcheck/00check.log:Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. ./CytoML.Rcheck/00check.log:See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ./CytoML.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./CytoML.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CytoML.Rcheck/00check.log:* checking examples ... OK ./CytoML.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./CytoML.Rcheck/00check.log:* checking tests ... OK ./CytoML.Rcheck/00check.log: Running ‘testthat.R’ ./CytoML.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CytoML.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CytoML.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./CytoML.Rcheck/00check.log: ‘HowToExportGatingSet.Rmd’using ‘UTF-8’... OK ./CytoML.Rcheck/00check.log: ‘cytobank2GatingSet.Rmd’using ‘UTF-8’... OK ./CytoML.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./CytoML.Rcheck/00check.log:* checking PDF version of manual ... OK ./CytoML.Rcheck/00check.log:* DONE ./CytoML.Rcheck/00check.log:Status: 2 WARNINGs, 7 NOTEs ELMER_2.9.5.tar.gz ./ELMER.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ELMER.Rcheck’ ./ELMER.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./ELMER.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ELMER.Rcheck/00check.log:* using session charset: UTF-8 ./ELMER.Rcheck/00check.log:* checking for file ‘ELMER/DESCRIPTION’ ... OK ./ELMER.Rcheck/00check.log:* this is package ‘ELMER’ version ‘2.9.5’ ./ELMER.Rcheck/00check.log:* package encoding: UTF-8 ./ELMER.Rcheck/00check.log:* checking package namespace information ... OK ./ELMER.Rcheck/00check.log:* checking package dependencies ... OK ./ELMER.Rcheck/00check.log:* checking if this is a source package ... OK ./ELMER.Rcheck/00check.log:* checking if there is a namespace ... OK ./ELMER.Rcheck/00check.log:* checking for executable files ... OK ./ELMER.Rcheck/00check.log:* checking for hidden files and directories ... OK ./ELMER.Rcheck/00check.log:* checking for portable file names ... OK ./ELMER.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ELMER.Rcheck/00check.log:* checking whether package ‘ELMER’ can be installed ... OK ./ELMER.Rcheck/00check.log:* checking installed package size ... NOTE ./ELMER.Rcheck/00check.log: installed size is 75.6Mb ./ELMER.Rcheck/00check.log: sub-directories of 1Mb or more: ./ELMER.Rcheck/00check.log: doc 75.1Mb ./ELMER.Rcheck/00check.log:* checking package directory ... OK ./ELMER.Rcheck/00check.log:* checking ‘build’ directory ... OK ./ELMER.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ELMER.Rcheck/00check.log:* checking top-level files ... OK ./ELMER.Rcheck/00check.log:* checking for left-over files ... OK ./ELMER.Rcheck/00check.log:* checking index information ... OK ./ELMER.Rcheck/00check.log:* checking package subdirectories ... OK ./ELMER.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ELMER.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ELMER.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ELMER.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ELMER.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ELMER.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ELMER.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ELMER.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ELMER.Rcheck/00check.log:* checking dependencies in R code ... OK ./ELMER.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ELMER.Rcheck/00check.log:* checking replacement functions ... OK ./ELMER.Rcheck/00check.log:* checking foreign function calls ... OK ./ELMER.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./ELMER.Rcheck/00check.log:addMutCol: no visible binding for global variable 'Hugo_Symbol' ./ELMER.Rcheck/00check.log:calcDistNearestTSS: no visible binding for global variable ./ELMER.Rcheck/00check.log: 'DistanceTSS' ./ELMER.Rcheck/00check.log:getRegionNearGenes : f: no visible binding for global variable 'Side' ./ELMER.Rcheck/00check.log:getRegionNearGenes: no visible binding for global variable 'ID' ./ELMER.Rcheck/00check.log:getTFtargets: no visible binding for global variable 'TF' ./ELMER.Rcheck/00check.log:heatmapGene: no visible global function definition for 'melt' ./ELMER.Rcheck/00check.log:heatmapGene: no visible binding for global variable 'mae' ./ELMER.Rcheck/00check.log:heatmapGene: no visible global function definition for 'stat_cor' ./ELMER.Rcheck/00check.log:Undefined global functions or variables: ./ELMER.Rcheck/00check.log: DistanceTSS Hugo_Symbol ID Side TF mae melt stat_cor ./ELMER.Rcheck/00check.log:* checking Rd files ... OK ./ELMER.Rcheck/00check.log:* checking Rd metadata ... OK ./ELMER.Rcheck/00check.log:* checking Rd cross-references ... OK ./ELMER.Rcheck/00check.log:* checking for missing documentation entries ... OK ./ELMER.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ELMER.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./ELMER.Rcheck/00check.log:Undocumented arguments in documentation object 'heatmapGene' ./ELMER.Rcheck/00check.log: ‘correlation.method’ ‘scatter.plot.width’ ‘scatter.plot.height’ ./ELMER.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./ELMER.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./ELMER.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./ELMER.Rcheck/00check.log:* checking Rd contents ... OK ./ELMER.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ELMER.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./ELMER.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./ELMER.Rcheck/00check.log:* checking examples ... OK ./ELMER.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./ELMER.Rcheck/00check.log:* checking tests ... OK ./ELMER.Rcheck/00check.log: Running ‘testthat.R’ ./ELMER.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./ELMER.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./ELMER.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./ELMER.Rcheck/00check.log: ‘analysis_data_input.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘analysis_diff_meth.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘analysis_get_pair.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘analysis_gui.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘analysis_motif_enrichment.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘analysis_regulatory_tf.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘index.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘input.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘pipe.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘plots_TF.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘plots_heatmap.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘plots_motif_enrichment.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘plots_scatter.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘plots_schematic.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log: ‘usecase.Rmd’using ‘UTF-8’... OK ./ELMER.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./ELMER.Rcheck/00check.log:Error(s) in re-building vignettes: ./ELMER.Rcheck/00check.log:--- re-building ‘analysis_data_input.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Loading required package: ELMER.data ./ELMER.Rcheck/00check.log:Attaching package: 'dplyr' ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:stats': ./ELMER.Rcheck/00check.log: filter, lag ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:base': ./ELMER.Rcheck/00check.log: intersect, setdiff, setequal, union ./ELMER.Rcheck/00check.log:Returning distal probes: 15561 ./ELMER.Rcheck/00check.log:Loading required package: SummarizedExperiment ./ELMER.Rcheck/00check.log:Loading required package: GenomicRanges ./ELMER.Rcheck/00check.log:Loading required package: stats4 ./ELMER.Rcheck/00check.log:Loading required package: BiocGenerics ./ELMER.Rcheck/00check.log:Loading required package: parallel ./ELMER.Rcheck/00check.log:Attaching package: 'BiocGenerics' ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:parallel': ./ELMER.Rcheck/00check.log: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, ./ELMER.Rcheck/00check.log: clusterExport, clusterMap, parApply, parCapply, parLapply, ./ELMER.Rcheck/00check.log: parLapplyLB, parRapply, parSapply, parSapplyLB ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:dplyr': ./ELMER.Rcheck/00check.log: combine, intersect, setdiff, union ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:stats': ./ELMER.Rcheck/00check.log: IQR, mad, sd, var, xtabs ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:base': ./ELMER.Rcheck/00check.log: Filter, Find, Map, Position, Reduce, anyDuplicated, append, ./ELMER.Rcheck/00check.log: as.data.frame, basename, cbind, colnames, dirname, do.call, ./ELMER.Rcheck/00check.log: duplicated, eval, evalq, get, grep, grepl, intersect, ./ELMER.Rcheck/00check.log: is.unsorted, lapply, mapply, match, mget, order, paste, pmax, ./ELMER.Rcheck/00check.log: pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, ./ELMER.Rcheck/00check.log: setdiff, sort, table, tapply, union, unique, unsplit, which, ./ELMER.Rcheck/00check.log: which.max, which.min ./ELMER.Rcheck/00check.log:Loading required package: S4Vectors ./ELMER.Rcheck/00check.log:Attaching package: 'S4Vectors' ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:dplyr': ./ELMER.Rcheck/00check.log: first, rename ./ELMER.Rcheck/00check.log:The following object is masked from 'package:base': ./ELMER.Rcheck/00check.log: expand.grid ./ELMER.Rcheck/00check.log:Loading required package: IRanges ./ELMER.Rcheck/00check.log:Attaching package: 'IRanges' ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:dplyr': ./ELMER.Rcheck/00check.log: collapse, desc, slice ./ELMER.Rcheck/00check.log:Loading required package: GenomeInfoDb ./ELMER.Rcheck/00check.log:Loading required package: Biobase ./ELMER.Rcheck/00check.log:Welcome to Bioconductor ./ELMER.Rcheck/00check.log: Vignettes contain introductory material; view with ./ELMER.Rcheck/00check.log: 'browseVignettes()'. To cite Bioconductor, see ./ELMER.Rcheck/00check.log: 'citation("Biobase")', and for packages 'citation("pkgname")'. ./ELMER.Rcheck/00check.log:Loading required package: DelayedArray ./ELMER.Rcheck/00check.log:Loading required package: matrixStats ./ELMER.Rcheck/00check.log:Attaching package: 'matrixStats' ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:Biobase': ./ELMER.Rcheck/00check.log: anyMissing, rowMedians ./ELMER.Rcheck/00check.log:The following object is masked from 'package:dplyr': ./ELMER.Rcheck/00check.log: count ./ELMER.Rcheck/00check.log:Loading required package: BiocParallel ./ELMER.Rcheck/00check.log:Attaching package: 'DelayedArray' ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:matrixStats': ./ELMER.Rcheck/00check.log: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:base': ./ELMER.Rcheck/00check.log: aperm, apply, rowsum ./ELMER.Rcheck/00check.log:=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ./ELMER.Rcheck/00check.log:Creating a SummarizedExperiment from gene expression input ./ELMER.Rcheck/00check.log:=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ./ELMER.Rcheck/00check.log:Creating a SummarizedExperiment from DNA methylation input ./ELMER.Rcheck/00check.log:Checking if samples have both DNA methylation and Gene expression and if they are in the same order... ./ELMER.Rcheck/00check.log:Starting to add information to samples ./ELMER.Rcheck/00check.log: => Add clinical information to samples ./ELMER.Rcheck/00check.log:Add FFPE information. More information at: ./ELMER.Rcheck/00check.log:=> https://cancergenome.nih.gov/cancersselected/biospeccriteria ./ELMER.Rcheck/00check.log:=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html ./ELMER.Rcheck/00check.log: => Adding subtype information to samples ./ELMER.Rcheck/00check.log:lusc subtype information from:doi:10.1038/nature11404 ./ELMER.Rcheck/00check.log:Creating MultiAssayExperiment ./ELMER.Rcheck/00check.log:MAE saved as: mae.rda ./ELMER.Rcheck/00check.log:--- finished re-building ‘analysis_data_input.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘analysis_diff_meth.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Quitting from lines 59-70 (analysis_diff_meth.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'analysis_diff_meth.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:could not find function "get.diff.meth" ./ELMER.Rcheck/00check.log:--- failed re-building ‘analysis_diff_meth.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘analysis_get_pair.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Loading required package: ELMER.data ./ELMER.Rcheck/00check.log:Attaching package: 'dplyr' ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:stats': ./ELMER.Rcheck/00check.log: filter, lag ./ELMER.Rcheck/00check.log:The following objects are masked from 'package:base': ./ELMER.Rcheck/00check.log: intersect, setdiff, setequal, union ./ELMER.Rcheck/00check.log:Warning in file(file, "rt") : ./ELMER.Rcheck/00check.log: cannot open file 'result/getMethdiff.hypo.probes.significant.csv': No such file or directory ./ELMER.Rcheck/00check.log:Quitting from lines 107-131 (analysis_get_pair.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'analysis_get_pair.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:cannot open the connection ./ELMER.Rcheck/00check.log:--- failed re-building ‘analysis_get_pair.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘analysis_gui.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Loading required package: ELMER.data ./ELMER.Rcheck/00check.log:--- finished re-building ‘analysis_gui.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘analysis_motif_enrichment.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Warning in file(file, "rt") : ./ELMER.Rcheck/00check.log: cannot open file 'result/getMethdiff.hypo.probes.significant.csv': No such file or directory ./ELMER.Rcheck/00check.log:Quitting from lines 58-72 (analysis_motif_enrichment.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:cannot open the connection ./ELMER.Rcheck/00check.log:--- failed re-building ‘analysis_motif_enrichment.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Warning in readChar(con, 5L, useBytes = TRUE) : ./ELMER.Rcheck/00check.log: cannot open compressed file 'result/getMotif.hypo.enriched.motifs.rda', probable reason 'No such file or directory' ./ELMER.Rcheck/00check.log:Quitting from lines 78-81 (analysis_regulatory_tf.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'analysis_regulatory_tf.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:cannot open the connection ./ELMER.Rcheck/00check.log:--- failed re-building ‘analysis_regulatory_tf.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘index.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:--- finished re-building ‘index.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘input.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Warning in data(elmer.data.example) : ./ELMER.Rcheck/00check.log: data set 'elmer.data.example' not found ./ELMER.Rcheck/00check.log:Warning in data(LUSC_meth_refined) : ./ELMER.Rcheck/00check.log: data set 'LUSC_meth_refined' not found ./ELMER.Rcheck/00check.log:Warning in data(LUSC_RNA_refined) : ./ELMER.Rcheck/00check.log: data set 'LUSC_RNA_refined' not found ./ELMER.Rcheck/00check.log:Quitting from lines 67-71 (input.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'input.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:object 'Meth' not found ./ELMER.Rcheck/00check.log:--- failed re-building ‘input.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘pipe.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:--- finished re-building ‘pipe.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘plots_TF.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Quitting from lines 33-38 (plots_TF.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'plots_TF.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:cannot open the connection ./ELMER.Rcheck/00check.log:--- failed re-building ‘plots_TF.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘plots_heatmap.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:--- finished re-building ‘plots_heatmap.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘plots_motif_enrichment.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Quitting from lines 28-32 (plots_motif_enrichment.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'plots_motif_enrichment.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:could not find function "motif.enrichment.plot" ./ELMER.Rcheck/00check.log:--- failed re-building ‘plots_motif_enrichment.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘plots_scatter.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Quitting from lines 37-42 (plots_scatter.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'plots_scatter.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:could not find function "scatter.plot" ./ELMER.Rcheck/00check.log:--- failed re-building ‘plots_scatter.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘plots_schematic.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:Warning in file(file, "rt") : ./ELMER.Rcheck/00check.log: cannot open file 'result/getPair.hypo.pairs.significant.csv': No such file or directory ./ELMER.Rcheck/00check.log:Quitting from lines 25-28 (plots_schematic.Rmd) ./ELMER.Rcheck/00check.log:Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics: ./ELMER.Rcheck/00check.log:cannot open the connection ./ELMER.Rcheck/00check.log:--- failed re-building ‘plots_schematic.Rmd’ ./ELMER.Rcheck/00check.log:--- re-building ‘usecase.Rmd’ using rmarkdown ./ELMER.Rcheck/00check.log:--- finished re-building ‘usecase.Rmd’ ./ELMER.Rcheck/00check.log:SUMMARY: processing the following files failed: ./ELMER.Rcheck/00check.log: ‘analysis_diff_meth.Rmd’ ‘analysis_get_pair.Rmd’ ./ELMER.Rcheck/00check.log: ‘analysis_motif_enrichment.Rmd’ ‘analysis_regulatory_tf.Rmd’ ./ELMER.Rcheck/00check.log: ‘input.Rmd’ ‘plots_TF.Rmd’ ‘plots_motif_enrichment.Rmd’ ./ELMER.Rcheck/00check.log: ‘plots_scatter.Rmd’ ‘plots_schematic.Rmd’ ./ELMER.Rcheck/00check.log:Error: Vignette re-building failed. ./ELMER.Rcheck/00check.log:Execution halted ./ELMER.Rcheck/00check.log:* checking PDF version of manual ... OK ./ELMER.Rcheck/00check.log:* DONE ./ELMER.Rcheck/00check.log:Status: 2 WARNINGs, 2 NOTEs eQTL_1.9.0.tar.gz ./eQTL.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/eQTL.Rcheck’ ./eQTL.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./eQTL.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./eQTL.Rcheck/00check.log:* using session charset: UTF-8 ./eQTL.Rcheck/00check.log:* checking for file ‘eQTL/DESCRIPTION’ ... OK ./eQTL.Rcheck/00check.log:* this is package ‘eQTL’ version ‘1.9.0’ ./eQTL.Rcheck/00check.log:* package encoding: UTF-8 ./eQTL.Rcheck/00check.log:* checking package namespace information ... OK ./eQTL.Rcheck/00check.log:* checking package dependencies ... NOTE ./eQTL.Rcheck/00check.log:Depends: includes the non-default packages: ./eQTL.Rcheck/00check.log: 'GGdata', 'GGtools', 'GenomeInfoDb', 'S4Vectors', 'SNPlocs.Hsapiens.dbSNP144.GRCh37', 'bibtex', 'biglm', 'data.table', 'doParallel', 'foreach', 'knitcitations', 'lumi', ./eQTL.Rcheck/00check.log: 'lumiHumanAll.db', 'parallel', 'rmeta', 'scatterplot3d', 'snpStats', 'grid', 'yri1kgv' ./eQTL.Rcheck/00check.log:Adding so many packages to the search path is excessive and importing selectively is preferable. ./eQTL.Rcheck/00check.log:* checking if this is a source package ... OK ./eQTL.Rcheck/00check.log:* checking if there is a namespace ... OK ./eQTL.Rcheck/00check.log:* checking for executable files ... OK ./eQTL.Rcheck/00check.log:* checking for hidden files and directories ... OK ./eQTL.Rcheck/00check.log:* checking for portable file names ... OK ./eQTL.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./eQTL.Rcheck/00check.log:* checking whether package ‘eQTL’ can be installed ... OK ./eQTL.Rcheck/00check.log:* checking installed package size ... NOTE ./eQTL.Rcheck/00check.log: installed size is 58.9Mb ./eQTL.Rcheck/00check.log: sub-directories of 1Mb or more: ./eQTL.Rcheck/00check.log: data 57.9Mb ./eQTL.Rcheck/00check.log:* checking package directory ... OK ./eQTL.Rcheck/00check.log:* checking ‘build’ directory ... OK ./eQTL.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./eQTL.Rcheck/00check.log:* checking top-level files ... OK ./eQTL.Rcheck/00check.log:* checking for left-over files ... OK ./eQTL.Rcheck/00check.log:* checking index information ... OK ./eQTL.Rcheck/00check.log:* checking package subdirectories ... OK ./eQTL.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./eQTL.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./eQTL.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./eQTL.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./eQTL.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./eQTL.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./eQTL.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./eQTL.Rcheck/00check.log:Undocumented code objects: ./eQTL.Rcheck/00check.log: 'partceu100k_dt' 'sensSave' ./eQTL.Rcheck/00check.log:Undocumented data sets: ./eQTL.Rcheck/00check.log: 'partceu100k_dt' 'sensSave' ./eQTL.Rcheck/00check.log:All user-level objects in a package should have documentation entries. ./eQTL.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./eQTL.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./eQTL.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./eQTL.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... WARNING ./eQTL.Rcheck/00check.log: ./eQTL.Rcheck/00check.log: Note: significantly better compression could be obtained ./eQTL.Rcheck/00check.log: by using R CMD build --resave-data ./eQTL.Rcheck/00check.log: old_size new_size compress ./eQTL.Rcheck/00check.log: partceu100k_dt.rda 58.4Mb 35.1Mb xz ./eQTL.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./eQTL.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./eQTL.Rcheck/00check.log:* checking examples ... NONE ./eQTL.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... NOTE ./eQTL.Rcheck/00check.log:'library' or 'require' calls not declared from: ./eQTL.Rcheck/00check.log: ‘ggplot2’ ‘reshape2’ ./eQTL.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./eQTL.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./eQTL.Rcheck/00check.log: ‘cloudeqtl.Rmd’using ‘UTF-8’... OK ./eQTL.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./eQTL.Rcheck/00check.log:* checking PDF version of manual ... OK ./eQTL.Rcheck/00check.log:* DONE ./eQTL.Rcheck/00check.log:Status: 2 WARNINGs, 3 NOTEs flowWorkspace_3.33.7.tar.gz ./flowWorkspace.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/flowWorkspace.Rcheck’ ./flowWorkspace.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./flowWorkspace.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./flowWorkspace.Rcheck/00check.log:* using session charset: UTF-8 ./flowWorkspace.Rcheck/00check.log:* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK ./flowWorkspace.Rcheck/00check.log:* checking extension type ... Package ./flowWorkspace.Rcheck/00check.log:* this is package ‘flowWorkspace’ version ‘3.33.7’ ./flowWorkspace.Rcheck/00check.log:* package encoding: UTF-8 ./flowWorkspace.Rcheck/00check.log:* checking package namespace information ... OK ./flowWorkspace.Rcheck/00check.log:* checking package dependencies ... OK ./flowWorkspace.Rcheck/00check.log:* checking if this is a source package ... OK ./flowWorkspace.Rcheck/00check.log:* checking if there is a namespace ... OK ./flowWorkspace.Rcheck/00check.log:* checking for executable files ... OK ./flowWorkspace.Rcheck/00check.log:* checking for hidden files and directories ... OK ./flowWorkspace.Rcheck/00check.log:* checking for portable file names ... OK ./flowWorkspace.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./flowWorkspace.Rcheck/00check.log:* checking whether package ‘flowWorkspace’ can be installed ... OK ./flowWorkspace.Rcheck/00check.log:* checking installed package size ... NOTE ./flowWorkspace.Rcheck/00check.log: installed size is 80.7Mb ./flowWorkspace.Rcheck/00check.log: sub-directories of 1Mb or more: ./flowWorkspace.Rcheck/00check.log: doc 1.4Mb ./flowWorkspace.Rcheck/00check.log: lib 56.0Mb ./flowWorkspace.Rcheck/00check.log: libs 22.3Mb ./flowWorkspace.Rcheck/00check.log:* checking package directory ... OK ./flowWorkspace.Rcheck/00check.log:* checking ‘build’ directory ... OK ./flowWorkspace.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./flowWorkspace.Rcheck/00check.log:Malformed Title field: should not end in a period. ./flowWorkspace.Rcheck/00check.log:Versioned 'LinkingTo' values for ./flowWorkspace.Rcheck/00check.log: ‘BH’ ‘RProtoBufLib’ ‘cytolib’ ./flowWorkspace.Rcheck/00check.log:are only usable in R >= 3.0.2 ./flowWorkspace.Rcheck/00check.log:* checking top-level files ... OK ./flowWorkspace.Rcheck/00check.log:* checking for left-over files ... OK ./flowWorkspace.Rcheck/00check.log:* checking index information ... OK ./flowWorkspace.Rcheck/00check.log:* checking package subdirectories ... OK ./flowWorkspace.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./flowWorkspace.Rcheck/00check.log:* checking R files for syntax errors ... OK ./flowWorkspace.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./flowWorkspace.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./flowWorkspace.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./flowWorkspace.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./flowWorkspace.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./flowWorkspace.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./flowWorkspace.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./flowWorkspace.Rcheck/00check.log:Namespaces in Imports field not imported from: ./flowWorkspace.Rcheck/00check.log: ‘RBGL’ ‘grDevices’ ‘graphics’ ‘utils’ ./flowWorkspace.Rcheck/00check.log: All declared Imports should be used. ./flowWorkspace.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./flowWorkspace.Rcheck/00check.log: ‘flowCore:::.estimateLogicle’ ‘flowCore:::checkClass’ ./flowWorkspace.Rcheck/00check.log: ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’ ./flowWorkspace.Rcheck/00check.log: ‘flowCore:::logicle_transform’ ‘flowCore:::updateTransformKeywords’ ./flowWorkspace.Rcheck/00check.log: ‘graph:::.makeEdgeKeys’ ‘lattice:::updateList’ ./flowWorkspace.Rcheck/00check.log: ‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’ ./flowWorkspace.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./flowWorkspace.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./flowWorkspace.Rcheck/00check.log:* checking replacement functions ... OK ./flowWorkspace.Rcheck/00check.log:* checking foreign function calls ... OK ./flowWorkspace.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./flowWorkspace.Rcheck/00check.log:.addGatingHierarchies: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:.addGatingHierarchies : : no visible global function ./flowWorkspace.Rcheck/00check.log: definition for ‘fj_ws_get_keywords’ ./flowWorkspace.Rcheck/00check.log:.computeCV : : no visible binding for global variable ./flowWorkspace.Rcheck/00check.log: ‘xml.count’ ./flowWorkspace.Rcheck/00check.log:.computeCV : : no visible binding for global variable ./flowWorkspace.Rcheck/00check.log: ‘openCyto.count’ ./flowWorkspace.Rcheck/00check.log:.computeCV : : : no visible global function ./flowWorkspace.Rcheck/00check.log: definition for ‘IQR’ ./flowWorkspace.Rcheck/00check.log:.computeCV : : : no visible global function ./flowWorkspace.Rcheck/00check.log: definition for ‘median’ ./flowWorkspace.Rcheck/00check.log:.computeCV_gh : : no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘IQR’ ./flowWorkspace.Rcheck/00check.log:.computeCV_gh : : no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘median’ ./flowWorkspace.Rcheck/00check.log:.graph_handler : asGraphNEL: no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘new’ ./flowWorkspace.Rcheck/00check.log:.graph_handler : asGraphNEL: no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘validObject’ ./flowWorkspace.Rcheck/00check.log:.load_gs: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:.load_gs: no visible global function definition for ‘.hasSlot’ ./flowWorkspace.Rcheck/00check.log:.load_gs: no visible global function definition for ‘slot’ ./flowWorkspace.Rcheck/00check.log:.load_gs: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:.mergeGates : : no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘extends’ ./flowWorkspace.Rcheck/00check.log:.plotGate: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:.plotGate: no visible global function definition for ‘as.formula’ ./flowWorkspace.Rcheck/00check.log:.preplot: no visible global function definition for ‘as’ ./flowWorkspace.Rcheck/00check.log:.preprocessMap: no visible binding for global variable ‘old’ ./flowWorkspace.Rcheck/00check.log:.preprocessMap: no visible binding for global variable ‘.’ ./flowWorkspace.Rcheck/00check.log:GatingSetList: no visible global function definition for ‘as’ ./flowWorkspace.Rcheck/00check.log:GatingSetList: no visible global function definition for ‘validObject’ ./flowWorkspace.Rcheck/00check.log:booleanFilter: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:booleanFilter: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:char2booleanFilter: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:flowWorkspace.par.init: no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘gray’ ./flowWorkspace.Rcheck/00check.log:gh_apply_to_new_fcs: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:gh_pop_compare_stats: no visible binding for global variable ‘node’ ./flowWorkspace.Rcheck/00check.log:gh_pop_get_count: no visible binding for global variable ‘count’ ./flowWorkspace.Rcheck/00check.log:gh_pop_get_proportion: no visible binding for global variable ‘percent’ ./flowWorkspace.Rcheck/00check.log:gs_get_singlecell_expression: no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘is’ ./flowWorkspace.Rcheck/00check.log:gs_get_singlecell_expression: no visible binding for global variable ./flowWorkspace.Rcheck/00check.log: ‘parallel’ ./flowWorkspace.Rcheck/00check.log:gs_pop_add: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:gs_pop_get_count_fast: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:gs_pop_get_count_with_meta: no visible binding for global variable ./flowWorkspace.Rcheck/00check.log: ‘sampleName’ ./flowWorkspace.Rcheck/00check.log:gs_pop_set_gate: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:gs_remove_redundant_nodes : : no visible global function ./flowWorkspace.Rcheck/00check.log: definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:gslist_to_gs: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:gslist_to_gs: no visible binding for global variable ‘slot’ ./flowWorkspace.Rcheck/00check.log:mkformula: no visible global function definition for ‘as.formula’ ./flowWorkspace.Rcheck/00check.log:pop.MFI: no visible binding for global variable ‘desc’ ./flowWorkspace.Rcheck/00check.log:save_gslist: no visible binding for global variable ‘slot’ ./flowWorkspace.Rcheck/00check.log:transformerList: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:transformerList: no visible binding for global variable ‘is’ ./flowWorkspace.Rcheck/00check.log:GatingSet,flowSet-ANY: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:[,GatingSet-ANY: no visible global function definition for ‘extends’ ./flowWorkspace.Rcheck/00check.log:[,GatingSetList-ANY: no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘callNextMethod’ ./flowWorkspace.Rcheck/00check.log:[,GatingSetList-ANY: no visible global function definition for ‘as’ ./flowWorkspace.Rcheck/00check.log:[[,GatingSet-character: no visible global function definition for ‘new’ ./flowWorkspace.Rcheck/00check.log:flowData,GatingSet: no visible binding for global variable ‘obj’ ./flowWorkspace.Rcheck/00check.log:gs_cyto_data,GatingSet: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:keyword,GatingSetList-character: no visible global function definition ./flowWorkspace.Rcheck/00check.log: for ‘selectMethod’ ./flowWorkspace.Rcheck/00check.log:keyword,GatingSetList-missing: no visible global function definition ./flowWorkspace.Rcheck/00check.log: for ‘selectMethod’ ./flowWorkspace.Rcheck/00check.log:pData<-,GatingSetList-data.frame: no visible global function definition ./flowWorkspace.Rcheck/00check.log: for ‘callNextMethod’ ./flowWorkspace.Rcheck/00check.log:pData<-,GatingSetList-data.frame: no visible global function definition ./flowWorkspace.Rcheck/00check.log: for ‘as’ ./flowWorkspace.Rcheck/00check.log:plotGate,GatingSetList-character: no visible global function definition ./flowWorkspace.Rcheck/00check.log: for ‘selectMethod’ ./flowWorkspace.Rcheck/00check.log:recompute,GatingSetList: no visible global function definition for ./flowWorkspace.Rcheck/00check.log: ‘selectMethod’ ./flowWorkspace.Rcheck/00check.log:setNode,GatingSet-character-ANY: no visible global function definition ./flowWorkspace.Rcheck/00check.log: for ‘is’ ./flowWorkspace.Rcheck/00check.log:transform,GatingSet: no visible global function definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:transform,GatingSet : : no visible global function ./flowWorkspace.Rcheck/00check.log: definition for ‘is’ ./flowWorkspace.Rcheck/00check.log:Undefined global functions or variables: ./flowWorkspace.Rcheck/00check.log: . .hasSlot IQR as as.formula callNextMethod count desc extends ./flowWorkspace.Rcheck/00check.log: fj_ws_get_keywords gray is median new node obj old openCyto.count ./flowWorkspace.Rcheck/00check.log: parallel percent sampleName selectMethod slot validObject xml.count ./flowWorkspace.Rcheck/00check.log:Consider adding ./flowWorkspace.Rcheck/00check.log: importFrom("grDevices", "gray") ./flowWorkspace.Rcheck/00check.log: importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends", ./flowWorkspace.Rcheck/00check.log: "is", "new", "selectMethod", "slot", "validObject") ./flowWorkspace.Rcheck/00check.log: importFrom("stats", "IQR", "as.formula", "median") ./flowWorkspace.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./flowWorkspace.Rcheck/00check.log:* checking Rd files ... OK ./flowWorkspace.Rcheck/00check.log:* checking Rd metadata ... OK ./flowWorkspace.Rcheck/00check.log:* checking Rd cross-references ... OK ./flowWorkspace.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./flowWorkspace.Rcheck/00check.log:Undocumented code objects: ./flowWorkspace.Rcheck/00check.log: ‘getChildren’ ‘getData’ ‘getGate’ ‘getNodes’ ‘getParent’ ./flowWorkspace.Rcheck/00check.log: ‘getPopStats’ ‘gs_cyto_data<-’ ./flowWorkspace.Rcheck/00check.log:Undocumented S4 methods: ./flowWorkspace.Rcheck/00check.log: generic '[[<-' and siglist 'GatingSet,ANY,ANY,GatingHierarchy' ./flowWorkspace.Rcheck/00check.log: generic 'flowData<-' and siglist 'GatingSet' ./flowWorkspace.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./flowWorkspace.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./flowWorkspace.Rcheck/00check.log:* checking for code/documentation mismatches ... WARNING ./flowWorkspace.Rcheck/00check.log:Codoc mismatches from documentation object 'GatingSet,GatingHierarchy,character-method': ./flowWorkspace.Rcheck/00check.log:gh_apply_to_new_fcs ./flowWorkspace.Rcheck/00check.log: Code: function(x, files, ...) ./flowWorkspace.Rcheck/00check.log: Docs: function(x, files, swap_cols = FALSE, ...) ./flowWorkspace.Rcheck/00check.log: Argument names in docs not in code: ./flowWorkspace.Rcheck/00check.log: swap_cols ./flowWorkspace.Rcheck/00check.log: Mismatches in argument names: ./flowWorkspace.Rcheck/00check.log: Position: 3 Code: ... Docs: swap_cols ./flowWorkspace.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./flowWorkspace.Rcheck/00check.log:Undocumented arguments in documentation object 'GatingSet,flowSet,ANY-method' ./flowWorkspace.Rcheck/00check.log: ‘x’ ./flowWorkspace.Rcheck/00check.log:Undocumented arguments in documentation object 'flowData' ./flowWorkspace.Rcheck/00check.log: ‘...’ ./flowWorkspace.Rcheck/00check.log:Duplicated \argument entries in documentation object 'getPopStats,GatingSet-method': ./flowWorkspace.Rcheck/00check.log: ‘x’ ‘...’ ./flowWorkspace.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./flowWorkspace.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./flowWorkspace.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./flowWorkspace.Rcheck/00check.log:* checking Rd contents ... OK ./flowWorkspace.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./flowWorkspace.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./flowWorkspace.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./flowWorkspace.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./flowWorkspace.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... NOTE ./flowWorkspace.Rcheck/00check.log:GNU make is a SystemRequirements. ./flowWorkspace.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./flowWorkspace.Rcheck/00check.log:* checking compiled code ... OK ./flowWorkspace.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./flowWorkspace.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./flowWorkspace.Rcheck/00check.log:* checking examples ... OK ./flowWorkspace.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./flowWorkspace.Rcheck/00check.log:* checking tests ... OK ./flowWorkspace.Rcheck/00check.log: Running ‘testthat.R’ ./flowWorkspace.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./flowWorkspace.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./flowWorkspace.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./flowWorkspace.Rcheck/00check.log: ‘HowToMergeGatingSet.Rmd’using ‘UTF-8’... OK ./flowWorkspace.Rcheck/00check.log: ‘flowWorkspace-Introduction.Rmd’using ‘UTF-8’... OK ./flowWorkspace.Rcheck/00check.log: ‘plotGate.Rmd’using ‘UTF-8’... OK ./flowWorkspace.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./flowWorkspace.Rcheck/00check.log:* checking PDF version of manual ... OK ./flowWorkspace.Rcheck/00check.log:* DONE ./flowWorkspace.Rcheck/00check.log:Status: 3 WARNINGs, 5 NOTEs geneXtendeR_1.11.0.tar.gz ./geneXtendeR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/geneXtendeR.Rcheck’ ./geneXtendeR.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./geneXtendeR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./geneXtendeR.Rcheck/00check.log:* using session charset: UTF-8 ./geneXtendeR.Rcheck/00check.log:* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK ./geneXtendeR.Rcheck/00check.log:* checking extension type ... Package ./geneXtendeR.Rcheck/00check.log:* this is package ‘geneXtendeR’ version ‘1.11.0’ ./geneXtendeR.Rcheck/00check.log:* package encoding: UTF-8 ./geneXtendeR.Rcheck/00check.log:* checking package namespace information ... OK ./geneXtendeR.Rcheck/00check.log:* checking package dependencies ... OK ./geneXtendeR.Rcheck/00check.log:* checking if this is a source package ... OK ./geneXtendeR.Rcheck/00check.log:* checking if there is a namespace ... OK ./geneXtendeR.Rcheck/00check.log:* checking for executable files ... OK ./geneXtendeR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./geneXtendeR.Rcheck/00check.log:* checking for portable file names ... OK ./geneXtendeR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./geneXtendeR.Rcheck/00check.log:* checking whether package ‘geneXtendeR’ can be installed ... WARNING ./geneXtendeR.Rcheck/00check.log:Found the following significant warnings: ./geneXtendeR.Rcheck/00check.log: annotate.c:106:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] ./geneXtendeR.Rcheck/00check.log: annotate.c:116:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] ./geneXtendeR.Rcheck/00check.log: extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] ./geneXtendeR.Rcheck/00check.log: extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] ./geneXtendeR.Rcheck/00check.log: extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] ./geneXtendeR.Rcheck/00check.log: extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] ./geneXtendeR.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/geneXtendeR.Rcheck/00install.out’ for details. ./geneXtendeR.Rcheck/00check.log:* checking installed package size ... NOTE ./geneXtendeR.Rcheck/00check.log: installed size is 11.5Mb ./geneXtendeR.Rcheck/00check.log: sub-directories of 1Mb or more: ./geneXtendeR.Rcheck/00check.log: data 5.8Mb ./geneXtendeR.Rcheck/00check.log: doc 1.9Mb ./geneXtendeR.Rcheck/00check.log: extdata 3.5Mb ./geneXtendeR.Rcheck/00check.log:* checking package directory ... OK ./geneXtendeR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./geneXtendeR.Rcheck/00check.log:Package listed in more than one of Depends, Imports, Suggests, Enhances: ./geneXtendeR.Rcheck/00check.log: ‘rtracklayer’ ./geneXtendeR.Rcheck/00check.log:A package should be listed in only one of these fields. ./geneXtendeR.Rcheck/00check.log:* checking top-level files ... OK ./geneXtendeR.Rcheck/00check.log:* checking for left-over files ... OK ./geneXtendeR.Rcheck/00check.log:* checking index information ... OK ./geneXtendeR.Rcheck/00check.log:* checking package subdirectories ... OK ./geneXtendeR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./geneXtendeR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./geneXtendeR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./geneXtendeR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./geneXtendeR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./geneXtendeR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./geneXtendeR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./geneXtendeR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./geneXtendeR.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./geneXtendeR.Rcheck/00check.log:Namespaces in Imports field not imported from: ./geneXtendeR.Rcheck/00check.log: ‘BiocStyle’ ‘SnowballC’ ‘org.Rn.eg.db’ ./geneXtendeR.Rcheck/00check.log: All declared Imports should be used. ./geneXtendeR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./geneXtendeR.Rcheck/00check.log:* checking replacement functions ... OK ./geneXtendeR.Rcheck/00check.log:* checking foreign function calls ... OK ./geneXtendeR.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./geneXtendeR.Rcheck/00check.log:.geneXtender: no visible binding for global variable ‘type’ ./geneXtendeR.Rcheck/00check.log:.geneXtender: no visible binding for global variable ‘seqid’ ./geneXtendeR.Rcheck/00check.log:.geneXtender: no visible binding for global variable ‘gene_id’ ./geneXtendeR.Rcheck/00check.log:.geneXtender: no visible binding for global variable ‘gene_name’ ./geneXtendeR.Rcheck/00check.log:annotate_n: no visible binding for global variable ‘..I’ ./geneXtendeR.Rcheck/00check.log:annotate_n: no visible binding for global variable ‘seqid’ ./geneXtendeR.Rcheck/00check.log:diffGO: no visible binding for global variable ‘rat’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible global function definition for ‘.’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘Distance-of-Gene-to-Nearest-Peak’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible global function definition for ‘sd’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ‘Chromosome’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ‘Gene-Start’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ‘Gene-End’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ‘Gene-ID’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ‘Gene-Name’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘Peaks-on-Gene-Body’ ./geneXtendeR.Rcheck/00check.log:gene_annotate: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘Number-of-Peaks-Associated-with-Gene’ ./geneXtendeR.Rcheck/00check.log:gene_lookup: no visible binding for global variable ‘gene_name_id’ ./geneXtendeR.Rcheck/00check.log:gene_lookup: no visible binding for global variable ‘gene_id’ ./geneXtendeR.Rcheck/00check.log:gene_lookup : internal_find: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘Chromosome’ ./geneXtendeR.Rcheck/00check.log:gene_lookup : internal_find: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘distance’ ./geneXtendeR.Rcheck/00check.log:gene_lookup : internal_find: no visible global function definition for ./geneXtendeR.Rcheck/00check.log: ‘na.omit’ ./geneXtendeR.Rcheck/00check.log:gene_lookup: no visible binding for global variable ‘..I’ ./geneXtendeR.Rcheck/00check.log:gene_lookup: no visible binding for global variable ‘distance’ ./geneXtendeR.Rcheck/00check.log:makeWordCloud: no visible binding for global variable ‘rat’ ./geneXtendeR.Rcheck/00check.log:meanPeakLength: no visible binding for global variable ‘rat’ ./geneXtendeR.Rcheck/00check.log:peaksInput: no visible binding for global variable ‘chr’ ./geneXtendeR.Rcheck/00check.log:peaksInput: no visible global function definition for ‘na.omit’ ./geneXtendeR.Rcheck/00check.log:peaksMerge: no visible binding for global variable ‘chr’ ./geneXtendeR.Rcheck/00check.log:peaksMerge: no visible binding for global variable ‘g’ ./geneXtendeR.Rcheck/00check.log:peaksMerge: no visible global function definition for ‘.’ ./geneXtendeR.Rcheck/00check.log:plotWordFreq : geneXtender: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘type’ ./geneXtendeR.Rcheck/00check.log:plotWordFreq : geneXtender: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘seqid’ ./geneXtendeR.Rcheck/00check.log:plotWordFreq : geneXtender: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘gene_id’ ./geneXtendeR.Rcheck/00check.log:plotWordFreq : geneXtender: no visible binding for global variable ./geneXtendeR.Rcheck/00check.log: ‘gene_name’ ./geneXtendeR.Rcheck/00check.log:Undefined global functions or variables: ./geneXtendeR.Rcheck/00check.log: . ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID ./geneXtendeR.Rcheck/00check.log: Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene ./geneXtendeR.Rcheck/00check.log: Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id ./geneXtendeR.Rcheck/00check.log: na.omit rat sd seqid type ./geneXtendeR.Rcheck/00check.log:Consider adding ./geneXtendeR.Rcheck/00check.log: importFrom("stats", "na.omit", "sd") ./geneXtendeR.Rcheck/00check.log:to your NAMESPACE file. ./geneXtendeR.Rcheck/00check.log:* checking Rd files ... OK ./geneXtendeR.Rcheck/00check.log:* checking Rd metadata ... OK ./geneXtendeR.Rcheck/00check.log:* checking Rd cross-references ... OK ./geneXtendeR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./geneXtendeR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./geneXtendeR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./geneXtendeR.Rcheck/00check.log:* checking Rd contents ... OK ./geneXtendeR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./geneXtendeR.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./geneXtendeR.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./geneXtendeR.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./geneXtendeR.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./geneXtendeR.Rcheck/00check.log:* checking compiled code ... OK ./geneXtendeR.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./geneXtendeR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./geneXtendeR.Rcheck/00check.log:* checking files in ‘vignettes’ ... NOTE ./geneXtendeR.Rcheck/00check.log:Files named as vignettes but with no recognized vignette engine: ./geneXtendeR.Rcheck/00check.log: ‘vignettes/geneXtendeR.Rnw’ ./geneXtendeR.Rcheck/00check.log:(Is a VignetteBuilder field missing?) ./geneXtendeR.Rcheck/00check.log:* checking examples ... OK ./geneXtendeR.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./geneXtendeR.Rcheck/00check.log:* checking tests ... OK ./geneXtendeR.Rcheck/00check.log: Running ‘testthat.R’ ./geneXtendeR.Rcheck/00check.log:* checking PDF version of manual ... OK ./geneXtendeR.Rcheck/00check.log:* DONE ./geneXtendeR.Rcheck/00check.log:Status: 1 WARNING, 5 NOTEs GenoGAM_2.3.4.tar.gz ./GenoGAM.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/GenoGAM.Rcheck’ ./GenoGAM.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./GenoGAM.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./GenoGAM.Rcheck/00check.log:* using session charset: UTF-8 ./GenoGAM.Rcheck/00check.log:* checking for file ‘GenoGAM/DESCRIPTION’ ... OK ./GenoGAM.Rcheck/00check.log:* checking extension type ... Package ./GenoGAM.Rcheck/00check.log:* this is package ‘GenoGAM’ version ‘2.3.4’ ./GenoGAM.Rcheck/00check.log:* package encoding: UTF-8 ./GenoGAM.Rcheck/00check.log:* checking package namespace information ... OK ./GenoGAM.Rcheck/00check.log:* checking package dependencies ... NOTE ./GenoGAM.Rcheck/00check.log:Depends: includes the non-default packages: ./GenoGAM.Rcheck/00check.log: 'SummarizedExperiment', 'HDF5Array', 'rhdf5', 'S4Vectors', 'Matrix', 'data.table' ./GenoGAM.Rcheck/00check.log:Adding so many packages to the search path is excessive and importing selectively is preferable. ./GenoGAM.Rcheck/00check.log:* checking if this is a source package ... OK ./GenoGAM.Rcheck/00check.log:* checking if there is a namespace ... OK ./GenoGAM.Rcheck/00check.log:* checking for executable files ... OK ./GenoGAM.Rcheck/00check.log:* checking for hidden files and directories ... OK ./GenoGAM.Rcheck/00check.log:* checking for portable file names ... OK ./GenoGAM.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./GenoGAM.Rcheck/00check.log:* checking whether package ‘GenoGAM’ can be installed ... WARNING ./GenoGAM.Rcheck/00check.log:Found the following significant warnings: ./GenoGAM.Rcheck/00check.log: Warning: replacing previous import ‘S4Vectors::na.omit’ by ‘stats::na.omit’ when loading ‘GenoGAM’ ./GenoGAM.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/GenoGAM.Rcheck/00install.out’ for details. ./GenoGAM.Rcheck/00check.log:* checking installed package size ... NOTE ./GenoGAM.Rcheck/00check.log: installed size is 8.9Mb ./GenoGAM.Rcheck/00check.log: sub-directories of 1Mb or more: ./GenoGAM.Rcheck/00check.log: R 1.2Mb ./GenoGAM.Rcheck/00check.log: doc 1.4Mb ./GenoGAM.Rcheck/00check.log: extdata 3.0Mb ./GenoGAM.Rcheck/00check.log: libs 3.1Mb ./GenoGAM.Rcheck/00check.log:* checking package directory ... OK ./GenoGAM.Rcheck/00check.log:* checking ‘build’ directory ... OK ./GenoGAM.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./GenoGAM.Rcheck/00check.log:* checking top-level files ... OK ./GenoGAM.Rcheck/00check.log:* checking for left-over files ... OK ./GenoGAM.Rcheck/00check.log:* checking index information ... OK ./GenoGAM.Rcheck/00check.log:* checking package subdirectories ... OK ./GenoGAM.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./GenoGAM.Rcheck/00check.log:* checking R files for syntax errors ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./GenoGAM.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./GenoGAM.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./GenoGAM.Rcheck/00check.log:Namespace in Imports field not imported from: ‘Biostrings’ ./GenoGAM.Rcheck/00check.log: All declared Imports should be used. ./GenoGAM.Rcheck/00check.log:Packages in Depends field not imported from: ./GenoGAM.Rcheck/00check.log: ‘Matrix’ ‘data.table’ ./GenoGAM.Rcheck/00check.log: These packages need to be imported from (in the NAMESPACE file) ./GenoGAM.Rcheck/00check.log: for when this namespace is loaded but not attached. ./GenoGAM.Rcheck/00check.log:':::' calls which should be '::': ./GenoGAM.Rcheck/00check.log: ‘DelayedArray:::getAutoBlockLength’ ‘DelayedArray:::read_block’ ./GenoGAM.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./GenoGAM.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./GenoGAM.Rcheck/00check.log:* checking replacement functions ... OK ./GenoGAM.Rcheck/00check.log:* checking foreign function calls ... OK ./GenoGAM.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./GenoGAM.Rcheck/00check.log:.GenoGAMFromHDF5: no visible binding for global variable ‘h5fits’ ./GenoGAM.Rcheck/00check.log:.GenoGAMFromHDF5: no visible binding for global variable ‘h5ses’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_default: no visible binding for global variable ‘pval’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_default: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘region’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_default: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘estimate’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_hdf5: no visible binding for global variable ‘pval’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_hdf5: no visible binding for global variable ‘region’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_hdf5: no visible binding for global variable ‘estimate’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_split: no visible binding for global variable ‘pval’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_split: no visible binding for global variable ‘region’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_split: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘estimate’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_split_hdf5: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘pval’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_split_hdf5: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘region’ ./GenoGAM.Rcheck/00check.log:.callBroadPeaks_split_hdf5: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘estimate’ ./GenoGAM.Rcheck/00check.log:.pvals_hdf5_split: no visible binding for global variable ‘chrom’ ./GenoGAM.Rcheck/00check.log:.setOptimalChunkSize: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘count.fields’ ./GenoGAM.Rcheck/00check.log:.shorth_hdf5 : COMBINE : : no visible binding for global ./GenoGAM.Rcheck/00check.log: variable ‘tmp’ ./GenoGAM.Rcheck/00check.log:callPeaks: no visible binding for global variable ‘fdr’ ./GenoGAM.Rcheck/00check.log:computeRegionSignificance: no visible binding for global variable ‘p’ ./GenoGAM.Rcheck/00check.log:computeRegionSignificance: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘region’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘par’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘plot’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘x11’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘lines’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘abline’ ./GenoGAM.Rcheck/00check.log:writeToBroadPeaks: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘write.table’ ./GenoGAM.Rcheck/00check.log:writeToNarrowPeaks: no visible binding for global variable ‘chromosome’ ./GenoGAM.Rcheck/00check.log:writeToNarrowPeaks: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘write.table’ ./GenoGAM.Rcheck/00check.log:Undefined global functions or variables: ./GenoGAM.Rcheck/00check.log: abline chrom chromosome count.fields estimate fdr h5fits h5ses lines ./GenoGAM.Rcheck/00check.log: p par plot pval region tmp write.table x11 ./GenoGAM.Rcheck/00check.log:Consider adding ./GenoGAM.Rcheck/00check.log: importFrom("grDevices", "x11") ./GenoGAM.Rcheck/00check.log: importFrom("graphics", "abline", "lines", "par", "plot") ./GenoGAM.Rcheck/00check.log: importFrom("utils", "count.fields", "write.table") ./GenoGAM.Rcheck/00check.log:to your NAMESPACE file. ./GenoGAM.Rcheck/00check.log:* checking Rd files ... OK ./GenoGAM.Rcheck/00check.log:* checking Rd metadata ... WARNING ./GenoGAM.Rcheck/00check.log:Rd files with duplicated alias 'GenoGAM': ./GenoGAM.Rcheck/00check.log: ‘GenoGAM-class.Rd’ ‘GenoGAM.Rd’ ./GenoGAM.Rcheck/00check.log:* checking Rd cross-references ... OK ./GenoGAM.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./GenoGAM.Rcheck/00check.log:Undocumented code objects: ./GenoGAM.Rcheck/00check.log: ‘getCountMatrix’ ‘is.HDF5’ ‘pvalue’ ./GenoGAM.Rcheck/00check.log:Undocumented S4 methods: ./GenoGAM.Rcheck/00check.log: generic 'dim' and siglist 'GenoGAMSetup' ./GenoGAM.Rcheck/00check.log: generic 'length' and siglist 'GenoGAMSetup' ./GenoGAM.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./GenoGAM.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./GenoGAM.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./GenoGAM.Rcheck/00check.log:* checking Rd \usage sections ... OK ./GenoGAM.Rcheck/00check.log:* checking Rd contents ... OK ./GenoGAM.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./GenoGAM.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./GenoGAM.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./GenoGAM.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./GenoGAM.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./GenoGAM.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./GenoGAM.Rcheck/00check.log:* checking compiled code ... OK ./GenoGAM.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./GenoGAM.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./GenoGAM.Rcheck/00check.log:* checking examples ... OK ./GenoGAM.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./GenoGAM.Rcheck/00check.log:* checking tests ... OK ./GenoGAM.Rcheck/00check.log: Running ‘testthat.R’ ./GenoGAM.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./GenoGAM.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./GenoGAM.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./GenoGAM.Rcheck/00check.log: ‘GenoGAM.Rmd’using ‘UTF-8’... OK ./GenoGAM.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./GenoGAM.Rcheck/00check.log:* checking PDF version of manual ... OK ./GenoGAM.Rcheck/00check.log:* DONE ./GenoGAM.Rcheck/00check.log:Status: 3 WARNINGs, 4 NOTEs genomation_1.17.0.tar.gz ./genomation.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/genomation.Rcheck’ ./genomation.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./genomation.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./genomation.Rcheck/00check.log:* using session charset: UTF-8 ./genomation.Rcheck/00check.log:* checking for file ‘genomation/DESCRIPTION’ ... OK ./genomation.Rcheck/00check.log:* checking extension type ... Package ./genomation.Rcheck/00check.log:* this is package ‘genomation’ version ‘1.17.0’ ./genomation.Rcheck/00check.log:* package encoding: latin1 ./genomation.Rcheck/00check.log:* checking package namespace information ... OK ./genomation.Rcheck/00check.log:* checking package dependencies ... OK ./genomation.Rcheck/00check.log:* checking if this is a source package ... OK ./genomation.Rcheck/00check.log:* checking if there is a namespace ... OK ./genomation.Rcheck/00check.log:* checking for executable files ... OK ./genomation.Rcheck/00check.log:* checking for hidden files and directories ... OK ./genomation.Rcheck/00check.log:* checking for portable file names ... OK ./genomation.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./genomation.Rcheck/00check.log:* checking whether package ‘genomation’ can be installed ... OK ./genomation.Rcheck/00check.log:* checking installed package size ... NOTE ./genomation.Rcheck/00check.log: installed size is 6.1Mb ./genomation.Rcheck/00check.log: sub-directories of 1Mb or more: ./genomation.Rcheck/00check.log: doc 3.5Mb ./genomation.Rcheck/00check.log: extdata 1.2Mb ./genomation.Rcheck/00check.log:* checking package directory ... OK ./genomation.Rcheck/00check.log:* checking ‘build’ directory ... OK ./genomation.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./genomation.Rcheck/00check.log:* checking top-level files ... OK ./genomation.Rcheck/00check.log:* checking for left-over files ... OK ./genomation.Rcheck/00check.log:* checking index information ... OK ./genomation.Rcheck/00check.log:* checking package subdirectories ... OK ./genomation.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./genomation.Rcheck/00check.log:* checking R files for syntax errors ... OK ./genomation.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./genomation.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./genomation.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./genomation.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./genomation.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./genomation.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./genomation.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./genomation.Rcheck/00check.log:Namespace in Imports field not imported from: ‘RUnit’ ./genomation.Rcheck/00check.log: All declared Imports should be used. ./genomation.Rcheck/00check.log:Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ ./genomation.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./genomation.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./genomation.Rcheck/00check.log:* checking replacement functions ... OK ./genomation.Rcheck/00check.log:* checking foreign function calls ... OK ./genomation.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./genomation.Rcheck/00check.log:ScoreMatrixBin,RleList-GRangesList: no visible binding for global ./genomation.Rcheck/00check.log: variable ‘id’ ./genomation.Rcheck/00check.log:ScoreMatrixBin,RleList-GRangesList: no visible global function ./genomation.Rcheck/00check.log: definition for ‘:=’ ./genomation.Rcheck/00check.log:Undefined global functions or variables: ./genomation.Rcheck/00check.log: := id ./genomation.Rcheck/00check.log:* checking Rd files ... OK ./genomation.Rcheck/00check.log:* checking Rd metadata ... OK ./genomation.Rcheck/00check.log:* checking Rd cross-references ... OK ./genomation.Rcheck/00check.log:* checking for missing documentation entries ... OK ./genomation.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./genomation.Rcheck/00check.log:* checking Rd \usage sections ... OK ./genomation.Rcheck/00check.log:* checking Rd contents ... OK ./genomation.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./genomation.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./genomation.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./genomation.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./genomation.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./genomation.Rcheck/00check.log:* checking compiled code ... OK ./genomation.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./genomation.Rcheck/00check.log:* checking files in ‘vignettes’ ... NOTE ./genomation.Rcheck/00check.log:The following directory looks like a leftover from 'knitr': ./genomation.Rcheck/00check.log: ‘cache’ ./genomation.Rcheck/00check.log:Please remove from your package. ./genomation.Rcheck/00check.log:* checking examples ... WARNING ./genomation.Rcheck/00check.log:Found the following significant warnings: ./genomation.Rcheck/00check.log: Warning: 'GenomicRangesList' is deprecated. ./genomation.Rcheck/00check.log:Deprecated functions may be defunct as soon as of the next release of R. ./genomation.Rcheck/00check.log:See ?Deprecated. ./genomation.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./genomation.Rcheck/00check.log:* checking tests ... OK ./genomation.Rcheck/00check.log: Running ‘genomation_unit_tests.R’ ./genomation.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./genomation.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./genomation.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./genomation.Rcheck/00check.log: ‘GenomationManual.Rmd’using ‘UTF-8’... OK ./genomation.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./genomation.Rcheck/00check.log:* checking PDF version of manual ... OK ./genomation.Rcheck/00check.log:* DONE ./genomation.Rcheck/00check.log:Status: 1 WARNING, 4 NOTEs ggcyto_1.13.2.tar.gz ./ggcyto.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ggcyto.Rcheck’ ./ggcyto.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./ggcyto.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ggcyto.Rcheck/00check.log:* using session charset: UTF-8 ./ggcyto.Rcheck/00check.log:* checking for file ‘ggcyto/DESCRIPTION’ ... OK ./ggcyto.Rcheck/00check.log:* checking extension type ... Package ./ggcyto.Rcheck/00check.log:* this is package ‘ggcyto’ version ‘1.13.2’ ./ggcyto.Rcheck/00check.log:* checking package namespace information ... OK ./ggcyto.Rcheck/00check.log:* checking package dependencies ... OK ./ggcyto.Rcheck/00check.log:* checking if this is a source package ... OK ./ggcyto.Rcheck/00check.log:* checking if there is a namespace ... OK ./ggcyto.Rcheck/00check.log:* checking for executable files ... OK ./ggcyto.Rcheck/00check.log:* checking for hidden files and directories ... NOTE ./ggcyto.Rcheck/00check.log:Found the following hidden files and directories: ./ggcyto.Rcheck/00check.log: .travis.yml ./ggcyto.Rcheck/00check.log:These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ./ggcyto.Rcheck/00check.log:* checking for portable file names ... OK ./ggcyto.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ggcyto.Rcheck/00check.log:* checking whether package ‘ggcyto’ can be installed ... OK ./ggcyto.Rcheck/00check.log:* checking installed package size ... NOTE ./ggcyto.Rcheck/00check.log: installed size is 5.9Mb ./ggcyto.Rcheck/00check.log: sub-directories of 1Mb or more: ./ggcyto.Rcheck/00check.log: doc 5.4Mb ./ggcyto.Rcheck/00check.log:* checking package directory ... OK ./ggcyto.Rcheck/00check.log:* checking ‘build’ directory ... OK ./ggcyto.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ggcyto.Rcheck/00check.log:* checking top-level files ... OK ./ggcyto.Rcheck/00check.log:* checking for left-over files ... OK ./ggcyto.Rcheck/00check.log:* checking index information ... OK ./ggcyto.Rcheck/00check.log:* checking package subdirectories ... OK ./ggcyto.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ggcyto.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ggcyto.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ggcyto.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ggcyto.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ggcyto.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ggcyto.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ggcyto.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ggcyto.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./ggcyto.Rcheck/00check.log:Namespace in Imports field not imported from: ‘scales’ ./ggcyto.Rcheck/00check.log: All declared Imports should be used. ./ggcyto.Rcheck/00check.log:':::' call which should be '::': ‘flowWorkspace:::gh_pop_is_negated’ ./ggcyto.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./ggcyto.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./ggcyto.Rcheck/00check.log: ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’ ./ggcyto.Rcheck/00check.log: ‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’ ./ggcyto.Rcheck/00check.log: ‘ggplot2:::as_gg_data_frame’ ‘ggplot2:::check_aesthetics’ ./ggcyto.Rcheck/00check.log: ‘ggplot2:::hex_binwidth’ ‘ggplot2:::is.waive’ ./ggcyto.Rcheck/00check.log: ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_labels’ ./ggcyto.Rcheck/00check.log: ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’ ./ggcyto.Rcheck/00check.log: ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_add_defaults’ ./ggcyto.Rcheck/00check.log: ‘ggplot2:::scales_list’ ‘ggplot2:::update_theme’ ./ggcyto.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./ggcyto.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ggcyto.Rcheck/00check.log:* checking replacement functions ... OK ./ggcyto.Rcheck/00check.log:* checking foreign function calls ... OK ./ggcyto.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./ggcyto.Rcheck/00check.log:.fs2dt: no visible binding for global variable ‘name’ ./ggcyto.Rcheck/00check.log:add_ggcyto: no visible binding for global variable ‘name’ ./ggcyto.Rcheck/00check.log:add_ggcyto: no visible global function definition for ‘modifyList’ ./ggcyto.Rcheck/00check.log:add_ggcyto: no visible binding for global variable ‘axis’ ./ggcyto.Rcheck/00check.log:add_ggcyto: no visible binding for global variable ‘desc’ ./ggcyto.Rcheck/00check.log:add_par: no visible global function definition for ‘modifyList’ ./ggcyto.Rcheck/00check.log:as.ggplot: no visible binding for global variable ‘axis’ ./ggcyto.Rcheck/00check.log:as.ggplot: no visible binding for global variable ‘name’ ./ggcyto.Rcheck/00check.log:as.ggplot : : no visible binding for global variable ‘axis’ ./ggcyto.Rcheck/00check.log:as.ggplot : : no visible binding for global variable ‘name’ ./ggcyto.Rcheck/00check.log:as.ggplot: no visible binding for global variable ‘density’ ./ggcyto.Rcheck/00check.log:autoplot.GatingHierarchy : : no visible global function ./ggcyto.Rcheck/00check.log: definition for ‘gray’ ./ggcyto.Rcheck/00check.log:autoplot.GatingSetList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:autoplot.ncdfFlowList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:density_fr_all : : no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘gray’ ./ggcyto.Rcheck/00check.log:fortify.GatingSetList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:fortify.ncdfFlowList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:fortify_fs.GatingSetList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:getFlowFrame.GatingSetList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:getFlowFrame.ncdfFlowList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:ggcyto.GatingSetList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:ggcyto.flowSet: no visible binding for global variable ‘name’ ./ggcyto.Rcheck/00check.log:ggcyto.flowSet: no visible binding for global variable ‘axis’ ./ggcyto.Rcheck/00check.log:ggcyto.ncdfFlowList: no visible global function definition for ./ggcyto.Rcheck/00check.log: ‘getS3method’ ./ggcyto.Rcheck/00check.log:ggcyto_arrange: no visible binding for global variable ‘name’ ./ggcyto.Rcheck/00check.log:Undefined global functions or variables: ./ggcyto.Rcheck/00check.log: axis density desc getS3method gray modifyList name ./ggcyto.Rcheck/00check.log:Consider adding ./ggcyto.Rcheck/00check.log: importFrom("grDevices", "gray") ./ggcyto.Rcheck/00check.log: importFrom("graphics", "axis") ./ggcyto.Rcheck/00check.log: importFrom("stats", "density") ./ggcyto.Rcheck/00check.log: importFrom("utils", "getS3method", "modifyList") ./ggcyto.Rcheck/00check.log:to your NAMESPACE file. ./ggcyto.Rcheck/00check.log:* checking Rd files ... OK ./ggcyto.Rcheck/00check.log:* checking Rd metadata ... OK ./ggcyto.Rcheck/00check.log:* checking Rd cross-references ... OK ./ggcyto.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./ggcyto.Rcheck/00check.log:Undocumented S4 methods: ./ggcyto.Rcheck/00check.log: generic '%+%' and siglist 'ggcyto' ./ggcyto.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./ggcyto.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./ggcyto.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ggcyto.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./ggcyto.Rcheck/00check.log:Undocumented arguments in documentation object 'fortify.filterList' ./ggcyto.Rcheck/00check.log: ‘data’ ‘nPoints’ ./ggcyto.Rcheck/00check.log:Undocumented arguments in documentation object 'fortify.polygonGate' ./ggcyto.Rcheck/00check.log: ‘nPoints’ ./ggcyto.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./ggcyto.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./ggcyto.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./ggcyto.Rcheck/00check.log:* checking Rd contents ... OK ./ggcyto.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ggcyto.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./ggcyto.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./ggcyto.Rcheck/00check.log:* checking examples ... OK ./ggcyto.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./ggcyto.Rcheck/00check.log:* checking tests ... OK ./ggcyto.Rcheck/00check.log: Running ‘testthat.R’ ./ggcyto.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./ggcyto.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./ggcyto.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./ggcyto.Rcheck/00check.log: ‘Top_features_of_ggcyto.Rmd’... OK ./ggcyto.Rcheck/00check.log: ‘autoplot.Rmd’... OK ./ggcyto.Rcheck/00check.log: ‘ggcyto.GatingSet.Rmd’... OK ./ggcyto.Rcheck/00check.log: ‘ggcyto.flowSet.Rmd’... OK ./ggcyto.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./ggcyto.Rcheck/00check.log:* checking PDF version of manual ... OK ./ggcyto.Rcheck/00check.log:* DONE ./ggcyto.Rcheck/00check.log:Status: 2 WARNINGs, 4 NOTEs HMMcopy_1.27.1.tar.gz ./HMMcopy.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/HMMcopy.Rcheck’ ./HMMcopy.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./HMMcopy.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./HMMcopy.Rcheck/00check.log:* using session charset: UTF-8 ./HMMcopy.Rcheck/00check.log:* checking for file ‘HMMcopy/DESCRIPTION’ ... OK ./HMMcopy.Rcheck/00check.log:* checking extension type ... Package ./HMMcopy.Rcheck/00check.log:* this is package ‘HMMcopy’ version ‘1.27.1’ ./HMMcopy.Rcheck/00check.log:* checking package namespace information ... OK ./HMMcopy.Rcheck/00check.log:* checking package dependencies ... OK ./HMMcopy.Rcheck/00check.log:* checking if this is a source package ... OK ./HMMcopy.Rcheck/00check.log:* checking if there is a namespace ... OK ./HMMcopy.Rcheck/00check.log:* checking for executable files ... OK ./HMMcopy.Rcheck/00check.log:* checking for hidden files and directories ... OK ./HMMcopy.Rcheck/00check.log:* checking for portable file names ... OK ./HMMcopy.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./HMMcopy.Rcheck/00check.log:* checking whether package ‘HMMcopy’ can be installed ... OK ./HMMcopy.Rcheck/00check.log:* checking installed package size ... OK ./HMMcopy.Rcheck/00check.log:* checking package directory ... OK ./HMMcopy.Rcheck/00check.log:* checking ‘build’ directory ... OK ./HMMcopy.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./HMMcopy.Rcheck/00check.log:* checking top-level files ... OK ./HMMcopy.Rcheck/00check.log:* checking for left-over files ... OK ./HMMcopy.Rcheck/00check.log:* checking index information ... OK ./HMMcopy.Rcheck/00check.log:* checking package subdirectories ... OK ./HMMcopy.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./HMMcopy.Rcheck/00check.log:* checking R files for syntax errors ... OK ./HMMcopy.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./HMMcopy.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./HMMcopy.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./HMMcopy.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./HMMcopy.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./HMMcopy.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./HMMcopy.Rcheck/00check.log:* checking dependencies in R code ... OK ./HMMcopy.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./HMMcopy.Rcheck/00check.log:* checking replacement functions ... OK ./HMMcopy.Rcheck/00check.log:* checking foreign function calls ... OK ./HMMcopy.Rcheck/00check.log:* checking R code for possible problems ... OK ./HMMcopy.Rcheck/00check.log:* checking Rd files ... OK ./HMMcopy.Rcheck/00check.log:* checking Rd metadata ... OK ./HMMcopy.Rcheck/00check.log:* checking Rd cross-references ... OK ./HMMcopy.Rcheck/00check.log:* checking for missing documentation entries ... OK ./HMMcopy.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./HMMcopy.Rcheck/00check.log:* checking Rd \usage sections ... OK ./HMMcopy.Rcheck/00check.log:* checking Rd contents ... OK ./HMMcopy.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./HMMcopy.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./HMMcopy.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./HMMcopy.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... WARNING ./HMMcopy.Rcheck/00check.log: ./HMMcopy.Rcheck/00check.log: Note: significantly better compression could be obtained ./HMMcopy.Rcheck/00check.log: by using R CMD build --resave-data ./HMMcopy.Rcheck/00check.log: old_size new_size compress ./HMMcopy.Rcheck/00check.log: tumour.rda 602Kb 390Kb xz ./HMMcopy.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./HMMcopy.Rcheck/00check.log:* checking compiled code ... OK ./HMMcopy.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./HMMcopy.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./HMMcopy.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./HMMcopy.Rcheck/00check.log:* checking examples ... OK ./HMMcopy.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./HMMcopy.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./HMMcopy.Rcheck/00check.log:* checking running R code from vignettes ... OK ./HMMcopy.Rcheck/00check.log: ‘HMMcopy.Rnw’... OK ./HMMcopy.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./HMMcopy.Rcheck/00check.log:* checking PDF version of manual ... OK ./HMMcopy.Rcheck/00check.log:* DONE ./HMMcopy.Rcheck/00check.log:Status: 1 WARNING iCNV_1.5.0.tar.gz ./iCNV.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/iCNV.Rcheck’ ./iCNV.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./iCNV.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./iCNV.Rcheck/00check.log:* using session charset: UTF-8 ./iCNV.Rcheck/00check.log:* checking for file ‘iCNV/DESCRIPTION’ ... OK ./iCNV.Rcheck/00check.log:* this is package ‘iCNV’ version ‘1.5.0’ ./iCNV.Rcheck/00check.log:* package encoding: UTF-8 ./iCNV.Rcheck/00check.log:* checking package namespace information ... OK ./iCNV.Rcheck/00check.log:* checking package dependencies ... OK ./iCNV.Rcheck/00check.log:* checking if this is a source package ... OK ./iCNV.Rcheck/00check.log:* checking if there is a namespace ... OK ./iCNV.Rcheck/00check.log:* checking for executable files ... OK ./iCNV.Rcheck/00check.log:* checking for hidden files and directories ... OK ./iCNV.Rcheck/00check.log:* checking for portable file names ... OK ./iCNV.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./iCNV.Rcheck/00check.log:* checking whether package ‘iCNV’ can be installed ... WARNING ./iCNV.Rcheck/00check.log:Found the following significant warnings: ./iCNV.Rcheck/00check.log: Note: break used in wrong context: no loop is visible ./iCNV.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/iCNV.Rcheck/00install.out’ for details. ./iCNV.Rcheck/00check.log:Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. ./iCNV.Rcheck/00check.log:* checking installed package size ... OK ./iCNV.Rcheck/00check.log:* checking package directory ... OK ./iCNV.Rcheck/00check.log:* checking ‘build’ directory ... OK ./iCNV.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./iCNV.Rcheck/00check.log:* checking top-level files ... OK ./iCNV.Rcheck/00check.log:* checking for left-over files ... OK ./iCNV.Rcheck/00check.log:* checking index information ... OK ./iCNV.Rcheck/00check.log:* checking package subdirectories ... OK ./iCNV.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./iCNV.Rcheck/00check.log:* checking R files for syntax errors ... OK ./iCNV.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./iCNV.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./iCNV.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./iCNV.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./iCNV.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./iCNV.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./iCNV.Rcheck/00check.log:* checking dependencies in R code ... OK ./iCNV.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./iCNV.Rcheck/00check.log:* checking replacement functions ... OK ./iCNV.Rcheck/00check.log:* checking foreign function calls ... OK ./iCNV.Rcheck/00check.log:* checking R code for possible problems ... OK ./iCNV.Rcheck/00check.log:* checking Rd files ... OK ./iCNV.Rcheck/00check.log:* checking Rd metadata ... OK ./iCNV.Rcheck/00check.log:* checking Rd cross-references ... OK ./iCNV.Rcheck/00check.log:* checking for missing documentation entries ... OK ./iCNV.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./iCNV.Rcheck/00check.log:* checking Rd \usage sections ... OK ./iCNV.Rcheck/00check.log:* checking Rd contents ... OK ./iCNV.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./iCNV.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./iCNV.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./iCNV.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./iCNV.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./iCNV.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./iCNV.Rcheck/00check.log:* checking examples ... OK ./iCNV.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./iCNV.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./iCNV.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./iCNV.Rcheck/00check.log: ‘iCNV-vignette.Rmd’using ‘UTF-8’... OK ./iCNV.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./iCNV.Rcheck/00check.log:* checking PDF version of manual ... OK ./iCNV.Rcheck/00check.log:* DONE ./iCNV.Rcheck/00check.log:Status: 1 WARNING methylPipe_1.19.0.tar.gz ./methylPipe.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/methylPipe.Rcheck’ ./methylPipe.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./methylPipe.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./methylPipe.Rcheck/00check.log:* using session charset: UTF-8 ./methylPipe.Rcheck/00check.log:* checking for file ‘methylPipe/DESCRIPTION’ ... OK ./methylPipe.Rcheck/00check.log:* checking extension type ... Package ./methylPipe.Rcheck/00check.log:* this is package ‘methylPipe’ version ‘1.19.0’ ./methylPipe.Rcheck/00check.log:* checking package namespace information ... OK ./methylPipe.Rcheck/00check.log:* checking package dependencies ... OK ./methylPipe.Rcheck/00check.log:* checking if this is a source package ... OK ./methylPipe.Rcheck/00check.log:* checking if there is a namespace ... OK ./methylPipe.Rcheck/00check.log:* checking for executable files ... OK ./methylPipe.Rcheck/00check.log:* checking for hidden files and directories ... OK ./methylPipe.Rcheck/00check.log:* checking for portable file names ... OK ./methylPipe.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./methylPipe.Rcheck/00check.log:* checking whether package ‘methylPipe’ can be installed ... OK ./methylPipe.Rcheck/00check.log:* checking installed package size ... OK ./methylPipe.Rcheck/00check.log:* checking package directory ... OK ./methylPipe.Rcheck/00check.log:* checking ‘build’ directory ... OK ./methylPipe.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./methylPipe.Rcheck/00check.log:* checking top-level files ... OK ./methylPipe.Rcheck/00check.log:* checking for left-over files ... OK ./methylPipe.Rcheck/00check.log:* checking index information ... OK ./methylPipe.Rcheck/00check.log:* checking package subdirectories ... OK ./methylPipe.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./methylPipe.Rcheck/00check.log:* checking R files for syntax errors ... OK ./methylPipe.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./methylPipe.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./methylPipe.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./methylPipe.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./methylPipe.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./methylPipe.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./methylPipe.Rcheck/00check.log:* checking dependencies in R code ... OK ./methylPipe.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./methylPipe.Rcheck/00check.log:* checking replacement functions ... OK ./methylPipe.Rcheck/00check.log:* checking foreign function calls ... OK ./methylPipe.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./methylPipe.Rcheck/00check.log:BSprepare : binomTestMulti: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'binom.test' ./methylPipe.Rcheck/00check.log:BSprepare : binomTestMulti : pVfun: no visible global function ./methylPipe.Rcheck/00check.log: definition for 'binom.test' ./methylPipe.Rcheck/00check.log:BSprepare : binomTestMulti: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'p.adjust' ./methylPipe.Rcheck/00check.log:chiCombP: no visible global function definition for 'pchisq' ./methylPipe.Rcheck/00check.log:consolidateDMRs: no visible global function definition for 'p.adjust' ./methylPipe.Rcheck/00check.log:plotMeth: no visible global function definition for 'rainbow' ./methylPipe.Rcheck/00check.log:process.hmc: no visible global function definition for 'write.table' ./methylPipe.Rcheck/00check.log:findDMR,BSdataSet : DMRchr: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'kruskal.test' ./methylPipe.Rcheck/00check.log:findDMR,BSdataSet : DMRchr: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'wilcox.test' ./methylPipe.Rcheck/00check.log:findDMR,BSdataSet: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'stopCluster' ./methylPipe.Rcheck/00check.log:findPMDs,BSdata : PMDchr: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'segmentPMDs' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'smooth.spline' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for 'box' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for 'axis' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for 'mtext' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'stopCluster' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.cor: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'par' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.cor: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'cor.test' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.cor: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'text' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.smooth: no visible global function ./methylPipe.Rcheck/00check.log: definition for 'points' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.smooth: no visible global function ./methylPipe.Rcheck/00check.log: definition for 'lines' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.hist: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'par' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.hist: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'hist' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.hist: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'rect' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'pairs' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'dist' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'hclust' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'dev.new' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'plot' ./methylPipe.Rcheck/00check.log:show,BSdata: no visible global function definition for 'organism' ./methylPipe.Rcheck/00check.log:show,BSdataSet: no visible global function definition for 'organism' ./methylPipe.Rcheck/00check.log:Undefined global functions or variables: ./methylPipe.Rcheck/00check.log: axis binom.test box cor.test dev.new dist hclust hist kruskal.test ./methylPipe.Rcheck/00check.log: lines mtext organism p.adjust pairs par pchisq plot points rainbow ./methylPipe.Rcheck/00check.log: rect segmentPMDs smooth.spline stopCluster text wilcox.test ./methylPipe.Rcheck/00check.log: write.table ./methylPipe.Rcheck/00check.log:Consider adding ./methylPipe.Rcheck/00check.log: importFrom("grDevices", "dev.new", "rainbow") ./methylPipe.Rcheck/00check.log: importFrom("graphics", "axis", "box", "hist", "lines", "mtext", ./methylPipe.Rcheck/00check.log: "pairs", "par", "plot", "points", "rect", "text") ./methylPipe.Rcheck/00check.log: importFrom("stats", "binom.test", "cor.test", "dist", "hclust", ./methylPipe.Rcheck/00check.log: "kruskal.test", "p.adjust", "pchisq", "smooth.spline", ./methylPipe.Rcheck/00check.log: "wilcox.test") ./methylPipe.Rcheck/00check.log: importFrom("utils", "write.table") ./methylPipe.Rcheck/00check.log:to your NAMESPACE file. ./methylPipe.Rcheck/00check.log:* checking Rd files ... OK ./methylPipe.Rcheck/00check.log:* checking Rd metadata ... OK ./methylPipe.Rcheck/00check.log:* checking Rd cross-references ... OK ./methylPipe.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./methylPipe.Rcheck/00check.log:Undocumented S4 methods: ./methylPipe.Rcheck/00check.log: generic '[' and siglist 'BSdataSet,ANY,ANY,ANY' ./methylPipe.Rcheck/00check.log: generic '[' and siglist 'GElist,ANY,ANY,ANY' ./methylPipe.Rcheck/00check.log: generic '[[<-' and siglist 'BSdataSet,ANY,ANY,ANY' ./methylPipe.Rcheck/00check.log: generic '[[<-' and siglist 'GElist,ANY,ANY,ANY' ./methylPipe.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./methylPipe.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./methylPipe.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./methylPipe.Rcheck/00check.log:* checking Rd \usage sections ... OK ./methylPipe.Rcheck/00check.log:* checking Rd contents ... OK ./methylPipe.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./methylPipe.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./methylPipe.Rcheck/00check.log:* checking compiled code ... OK ./methylPipe.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./methylPipe.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./methylPipe.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./methylPipe.Rcheck/00check.log:* checking examples ... WARNING ./methylPipe.Rcheck/00check.log:Found the following significant warnings: ./methylPipe.Rcheck/00check.log: Warning: working directory was changed to '/tmp/RtmprBriZm', resetting ./methylPipe.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./methylPipe.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./methylPipe.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./methylPipe.Rcheck/00check.log: ‘methylPipe.rnw’... OK ./methylPipe.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./methylPipe.Rcheck/00check.log:* checking PDF version of manual ... OK ./methylPipe.Rcheck/00check.log:* DONE ./methylPipe.Rcheck/00check.log:Status: 2 WARNINGs, 1 NOTE MinimumDistance_1.29.2.tar.gz ./MinimumDistance.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/MinimumDistance.Rcheck’ ./MinimumDistance.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./MinimumDistance.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./MinimumDistance.Rcheck/00check.log:* using session charset: UTF-8 ./MinimumDistance.Rcheck/00check.log:* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK ./MinimumDistance.Rcheck/00check.log:* this is package ‘MinimumDistance’ version ‘1.29.2’ ./MinimumDistance.Rcheck/00check.log:* checking package namespace information ... OK ./MinimumDistance.Rcheck/00check.log:* checking package dependencies ... OK ./MinimumDistance.Rcheck/00check.log:* checking if this is a source package ... OK ./MinimumDistance.Rcheck/00check.log:* checking if there is a namespace ... OK ./MinimumDistance.Rcheck/00check.log:* checking for executable files ... OK ./MinimumDistance.Rcheck/00check.log:* checking for hidden files and directories ... OK ./MinimumDistance.Rcheck/00check.log:* checking for portable file names ... OK ./MinimumDistance.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether package ‘MinimumDistance’ can be installed ... OK ./MinimumDistance.Rcheck/00check.log:* checking installed package size ... OK ./MinimumDistance.Rcheck/00check.log:* checking package directory ... OK ./MinimumDistance.Rcheck/00check.log:* checking ‘build’ directory ... OK ./MinimumDistance.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./MinimumDistance.Rcheck/00check.log:* checking top-level files ... OK ./MinimumDistance.Rcheck/00check.log:* checking for left-over files ... OK ./MinimumDistance.Rcheck/00check.log:* checking index information ... OK ./MinimumDistance.Rcheck/00check.log:* checking package subdirectories ... OK ./MinimumDistance.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./MinimumDistance.Rcheck/00check.log:* checking R files for syntax errors ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./MinimumDistance.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./MinimumDistance.Rcheck/00check.log:* checking dependencies in R code ... OK ./MinimumDistance.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./MinimumDistance.Rcheck/00check.log:* checking replacement functions ... OK ./MinimumDistance.Rcheck/00check.log:* checking foreign function calls ... OK ./MinimumDistance.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./MinimumDistance.Rcheck/00check.log:callDenovoSegments: no visible global function definition for ./MinimumDistance.Rcheck/00check.log: ‘read.bsfiles’ ./MinimumDistance.Rcheck/00check.log:pruneTrioSet: no visible global function definition for ./MinimumDistance.Rcheck/00check.log: ‘RangedDataList’ ./MinimumDistance.Rcheck/00check.log:read.bsfiles2: no visible binding for global variable ‘read.bsfiles’ ./MinimumDistance.Rcheck/00check.log:GenomeAnnotatedDataFrameFrom,character: no visible global function ./MinimumDistance.Rcheck/00check.log: definition for ‘read.bsfiles’ ./MinimumDistance.Rcheck/00check.log:calculateMindist,list: no visible binding for global variable ‘elt’ ./MinimumDistance.Rcheck/00check.log:Undefined global functions or variables: ./MinimumDistance.Rcheck/00check.log: RangedDataList elt read.bsfiles ./MinimumDistance.Rcheck/00check.log:* checking Rd files ... OK ./MinimumDistance.Rcheck/00check.log:* checking Rd metadata ... OK ./MinimumDistance.Rcheck/00check.log:* checking Rd cross-references ... OK ./MinimumDistance.Rcheck/00check.log:* checking for missing documentation entries ... OK ./MinimumDistance.Rcheck/00check.log:* checking for code/documentation mismatches ... WARNING ./MinimumDistance.Rcheck/00check.log:Functions or methods with usage in documentation object 'coerce' but not in code: ./MinimumDistance.Rcheck/00check.log: ‘as’ ./MinimumDistance.Rcheck/00check.log:* checking Rd \usage sections ... OK ./MinimumDistance.Rcheck/00check.log:* checking Rd contents ... OK ./MinimumDistance.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./MinimumDistance.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./MinimumDistance.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./MinimumDistance.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./MinimumDistance.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./MinimumDistance.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./MinimumDistance.Rcheck/00check.log:* checking include directives in Makefiles ... OK ./MinimumDistance.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking examples ... OK ./MinimumDistance.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking tests ... OK ./MinimumDistance.Rcheck/00check.log: Running ‘doRUnit.R’ ./MinimumDistance.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./MinimumDistance.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking running R code from vignettes ... OK ./MinimumDistance.Rcheck/00check.log: ‘MinimumDistance.Rnw’... OK ./MinimumDistance.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./MinimumDistance.Rcheck/00check.log:* checking PDF version of manual ... OK ./MinimumDistance.Rcheck/00check.log:* DONE ./MinimumDistance.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE MSnID_1.19.0.tar.gz ./MSnID.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/MSnID.Rcheck’ ./MSnID.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./MSnID.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./MSnID.Rcheck/00check.log:* using session charset: UTF-8 ./MSnID.Rcheck/00check.log:* checking for file ‘MSnID/DESCRIPTION’ ... OK ./MSnID.Rcheck/00check.log:* checking extension type ... Package ./MSnID.Rcheck/00check.log:* this is package ‘MSnID’ version ‘1.19.0’ ./MSnID.Rcheck/00check.log:* checking package namespace information ... OK ./MSnID.Rcheck/00check.log:* checking package dependencies ... OK ./MSnID.Rcheck/00check.log:* checking if this is a source package ... OK ./MSnID.Rcheck/00check.log:* checking if there is a namespace ... OK ./MSnID.Rcheck/00check.log:* checking for executable files ... OK ./MSnID.Rcheck/00check.log:* checking for hidden files and directories ... OK ./MSnID.Rcheck/00check.log:* checking for portable file names ... OK ./MSnID.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./MSnID.Rcheck/00check.log:* checking whether package ‘MSnID’ can be installed ... OK ./MSnID.Rcheck/00check.log:* checking installed package size ... OK ./MSnID.Rcheck/00check.log:* checking package directory ... OK ./MSnID.Rcheck/00check.log:* checking ‘build’ directory ... OK ./MSnID.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./MSnID.Rcheck/00check.log:* checking top-level files ... OK ./MSnID.Rcheck/00check.log:* checking for left-over files ... OK ./MSnID.Rcheck/00check.log:* checking index information ... OK ./MSnID.Rcheck/00check.log:* checking package subdirectories ... OK ./MSnID.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./MSnID.Rcheck/00check.log:* checking R files for syntax errors ... OK ./MSnID.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./MSnID.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./MSnID.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./MSnID.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./MSnID.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./MSnID.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./MSnID.Rcheck/00check.log:* checking dependencies in R code ... OK ./MSnID.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./MSnID.Rcheck/00check.log:* checking replacement functions ... OK ./MSnID.Rcheck/00check.log:* checking foreign function calls ... OK ./MSnID.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./MSnID.Rcheck/00check.log:.construct_optimization_grid : : no visible global function ./MSnID.Rcheck/00check.log: definition for ‘quantile’ ./MSnID.Rcheck/00check.log:.get_num_pep_for_fdr: no visible global function definition for ‘rnorm’ ./MSnID.Rcheck/00check.log:.optimize_filter: no visible global function definition for ‘optim’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR: no visible binding for global variable ‘i’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘spectrumID’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘name’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘mass’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘location’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘modification’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘DatabaseAccess’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘DatabaseDescription’ ./MSnID.Rcheck/00check.log:.read_mzIDs.mzR.engine.single.file: no visible binding for global ./MSnID.Rcheck/00check.log: variable ‘DBseqLength’ ./MSnID.Rcheck/00check.log:infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for ./MSnID.Rcheck/00check.log: global variable ‘accession’ ./MSnID.Rcheck/00check.log:infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for ./MSnID.Rcheck/00check.log: global variable ‘N’ ./MSnID.Rcheck/00check.log:infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for ./MSnID.Rcheck/00check.log: global variable ‘pepSeq’ ./MSnID.Rcheck/00check.log:recalibrate,MSnID: no visible global function definition for ‘median’ ./MSnID.Rcheck/00check.log:recalibrate,MSnID: no visible global function definition for ‘density’ ./MSnID.Rcheck/00check.log:Undefined global functions or variables: ./MSnID.Rcheck/00check.log: DBseqLength DatabaseAccess DatabaseDescription N accession density i ./MSnID.Rcheck/00check.log: location mass median modification name optim pepSeq quantile rnorm ./MSnID.Rcheck/00check.log: spectrumID ./MSnID.Rcheck/00check.log:Consider adding ./MSnID.Rcheck/00check.log: importFrom("stats", "density", "median", "optim", "quantile", "rnorm") ./MSnID.Rcheck/00check.log:to your NAMESPACE file. ./MSnID.Rcheck/00check.log:* checking Rd files ... OK ./MSnID.Rcheck/00check.log:* checking Rd metadata ... OK ./MSnID.Rcheck/00check.log:* checking Rd cross-references ... WARNING ./MSnID.Rcheck/00check.log:Missing link or links in documentation object 'read_mzIDs.Rd': ./MSnID.Rcheck/00check.log: ‘[mzR]{mzR-package}’ ./MSnID.Rcheck/00check.log:See section 'Cross-references' in the 'Writing R Extensions' manual. ./MSnID.Rcheck/00check.log:* checking for missing documentation entries ... OK ./MSnID.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./MSnID.Rcheck/00check.log:* checking Rd \usage sections ... OK ./MSnID.Rcheck/00check.log:* checking Rd contents ... OK ./MSnID.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./MSnID.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./MSnID.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./MSnID.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./MSnID.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./MSnID.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./MSnID.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./MSnID.Rcheck/00check.log:* checking examples ... OK ./MSnID.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./MSnID.Rcheck/00check.log:* checking tests ... OK ./MSnID.Rcheck/00check.log: Running ‘runTests.R’ ./MSnID.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./MSnID.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./MSnID.Rcheck/00check.log:* checking running R code from vignettes ... OK ./MSnID.Rcheck/00check.log: ‘msnid_vignette.Rnw’... OK ./MSnID.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./MSnID.Rcheck/00check.log:* checking PDF version of manual ... OK ./MSnID.Rcheck/00check.log:* DONE ./MSnID.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE MSstats_3.17.1.tar.gz MSstatsTMT_1.3.2.tar.gz ./MSstats.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/MSstats.Rcheck’ ./MSstats.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./MSstats.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./MSstats.Rcheck/00check.log:* using session charset: UTF-8 ./MSstats.Rcheck/00check.log:* checking for file ‘MSstats/DESCRIPTION’ ... OK ./MSstats.Rcheck/00check.log:* this is package ‘MSstats’ version ‘3.17.1’ ./MSstats.Rcheck/00check.log:* package encoding: UTF-8 ./MSstats.Rcheck/00check.log:* checking package namespace information ... OK ./MSstats.Rcheck/00check.log:* checking package dependencies ... OK ./MSstats.Rcheck/00check.log:* checking if this is a source package ... OK ./MSstats.Rcheck/00check.log:* checking if there is a namespace ... OK ./MSstats.Rcheck/00check.log:* checking for executable files ... OK ./MSstats.Rcheck/00check.log:* checking for hidden files and directories ... OK ./MSstats.Rcheck/00check.log:* checking for portable file names ... OK ./MSstats.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./MSstats.Rcheck/00check.log:* checking whether package ‘MSstats’ can be installed ... WARNING ./MSstats.Rcheck/00check.log:Found the following significant warnings: ./MSstats.Rcheck/00check.log: Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’ ./MSstats.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/MSstats.Rcheck/00install.out’ for details. ./MSstats.Rcheck/00check.log:* checking installed package size ... OK ./MSstats.Rcheck/00check.log:* checking package directory ... OK ./MSstats.Rcheck/00check.log:* checking ‘build’ directory ... OK ./MSstats.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./MSstats.Rcheck/00check.log:* checking top-level files ... OK ./MSstats.Rcheck/00check.log:* checking for left-over files ... OK ./MSstats.Rcheck/00check.log:* checking index information ... OK ./MSstats.Rcheck/00check.log:* checking package subdirectories ... OK ./MSstats.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./MSstats.Rcheck/00check.log:* checking R files for syntax errors ... OK ./MSstats.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./MSstats.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./MSstats.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./MSstats.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./MSstats.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./MSstats.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./MSstats.Rcheck/00check.log:* checking dependencies in R code ... OK ./MSstats.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./MSstats.Rcheck/00check.log:* checking replacement functions ... OK ./MSstats.Rcheck/00check.log:* checking foreign function calls ... OK ./MSstats.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./MSstats.Rcheck/00check.log:.iter.wls.fit.model: no visible binding for global variable ‘weight’ ./MSstats.Rcheck/00check.log:.runQuantification: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘datafeature’ ./MSstats.Rcheck/00check.log:.runQuantification: no visible binding for global variable ‘ount’ ./MSstats.Rcheck/00check.log:DIAUmpiretoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘Selected_fragments’ ./MSstats.Rcheck/00check.log:DIAUmpiretoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘Selected_peptides’ ./MSstats.Rcheck/00check.log:DIAUmpiretoMSstatsFormat: no visible binding for global variable ‘fea’ ./MSstats.Rcheck/00check.log:DIAUmpiretoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘Intensity’ ./MSstats.Rcheck/00check.log:OpenMStoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘missing.col’ ./MSstats.Rcheck/00check.log:OpenMStoMSstatsFormat: no visible binding for global variable ‘fea’ ./MSstats.Rcheck/00check.log:OpenMStoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘Intensity’ ./MSstats.Rcheck/00check.log:OpenMStoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘PeptideSequence’ ./MSstats.Rcheck/00check.log:OpenMStoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘ProteinName’ ./MSstats.Rcheck/00check.log:OpenSWATHtoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘missing.col’ ./MSstats.Rcheck/00check.log:OpenSWATHtoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘aggr_Fragment_Annotation’ ./MSstats.Rcheck/00check.log:OpenSWATHtoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘aggr_Peak_Area’ ./MSstats.Rcheck/00check.log:OpenSWATHtoMSstatsFormat: no visible binding for global variable ‘fea’ ./MSstats.Rcheck/00check.log:OpenSWATHtoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘Intensity’ ./MSstats.Rcheck/00check.log:OpenSWATHtoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘PeptideSequence’ ./MSstats.Rcheck/00check.log:OpenSWATHtoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘ProteinName’ ./MSstats.Rcheck/00check.log:PDtoMSstatsFormat: no visible binding for global variable ‘fea’ ./MSstats.Rcheck/00check.log:PDtoMSstatsFormat: no visible binding for global variable ‘Intensity’ ./MSstats.Rcheck/00check.log:SkylinetoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘PeptideSequence’ ./MSstats.Rcheck/00check.log:SkylinetoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘ProteinName’ ./MSstats.Rcheck/00check.log:SkylinetoMSstatsFormat: no visible binding for global variable ‘fea’ ./MSstats.Rcheck/00check.log:SkylinetoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘Intensity’ ./MSstats.Rcheck/00check.log:SpectronauttoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘missing.col’ ./MSstats.Rcheck/00check.log:SpectronauttoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘fea’ ./MSstats.Rcheck/00check.log:SpectronauttoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘Intensity’ ./MSstats.Rcheck/00check.log:SpectronauttoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘PeptideSequence’ ./MSstats.Rcheck/00check.log:SpectronauttoMSstatsFormat: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘ProteinName’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘.resid’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘is_olr’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘log2inty’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘feature’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘nb_run’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘resid_null’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘svar_feature’ ./MSstats.Rcheck/00check.log:calc_fvar: no visible binding for global variable ‘svar_ref’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘FEATURE’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘ncount’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘ABUNDANCE’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘RUN’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘FRACTION’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘PROTEIN’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘INTENSITY’ ./MSstats.Rcheck/00check.log:dataProcess: no visible binding for global variable ‘LABEL’ ./MSstats.Rcheck/00check.log:dataProcessPlots: no visible binding for global variable ‘RUN’ ./MSstats.Rcheck/00check.log:dataProcessPlots: no visible binding for global variable ‘ABUNDANCE’ ./MSstats.Rcheck/00check.log:dataProcessPlots: no visible binding for global variable ‘Name’ ./MSstats.Rcheck/00check.log:dataProcessPlots: no visible binding for global variable ‘analysis’ ./MSstats.Rcheck/00check.log:dataProcessPlots: no visible binding for global variable ‘Mean’ ./MSstats.Rcheck/00check.log:dataProcessPlots: no visible binding for global variable ‘ciw’ ./MSstats.Rcheck/00check.log:designSampleSizeClassificationPlots: no visible binding for global ./MSstats.Rcheck/00check.log: variable ‘Train_size’ ./MSstats.Rcheck/00check.log:designSampleSizeClassificationPlots: no visible binding for global ./MSstats.Rcheck/00check.log: variable ‘Protein_number’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘PROTEIN’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘PEPTIDE’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘FEATURE’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘originalRUN’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘LABEL’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘ABUNDANCE’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘censored’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘log2inty’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘is_censored’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘is_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘protein’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘peptide’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘run’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘label’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘nb_run’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘nb_feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘nb_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘nb_full’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘pi_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘min_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘is_lowcvr’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘cover_feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘rlm_fit’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘s_resid’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘df_resid’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘var_resid_eb’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘s_resid_eb’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘is_olr’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘var_feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data: no visible binding for global variable ‘svar_feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘PROTEIN’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘PEPTIDE’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘FEATURE’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘originalRUN’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘LABEL’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘ABUNDANCE’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘censored’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘log2inty’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘is_censored’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘is_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘protein’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘peptide’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘run’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘label’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘nb_feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘nb_run’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘nb_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘nb_full’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘pi_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘min_obs’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘is_lowcvr’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘cover_feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘rlm_fit’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘s_resid’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘df_resid’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘var_resid_eb’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘s_resid_eb’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ‘is_olr’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘var_feature’ ./MSstats.Rcheck/00check.log:flag_noninf_data_nbftr: no visible binding for global variable ./MSstats.Rcheck/00check.log: ‘svar_feature’ ./MSstats.Rcheck/00check.log:flag_outlier: no visible binding for global variable ‘.resid’ ./MSstats.Rcheck/00check.log:flag_outlier: no visible binding for global variable ‘run’ ./MSstats.Rcheck/00check.log:flag_outlier: no visible binding for global variable ‘feature’ ./MSstats.Rcheck/00check.log:flag_outlier: no visible binding for global variable ‘is_olr’ ./MSstats.Rcheck/00check.log:groupComparisonPlots: no visible binding for global variable ‘Protein’ ./MSstats.Rcheck/00check.log:groupComparisonPlots: no visible binding for global variable ‘logFC’ ./MSstats.Rcheck/00check.log:groupComparisonPlots: no visible binding for global variable ‘ciw’ ./MSstats.Rcheck/00check.log:linear_quantlim: no visible binding for global variable ‘label’ ./MSstats.Rcheck/00check.log:modelBasedQCPlots: no visible binding for global variable ‘residual’ ./MSstats.Rcheck/00check.log:nonlinear_quantlim: no visible binding for global variable ‘label’ ./MSstats.Rcheck/00check.log:plot_quantlim: no visible binding for global variable ‘x’ ./MSstats.Rcheck/00check.log:plot_quantlim: no visible binding for global variable ‘y’ ./MSstats.Rcheck/00check.log:plot_quantlim: no visible binding for global variable ‘ymin’ ./MSstats.Rcheck/00check.log:plot_quantlim: no visible binding for global variable ‘ymax’ ./MSstats.Rcheck/00check.log:plot_quantlim: no visible binding for global variable ‘shape’ ./MSstats.Rcheck/00check.log:Undefined global functions or variables: ./MSstats.Rcheck/00check.log: .resid ABUNDANCE FEATURE FRACTION INTENSITY Intensity LABEL Mean Name ./MSstats.Rcheck/00check.log: PEPTIDE PROTEIN PeptideSequence Protein ProteinName Protein_number ./MSstats.Rcheck/00check.log: RUN Selected_fragments Selected_peptides Train_size ./MSstats.Rcheck/00check.log: aggr_Fragment_Annotation aggr_Peak_Area analysis censored ciw ./MSstats.Rcheck/00check.log: cover_feature datafeature df_resid fea feature is_censored is_lowcvr ./MSstats.Rcheck/00check.log: is_obs is_olr label log2inty logFC min_obs missing.col nb_feature ./MSstats.Rcheck/00check.log: nb_full nb_obs nb_run ncount originalRUN ount peptide pi_obs protein ./MSstats.Rcheck/00check.log: resid_null residual rlm_fit run s_resid s_resid_eb shape svar_feature ./MSstats.Rcheck/00check.log: svar_ref var_feature var_resid_eb weight x y ymax ymin ./MSstats.Rcheck/00check.log:* checking Rd files ... OK ./MSstats.Rcheck/00check.log:* checking Rd metadata ... OK ./MSstats.Rcheck/00check.log:* checking Rd cross-references ... OK ./MSstats.Rcheck/00check.log:* checking for missing documentation entries ... OK ./MSstats.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./MSstats.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./MSstats.Rcheck/00check.log:Duplicated \argument entries in documentation object 'dataProcess': ./MSstats.Rcheck/00check.log: ‘featureSubset’ ./MSstats.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./MSstats.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./MSstats.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./MSstats.Rcheck/00check.log:* checking Rd contents ... OK ./MSstats.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./MSstats.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./MSstats.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./MSstats.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./MSstats.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./MSstats.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./MSstats.Rcheck/00check.log:* checking examples ... OK ./MSstats.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./MSstats.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./MSstats.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./MSstats.Rcheck/00check.log: ‘MSstats.Rmd’using ‘UTF-8’... OK ./MSstats.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./MSstats.Rcheck/00check.log:* checking PDF version of manual ... OK ./MSstats.Rcheck/00check.log:* DONE ./MSstats.Rcheck/00check.log:Status: 2 WARNINGs, 1 NOTE netSmooth_1.5.1.tar.gz ./netSmooth.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/netSmooth.Rcheck’ ./netSmooth.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./netSmooth.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./netSmooth.Rcheck/00check.log:* using session charset: UTF-8 ./netSmooth.Rcheck/00check.log:* checking for file ‘netSmooth/DESCRIPTION’ ... OK ./netSmooth.Rcheck/00check.log:* checking extension type ... Package ./netSmooth.Rcheck/00check.log:* this is package ‘netSmooth’ version ‘1.5.1’ ./netSmooth.Rcheck/00check.log:* package encoding: UTF-8 ./netSmooth.Rcheck/00check.log:* checking package namespace information ... OK ./netSmooth.Rcheck/00check.log:* checking package dependencies ... OK ./netSmooth.Rcheck/00check.log:* checking if this is a source package ... OK ./netSmooth.Rcheck/00check.log:* checking if there is a namespace ... OK ./netSmooth.Rcheck/00check.log:* checking for executable files ... OK ./netSmooth.Rcheck/00check.log:* checking for hidden files and directories ... NOTE ./netSmooth.Rcheck/00check.log:Found the following hidden files and directories: ./netSmooth.Rcheck/00check.log: .travis.yml ./netSmooth.Rcheck/00check.log:These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ./netSmooth.Rcheck/00check.log:* checking for portable file names ... OK ./netSmooth.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./netSmooth.Rcheck/00check.log:* checking whether package ‘netSmooth’ can be installed ... OK ./netSmooth.Rcheck/00check.log:* checking installed package size ... NOTE ./netSmooth.Rcheck/00check.log: installed size is 6.0Mb ./netSmooth.Rcheck/00check.log: sub-directories of 1Mb or more: ./netSmooth.Rcheck/00check.log: data 3.4Mb ./netSmooth.Rcheck/00check.log: doc 2.4Mb ./netSmooth.Rcheck/00check.log:* checking package directory ... OK ./netSmooth.Rcheck/00check.log:* checking ‘build’ directory ... OK ./netSmooth.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./netSmooth.Rcheck/00check.log:* checking top-level files ... OK ./netSmooth.Rcheck/00check.log:* checking for left-over files ... OK ./netSmooth.Rcheck/00check.log:* checking index information ... OK ./netSmooth.Rcheck/00check.log:* checking package subdirectories ... OK ./netSmooth.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./netSmooth.Rcheck/00check.log:* checking R files for syntax errors ... OK ./netSmooth.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./netSmooth.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./netSmooth.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./netSmooth.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./netSmooth.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./netSmooth.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./netSmooth.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./netSmooth.Rcheck/00check.log:Namespace in Imports field not imported from: ‘methods’ ./netSmooth.Rcheck/00check.log: All declared Imports should be used. ./netSmooth.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./netSmooth.Rcheck/00check.log:* checking replacement functions ... OK ./netSmooth.Rcheck/00check.log:* checking foreign function calls ... OK ./netSmooth.Rcheck/00check.log:* checking R code for possible problems ... OK ./netSmooth.Rcheck/00check.log:* checking Rd files ... OK ./netSmooth.Rcheck/00check.log:* checking Rd metadata ... OK ./netSmooth.Rcheck/00check.log:* checking Rd cross-references ... OK ./netSmooth.Rcheck/00check.log:* checking for missing documentation entries ... OK ./netSmooth.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./netSmooth.Rcheck/00check.log:* checking Rd \usage sections ... OK ./netSmooth.Rcheck/00check.log:* checking Rd contents ... OK ./netSmooth.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./netSmooth.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./netSmooth.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./netSmooth.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./netSmooth.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./netSmooth.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./netSmooth.Rcheck/00check.log:* checking examples ... WARNING ./netSmooth.Rcheck/00check.log:Found the following significant warnings: ./netSmooth.Rcheck/00check.log: Warning: 'use_size_factors=FALSE' is deprecated. ./netSmooth.Rcheck/00check.log: Warning: 'use_size_factors=FALSE' is deprecated. ./netSmooth.Rcheck/00check.log: Warning: 'use_size_factors=FALSE' is deprecated. ./netSmooth.Rcheck/00check.log: Warning: 'use_size_factors=FALSE' is deprecated. ./netSmooth.Rcheck/00check.log: Warning: 'use_size_factors=FALSE' is deprecated. ./netSmooth.Rcheck/00check.log:Deprecated functions may be defunct as soon as of the next release of R. ./netSmooth.Rcheck/00check.log:See ?Deprecated. ./netSmooth.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./netSmooth.Rcheck/00check.log:* checking tests ... OK ./netSmooth.Rcheck/00check.log: Running ‘testthat.R’ ./netSmooth.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./netSmooth.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./netSmooth.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./netSmooth.Rcheck/00check.log: ‘buildingPPIsFromStringDB.Rmd’using ‘UTF-8’... OK ./netSmooth.Rcheck/00check.log: ‘netSmoothIntro.Rmd’using ‘UTF-8’... OK ./netSmooth.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./netSmooth.Rcheck/00check.log:* checking PDF version of manual ... OK ./netSmooth.Rcheck/00check.log:* DONE ./netSmooth.Rcheck/00check.log:Status: 1 WARNING, 3 NOTEs openCyto_1.23.5.tar.gz ./openCyto.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/openCyto.Rcheck’ ./openCyto.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./openCyto.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./openCyto.Rcheck/00check.log:* using session charset: UTF-8 ./openCyto.Rcheck/00check.log:* checking for file ‘openCyto/DESCRIPTION’ ... OK ./openCyto.Rcheck/00check.log:* checking extension type ... Package ./openCyto.Rcheck/00check.log:* this is package ‘openCyto’ version ‘1.23.5’ ./openCyto.Rcheck/00check.log:* package encoding: UTF-8 ./openCyto.Rcheck/00check.log:* checking package namespace information ... OK ./openCyto.Rcheck/00check.log:* checking package dependencies ... OK ./openCyto.Rcheck/00check.log:* checking if this is a source package ... OK ./openCyto.Rcheck/00check.log:* checking if there is a namespace ... OK ./openCyto.Rcheck/00check.log:* checking for executable files ... OK ./openCyto.Rcheck/00check.log:* checking for hidden files and directories ... NOTE ./openCyto.Rcheck/00check.log:Found the following hidden files and directories: ./openCyto.Rcheck/00check.log: .travis.yml ./openCyto.Rcheck/00check.log:These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ./openCyto.Rcheck/00check.log:* checking for portable file names ... OK ./openCyto.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./openCyto.Rcheck/00check.log:* checking whether package ‘openCyto’ can be installed ... OK ./openCyto.Rcheck/00check.log:* checking installed package size ... NOTE ./openCyto.Rcheck/00check.log: installed size is 6.7Mb ./openCyto.Rcheck/00check.log: sub-directories of 1Mb or more: ./openCyto.Rcheck/00check.log: doc 2.5Mb ./openCyto.Rcheck/00check.log: libs 3.2Mb ./openCyto.Rcheck/00check.log:* checking package directory ... OK ./openCyto.Rcheck/00check.log:* checking ‘build’ directory ... OK ./openCyto.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./openCyto.Rcheck/00check.log:* checking top-level files ... OK ./openCyto.Rcheck/00check.log:* checking for left-over files ... OK ./openCyto.Rcheck/00check.log:* checking index information ... OK ./openCyto.Rcheck/00check.log:* checking package subdirectories ... OK ./openCyto.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./openCyto.Rcheck/00check.log:* checking R files for syntax errors ... OK ./openCyto.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./openCyto.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./openCyto.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./openCyto.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./openCyto.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./openCyto.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./openCyto.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./openCyto.Rcheck/00check.log:'library' or 'require' call to ‘parallel’ in package code. ./openCyto.Rcheck/00check.log: Please use :: or requireNamespace() instead. ./openCyto.Rcheck/00check.log: See section 'Suggested packages' in the 'Writing R Extensions' manual. ./openCyto.Rcheck/00check.log:Namespace in Imports field not imported from: ‘flowViz’ ./openCyto.Rcheck/00check.log: All declared Imports should be used. ./openCyto.Rcheck/00check.log:':::' call which should be '::': ‘flowWorkspace:::gh_pop_is_negated’ ./openCyto.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./openCyto.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./openCyto.Rcheck/00check.log: ‘flowClust:::.ellipsePoints’ ‘flowStats:::drvkde’ ./openCyto.Rcheck/00check.log: ‘flowStats:::warpSetNCDF’ ‘flowWorkspace:::.addGate’ ./openCyto.Rcheck/00check.log: ‘flowWorkspace:::.cpp_addGate’ ‘flowWorkspace:::.cpp_boolGating’ ./openCyto.Rcheck/00check.log: ‘flowWorkspace:::.cpp_setIndices’ ./openCyto.Rcheck/00check.log: ‘flowWorkspace:::.getAllDescendants’ ./openCyto.Rcheck/00check.log: ‘flowWorkspace:::filter_to_list.booleanFilter’ ./openCyto.Rcheck/00check.log: ‘flowWorkspace:::filter_to_list.rectangleGate’ ‘lattice:::updateList’ ./openCyto.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./openCyto.Rcheck/00check.log:There are ::: calls to the package's namespace in its code. A package ./openCyto.Rcheck/00check.log: almost never needs to use ::: for its own objects: ./openCyto.Rcheck/00check.log: ‘groupBy’ ‘isCollapse’ ‘ppMethod’ ‘unlockNamespace’ ./openCyto.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./openCyto.Rcheck/00check.log:* checking replacement functions ... OK ./openCyto.Rcheck/00check.log:* checking foreign function calls ... OK ./openCyto.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./openCyto.Rcheck/00check.log:Found the following possibly unsafe calls: ./openCyto.Rcheck/00check.log:File ‘openCyto/R/pluginFramework.R’: ./openCyto.Rcheck/00check.log: unlockBinding(methodName, ENV) ./openCyto.Rcheck/00check.log: unlockBinding(methodName, ENV) ./openCyto.Rcheck/00check.log:.boundary: no visible global function definition for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.center_mode: no visible global function definition for ‘density’ ./openCyto.Rcheck/00check.log:.find_peaks: no visible global function definition for ‘density’ ./openCyto.Rcheck/00check.log:.find_peaks: no visible global function definition for ‘points’ ./openCyto.Rcheck/00check.log:.find_valleys: no visible global function definition for ‘density’ ./openCyto.Rcheck/00check.log:.gateToFilterResult: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:.gateToFilterResult: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:.gate_tail: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:.gate_tail: no visible global function definition for ‘exprs<-’ ./openCyto.Rcheck/00check.log:.gate_tail: no visible global function definition for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible global function definition for ‘new’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible binding for global variable ‘pop’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible binding for global variable ‘gating_method’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible binding for global variable ‘gating_args’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘collapseDataForGating’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_method’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_args’ ./openCyto.Rcheck/00check.log:.gatingTemplate: no visible global function definition for ‘extends’ ./openCyto.Rcheck/00check.log:.gating_adaptor: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:.gating_adaptor: no visible global function definition for ‘na.omit’ ./openCyto.Rcheck/00check.log:.gating_adaptor: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.gating_adaptor: no visible global function definition for ‘filters’ ./openCyto.Rcheck/00check.log:.gating_adaptor: no visible global function definition for ‘extends’ ./openCyto.Rcheck/00check.log:.gating_gtMethod : : no visible global function definition ./openCyto.Rcheck/00check.log: for ‘extends’ ./openCyto.Rcheck/00check.log:.gating_gtMethod: no visible global function definition for ‘extends’ ./openCyto.Rcheck/00check.log:.gating_refGate : : no visible global function definition ./openCyto.Rcheck/00check.log: for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.gating_refGate: no visible global function definition for ‘filterList’ ./openCyto.Rcheck/00check.log:.gen_1dgate : : no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘parent’ ./openCyto.Rcheck/00check.log:.gen_1dgate : : no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘gating_method’ ./openCyto.Rcheck/00check.log:.gen_1dgate : : no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘gating_args’ ./openCyto.Rcheck/00check.log:.gen_1dgate : : no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘collapseDataForGating’ ./openCyto.Rcheck/00check.log:.gen_1dgate : : no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_method’ ./openCyto.Rcheck/00check.log:.gen_1dgate : : no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_args’ ./openCyto.Rcheck/00check.log:.gen_dummy_ref_gate: no visible binding for global variable ‘parent’ ./openCyto.Rcheck/00check.log:.gen_dummy_ref_gate : : no visible binding for global ./openCyto.Rcheck/00check.log: variable ‘pop’ ./openCyto.Rcheck/00check.log:.gen_dummy_ref_gate : : no visible binding for global ./openCyto.Rcheck/00check.log: variable ‘gating_method’ ./openCyto.Rcheck/00check.log:.gen_dummy_ref_gate : : no visible binding for global ./openCyto.Rcheck/00check.log: variable ‘gating_args’ ./openCyto.Rcheck/00check.log:.gen_dummy_ref_gate : : no visible binding for global ./openCyto.Rcheck/00check.log: variable ‘collapseDataForGating’ ./openCyto.Rcheck/00check.log:.gen_dummy_ref_gate : : no visible binding for global ./openCyto.Rcheck/00check.log: variable ‘preprocessing_method’ ./openCyto.Rcheck/00check.log:.gen_dummy_ref_gate : : no visible binding for global ./openCyto.Rcheck/00check.log: variable ‘preprocessing_args’ ./openCyto.Rcheck/00check.log:.gen_refGate: no visible binding for global variable ‘parent’ ./openCyto.Rcheck/00check.log:.gen_refGate: no visible binding for global variable ‘gating_args’ ./openCyto.Rcheck/00check.log:.getEllipse: no visible global function definition for ‘qf’ ./openCyto.Rcheck/00check.log:.getEllipse: no visible global function definition for ‘qchisq’ ./openCyto.Rcheck/00check.log:.getEllipseGate: no visible global function definition for ‘qf’ ./openCyto.Rcheck/00check.log:.getEllipseGate: no visible global function definition for ‘qchisq’ ./openCyto.Rcheck/00check.log:.getEllipseGate: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘polygonGate’ ./openCyto.Rcheck/00check.log:.getEllipseGate: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘ellipsoidGate’ ./openCyto.Rcheck/00check.log:.getFullPath: no visible binding for global variable ‘parent’ ./openCyto.Rcheck/00check.log:.improvedMindensity: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘density’ ./openCyto.Rcheck/00check.log:.improvedMindensity: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘smooth.spline’ ./openCyto.Rcheck/00check.log:.improvedMindensity: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘predict’ ./openCyto.Rcheck/00check.log:.improvedMindensity: no visible global function definition for ‘median’ ./openCyto.Rcheck/00check.log:.improvedMindensity : .plots: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘abline’ ./openCyto.Rcheck/00check.log:.improvedMindensity: no visible global function definition for ‘par’ ./openCyto.Rcheck/00check.log:.improvedMindensity: no visible global function definition for ‘abline’ ./openCyto.Rcheck/00check.log:.plotTree: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:.plotTree: no visible global function definition for ‘par’ ./openCyto.Rcheck/00check.log:.plotTree: no visible global function definition for ‘legend’ ./openCyto.Rcheck/00check.log:.preprocess_csv: no visible binding for global variable ‘pop’ ./openCyto.Rcheck/00check.log:.preprocess_csv: no visible binding for global variable ‘parent’ ./openCyto.Rcheck/00check.log:.preprocess_csv: no visible binding for global variable ‘gating_method’ ./openCyto.Rcheck/00check.log:.preprocess_csv: no visible binding for global variable ‘gating_args’ ./openCyto.Rcheck/00check.log:.preprocess_csv: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘collapseDataForGating’ ./openCyto.Rcheck/00check.log:.preprocess_csv: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_method’ ./openCyto.Rcheck/00check.log:.preprocess_csv: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_args’ ./openCyto.Rcheck/00check.log:.preprocess_row: no visible binding for global variable ‘pop’ ./openCyto.Rcheck/00check.log:.preprocess_row: no visible binding for global variable ‘gating_method’ ./openCyto.Rcheck/00check.log:.preprocess_row: no visible binding for global variable ‘parent’ ./openCyto.Rcheck/00check.log:.preprocess_row: no visible binding for global variable ‘gating_args’ ./openCyto.Rcheck/00check.log:.preprocess_row: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_method’ ./openCyto.Rcheck/00check.log:.preprocess_row: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘preprocessing_args’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d: no visible global function definition for ‘fsApply’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d : : no visible global function definition ./openCyto.Rcheck/00check.log: for ‘exprs’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d: no visible global function definition for ‘hclust’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d: no visible global function definition for ‘dist’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d: no visible global function definition for ‘median’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d: no visible global function definition for ‘cutree’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d: no visible global function definition for ‘kmeans’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d : : no visible global function definition ./openCyto.Rcheck/00check.log: for ‘sd’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d: no visible binding for global variable ‘var’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d : : no visible global function definition ./openCyto.Rcheck/00check.log: for ‘embed’ ./openCyto.Rcheck/00check.log:.prior_flowClust1d : : no visible binding for global ./openCyto.Rcheck/00check.log: variable ‘var’ ./openCyto.Rcheck/00check.log:.prior_kmeans : : no visible global function definition for ./openCyto.Rcheck/00check.log: ‘exprs’ ./openCyto.Rcheck/00check.log:.prior_kmeans : : no visible global function definition for ./openCyto.Rcheck/00check.log: ‘kmeans’ ./openCyto.Rcheck/00check.log:.prior_kmeans : : : no visible global function ./openCyto.Rcheck/00check.log: definition for ‘cov’ ./openCyto.Rcheck/00check.log:.prior_kmeans : : no visible global function definition for ./openCyto.Rcheck/00check.log: ‘dist’ ./openCyto.Rcheck/00check.log:.prior_kmeans: no visible binding for global variable ‘cov.wt’ ./openCyto.Rcheck/00check.log:.quadGate2rectangleGates: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.quadGate2rectangleGates: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘filters’ ./openCyto.Rcheck/00check.log:.quantile_flowClust : cdf_target : : no visible global ./openCyto.Rcheck/00check.log: function definition for ‘pt’ ./openCyto.Rcheck/00check.log:.quantile_flowClust : cdf_target: no visible global function definition ./openCyto.Rcheck/00check.log: for ‘weighted.mean’ ./openCyto.Rcheck/00check.log:.quantile_flowClust: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘uniroot’ ./openCyto.Rcheck/00check.log:.read.FCS.csv: no visible global function definition for ‘new’ ./openCyto.Rcheck/00check.log:.read.FCS.csv: no visible global function definition for ‘parameters<-’ ./openCyto.Rcheck/00check.log:.read.flowSet.csv: no visible global function definition for ‘flowSet’ ./openCyto.Rcheck/00check.log:.standardize_flowFrame: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘exprs’ ./openCyto.Rcheck/00check.log:.standardize_flowFrame: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘exprs<-’ ./openCyto.Rcheck/00check.log:.standardize_flowset: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘fsApply’ ./openCyto.Rcheck/00check.log:.standardize_flowset: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘flowSet’ ./openCyto.Rcheck/00check.log:.standardize_flowset: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:.tailgate: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:.tailgate: no visible global function definition for ‘exprs<-’ ./openCyto.Rcheck/00check.log:.tailgate: no visible global function definition for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.truncate_flowframe: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.truncate_flowframe: no visible global function definition for ‘Subset’ ./openCyto.Rcheck/00check.log:.truncate_flowset: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:.truncate_flowset: no visible global function definition for ‘Subset’ ./openCyto.Rcheck/00check.log:.unique_check_alias: no visible binding for global variable ‘parent’ ./openCyto.Rcheck/00check.log:as.data.table.gatingTemplate : : no visible global function ./openCyto.Rcheck/00check.log: definition for ‘extends’ ./openCyto.Rcheck/00check.log:fcEllipsoidGate: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:fcFilterList : : no visible global function definition for ./openCyto.Rcheck/00check.log: ‘extends’ ./openCyto.Rcheck/00check.log:fcFilterList: no visible global function definition for ‘filterList’ ./openCyto.Rcheck/00check.log:fcFilterList: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:fcPolygonGate: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:fcRectangleGate: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:fcTree: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:fcTree: no visible global function definition for ‘new’ ./openCyto.Rcheck/00check.log:gate_flowclust_1d: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_flowclust_1d: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:gate_flowclust_1d: no visible global function definition for ‘abline’ ./openCyto.Rcheck/00check.log:gate_flowclust_1d: no visible global function definition for ‘rainbow’ ./openCyto.Rcheck/00check.log:gate_flowclust_1d: no visible global function definition for ‘lines’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ‘new’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ‘dist’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ‘qchisq’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ‘sd’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘polygonGate’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ‘lines’ ./openCyto.Rcheck/00check.log:gate_flowclust_2d: no visible global function definition for ‘points’ ./openCyto.Rcheck/00check.log:gate_mindensity: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_mindensity: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:gate_mindensity2: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_mindensity2: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:gate_quad_sequential : : no visible global function ./openCyto.Rcheck/00check.log: definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_quad_sequential: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘filter’ ./openCyto.Rcheck/00check.log:gate_quad_sequential: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:gate_quad_sequential : : no visible global function ./openCyto.Rcheck/00check.log: definition for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:gate_quad_sequential: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘filters’ ./openCyto.Rcheck/00check.log:gate_quad_tmix: no visible global function definition for ‘filter’ ./openCyto.Rcheck/00check.log:gate_quad_tmix: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:gate_quad_tmix: no visible global function definition for ‘polygonGate’ ./openCyto.Rcheck/00check.log:gate_quad_tmix: no visible global function definition for ‘filters’ ./openCyto.Rcheck/00check.log:gate_quantile: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_quantile: no visible global function definition for ‘quantile’ ./openCyto.Rcheck/00check.log:gate_quantile: no visible global function definition for ‘hist’ ./openCyto.Rcheck/00check.log:gate_quantile: no visible global function definition for ‘density’ ./openCyto.Rcheck/00check.log:gate_quantile: no visible global function definition for ‘abline’ ./openCyto.Rcheck/00check.log:gate_quantile: no visible global function definition for ‘text’ ./openCyto.Rcheck/00check.log:gate_quantile: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:gate_tail: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_tail: no visible global function definition for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:gate_tautstring: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:gate_tautstring: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rectangleGate’ ./openCyto.Rcheck/00check.log:gs_add_gating_method: no visible global function definition for ‘is’ ./openCyto.Rcheck/00check.log:gs_add_gating_method_init: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘is’ ./openCyto.Rcheck/00check.log:gs_remove_gating_method: no visible global function definition for ‘is’ ./openCyto.Rcheck/00check.log:mindensity: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:mindensity: no visible global function definition for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:ocRectRefGate: no visible global function definition for ‘as’ ./openCyto.Rcheck/00check.log:quadGate.tmix: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘quad_gate_tmix’ ./openCyto.Rcheck/00check.log:tailgate: no visible global function definition for ‘exprs’ ./openCyto.Rcheck/00check.log:tailgate: no visible global function definition for ‘rectangleGate’ ./openCyto.Rcheck/00check.log:coerce,ncdfFlowList-flowFrame: no visible global function definition ./openCyto.Rcheck/00check.log: for ‘selectMethod’ ./openCyto.Rcheck/00check.log:coerce,ncdfFlowSet-flowFrame: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘fsApply’ ./openCyto.Rcheck/00check.log:coerce,ncdfFlowSet-flowFrame : : no visible global function ./openCyto.Rcheck/00check.log: definition for ‘exprs’ ./openCyto.Rcheck/00check.log:coerce,ncdfFlowSet-flowFrame: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘new’ ./openCyto.Rcheck/00check.log:gatingTemplate,character: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘isMultiPops’ ./openCyto.Rcheck/00check.log:gatingTemplate,character: no visible binding for global variable ‘pop’ ./openCyto.Rcheck/00check.log:gatingTemplate,character: no visible binding for global variable ./openCyto.Rcheck/00check.log: ‘gating_args’ ./openCyto.Rcheck/00check.log:plot,fcFilterList-ANY : : no visible global function ./openCyto.Rcheck/00check.log: definition for ‘dnorm’ ./openCyto.Rcheck/00check.log:plot,fcFilterList-ANY: no visible global function definition for ‘hist’ ./openCyto.Rcheck/00check.log:plot,fcFilterList-ANY: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘exprs’ ./openCyto.Rcheck/00check.log:plot,fcFilterList-ANY: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘lines’ ./openCyto.Rcheck/00check.log:plot,fcFilterList-ANY: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘rainbow’ ./openCyto.Rcheck/00check.log:plot,fcFilterList-ANY: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘abline’ ./openCyto.Rcheck/00check.log:show,fcFilter: no visible global function definition for ./openCyto.Rcheck/00check.log: ‘callNextMethod’ ./openCyto.Rcheck/00check.log:Undefined global functions or variables: ./openCyto.Rcheck/00check.log: Subset abline as callNextMethod collapseDataForGating cov cov.wt ./openCyto.Rcheck/00check.log: cutree density dist dnorm ellipsoidGate embed exprs exprs<- extends ./openCyto.Rcheck/00check.log: filter filterList filters flowSet fsApply gating_args gating_method ./openCyto.Rcheck/00check.log: hclust hist is isMultiPops kmeans legend lines median na.omit new par ./openCyto.Rcheck/00check.log: parameters<- parent points polygonGate pop predict preprocessing_args ./openCyto.Rcheck/00check.log: preprocessing_method pt qchisq qf quad_gate_tmix quantile rainbow ./openCyto.Rcheck/00check.log: rectangleGate sd selectMethod smooth.spline text uniroot var ./openCyto.Rcheck/00check.log: weighted.mean ./openCyto.Rcheck/00check.log:Consider adding ./openCyto.Rcheck/00check.log: importFrom("grDevices", "rainbow") ./openCyto.Rcheck/00check.log: importFrom("graphics", "abline", "hist", "legend", "lines", "par", ./openCyto.Rcheck/00check.log: "points", "text") ./openCyto.Rcheck/00check.log: importFrom("methods", "as", "callNextMethod", "extends", "is", "new", ./openCyto.Rcheck/00check.log: "selectMethod") ./openCyto.Rcheck/00check.log: importFrom("stats", "cov", "cov.wt", "cutree", "density", "dist", ./openCyto.Rcheck/00check.log: "dnorm", "embed", "filter", "hclust", "kmeans", "median", ./openCyto.Rcheck/00check.log: "na.omit", "predict", "pt", "qchisq", "qf", "quantile", ./openCyto.Rcheck/00check.log: "sd", "smooth.spline", "uniroot", "var", "weighted.mean") ./openCyto.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./openCyto.Rcheck/00check.log:* checking Rd files ... OK ./openCyto.Rcheck/00check.log:* checking Rd metadata ... OK ./openCyto.Rcheck/00check.log:* checking Rd cross-references ... WARNING ./openCyto.Rcheck/00check.log:Missing link or links in documentation object 'openCyto.Rd': ./openCyto.Rcheck/00check.log: ‘[openCyto:gating-methods]{gating}’ ./openCyto.Rcheck/00check.log:See section 'Cross-references' in the 'Writing R Extensions' manual. ./openCyto.Rcheck/00check.log:* checking for missing documentation entries ... OK ./openCyto.Rcheck/00check.log:* checking for code/documentation mismatches ... WARNING ./openCyto.Rcheck/00check.log:Codoc mismatches from documentation object 'gs_add_gating_method_init': ./openCyto.Rcheck/00check.log:gs_add_gating_method_init ./openCyto.Rcheck/00check.log: Code: function(gs = NULL) ./openCyto.Rcheck/00check.log: Docs: function(GatingSet) ./openCyto.Rcheck/00check.log: Argument names in code not in docs: ./openCyto.Rcheck/00check.log: gs ./openCyto.Rcheck/00check.log: Argument names in docs not in code: ./openCyto.Rcheck/00check.log: GatingSet ./openCyto.Rcheck/00check.log: Mismatches in argument names: ./openCyto.Rcheck/00check.log: Position: 1 Code: gs Docs: GatingSet ./openCyto.Rcheck/00check.log:gs_add_gating_method_init ./openCyto.Rcheck/00check.log: Code: function(gs = NULL) ./openCyto.Rcheck/00check.log: Docs: function(GatingSetList) ./openCyto.Rcheck/00check.log: Argument names in code not in docs: ./openCyto.Rcheck/00check.log: gs ./openCyto.Rcheck/00check.log: Argument names in docs not in code: ./openCyto.Rcheck/00check.log: GatingSetList ./openCyto.Rcheck/00check.log: Mismatches in argument names: ./openCyto.Rcheck/00check.log: Position: 1 Code: gs Docs: GatingSetList ./openCyto.Rcheck/00check.log:gs_add_gating_method_init ./openCyto.Rcheck/00check.log: Code: function(gs = NULL) ./openCyto.Rcheck/00check.log: Docs: function() ./openCyto.Rcheck/00check.log: Argument names in code not in docs: ./openCyto.Rcheck/00check.log: gs ./openCyto.Rcheck/00check.log:Codoc mismatches from documentation object 'gs_remove_gating_method': ./openCyto.Rcheck/00check.log:gs_remove_gating_method ./openCyto.Rcheck/00check.log: Code: function(gs) ./openCyto.Rcheck/00check.log: Docs: function(GatingSet) ./openCyto.Rcheck/00check.log: Argument names in code not in docs: ./openCyto.Rcheck/00check.log: gs ./openCyto.Rcheck/00check.log: Argument names in docs not in code: ./openCyto.Rcheck/00check.log: GatingSet ./openCyto.Rcheck/00check.log: Mismatches in argument names: ./openCyto.Rcheck/00check.log: Position: 1 Code: gs Docs: GatingSet ./openCyto.Rcheck/00check.log:gs_remove_gating_method ./openCyto.Rcheck/00check.log: Code: function(gs) ./openCyto.Rcheck/00check.log: Docs: function(GatingSetList) ./openCyto.Rcheck/00check.log: Argument names in code not in docs: ./openCyto.Rcheck/00check.log: gs ./openCyto.Rcheck/00check.log: Argument names in docs not in code: ./openCyto.Rcheck/00check.log: GatingSetList ./openCyto.Rcheck/00check.log: Mismatches in argument names: ./openCyto.Rcheck/00check.log: Position: 1 Code: gs Docs: GatingSetList ./openCyto.Rcheck/00check.log:* checking Rd \usage sections ... WARNING ./openCyto.Rcheck/00check.log:Undocumented arguments in documentation object 'gs_add_gating_method_init' ./openCyto.Rcheck/00check.log: ‘GatingSet’ ‘GatingSetList’ ‘gs’ ./openCyto.Rcheck/00check.log:Undocumented arguments in documentation object 'gs_remove_gating_method' ./openCyto.Rcheck/00check.log: ‘GatingSet’ ‘GatingSetList’ ./openCyto.Rcheck/00check.log:Documented arguments not in \usage in documentation object 'gt_gating': ./openCyto.Rcheck/00check.log: ‘env_fct’ ./openCyto.Rcheck/00check.log:Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. ./openCyto.Rcheck/00check.log:The \usage entries must correspond to syntactically valid R code. ./openCyto.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./openCyto.Rcheck/00check.log:* checking Rd contents ... OK ./openCyto.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./openCyto.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./openCyto.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./openCyto.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./openCyto.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./openCyto.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./openCyto.Rcheck/00check.log:* checking compiled code ... OK ./openCyto.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./openCyto.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./openCyto.Rcheck/00check.log:* checking examples ... OK ./openCyto.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./openCyto.Rcheck/00check.log:* checking tests ... OK ./openCyto.Rcheck/00check.log: Running ‘testthat.R’ ./openCyto.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... NOTE ./openCyto.Rcheck/00check.log:'::' or ':::' import not declared from: ‘gridExtra’ ./openCyto.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./openCyto.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./openCyto.Rcheck/00check.log: ‘HowToAutoGating.Rmd’using ‘UTF-8’... OK ./openCyto.Rcheck/00check.log: ‘HowToWriteCSVTemplate.Rmd’using ‘UTF-8’... OK ./openCyto.Rcheck/00check.log: ‘openCytoVignette.Rmd’using ‘UTF-8’... OK ./openCyto.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./openCyto.Rcheck/00check.log:* checking PDF version of manual ... OK ./openCyto.Rcheck/00check.log:* DONE ./openCyto.Rcheck/00check.log:Status: 3 WARNINGs, 5 NOTEs QUALIFIER_1.29.1.tar.gz ./QUALIFIER.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/QUALIFIER.Rcheck’ ./QUALIFIER.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./QUALIFIER.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./QUALIFIER.Rcheck/00check.log:* using session charset: UTF-8 ./QUALIFIER.Rcheck/00check.log:* checking for file ‘QUALIFIER/DESCRIPTION’ ... OK ./QUALIFIER.Rcheck/00check.log:* checking extension type ... Package ./QUALIFIER.Rcheck/00check.log:* this is package ‘QUALIFIER’ version ‘1.29.1’ ./QUALIFIER.Rcheck/00check.log:* checking package namespace information ... OK ./QUALIFIER.Rcheck/00check.log:* checking package dependencies ... NOTE ./QUALIFIER.Rcheck/00check.log:Depends: includes the non-default packages: ./QUALIFIER.Rcheck/00check.log: 'flowCore', 'flowViz', 'ncdfFlow', 'flowWorkspace', 'data.table', 'reshape' ./QUALIFIER.Rcheck/00check.log:Adding so many packages to the search path is excessive and importing selectively is preferable. ./QUALIFIER.Rcheck/00check.log:* checking if this is a source package ... OK ./QUALIFIER.Rcheck/00check.log:* checking if there is a namespace ... OK ./QUALIFIER.Rcheck/00check.log:* checking for executable files ... OK ./QUALIFIER.Rcheck/00check.log:* checking for hidden files and directories ... OK ./QUALIFIER.Rcheck/00check.log:* checking for portable file names ... OK ./QUALIFIER.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./QUALIFIER.Rcheck/00check.log:* checking whether package ‘QUALIFIER’ can be installed ... OK ./QUALIFIER.Rcheck/00check.log:* checking installed package size ... OK ./QUALIFIER.Rcheck/00check.log:* checking package directory ... OK ./QUALIFIER.Rcheck/00check.log:* checking ‘build’ directory ... OK ./QUALIFIER.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./QUALIFIER.Rcheck/00check.log:Packages listed in more than one of Depends, Imports, Suggests, Enhances: ./QUALIFIER.Rcheck/00check.log: ‘flowCore’ ‘flowViz’ ‘flowWorkspace’ ./QUALIFIER.Rcheck/00check.log:A package should be listed in only one of these fields. ./QUALIFIER.Rcheck/00check.log:* checking top-level files ... OK ./QUALIFIER.Rcheck/00check.log:* checking for left-over files ... OK ./QUALIFIER.Rcheck/00check.log:* checking index information ... OK ./QUALIFIER.Rcheck/00check.log:* checking package subdirectories ... OK ./QUALIFIER.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./QUALIFIER.Rcheck/00check.log:* checking R files for syntax errors ... OK ./QUALIFIER.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./QUALIFIER.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./QUALIFIER.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./QUALIFIER.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./QUALIFIER.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./QUALIFIER.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./QUALIFIER.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./QUALIFIER.Rcheck/00check.log:Namespaces in Imports field not imported from: ./QUALIFIER.Rcheck/00check.log: ‘flowViz’ ‘grDevices’ ‘methods’ ./QUALIFIER.Rcheck/00check.log: All declared Imports should be used. ./QUALIFIER.Rcheck/00check.log:Packages in Depends field not imported from: ./QUALIFIER.Rcheck/00check.log: ‘data.table’ ‘flowCore’ ‘flowViz’ ‘ncdfFlow’ ‘reshape’ ./QUALIFIER.Rcheck/00check.log: These packages need to be imported from (in the NAMESPACE file) ./QUALIFIER.Rcheck/00check.log: for when this namespace is loaded but not attached. ./QUALIFIER.Rcheck/00check.log:':::' call which should be '::': ‘flowWorkspace:::mkformula’ ./QUALIFIER.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./QUALIFIER.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./QUALIFIER.Rcheck/00check.log: ‘flowWorkspace:::.formulaParser’ ‘flowWorkspace:::.getPopStat’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::calculateGridLayout’ ‘lattice:::checkArgsAndCall’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::chooseFace’ ‘lattice:::compute.layout’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::drawInViewport’ ‘lattice:::evaluate.legend’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::getFunctionOrName’ ‘lattice:::getLabelList’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::grobFromLabelList’ ‘lattice:::lattice.getStatus’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::lattice.setStatus’ ‘lattice:::layoutNCol’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::layoutNRow’ ‘lattice:::paste.and.draw’ ./QUALIFIER.Rcheck/00check.log: ‘lattice:::updateList’ ./QUALIFIER.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./QUALIFIER.Rcheck/00check.log:There are ::: calls to the package's namespace in its code. A package ./QUALIFIER.Rcheck/00check.log: almost never needs to use ::: for its own objects: ./QUALIFIER.Rcheck/00check.log: ‘getName’ ‘height’ ‘width’ ./QUALIFIER.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./QUALIFIER.Rcheck/00check.log:* checking replacement functions ... OK ./QUALIFIER.Rcheck/00check.log:* checking foreign function calls ... OK ./QUALIFIER.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./QUALIFIER.Rcheck/00check.log:.TubeNameMapping: no visible global function definition for ‘pData’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible global function definition for ‘getData’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible binding for global variable ‘value’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible global function definition for ‘:=’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible binding for global variable ‘stats’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible binding for global variable ‘sid’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible binding for global variable ‘channel’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible binding for global variable ‘stain’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible binding for global variable ‘population’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible binding for global variable ‘node’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible global function definition for ‘setcolorder’ ./QUALIFIER.Rcheck/00check.log:.addStats: no visible global function definition for ‘rbindlist’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.env: no visible global function definition for ‘:=’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.env: no visible global function definition for ‘rbindlist’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.env: no visible binding for global variable ‘sid’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh: no visible global function definition for ‘sampleNames’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘gh_get_transformations’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘gs_get_pop_paths’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘gh_pop_get_data’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh: no visible global function definition for ‘pData’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh: no visible global function definition for ‘parameters’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘gh_pop_get_gate’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘parameters’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘data.table’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘exprs’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘rbindlist’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘gh_pop_get_data’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘:=’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible binding for global variable ./QUALIFIER.Rcheck/00check.log: ‘node’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh : : no visible binding for global variable ./QUALIFIER.Rcheck/00check.log: ‘population’ ./QUALIFIER.Rcheck/00check.log:.getQAStats.gh: no visible global function definition for ‘rbindlist’ ./QUALIFIER.Rcheck/00check.log:.parseTubeID: no visible global function definition for ‘pData’ ./QUALIFIER.Rcheck/00check.log:.parseTubeID: no visible global function definition for ‘pData<-’ ./QUALIFIER.Rcheck/00check.log:.qaCheck: no visible global function definition for ‘getData’ ./QUALIFIER.Rcheck/00check.log:.qaCheck: no visible global function definition for ‘rename’ ./QUALIFIER.Rcheck/00check.log:.qaCheck : .funcOutlierGrp: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘IQR’ ./QUALIFIER.Rcheck/00check.log:.qaCheck : .funcOutlierGrp: no visible binding for global variable ./QUALIFIER.Rcheck/00check.log: ‘.SD’ ./QUALIFIER.Rcheck/00check.log:.qaCheck : .funcOutlierGrp: no visible binding for global variable ‘V1’ ./QUALIFIER.Rcheck/00check.log:.qaCheck : .funcOutlierGrp: no visible binding for global variable ./QUALIFIER.Rcheck/00check.log: ‘sid’ ./QUALIFIER.Rcheck/00check.log:.qaCheck: no visible binding for global variable ‘.SD’ ./QUALIFIER.Rcheck/00check.log:.qaCheck: no visible binding for global variable ‘V1’ ./QUALIFIER.Rcheck/00check.log:.qaCheck : .funcOutlier: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘as.formula’ ./QUALIFIER.Rcheck/00check.log:.qaCheck : .funcOutlier: no visible binding for global variable ‘sid’ ./QUALIFIER.Rcheck/00check.log:.queryStats : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘pData’ ./QUALIFIER.Rcheck/00check.log:.queryStats: no visible global function definition for ‘pData’ ./QUALIFIER.Rcheck/00check.log:.queryStats: no visible binding for global variable ‘stats’ ./QUALIFIER.Rcheck/00check.log:.read.qaTask : : no visible binding for global variable ./QUALIFIER.Rcheck/00check.log: ‘aoutlierFunc_args’ ./QUALIFIER.Rcheck/00check.log:.read.qaTask : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘new’ ./QUALIFIER.Rcheck/00check.log:.read.qaTask : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘as.formula’ ./QUALIFIER.Rcheck/00check.log:.setupPlotTheme: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘standard.theme’ ./QUALIFIER.Rcheck/00check.log:.setupPlotTheme: no visible global function definition for ‘gray’ ./QUALIFIER.Rcheck/00check.log:.timelineplot: no visible global function definition for ‘exprs’ ./QUALIFIER.Rcheck/00check.log:.timelineplot: no visible global function definition for ‘median’ ./QUALIFIER.Rcheck/00check.log:clearCheck: no visible global function definition for ‘getData’ ./QUALIFIER.Rcheck/00check.log:createDbSchema: no visible global function definition for ‘rename’ ./QUALIFIER.Rcheck/00check.log:load_db: no visible global function definition for ‘l_ply’ ./QUALIFIER.Rcheck/00check.log:load_db : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘load_gs’ ./QUALIFIER.Rcheck/00check.log:makeQaTask: no visible global function definition for ‘new’ ./QUALIFIER.Rcheck/00check.log:makeQaTask: no visible global function definition for ‘as.formula’ ./QUALIFIER.Rcheck/00check.log:outlier.norm: no visible global function definition for ‘median’ ./QUALIFIER.Rcheck/00check.log:outlier.norm: no visible global function definition for ‘mad’ ./QUALIFIER.Rcheck/00check.log:outlier.norm: no visible global function definition for ‘pnorm’ ./QUALIFIER.Rcheck/00check.log:outlier.plot: no visible global function definition for ‘abline’ ./QUALIFIER.Rcheck/00check.log:outlier.t: no visible global function definition for ‘optim’ ./QUALIFIER.Rcheck/00check.log:outlier.t : : no visible global function definition for ‘dt’ ./QUALIFIER.Rcheck/00check.log:outlier.t: no visible global function definition for ‘pt’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘trellis.par.get’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘current.panel.limits’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible global function definition for ‘:=’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible binding for global variable ‘.BY’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible binding for global variable ‘.SD’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.polygon’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.segments’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.points’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible binding for global variable ‘outlier’ ./QUALIFIER.Rcheck/00check.log:panel.bwplotEx: no visible binding for global variable ‘gOutlier’ ./QUALIFIER.Rcheck/00check.log:panel.xyplot.flowsetEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.xyplot.flowset’ ./QUALIFIER.Rcheck/00check.log:panel.xyplot.qa: no visible global function definition for ‘coef’ ./QUALIFIER.Rcheck/00check.log:panel.xyplot.qa: no visible global function definition for ‘pt’ ./QUALIFIER.Rcheck/00check.log:panel.xyplot.qa: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘coefficients’ ./QUALIFIER.Rcheck/00check.log:panel.xyplot.qa: no visible global function definition for ‘panel.text’ ./QUALIFIER.Rcheck/00check.log:panel.xyplot.qa: no visible global function definition for ‘quantile’ ./QUALIFIER.Rcheck/00check.log:panel.xyplot.qa: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.abline’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘trellis.par.get’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible binding for global variable ‘panel.grid’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible binding for global variable ‘panel.abline’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.superpose’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.points’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible global function definition for ‘panel.lines’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.lmline’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible global function definition for ‘panel.loess’ ./QUALIFIER.Rcheck/00check.log:panel.xyplotEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘panel.linejoin’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible global function definition for ‘description’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘lattice.options’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible global function definition for ‘getData’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible global function definition for ‘:=’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible binding for global variable ‘outlier’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible binding for global variable ‘gOutlier’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible global function definition for ‘rename’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible global function definition for ‘dev.off’ ./QUALIFIER.Rcheck/00check.log:plot.qaTask: no visible global function definition for ‘png’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible binding for global variable ./QUALIFIER.Rcheck/00check.log: ‘packet.panel.default’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘lattice.getOption’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ‘dev.list’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘trellis.device’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘trellis.par.get’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘trellis.par.set’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘lattice.options’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘trellis.grobname’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘trellis.vpname’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ‘par’ ./QUALIFIER.Rcheck/00check.log:plot.trellisEx: no visible global function definition for ‘panel.fill’ ./QUALIFIER.Rcheck/00check.log:proportion.outliers.mle: no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘optim’ ./QUALIFIER.Rcheck/00check.log:proportion.outliers.mle : : no visible global function ./QUALIFIER.Rcheck/00check.log: definition for ‘dbeta’ 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‘as.formula’ ./QUALIFIER.Rcheck/00check.log:qa.GroupPlot: no visible binding for global variable ‘name’ ./QUALIFIER.Rcheck/00check.log:qaWrite.list: no visible global function definition for ‘getData’ ./QUALIFIER.Rcheck/00check.log:qaWrite.summary: no visible global function definition for ‘getData’ ./QUALIFIER.Rcheck/00check.log:qaWrite.summary: no visible global function definition for ‘pData’ ./QUALIFIER.Rcheck/00check.log:qaWrite.summary: no visible global function definition for ‘cast’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task: no visible global function definition for ‘getData’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task: no visible global function definition for ‘pData’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task: no visible global function definition for ‘rename’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task: no visible global function definition for ‘description’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task: no visible global function definition for ‘as.formula’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task: no visible global function definition for ‘melt’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task: no visible global function definition for ‘cast’ ./QUALIFIER.Rcheck/00check.log:qaWrite.task : : no visible global function definition for ./QUALIFIER.Rcheck/00check.log: ‘getData’ ./QUALIFIER.Rcheck/00check.log:read.qaTask: no visible global function definition for ‘read.csv’ ./QUALIFIER.Rcheck/00check.log:read.qaTask: no visible global function definition for ‘fread’ ./QUALIFIER.Rcheck/00check.log:saveToDB: no visible global function definition for ‘pData’ ./QUALIFIER.Rcheck/00check.log:saveToDB: no visible global function definition for ‘fread’ ./QUALIFIER.Rcheck/00check.log:saveToDB: no visible binding for global variable ‘name’ ./QUALIFIER.Rcheck/00check.log:saveToDB: no visible global function definition for ‘sampleNames’ ./QUALIFIER.Rcheck/00check.log:saveToDB: no visible global function definition for ‘pData<-’ 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./QUALIFIER.Rcheck/00check.log:Undefined global functions or variables: ./QUALIFIER.Rcheck/00check.log: .BY .SD := IQR V1 abline aoutlierFunc_args as.formula cast channel ./QUALIFIER.Rcheck/00check.log: coef coefficients current.panel.limits data.table dbeta description ./QUALIFIER.Rcheck/00check.log: dev.list dev.off dt exprs extends flowSet fread gOutlier getData ./QUALIFIER.Rcheck/00check.log: gh_get_transformations gh_pop_get_data gh_pop_get_gate ./QUALIFIER.Rcheck/00check.log: gh_pop_get_proportion gray gs_get_pop_paths gs_pop_get_parent l_ply ./QUALIFIER.Rcheck/00check.log: lattice.getOption lattice.options load_gs mad median melt name new ./QUALIFIER.Rcheck/00check.log: node optim outlier pData pData<- packet.panel.default panel.abline ./QUALIFIER.Rcheck/00check.log: panel.fill panel.grid panel.linejoin panel.lines panel.lmline ./QUALIFIER.Rcheck/00check.log: panel.loess panel.points panel.polygon panel.segments panel.superpose ./QUALIFIER.Rcheck/00check.log: panel.text panel.xyplot.flowset par parameters pbeta png pnorm ./QUALIFIER.Rcheck/00check.log: population pt quantile rbindlist read.csv rename sampleNames save_gs ./QUALIFIER.Rcheck/00check.log: setcolorder sid stain standard.theme stats trellis.device ./QUALIFIER.Rcheck/00check.log: trellis.grobname trellis.par.get trellis.par.set trellis.vpname value ./QUALIFIER.Rcheck/00check.log:Consider adding ./QUALIFIER.Rcheck/00check.log: importFrom("grDevices", "dev.list", "dev.off", "gray", "png") ./QUALIFIER.Rcheck/00check.log: importFrom("graphics", "abline", "par") ./QUALIFIER.Rcheck/00check.log: importFrom("methods", "extends", "new") ./QUALIFIER.Rcheck/00check.log: importFrom("stats", "IQR", "as.formula", "coef", "coefficients", ./QUALIFIER.Rcheck/00check.log: "dbeta", "dt", "mad", "median", "optim", "pbeta", "pnorm", ./QUALIFIER.Rcheck/00check.log: "pt", "quantile") ./QUALIFIER.Rcheck/00check.log: importFrom("utils", "read.csv") ./QUALIFIER.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./QUALIFIER.Rcheck/00check.log:* checking Rd files ... OK ./QUALIFIER.Rcheck/00check.log:* checking Rd metadata ... OK ./QUALIFIER.Rcheck/00check.log:* checking Rd cross-references ... WARNING ./QUALIFIER.Rcheck/00check.log:Missing link or links in documentation object 'getQAStats.Rd': ./QUALIFIER.Rcheck/00check.log: ‘flowjo_to_gatingset’ ./QUALIFIER.Rcheck/00check.log:See section 'Cross-references' in the 'Writing R Extensions' manual. ./QUALIFIER.Rcheck/00check.log:* checking for missing documentation entries ... OK ./QUALIFIER.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./QUALIFIER.Rcheck/00check.log:* checking Rd \usage sections ... OK ./QUALIFIER.Rcheck/00check.log:* checking Rd contents ... OK ./QUALIFIER.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./QUALIFIER.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./QUALIFIER.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./QUALIFIER.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./QUALIFIER.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... NOTE ./QUALIFIER.Rcheck/00check.log:The following files should probably not be installed: ./QUALIFIER.Rcheck/00check.log: ‘QUALIFIER-plot-MNC-scatter.png’, ‘QUALIFIER-plot-subset2.png’ ./QUALIFIER.Rcheck/00check.log:Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, ./QUALIFIER.Rcheck/00check.log:or move the vignette sources from ‘inst/doc’ to ‘vignettes’. ./QUALIFIER.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./QUALIFIER.Rcheck/00check.log:* checking examples ... OK ./QUALIFIER.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./QUALIFIER.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./QUALIFIER.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./QUALIFIER.Rcheck/00check.log: ‘QUALIFIER.Rmd’... OK ./QUALIFIER.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./QUALIFIER.Rcheck/00check.log:* checking PDF version of manual ... OK ./QUALIFIER.Rcheck/00check.log:* DONE ./QUALIFIER.Rcheck/00check.log:Status: 1 WARNING, 5 NOTEs RegParallel_1.3.1.tar.gz ./RegParallel.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/RegParallel.Rcheck’ ./RegParallel.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./RegParallel.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./RegParallel.Rcheck/00check.log:* using session charset: UTF-8 ./RegParallel.Rcheck/00check.log:* checking for file ‘RegParallel/DESCRIPTION’ ... OK ./RegParallel.Rcheck/00check.log:* checking extension type ... Package ./RegParallel.Rcheck/00check.log:* this is package ‘RegParallel’ version ‘1.3.1’ ./RegParallel.Rcheck/00check.log:* checking package namespace information ... OK ./RegParallel.Rcheck/00check.log:* checking package dependencies ... NOTE ./RegParallel.Rcheck/00check.log:Depends: includes the non-default packages: ./RegParallel.Rcheck/00check.log: 'doParallel', 'foreach', 'parallel', 'iterators', 'data.table', 'stringr', 'survival', 'arm', 'MASS' ./RegParallel.Rcheck/00check.log:Adding so many packages to the search path is excessive and importing selectively is preferable. ./RegParallel.Rcheck/00check.log:* checking if this is a source package ... OK ./RegParallel.Rcheck/00check.log:* checking if there is a namespace ... OK ./RegParallel.Rcheck/00check.log:* checking for executable files ... OK ./RegParallel.Rcheck/00check.log:* checking for hidden files and directories ... OK ./RegParallel.Rcheck/00check.log:* checking for portable file names ... OK ./RegParallel.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./RegParallel.Rcheck/00check.log:* checking whether package ‘RegParallel’ can be installed ... OK ./RegParallel.Rcheck/00check.log:* checking installed package size ... OK ./RegParallel.Rcheck/00check.log:* checking package directory ... OK ./RegParallel.Rcheck/00check.log:* checking ‘build’ directory ... OK ./RegParallel.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./RegParallel.Rcheck/00check.log:* checking top-level files ... OK ./RegParallel.Rcheck/00check.log:* checking for left-over files ... OK ./RegParallel.Rcheck/00check.log:* checking index information ... OK ./RegParallel.Rcheck/00check.log:* checking package subdirectories ... OK ./RegParallel.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./RegParallel.Rcheck/00check.log:* checking R files for syntax errors ... OK ./RegParallel.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./RegParallel.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./RegParallel.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./RegParallel.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./RegParallel.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./RegParallel.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./RegParallel.Rcheck/00check.log:* checking dependencies in R code ... OK ./RegParallel.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./RegParallel.Rcheck/00check.log:* checking replacement functions ... OK ./RegParallel.Rcheck/00check.log:* checking foreign function calls ... OK ./RegParallel.Rcheck/00check.log:* checking R code for possible problems ... OK ./RegParallel.Rcheck/00check.log:* checking Rd files ... OK ./RegParallel.Rcheck/00check.log:* checking Rd metadata ... OK ./RegParallel.Rcheck/00check.log:* checking Rd cross-references ... OK ./RegParallel.Rcheck/00check.log:* checking for missing documentation entries ... OK ./RegParallel.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./RegParallel.Rcheck/00check.log:* checking Rd \usage sections ... OK ./RegParallel.Rcheck/00check.log:* checking Rd contents ... OK ./RegParallel.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./RegParallel.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./RegParallel.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./RegParallel.Rcheck/00check.log:* checking examples ... OK ./RegParallel.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./RegParallel.Rcheck/00check.log:* checking tests ... OK ./RegParallel.Rcheck/00check.log: Running ‘runTests.R’ ./RegParallel.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./RegParallel.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./RegParallel.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./RegParallel.Rcheck/00check.log: ‘RegParallel.Rmd’using ‘UTF-8’... OK ./RegParallel.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./RegParallel.Rcheck/00check.log:Error(s) in re-building vignettes: ./RegParallel.Rcheck/00check.log:--- re-building ‘RegParallel.Rmd’ using rmarkdown ./RegParallel.Rcheck/00check.log:Loading required package: doParallel ./RegParallel.Rcheck/00check.log:Loading required package: foreach ./RegParallel.Rcheck/00check.log:Loading required package: iterators ./RegParallel.Rcheck/00check.log:Loading required package: parallel ./RegParallel.Rcheck/00check.log:Loading required package: data.table ./RegParallel.Rcheck/00check.log:Loading required package: stringr ./RegParallel.Rcheck/00check.log:Loading required package: survival ./RegParallel.Rcheck/00check.log:Loading required package: arm ./RegParallel.Rcheck/00check.log:Loading required package: MASS ./RegParallel.Rcheck/00check.log:Loading required package: Matrix ./RegParallel.Rcheck/00check.log:Loading required package: lme4 ./RegParallel.Rcheck/00check.log:arm (Version 1.10-1, built: 2018-4-12) ./RegParallel.Rcheck/00check.log:Working directory is /home/mdowle/build/revdeplib/RegParallel.Rcheck/vign_test/RegParallel/vignettes ./RegParallel.Rcheck/00check.log:Loading required package: SummarizedExperiment ./RegParallel.Rcheck/00check.log:Loading required package: GenomicRanges ./RegParallel.Rcheck/00check.log:Loading required package: stats4 ./RegParallel.Rcheck/00check.log:Loading required package: BiocGenerics ./RegParallel.Rcheck/00check.log:Attaching package: 'BiocGenerics' ./RegParallel.Rcheck/00check.log:The following object is masked from 'package:Matrix': ./RegParallel.Rcheck/00check.log: which ./RegParallel.Rcheck/00check.log:The following objects are masked from 'package:parallel': ./RegParallel.Rcheck/00check.log: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, ./RegParallel.Rcheck/00check.log: clusterExport, clusterMap, parApply, parCapply, parLapply, ./RegParallel.Rcheck/00check.log: parLapplyLB, parRapply, parSapply, parSapplyLB ./RegParallel.Rcheck/00check.log:The following objects are masked from 'package:stats': ./RegParallel.Rcheck/00check.log: IQR, mad, sd, var, xtabs ./RegParallel.Rcheck/00check.log:The following objects are masked from 'package:base': ./RegParallel.Rcheck/00check.log: Filter, Find, Map, Position, Reduce, anyDuplicated, append, ./RegParallel.Rcheck/00check.log: as.data.frame, basename, cbind, colnames, dirname, do.call, ./RegParallel.Rcheck/00check.log: duplicated, eval, evalq, get, grep, grepl, intersect, ./RegParallel.Rcheck/00check.log: is.unsorted, lapply, mapply, match, mget, order, paste, pmax, ./RegParallel.Rcheck/00check.log: pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, ./RegParallel.Rcheck/00check.log: setdiff, sort, table, tapply, union, unique, unsplit, which, ./RegParallel.Rcheck/00check.log: which.max, which.min ./RegParallel.Rcheck/00check.log:Loading required package: S4Vectors ./RegParallel.Rcheck/00check.log:Attaching package: 'S4Vectors' ./RegParallel.Rcheck/00check.log:The following object is masked from 'package:Matrix': ./RegParallel.Rcheck/00check.log: expand ./RegParallel.Rcheck/00check.log:The following objects are masked from 'package:data.table': ./RegParallel.Rcheck/00check.log: first, second ./RegParallel.Rcheck/00check.log:The following object is masked from 'package:base': ./RegParallel.Rcheck/00check.log: expand.grid ./RegParallel.Rcheck/00check.log:Loading required package: IRanges ./RegParallel.Rcheck/00check.log:Attaching package: 'IRanges' ./RegParallel.Rcheck/00check.log:The following object is masked from 'package:data.table': ./RegParallel.Rcheck/00check.log: shift ./RegParallel.Rcheck/00check.log:Loading required package: GenomeInfoDb ./RegParallel.Rcheck/00check.log:Loading required package: Biobase ./RegParallel.Rcheck/00check.log:Welcome to Bioconductor ./RegParallel.Rcheck/00check.log: Vignettes contain introductory material; view with ./RegParallel.Rcheck/00check.log: 'browseVignettes()'. To cite Bioconductor, see ./RegParallel.Rcheck/00check.log: 'citation("Biobase")', and for packages 'citation("pkgname")'. ./RegParallel.Rcheck/00check.log:Loading required package: DelayedArray ./RegParallel.Rcheck/00check.log:Loading required package: matrixStats ./RegParallel.Rcheck/00check.log:Attaching package: 'matrixStats' ./RegParallel.Rcheck/00check.log:The following objects are masked from 'package:Biobase': ./RegParallel.Rcheck/00check.log: anyMissing, rowMedians ./RegParallel.Rcheck/00check.log:Loading required package: BiocParallel ./RegParallel.Rcheck/00check.log:Attaching package: 'DelayedArray' ./RegParallel.Rcheck/00check.log:The following objects are masked from 'package:matrixStats': ./RegParallel.Rcheck/00check.log: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges ./RegParallel.Rcheck/00check.log:The following objects are masked from 'package:base': ./RegParallel.Rcheck/00check.log: aperm, apply, rowsum ./RegParallel.Rcheck/00check.log:estimating size factors ./RegParallel.Rcheck/00check.log:estimating dispersions ./RegParallel.Rcheck/00check.log:gene-wise dispersion estimates ./RegParallel.Rcheck/00check.log:mean-dispersion relationship ./RegParallel.Rcheck/00check.log:final dispersion estimates ./RegParallel.Rcheck/00check.log:fitting model and testing ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:#RegParallel ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:System is: ./RegParallel.Rcheck/00check.log:-- Linux ./RegParallel.Rcheck/00check.log:Blocksize: ./RegParallel.Rcheck/00check.log:-- 500 ./RegParallel.Rcheck/00check.log:170 variables have all zeros! Removing these... ./RegParallel.Rcheck/00check.log:Now testing 2821 variables ./RegParallel.Rcheck/00check.log:Cores / Threads: ./RegParallel.Rcheck/00check.log:-- 3 ./RegParallel.Rcheck/00check.log:Terms included in model: ./RegParallel.Rcheck/00check.log:-- dex ./RegParallel.Rcheck/00check.log:First 5 formulae: ./RegParallel.Rcheck/00check.log:-- dex ~ ENSG00000000003 ./RegParallel.Rcheck/00check.log:-- dex ~ ENSG00000000419 ./RegParallel.Rcheck/00check.log:-- dex ~ ENSG00000000457 ./RegParallel.Rcheck/00check.log:-- dex ~ ENSG00000000460 ./RegParallel.Rcheck/00check.log:-- dex ~ ENSG00000000938 ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 1 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 1; index2: 500 ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 2 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 501; index2: 1000 ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 3 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 1001; index2: 1500 ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: 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not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 5 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 2001; index2: 2500 ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 4 of 6 ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:-- index1: 1501; index2: 2000 ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Processing final batch 6 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 2501; index2: 2821 ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: algorithm did not converge ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred ./RegParallel.Rcheck/00check.log:Done! ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:#RegParallel ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:System is: ./RegParallel.Rcheck/00check.log:-- Linux ./RegParallel.Rcheck/00check.log:Blocksize: ./RegParallel.Rcheck/00check.log:-- 500 ./RegParallel.Rcheck/00check.log:101 variables have all zeros! Removing these... ./RegParallel.Rcheck/00check.log:Now testing 1890 variables ./RegParallel.Rcheck/00check.log:Cores / Threads: ./RegParallel.Rcheck/00check.log:-- 3 ./RegParallel.Rcheck/00check.log:Terms included in model: ./RegParallel.Rcheck/00check.log:-- cell ./RegParallel.Rcheck/00check.log:First 5 formulae: ./RegParallel.Rcheck/00check.log:-- ENSG00000000003 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000419 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000457 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000460 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000938 ~ cell ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 1 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 1; index2: 500 ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 2 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 501; index2: 1000 ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 3 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 1001; index2: 1500 ./RegParallel.Rcheck/00check.log:Processing final batch 4 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 1501; index2: 1890 ./RegParallel.Rcheck/00check.log:Done! ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:#RegParallel ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:System is: ./RegParallel.Rcheck/00check.log:-- Linux ./RegParallel.Rcheck/00check.log:Blocksize: ./RegParallel.Rcheck/00check.log:-- 500 ./RegParallel.Rcheck/00check.log:101 variables have all zeros! Removing these... ./RegParallel.Rcheck/00check.log:Now testing 1890 variables ./RegParallel.Rcheck/00check.log:Cores / Threads: ./RegParallel.Rcheck/00check.log:-- 3 ./RegParallel.Rcheck/00check.log:Terms included in model: ./RegParallel.Rcheck/00check.log:-- cell ./RegParallel.Rcheck/00check.log:First 5 formulae: ./RegParallel.Rcheck/00check.log:-- ENSG00000000003 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000419 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000457 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000460 ~ cell ./RegParallel.Rcheck/00check.log:-- ENSG00000000938 ~ cell ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 1 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 1; index2: 500 ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 2 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 501; index2: 1000 ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 3 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 1001; index2: 1500 ./RegParallel.Rcheck/00check.log:Processing final batch 4 of 4 ./RegParallel.Rcheck/00check.log:-- index1: 1501; index2: 1890 ./RegParallel.Rcheck/00check.log:Done! ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:#RegParallel ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:System is: ./RegParallel.Rcheck/00check.log:-- Linux ./RegParallel.Rcheck/00check.log:Blocksize: ./RegParallel.Rcheck/00check.log:-- 500 ./RegParallel.Rcheck/00check.log:170 variables have all zeros! Removing these... ./RegParallel.Rcheck/00check.log:Now testing 2821 variables ./RegParallel.Rcheck/00check.log:Cores / Threads: ./RegParallel.Rcheck/00check.log:-- 3 ./RegParallel.Rcheck/00check.log:Terms included in model: ./RegParallel.Rcheck/00check.log:-- dex ./RegParallel.Rcheck/00check.log:First 5 formulae: ./RegParallel.Rcheck/00check.log:-- ENSG00000000003 ~ dex ./RegParallel.Rcheck/00check.log:-- ENSG00000000419 ~ dex ./RegParallel.Rcheck/00check.log:-- ENSG00000000457 ~ dex ./RegParallel.Rcheck/00check.log:-- ENSG00000000460 ~ dex ./RegParallel.Rcheck/00check.log:-- ENSG00000000938 ~ dex ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 1 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 1; index2: 500 ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 2 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 501; index2: 1000 ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 3 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 1001; index2: 1500 ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Processing final batch 6 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 2501; index2: 2821 ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 4 of 6 ./RegParallel.Rcheck/00check.log:-- index1: 1501; index2: 2000 ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Processing 500 formulae, batch 5 of 6 ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:-- index1: 2001; index2: 2500 ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : iteration limit reached ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in sqrt(1/i) : NaNs produced ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > : ./RegParallel.Rcheck/00check.log: iteration limit reached ./RegParallel.Rcheck/00check.log:Done! ./RegParallel.Rcheck/00check.log:Warning in rm(dds, nbdata, nbcounts, rlogdata, rlogcounts, data, airway) : ./RegParallel.Rcheck/00check.log: object 'data' not found ./RegParallel.Rcheck/00check.log:Setting options('download.file.method.GEOquery'='auto') ./RegParallel.Rcheck/00check.log:Setting options('GEOquery.inmemory.gpl'=FALSE) ./RegParallel.Rcheck/00check.log:Found 1 file(s) ./RegParallel.Rcheck/00check.log:GSE2990_series_matrix.txt.gz ./RegParallel.Rcheck/00check.log:trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2990/matrix/GSE2990_series_matrix.txt.gz' ./RegParallel.Rcheck/00check.log:Content type 'application/x-gzip' length 16680570 bytes (15.9 MB) ./RegParallel.Rcheck/00check.log:================================================== ./RegParallel.Rcheck/00check.log:downloaded 15.9 MB ./RegParallel.Rcheck/00check.log:Parsed with column specification: ./RegParallel.Rcheck/00check.log:cols( ./RegParallel.Rcheck/00check.log: .default = col_double(), ./RegParallel.Rcheck/00check.log: ID_REF = col_character() ./RegParallel.Rcheck/00check.log:) ./RegParallel.Rcheck/00check.log:See spec(...) for full column specifications. ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:#RegParallel ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:System is: ./RegParallel.Rcheck/00check.log:-- Linux ./RegParallel.Rcheck/00check.log:Blocksize: ./RegParallel.Rcheck/00check.log:-- 2000 ./RegParallel.Rcheck/00check.log:Cores / Threads: ./RegParallel.Rcheck/00check.log:-- 3 ./RegParallel.Rcheck/00check.log:Terms included in model: ./RegParallel.Rcheck/00check.log:-- Time.RFS ./RegParallel.Rcheck/00check.log:-- Distant.RFS ./RegParallel.Rcheck/00check.log:First 5 formulae: ./RegParallel.Rcheck/00check.log:-- Surv(Time.RFS, Distant.RFS) ~ X1007_s_at ./RegParallel.Rcheck/00check.log:-- Surv(Time.RFS, Distant.RFS) ~ X1053_at ./RegParallel.Rcheck/00check.log:-- Surv(Time.RFS, Distant.RFS) ~ X117_at ./RegParallel.Rcheck/00check.log:-- Surv(Time.RFS, Distant.RFS) ~ X121_at ./RegParallel.Rcheck/00check.log:-- Surv(Time.RFS, Distant.RFS) ~ X1255_g_at ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 1 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 1; index2: 2000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 2 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 2001; index2: 4000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 3 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 4001; index2: 6000 ./RegParallel.Rcheck/00check.log:Warning in fitter(X, Y, strats, offset, init, control, weights = weights, : ./RegParallel.Rcheck/00check.log: Loglik converged before variable 1 ; coefficient may be infinite. ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 4 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 6001; index2: 8000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 5 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 8001; index2: 10000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 6 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 10001; index2: 12000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 7 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 12001; index2: 14000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 8 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 14001; index2: 16000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 9 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 16001; index2: 18000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 10 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 18001; index2: 20000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 11 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 20001; index2: 22000 ./RegParallel.Rcheck/00check.log:Processing final batch 12 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 22001; index2: 22215 ./RegParallel.Rcheck/00check.log:Warning in fitter(X, Y, strats, offset, init, control, weights = weights, : ./RegParallel.Rcheck/00check.log: Loglik converged before variable 1 ; coefficient may be infinite. ./RegParallel.Rcheck/00check.log:Done! ./RegParallel.Rcheck/00check.log:Cache found ./RegParallel.Rcheck/00check.log:Loading required package: ggplot2 ./RegParallel.Rcheck/00check.log:Loading required package: ggpubr ./RegParallel.Rcheck/00check.log:Warning in eval(expr, envir, enclos) : NAs introduced by coercion ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:#RegParallel ./RegParallel.Rcheck/00check.log:############################## ./RegParallel.Rcheck/00check.log:System is: ./RegParallel.Rcheck/00check.log:-- Linux ./RegParallel.Rcheck/00check.log:Blocksize: ./RegParallel.Rcheck/00check.log:-- 2000 ./RegParallel.Rcheck/00check.log:Cores / Threads: ./RegParallel.Rcheck/00check.log:-- 3 ./RegParallel.Rcheck/00check.log:Terms included in model: ./RegParallel.Rcheck/00check.log:-- ER ./RegParallel.Rcheck/00check.log:-- Age ./RegParallel.Rcheck/00check.log:-- Grade ./RegParallel.Rcheck/00check.log:First 5 formulae: ./RegParallel.Rcheck/00check.log:-- ER ~ X1007_s_at + Age + strata(Grade) ./RegParallel.Rcheck/00check.log:-- ER ~ X1053_at + Age + strata(Grade) ./RegParallel.Rcheck/00check.log:-- ER ~ X117_at + Age + strata(Grade) ./RegParallel.Rcheck/00check.log:-- ER ~ X121_at + Age + strata(Grade) ./RegParallel.Rcheck/00check.log:-- ER ~ X1255_g_at + Age + strata(Grade) ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 1 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 1; index2: 2000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 2 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 2001; index2: 4000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 3 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 4001; index2: 6000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 6 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 10001; index2: 12000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 4 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 6001; index2: 8000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 5 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 8001; index2: 10000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 7 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 12001; index2: 14000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 9 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 16001; index2: 18000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 8 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 14001; index2: 16000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 10 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 18001; index2: 20000 ./RegParallel.Rcheck/00check.log:Processing 2000 formulae, batch 11 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 20001; index2: 22000 ./RegParallel.Rcheck/00check.log:Processing final batch 12 of 12 ./RegParallel.Rcheck/00check.log:-- index1: 22001; index2: 22215 ./RegParallel.Rcheck/00check.log:Done! ./RegParallel.Rcheck/00check.log:Quitting from lines 356-399 (RegParallel.Rmd) ./RegParallel.Rcheck/00check.log:Error: processing vignette 'RegParallel.Rmd' failed with diagnostics: ./RegParallel.Rcheck/00check.log:failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no" ./RegParallel.Rcheck/00check.log:--- failed re-building ‘RegParallel.Rmd’ ./RegParallel.Rcheck/00check.log:SUMMARY: processing the following file failed: ./RegParallel.Rcheck/00check.log: ‘RegParallel.Rmd’ ./RegParallel.Rcheck/00check.log:Error: Vignette re-building failed. ./RegParallel.Rcheck/00check.log:Execution halted ./RegParallel.Rcheck/00check.log:* checking PDF version of manual ... OK ./RegParallel.Rcheck/00check.log:* DONE ./RegParallel.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE RiboProfiling_1.15.0.tar.gz ./RiboProfiling.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/RiboProfiling.Rcheck’ ./RiboProfiling.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./RiboProfiling.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./RiboProfiling.Rcheck/00check.log:* using session charset: UTF-8 ./RiboProfiling.Rcheck/00check.log:* checking for file ‘RiboProfiling/DESCRIPTION’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking extension type ... Package ./RiboProfiling.Rcheck/00check.log:* this is package ‘RiboProfiling’ version ‘1.15.0’ ./RiboProfiling.Rcheck/00check.log:* checking package namespace information ... OK ./RiboProfiling.Rcheck/00check.log:* checking package dependencies ... OK ./RiboProfiling.Rcheck/00check.log:* checking if this is a source package ... OK ./RiboProfiling.Rcheck/00check.log:* checking if there is a namespace ... OK ./RiboProfiling.Rcheck/00check.log:* checking for executable files ... OK ./RiboProfiling.Rcheck/00check.log:* checking for hidden files and directories ... OK ./RiboProfiling.Rcheck/00check.log:* checking for portable file names ... OK ./RiboProfiling.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether package ‘RiboProfiling’ can be installed ... WARNING ./RiboProfiling.Rcheck/00check.log:Found the following significant warnings: ./RiboProfiling.Rcheck/00check.log: Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’ ./RiboProfiling.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/RiboProfiling.Rcheck/00install.out’ for details. ./RiboProfiling.Rcheck/00check.log:* checking installed package size ... OK ./RiboProfiling.Rcheck/00check.log:* checking package directory ... OK ./RiboProfiling.Rcheck/00check.log:* checking ‘build’ directory ... OK ./RiboProfiling.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./RiboProfiling.Rcheck/00check.log:* checking top-level files ... OK ./RiboProfiling.Rcheck/00check.log:* checking for left-over files ... OK ./RiboProfiling.Rcheck/00check.log:* checking index information ... OK ./RiboProfiling.Rcheck/00check.log:* checking package subdirectories ... OK ./RiboProfiling.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./RiboProfiling.Rcheck/00check.log:* checking R files for syntax errors ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./RiboProfiling.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./RiboProfiling.Rcheck/00check.log:* checking dependencies in R code ... OK ./RiboProfiling.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./RiboProfiling.Rcheck/00check.log:* checking replacement functions ... OK ./RiboProfiling.Rcheck/00check.log:* checking foreign function calls ... OK ./RiboProfiling.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./RiboProfiling.Rcheck/00check.log:applyShiftFeature: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:aroundPromoter: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:codonInfo: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:countShiftReads: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:histMatchLength: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:orfRelativePos: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:plotSummarizedCov: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:readStartCov: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:readsToStartOrEnd: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:riboSeqFromBAM: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:Undefined global functions or variables: ./RiboProfiling.Rcheck/00check.log: is ./RiboProfiling.Rcheck/00check.log:Consider adding ./RiboProfiling.Rcheck/00check.log: importFrom("methods", "is") ./RiboProfiling.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./RiboProfiling.Rcheck/00check.log:* checking Rd files ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd metadata ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd cross-references ... OK ./RiboProfiling.Rcheck/00check.log:* checking for missing documentation entries ... OK ./RiboProfiling.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd \usage sections ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd contents ... OK ./RiboProfiling.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./RiboProfiling.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./RiboProfiling.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./RiboProfiling.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./RiboProfiling.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking examples ... OK ./RiboProfiling.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking tests ... OK ./RiboProfiling.Rcheck/00check.log: Running ‘testthat.R’ ./RiboProfiling.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./RiboProfiling.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./RiboProfiling.Rcheck/00check.log: ‘RiboProfiling.Rnw’... OK ./RiboProfiling.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./RiboProfiling.Rcheck/00check.log:* checking PDF version of manual ... OK ./RiboProfiling.Rcheck/00check.log:* DONE ./RiboProfiling.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE S4Vectors_0.23.21.tar.gz ./S4Vectors.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/S4Vectors.Rcheck’ ./S4Vectors.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./S4Vectors.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./S4Vectors.Rcheck/00check.log:* using session charset: UTF-8 ./S4Vectors.Rcheck/00check.log:* checking for file ‘S4Vectors/DESCRIPTION’ ... OK ./S4Vectors.Rcheck/00check.log:* this is package ‘S4Vectors’ version ‘0.23.21’ ./S4Vectors.Rcheck/00check.log:* package encoding: UTF-8 ./S4Vectors.Rcheck/00check.log:* checking package namespace information ... OK ./S4Vectors.Rcheck/00check.log:* checking package dependencies ... OK ./S4Vectors.Rcheck/00check.log:* checking if this is a source package ... OK ./S4Vectors.Rcheck/00check.log:* checking if there is a namespace ... OK ./S4Vectors.Rcheck/00check.log:* checking for executable files ... OK ./S4Vectors.Rcheck/00check.log:* checking for hidden files and directories ... OK ./S4Vectors.Rcheck/00check.log:* checking for portable file names ... OK ./S4Vectors.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./S4Vectors.Rcheck/00check.log:* checking whether package ‘S4Vectors’ can be installed ... OK ./S4Vectors.Rcheck/00check.log:* checking installed package size ... OK ./S4Vectors.Rcheck/00check.log:* checking package directory ... OK ./S4Vectors.Rcheck/00check.log:* checking ‘build’ directory ... OK ./S4Vectors.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./S4Vectors.Rcheck/00check.log:* checking top-level files ... OK ./S4Vectors.Rcheck/00check.log:* checking for left-over files ... OK ./S4Vectors.Rcheck/00check.log:* checking index information ... OK ./S4Vectors.Rcheck/00check.log:* checking package subdirectories ... OK ./S4Vectors.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./S4Vectors.Rcheck/00check.log:* checking R files for syntax errors ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./S4Vectors.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./S4Vectors.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./S4Vectors.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./S4Vectors.Rcheck/00check.log: ‘data.table:::as.data.frame.data.table’ ./S4Vectors.Rcheck/00check.log: ‘stats:::na.exclude.data.frame’ ‘stats:::na.omit.data.frame’ ./S4Vectors.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./S4Vectors.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./S4Vectors.Rcheck/00check.log:* checking replacement functions ... OK ./S4Vectors.Rcheck/00check.log:* checking foreign function calls ... OK ./S4Vectors.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./S4Vectors.Rcheck/00check.log:evalSeparately,FilterRules : : no visible global function ./S4Vectors.Rcheck/00check.log: definition for ‘.’ ./S4Vectors.Rcheck/00check.log:Undefined global functions or variables: ./S4Vectors.Rcheck/00check.log: . ./S4Vectors.Rcheck/00check.log:* checking Rd files ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd metadata ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd cross-references ... WARNING ./S4Vectors.Rcheck/00check.log:Missing link or links in documentation object 'Vector-comparison.Rd': ./S4Vectors.Rcheck/00check.log: ‘[IRanges]{IntegerRanges-comparison}’ ./S4Vectors.Rcheck/00check.log:See section 'Cross-references' in the 'Writing R Extensions' manual. ./S4Vectors.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./S4Vectors.Rcheck/00check.log:Undocumented code objects: ./S4Vectors.Rcheck/00check.log: ‘head.LLint’ ‘pcompareRecursively’ ‘t.HitsList’ ‘tail.LLint’ ./S4Vectors.Rcheck/00check.log: ‘transform.Vector’ ‘window.LLint’ ./S4Vectors.Rcheck/00check.log:Undocumented S4 methods: ./S4Vectors.Rcheck/00check.log: generic '!' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic '<=' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic '<=' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic '<=' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic '==' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic '==' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic '==' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic '[' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic '[<-' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'anyNA' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'by' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'coerce' and siglist 'ANY,DataTable_OR_NULL' ./S4Vectors.Rcheck/00check.log: generic 'countMatches' and siglist 'ANY' ./S4Vectors.Rcheck/00check.log: generic 'do.call' and siglist 'ANY,List' ./S4Vectors.Rcheck/00check.log: generic 'droplevels' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'duplicated' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'eval' and siglist 'expression,Vector' ./S4Vectors.Rcheck/00check.log: generic 'eval' and siglist 'language,Vector' ./S4Vectors.Rcheck/00check.log: generic 'extractCOLS' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'DataFrame,ANY' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'LLint,ANY' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'LLint,NSBS' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'LLint,RangeNSBS' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'Vector,ANY' ./S4Vectors.Rcheck/00check.log: generic 'filterRules' and siglist 'FilterResults' ./S4Vectors.Rcheck/00check.log: generic 'from' and siglist 'HitsList' ./S4Vectors.Rcheck/00check.log: generic 'getListElement' and siglist 'SimpleList' ./S4Vectors.Rcheck/00check.log: generic 'grep' and siglist 'ANY,Rle' ./S4Vectors.Rcheck/00check.log: generic 'grepl' and siglist 'ANY,Rle' ./S4Vectors.Rcheck/00check.log: generic 'head' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'is.na' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'is.unsorted' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,Vector' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,vector' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic 'max' and siglist 'NSBS' ./S4Vectors.Rcheck/00check.log: generic 'mergeROWS' and siglist 'ANY' ./S4Vectors.Rcheck/00check.log: generic 'mergeROWS' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'mergeROWS' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'normalizeSingleBracketReplacementValue' and siglist ./S4Vectors.Rcheck/00check.log: 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'normalizeSingleBracketReplacementValue' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'order' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'pcompare' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic 'pcompare' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic 'pcompare' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic 'pcompareRecursively' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'pcompareRecursively' and siglist 'list' ./S4Vectors.Rcheck/00check.log: generic 'rank' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'rep.int' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'rep' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'replaceCOLS' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'replaceROWS' and siglist 'ANY' ./S4Vectors.Rcheck/00check.log: generic 'replaceROWS' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'replaceROWS' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'replaceROWS' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'sort' and siglist 'DataTable' ./S4Vectors.Rcheck/00check.log: generic 'sort' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'splitAsList' and siglist 'ANY' ./S4Vectors.Rcheck/00check.log: generic 'splitAsList' and siglist 'SortedByQueryHits' ./S4Vectors.Rcheck/00check.log: generic 'summary' and siglist 'FilterResults' ./S4Vectors.Rcheck/00check.log: generic 't' and siglist 'Pairs' ./S4Vectors.Rcheck/00check.log: generic 'tail' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'to' and siglist 'HitsList' ./S4Vectors.Rcheck/00check.log: generic 'transform' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'unique' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'unique' and siglist 'SimpleList' ./S4Vectors.Rcheck/00check.log: generic 'window' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'with' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'xtabs' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./S4Vectors.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./S4Vectors.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd \usage sections ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd contents ... OK ./S4Vectors.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./S4Vectors.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./S4Vectors.Rcheck/00check.log:* checking compiled code ... OK ./S4Vectors.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./S4Vectors.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./S4Vectors.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./S4Vectors.Rcheck/00check.log:* checking examples ... OK ./S4Vectors.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./S4Vectors.Rcheck/00check.log:* checking tests ... OK ./S4Vectors.Rcheck/00check.log: Running ‘run_unitTests.R’ ./S4Vectors.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./S4Vectors.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./S4Vectors.Rcheck/00check.log:* checking running R code from vignettes ... OK ./S4Vectors.Rcheck/00check.log: ‘RleTricks.Rnw’using ‘UTF-8’... OK ./S4Vectors.Rcheck/00check.log: ‘S4QuickOverview.Rnw’using ‘UTF-8’... OK ./S4Vectors.Rcheck/00check.log: ‘S4VectorsOverview.Rnw’using ‘UTF-8’... OK ./S4Vectors.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./S4Vectors.Rcheck/00check.log:* checking PDF version of manual ... OK ./S4Vectors.Rcheck/00check.log:* DONE ./S4Vectors.Rcheck/00check.log:Status: 2 WARNINGs, 2 NOTEs SISPA_1.15.0.tar.gz ./SISPA.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/SISPA.Rcheck’ ./SISPA.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./SISPA.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./SISPA.Rcheck/00check.log:* using session charset: UTF-8 ./SISPA.Rcheck/00check.log:* checking for file ‘SISPA/DESCRIPTION’ ... OK ./SISPA.Rcheck/00check.log:* checking extension type ... Package ./SISPA.Rcheck/00check.log:* this is package ‘SISPA’ version ‘1.15.0’ ./SISPA.Rcheck/00check.log:* checking package namespace information ... OK ./SISPA.Rcheck/00check.log:* checking package dependencies ... OK ./SISPA.Rcheck/00check.log:* checking if this is a source package ... OK ./SISPA.Rcheck/00check.log:* checking if there is a namespace ... OK ./SISPA.Rcheck/00check.log:* checking for executable files ... OK ./SISPA.Rcheck/00check.log:* checking for hidden files and directories ... OK ./SISPA.Rcheck/00check.log:* checking for portable file names ... OK ./SISPA.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./SISPA.Rcheck/00check.log:* checking whether package ‘SISPA’ can be installed ... OK ./SISPA.Rcheck/00check.log:* checking installed package size ... OK ./SISPA.Rcheck/00check.log:* checking package directory ... OK ./SISPA.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./SISPA.Rcheck/00check.log:* checking top-level files ... OK ./SISPA.Rcheck/00check.log:* checking for left-over files ... OK ./SISPA.Rcheck/00check.log:* checking index information ... OK ./SISPA.Rcheck/00check.log:* checking package subdirectories ... OK ./SISPA.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./SISPA.Rcheck/00check.log:* checking R files for syntax errors ... OK ./SISPA.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./SISPA.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./SISPA.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./SISPA.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./SISPA.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./SISPA.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./SISPA.Rcheck/00check.log:* checking dependencies in R code ... OK ./SISPA.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./SISPA.Rcheck/00check.log:* checking replacement functions ... OK ./SISPA.Rcheck/00check.log:* checking foreign function calls ... OK ./SISPA.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./SISPA.Rcheck/00check.log:cptSamples : cptsPlot: no visible global function definition for ./SISPA.Rcheck/00check.log: ‘abline’ ./SISPA.Rcheck/00check.log:cptSamples : cptsPlot: no visible global function definition for ‘text’ ./SISPA.Rcheck/00check.log:Undefined global functions or variables: ./SISPA.Rcheck/00check.log: abline text ./SISPA.Rcheck/00check.log:Consider adding ./SISPA.Rcheck/00check.log: importFrom("graphics", "abline", "text") ./SISPA.Rcheck/00check.log:to your NAMESPACE file. ./SISPA.Rcheck/00check.log:* checking Rd files ... OK ./SISPA.Rcheck/00check.log:* checking Rd metadata ... OK ./SISPA.Rcheck/00check.log:* checking Rd cross-references ... OK ./SISPA.Rcheck/00check.log:* checking for missing documentation entries ... OK ./SISPA.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./SISPA.Rcheck/00check.log:* checking Rd \usage sections ... OK ./SISPA.Rcheck/00check.log:* checking Rd contents ... OK ./SISPA.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./SISPA.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./SISPA.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./SISPA.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./SISPA.Rcheck/00check.log:* checking files in ‘vignettes’ ... WARNING ./SISPA.Rcheck/00check.log:Files in the 'vignettes' directory but no files in 'inst/doc': ./SISPA.Rcheck/00check.log: ‘SISPA.Rmd’, ‘SISPA.md’, ‘SISPA_data.Rda’, ‘SISPA_files/figure-html/unnamed-chunk-2-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-3-1.png’, ./SISPA.Rcheck/00check.log: ‘SISPA_files/figure-html/unnamed-chunk-4-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-5-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-6-1.png’, ./SISPA.Rcheck/00check.log: ‘SISPA_files/figure-html/unnamed-chunk-7-1.png’, ‘sispa_overview.png’ ./SISPA.Rcheck/00check.log:Files named as vignettes but with no recognized vignette engine: ./SISPA.Rcheck/00check.log: ‘vignettes/SISPA.Rmd’ ./SISPA.Rcheck/00check.log:(Is a VignetteBuilder field missing?) ./SISPA.Rcheck/00check.log:* checking examples ... OK ./SISPA.Rcheck/00check.log:* checking PDF version of manual ... OK ./SISPA.Rcheck/00check.log:* DONE ./SISPA.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE TFutils_1.5.13.tar.gz ./TFutils.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/TFutils.Rcheck’ ./TFutils.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./TFutils.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./TFutils.Rcheck/00check.log:* using session charset: UTF-8 ./TFutils.Rcheck/00check.log:* checking for file ‘TFutils/DESCRIPTION’ ... OK ./TFutils.Rcheck/00check.log:* this is package ‘TFutils’ version ‘1.5.13’ ./TFutils.Rcheck/00check.log:* package encoding: UTF-8 ./TFutils.Rcheck/00check.log:* checking package namespace information ... OK ./TFutils.Rcheck/00check.log:* checking package dependencies ... OK ./TFutils.Rcheck/00check.log:* checking if this is a source package ... OK ./TFutils.Rcheck/00check.log:* checking if there is a namespace ... OK ./TFutils.Rcheck/00check.log:* checking for executable files ... OK ./TFutils.Rcheck/00check.log:* checking for hidden files and directories ... OK ./TFutils.Rcheck/00check.log:* checking for portable file names ... OK ./TFutils.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./TFutils.Rcheck/00check.log:* checking whether package ‘TFutils’ can be installed ... OK ./TFutils.Rcheck/00check.log:* checking installed package size ... NOTE ./TFutils.Rcheck/00check.log: installed size is 7.6Mb ./TFutils.Rcheck/00check.log: sub-directories of 1Mb or more: ./TFutils.Rcheck/00check.log: data 3.5Mb ./TFutils.Rcheck/00check.log: doc 2.2Mb ./TFutils.Rcheck/00check.log: lambert 1.4Mb ./TFutils.Rcheck/00check.log:* checking package directory ... OK ./TFutils.Rcheck/00check.log:* checking ‘build’ directory ... OK ./TFutils.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./TFutils.Rcheck/00check.log:Package listed in more than one of Depends, Imports, Suggests, Enhances: ./TFutils.Rcheck/00check.log: ‘Rsamtools’ ./TFutils.Rcheck/00check.log:A package should be listed in only one of these fields. ./TFutils.Rcheck/00check.log:* checking top-level files ... OK ./TFutils.Rcheck/00check.log:* checking for left-over files ... OK ./TFutils.Rcheck/00check.log:* checking index information ... OK ./TFutils.Rcheck/00check.log:* checking package subdirectories ... OK ./TFutils.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./TFutils.Rcheck/00check.log:* checking R files for syntax errors ... OK ./TFutils.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./TFutils.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./TFutils.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./TFutils.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./TFutils.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./TFutils.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./TFutils.Rcheck/00check.log:* checking dependencies in R code ... WARNING ./TFutils.Rcheck/00check.log:'::' or ':::' imports not declared from: ./TFutils.Rcheck/00check.log: 'BiocFileCache' 'DT' 'httr' 'readxl' 'rjson' ./TFutils.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./TFutils.Rcheck/00check.log:* checking replacement functions ... OK ./TFutils.Rcheck/00check.log:* checking foreign function calls ... OK ./TFutils.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./TFutils.Rcheck/00check.log:browse_lambert_gwaslinks: no visible global function definition for ./TFutils.Rcheck/00check.log: ‘read.csv’ ./TFutils.Rcheck/00check.log:directHitsInCISBP: no visible binding for global variable ./TFutils.Rcheck/00check.log: ‘DISEASE.TRAIT’ ./TFutils.Rcheck/00check.log:directHitsInCISBP: no visible binding for global variable ‘MAPPED_GENE’ ./TFutils.Rcheck/00check.log:directHitsInCISBP: no visible binding for global variable ‘cisbpTFcat’ ./TFutils.Rcheck/00check.log:directHitsInCISBP: no visible binding for global variable ‘HGNC’ ./TFutils.Rcheck/00check.log:directHitsInCISBP: no visible binding for global variable ‘Family_Name’ ./TFutils.Rcheck/00check.log:fimo_granges: no visible global function definition for ‘rowRanges<-’ ./TFutils.Rcheck/00check.log:fimo_granges : proctext: no visible global function definition for ./TFutils.Rcheck/00check.log: ‘read.delim’ ./TFutils.Rcheck/00check.log:fimo_granges: no visible global function definition for ‘reduceByRange’ ./TFutils.Rcheck/00check.log:fimo_granges : : no visible global function definition for ./TFutils.Rcheck/00check.log: ‘seqinfo<-’ ./TFutils.Rcheck/00check.log:retrieve_lambert_main: no visible global function definition for ./TFutils.Rcheck/00check.log: ‘bfcadd’ ./TFutils.Rcheck/00check.log:setupHIZE: no visible global function definition for ‘read.delim’ ./TFutils.Rcheck/00check.log:tffamCirc.prep: no visible binding for global variable ‘TF family’ ./TFutils.Rcheck/00check.log:tffamCirc.prep: no visible binding for global variable ‘TFfamily’ ./TFutils.Rcheck/00check.log:tffamCirc.prep: no visible binding for global variable ‘Transcription ./TFutils.Rcheck/00check.log: factor’ ./TFutils.Rcheck/00check.log:topTraitsOfTargets: no visible global function definition for ‘mcols’ ./TFutils.Rcheck/00check.log:topTraitsOfTargets: no visible binding for global variable ./TFutils.Rcheck/00check.log: ‘DISEASE.TRAIT’ ./TFutils.Rcheck/00check.log:Undefined global functions or variables: ./TFutils.Rcheck/00check.log: DISEASE.TRAIT Family_Name HGNC MAPPED_GENE TF family TFfamily ./TFutils.Rcheck/00check.log: Transcription factor bfcadd cisbpTFcat mcols read.csv read.delim ./TFutils.Rcheck/00check.log: reduceByRange rowRanges<- seqinfo<- ./TFutils.Rcheck/00check.log:Consider adding ./TFutils.Rcheck/00check.log: importFrom("base", "factor") ./TFutils.Rcheck/00check.log: importFrom("stats", "family") ./TFutils.Rcheck/00check.log: importFrom("utils", "read.csv", "read.delim") ./TFutils.Rcheck/00check.log:to your NAMESPACE file. ./TFutils.Rcheck/00check.log:* checking Rd files ... OK ./TFutils.Rcheck/00check.log:* checking Rd metadata ... OK ./TFutils.Rcheck/00check.log:* checking Rd cross-references ... OK ./TFutils.Rcheck/00check.log:* checking for missing documentation entries ... OK ./TFutils.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./TFutils.Rcheck/00check.log:* checking Rd \usage sections ... OK ./TFutils.Rcheck/00check.log:* checking Rd contents ... OK ./TFutils.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./TFutils.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./TFutils.Rcheck/00check.log:* checking data for non-ASCII characters ... NOTE ./TFutils.Rcheck/00check.log: Note: found 62 marked UTF-8 strings ./TFutils.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./TFutils.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./TFutils.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./TFutils.Rcheck/00check.log:* checking include directives in Makefiles ... OK ./TFutils.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./TFutils.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./TFutils.Rcheck/00check.log:* checking examples ... OK ./TFutils.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./TFutils.Rcheck/00check.log:* checking tests ... OK ./TFutils.Rcheck/00check.log: Running ‘testthat.R’ ./TFutils.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./TFutils.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./TFutils.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./TFutils.Rcheck/00check.log: ‘TFutils.Rmd’using ‘UTF-8’... OK ./TFutils.Rcheck/00check.log: ‘fimo16.Rmd’using ‘UTF-8’... OK ./TFutils.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./TFutils.Rcheck/00check.log:* checking PDF version of manual ... OK ./TFutils.Rcheck/00check.log:* DONE ./TFutils.Rcheck/00check.log:Status: 1 WARNING, 4 NOTEs TitanCNA_1.23.1.tar.gz ./TitanCNA.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/TitanCNA.Rcheck’ ./TitanCNA.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./TitanCNA.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./TitanCNA.Rcheck/00check.log:* using session charset: UTF-8 ./TitanCNA.Rcheck/00check.log:* checking for file ‘TitanCNA/DESCRIPTION’ ... OK ./TitanCNA.Rcheck/00check.log:* checking extension type ... Package ./TitanCNA.Rcheck/00check.log:* this is package ‘TitanCNA’ version ‘1.23.1’ ./TitanCNA.Rcheck/00check.log:* checking package namespace information ... OK ./TitanCNA.Rcheck/00check.log:* checking package dependencies ... OK ./TitanCNA.Rcheck/00check.log:* checking if this is a source package ... OK ./TitanCNA.Rcheck/00check.log:* checking if there is a namespace ... OK ./TitanCNA.Rcheck/00check.log:* checking for executable files ... OK ./TitanCNA.Rcheck/00check.log:* checking for hidden files and directories ... OK ./TitanCNA.Rcheck/00check.log:* checking for portable file names ... OK ./TitanCNA.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./TitanCNA.Rcheck/00check.log:* checking whether package ‘TitanCNA’ can be installed ... WARNING ./TitanCNA.Rcheck/00check.log:Found the following significant warnings: ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log: Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’ ./TitanCNA.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/TitanCNA.Rcheck/00install.out’ for details. ./TitanCNA.Rcheck/00check.log:* checking installed package size ... NOTE ./TitanCNA.Rcheck/00check.log: installed size is 7.5Mb ./TitanCNA.Rcheck/00check.log: sub-directories of 1Mb or more: ./TitanCNA.Rcheck/00check.log: data 1.7Mb ./TitanCNA.Rcheck/00check.log: extdata 4.9Mb ./TitanCNA.Rcheck/00check.log:* checking package directory ... OK ./TitanCNA.Rcheck/00check.log:* checking ‘build’ directory ... OK ./TitanCNA.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./TitanCNA.Rcheck/00check.log:* checking top-level files ... OK ./TitanCNA.Rcheck/00check.log:* checking for left-over files ... OK ./TitanCNA.Rcheck/00check.log:* checking index information ... OK ./TitanCNA.Rcheck/00check.log:* checking package subdirectories ... OK ./TitanCNA.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./TitanCNA.Rcheck/00check.log:* checking R files for syntax errors ... OK ./TitanCNA.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./TitanCNA.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./TitanCNA.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./TitanCNA.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./TitanCNA.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./TitanCNA.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./TitanCNA.Rcheck/00check.log:* checking dependencies in R code ... OK ./TitanCNA.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./TitanCNA.Rcheck/00check.log:* checking replacement functions ... OK ./TitanCNA.Rcheck/00check.log:* checking foreign function calls ... OK ./TitanCNA.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./TitanCNA.Rcheck/00check.log:computeSDbwIndex: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘ClonalCluster’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Median_HaplotypeRatio’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘Chromosome’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘Copy_Number’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘logR_Copy_Number’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘Median_logR’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Cellular_Prevalence’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘Chr’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘LogRatio’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘CellularPrevalence’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Corrected_Ratio’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Corrected_Copy_Number’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Corrected_Call’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘TITAN_call’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Corrected_MajorCN’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘MajorCN’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Corrected_MinorCN’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘MinorCN’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘CopyNumber’ ./TitanCNA.Rcheck/00check.log:correctIntegerCN: no visible binding for global variable ‘TITANcall’ ./TitanCNA.Rcheck/00check.log:correctReadDepth: no visible global function definition for ‘queryHits’ ./TitanCNA.Rcheck/00check.log:correctReadcount: no visible global function definition for ‘loess’ ./TitanCNA.Rcheck/00check.log:correctReadcount: no visible global function definition for ‘predict’ ./TitanCNA.Rcheck/00check.log:correctReadcount: no visible global function definition for ‘approxfun’ ./TitanCNA.Rcheck/00check.log:correctReadcount: no visible global function definition for ‘lowess’ ./TitanCNA.Rcheck/00check.log:extendSegments: no visible binding for global variable ‘Start’ ./TitanCNA.Rcheck/00check.log:extendSegments: no visible binding for global variable ‘End’ ./TitanCNA.Rcheck/00check.log:extendSegments: no visible binding for global variable ‘Chromosome’ ./TitanCNA.Rcheck/00check.log:extendSegments: no visible binding for global variable ‘Start.snp’ ./TitanCNA.Rcheck/00check.log:extendSegments: no visible binding for global variable ‘End.snp’ ./TitanCNA.Rcheck/00check.log:extendSegments: no visible binding for global variable ‘Start.telo’ ./TitanCNA.Rcheck/00check.log:extendSegments: no visible binding for global variable ‘seq.info’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘PileupParam’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘BcfFile’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘scanBcf’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘ScanBamParam’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘scanBamFlag’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘BamFile’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘pileup’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘xtabs’ ./TitanCNA.Rcheck/00check.log:extractAlleleReadCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘write.table’ ./TitanCNA.Rcheck/00check.log:getHaplotypesFromVCF: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘rowRanges<-’ ./TitanCNA.Rcheck/00check.log:getHaplotypesFromVCF: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘rowRanges’ ./TitanCNA.Rcheck/00check.log:getHaplotypesFromVCF: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘na.omit’ ./TitanCNA.Rcheck/00check.log:getHaplotypesFromVCF: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘unstrsplit’ ./TitanCNA.Rcheck/00check.log:getHaplotypesFromVCF: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘queryHits’ ./TitanCNA.Rcheck/00check.log:getHaplotypesFromVCF: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘DataFrame’ ./TitanCNA.Rcheck/00check.log:getOverlap: no visible global function definition for ‘as’ ./TitanCNA.Rcheck/00check.log:getOverlap: no visible global function definition for ‘queryHits’ ./TitanCNA.Rcheck/00check.log:getOverlap: no visible global function definition for ‘subjectHits’ ./TitanCNA.Rcheck/00check.log:getPositionOverlap: no visible global function definition for ‘as’ ./TitanCNA.Rcheck/00check.log:getSubcloneProfiles: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘read.delim’ ./TitanCNA.Rcheck/00check.log:getSubcloneProfiles: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘CopyNumber’ ./TitanCNA.Rcheck/00check.log:getSubcloneProfiles: no visible binding for global variable ‘TITANcall’ ./TitanCNA.Rcheck/00check.log:keepChr: no visible global function definition for ‘as’ ./TitanCNA.Rcheck/00check.log:loadAlleleCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘read.delim’ ./TitanCNA.Rcheck/00check.log:loadBXcountsFromBEDDir: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘BXcounts’ ./TitanCNA.Rcheck/00check.log:loadBXcountsFromBEDDir: no visible binding for global variable ‘BX’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘read.delim’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘subjectHits’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘as’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘phasedAlleleFraction’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘phasedCount’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘depth’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘SNPs’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeFraction’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeDepth.sum’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeBinDepth.sum’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeDepth.mean’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeBinDepth.mean’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘phaseSet’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘haplotypeBin’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeFraction.symmetric’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeDepth.sum.symmetric’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeDepth.mean.symmetric’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘.’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘na.omit’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘phasedCount.haploSymmetric’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘nonRef’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘phaseSet.aggr’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeRatio’ ./TitanCNA.Rcheck/00check.log:loadHaplotypeAlleleCounts: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘tumDepth’ ./TitanCNA.Rcheck/00check.log:loadReadCountsFromBed: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘excludeCentromere’ ./TitanCNA.Rcheck/00check.log:loadReadCountsFromBed: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘filterByTargetedSequences’ ./TitanCNA.Rcheck/00check.log:mergeSegsByCol: no visible binding for global variable ‘Median_Ratio’ ./TitanCNA.Rcheck/00check.log:mergeSegsByCol: no visible binding for global variable ‘Median_logR’ ./TitanCNA.Rcheck/00check.log:mergeSegsByCol: no visible binding for global variable ‘End’ ./TitanCNA.Rcheck/00check.log:mergeSegsByCol: no visible binding for global variable ‘Length.snp.’ ./TitanCNA.Rcheck/00check.log:outlierObslik: no visible global function definition for ‘dunif’ ./TitanCNA.Rcheck/00check.log:outputModelParameters: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘write.table’ ./TitanCNA.Rcheck/00check.log:outputTitanResults: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘write.table’ ./TitanCNA.Rcheck/00check.log:outputTitanSegments: no visible binding for global variable ‘Sample’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible binding for global variable ‘Allele.1’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible binding for global variable ‘LogRatio’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible binding for global variable ‘Allele.2’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible binding for global variable ‘Chr’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible binding for global variable ‘TITANcall’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible binding for global variable ‘CopyNumber’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible global function definition for ‘points’ ./TitanCNA.Rcheck/00check.log:plotAllelicCN: no visible global function definition for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotAllelicRatio: no visible binding for global variable ‘Chr’ ./TitanCNA.Rcheck/00check.log:plotAllelicRatio: no visible binding for global variable ‘TITANcall’ ./TitanCNA.Rcheck/00check.log:plotAllelicRatio: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotAllelicRatio: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotAllelicRatio: no visible binding for global variable ‘AllelicRatio’ ./TitanCNA.Rcheck/00check.log:plotAllelicRatio: no visible global function definition for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible binding for global variable ‘LogRatio’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible binding for global variable ‘Median_logR’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible binding for global variable ‘Chr’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible binding for global variable ‘TITANcall’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible global function definition for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible binding for global variable ‘Chromosome’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr : : no visible global function definition ./TitanCNA.Rcheck/00check.log: for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘End_Position.bp.’ ./TitanCNA.Rcheck/00check.log:plotCNlogRByChr: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Start_Position.bp.’ ./TitanCNA.Rcheck/00check.log:plotChrLines: no visible global function definition for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotChrLines: no visible global function definition for ‘axis’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘ClonalCluster’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘CellularPrevalence’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible binding for global variable ‘TITANcall’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible binding for global variable ‘Chr’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible global function definition for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotClonalFrequency: no visible global function definition for ‘mtext’ ./TitanCNA.Rcheck/00check.log:plotGeneAnnotation: no visible global function definition for ‘abline’ ./TitanCNA.Rcheck/00check.log:plotGeneAnnotation: no visible global function definition for ‘mtext’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeRatio.1’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeRatio’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘HaplotypeRatio.2’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible binding for global variable ‘Chr’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘TITANcall’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘points’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘AllelicRatio’ ./TitanCNA.Rcheck/00check.log:plotHaplotypeFraction: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘lines’ ./TitanCNA.Rcheck/00check.log:plotIdiogram.hg38: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotIdiogram.hg38: no visible binding for global variable ‘lsegments’ ./TitanCNA.Rcheck/00check.log:plotIdiogram.hg38: no visible binding for global variable ‘lpolygon’ ./TitanCNA.Rcheck/00check.log:plotIdiogram.hg38: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotIdiogram.hg38: no visible global function definition for ‘axis’ ./TitanCNA.Rcheck/00check.log:plotIdiogram.hg38: no visible global function definition for ‘text’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible binding for global variable ‘Chromosome’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible binding for global variable ‘TITAN_call’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘End_Position.bp.’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible global function definition for ‘.’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Start_Position.bp.’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible binding for global variable ‘MajorCN’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible binding for global variable ‘MinorCN’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians : : no visible global function definition ./TitanCNA.Rcheck/00check.log: for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible global function definition for ‘lines’ ./TitanCNA.Rcheck/00check.log:plotSegmentMedians: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Copy_Number’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible binding for global variable ‘Chr’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible global function definition for ‘par’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘CopyNumber’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible global function definition for ‘plot’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible global function definition for ‘axis’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible global function definition for ./TitanCNA.Rcheck/00check.log: ‘points’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible global function definition for ‘mtext’ ./TitanCNA.Rcheck/00check.log:plotSubcloneProfiles: no visible global function definition for ‘lines’ ./TitanCNA.Rcheck/00check.log:printSDbw: no visible global function definition for ‘write.table’ ./TitanCNA.Rcheck/00check.log:removeCentromereSegs: no visible binding for global variable ./TitanCNA.Rcheck/00check.log: ‘Chromosome’ ./TitanCNA.Rcheck/00check.log:removeCentromereSegs: no visible binding for global variable ‘Start’ ./TitanCNA.Rcheck/00check.log:removeCentromereSegs: no visible binding for global variable ‘End’ ./TitanCNA.Rcheck/00check.log:removeEmptyClusters: no visible global function definition for ‘tail’ ./TitanCNA.Rcheck/00check.log:runEMclonalCN: no visible binding for global variable ‘head’ ./TitanCNA.Rcheck/00check.log:updateParameters: no visible global function definition for ‘uniroot’ ./TitanCNA.Rcheck/00check.log:Undefined global functions or variables: ./TitanCNA.Rcheck/00check.log: . Allele.1 Allele.2 AllelicRatio BX BXcounts BamFile BcfFile ./TitanCNA.Rcheck/00check.log: CellularPrevalence Cellular_Prevalence Chr Chromosome ClonalCluster ./TitanCNA.Rcheck/00check.log: CopyNumber Copy_Number Corrected_Call Corrected_Copy_Number ./TitanCNA.Rcheck/00check.log: Corrected_MajorCN Corrected_MinorCN Corrected_Ratio DataFrame End ./TitanCNA.Rcheck/00check.log: End.snp End_Position.bp. HaplotypeBinDepth.mean HaplotypeBinDepth.sum ./TitanCNA.Rcheck/00check.log: HaplotypeDepth.mean HaplotypeDepth.mean.symmetric HaplotypeDepth.sum ./TitanCNA.Rcheck/00check.log: HaplotypeDepth.sum.symmetric HaplotypeFraction ./TitanCNA.Rcheck/00check.log: HaplotypeFraction.symmetric HaplotypeRatio HaplotypeRatio.1 ./TitanCNA.Rcheck/00check.log: HaplotypeRatio.2 Length.snp. LogRatio MajorCN Median_HaplotypeRatio ./TitanCNA.Rcheck/00check.log: Median_Ratio Median_logR MinorCN PileupParam SNPs Sample ScanBamParam ./TitanCNA.Rcheck/00check.log: Start Start.snp Start.telo Start_Position.bp. TITAN_call TITANcall ./TitanCNA.Rcheck/00check.log: abline approxfun as axis depth dunif excludeCentromere ./TitanCNA.Rcheck/00check.log: filterByTargetedSequences haplotypeBin head lines loess ./TitanCNA.Rcheck/00check.log: logR_Copy_Number lowess lpolygon lsegments mtext na.omit nonRef par ./TitanCNA.Rcheck/00check.log: phaseSet phaseSet.aggr phasedAlleleFraction phasedCount ./TitanCNA.Rcheck/00check.log: phasedCount.haploSymmetric pileup plot points predict queryHits ./TitanCNA.Rcheck/00check.log: read.delim rowRanges rowRanges<- scanBamFlag scanBcf seq.info ./TitanCNA.Rcheck/00check.log: subjectHits tail text tumDepth uniroot unstrsplit write.table xtabs ./TitanCNA.Rcheck/00check.log:Consider adding ./TitanCNA.Rcheck/00check.log: importFrom("graphics", "abline", "axis", "lines", "mtext", "par", ./TitanCNA.Rcheck/00check.log: "plot", "points", "text") ./TitanCNA.Rcheck/00check.log: importFrom("methods", "as") ./TitanCNA.Rcheck/00check.log: importFrom("stats", "approxfun", "dunif", "loess", "lowess", "na.omit", ./TitanCNA.Rcheck/00check.log: "predict", "uniroot", "xtabs") ./TitanCNA.Rcheck/00check.log: importFrom("utils", "head", "read.delim", "tail", "write.table") ./TitanCNA.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./TitanCNA.Rcheck/00check.log:* checking Rd files ... NOTE ./TitanCNA.Rcheck/00check.log:prepare_Rd: correctCN.Rd:51-53: Dropping empty section \details ./TitanCNA.Rcheck/00check.log:* checking Rd metadata ... OK ./TitanCNA.Rcheck/00check.log:* checking Rd cross-references ... NOTE ./TitanCNA.Rcheck/00check.log:Package unavailable to check Rd xrefs: ‘list’ ./TitanCNA.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./TitanCNA.Rcheck/00check.log:Undocumented code objects: ./TitanCNA.Rcheck/00check.log: ‘plotIdiogram.hg38’ ./TitanCNA.Rcheck/00check.log:All user-level objects in a package should have documentation entries. ./TitanCNA.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./TitanCNA.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./TitanCNA.Rcheck/00check.log:* checking Rd \usage sections ... OK ./TitanCNA.Rcheck/00check.log:* checking Rd contents ... OK ./TitanCNA.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./TitanCNA.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./TitanCNA.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./TitanCNA.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./TitanCNA.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./TitanCNA.Rcheck/00check.log:* checking compiled code ... OK ./TitanCNA.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./TitanCNA.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./TitanCNA.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./TitanCNA.Rcheck/00check.log:* checking examples ... OK ./TitanCNA.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./TitanCNA.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./TitanCNA.Rcheck/00check.log:* checking running R code from vignettes ... OK ./TitanCNA.Rcheck/00check.log: ‘TitanCNA.Rnw’using ‘UTF-8’... OK ./TitanCNA.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./TitanCNA.Rcheck/00check.log:* checking PDF version of manual ... OK ./TitanCNA.Rcheck/00check.log:* DONE ./TitanCNA.Rcheck/00check.log:Status: 2 WARNINGs, 4 NOTEs Ularcirc_1.3.1.tar.gz ./Ularcirc.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/Ularcirc.Rcheck’ ./Ularcirc.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./Ularcirc.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./Ularcirc.Rcheck/00check.log:* using session charset: UTF-8 ./Ularcirc.Rcheck/00check.log:* checking for file ‘Ularcirc/DESCRIPTION’ ... OK ./Ularcirc.Rcheck/00check.log:* checking extension type ... Package ./Ularcirc.Rcheck/00check.log:* this is package ‘Ularcirc’ version ‘1.3.1’ ./Ularcirc.Rcheck/00check.log:* package encoding: UTF-8 ./Ularcirc.Rcheck/00check.log:* checking package namespace information ... OK ./Ularcirc.Rcheck/00check.log:* checking package dependencies ... OK ./Ularcirc.Rcheck/00check.log:* checking if this is a source package ... OK ./Ularcirc.Rcheck/00check.log:* checking if there is a namespace ... OK ./Ularcirc.Rcheck/00check.log:* checking for executable files ... OK ./Ularcirc.Rcheck/00check.log:* checking for hidden files and directories ... OK ./Ularcirc.Rcheck/00check.log:* checking for portable file names ... OK ./Ularcirc.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./Ularcirc.Rcheck/00check.log:* checking whether package ‘Ularcirc’ can be installed ... OK ./Ularcirc.Rcheck/00check.log:* checking installed package size ... NOTE ./Ularcirc.Rcheck/00check.log: installed size is 5.8Mb ./Ularcirc.Rcheck/00check.log: sub-directories of 1Mb or more: ./Ularcirc.Rcheck/00check.log: doc 1.1Mb ./Ularcirc.Rcheck/00check.log: extdata 4.3Mb ./Ularcirc.Rcheck/00check.log:* checking package directory ... OK ./Ularcirc.Rcheck/00check.log:* checking ‘build’ directory ... OK ./Ularcirc.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./Ularcirc.Rcheck/00check.log:* checking top-level files ... OK ./Ularcirc.Rcheck/00check.log:* checking for left-over files ... OK ./Ularcirc.Rcheck/00check.log:* checking index information ... OK ./Ularcirc.Rcheck/00check.log:* checking package subdirectories ... OK ./Ularcirc.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./Ularcirc.Rcheck/00check.log:* checking R files for syntax errors ... OK ./Ularcirc.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./Ularcirc.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./Ularcirc.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./Ularcirc.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./Ularcirc.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./Ularcirc.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./Ularcirc.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./Ularcirc.Rcheck/00check.log:Namespaces in Imports field not imported from: ./Ularcirc.Rcheck/00check.log: ‘DT’ ‘GenomeInfoDb’ ‘GenomeInfoDbData’ ‘GenomicFeatures’ ‘Sushi’ ./Ularcirc.Rcheck/00check.log: ‘data.table’ ‘ggplot2’ ‘ggrepel’ ‘gsubfn’ ‘httpuv’ ‘mirbase.db’ ./Ularcirc.Rcheck/00check.log: ‘moments’ ‘shinyFiles’ ‘yaml’ ./Ularcirc.Rcheck/00check.log: All declared Imports should be used. ./Ularcirc.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./Ularcirc.Rcheck/00check.log:* checking replacement functions ... OK ./Ularcirc.Rcheck/00check.log:* checking foreign function calls ... OK ./Ularcirc.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘genes’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘GRanges’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible binding for global variable ./Ularcirc.Rcheck/00check.log: ‘strand’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘findOverlaps’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘invertStrand’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘subjectHits’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘select’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible binding for global variable ./Ularcirc.Rcheck/00check.log: ‘GeneList’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible binding for global variable ./Ularcirc.Rcheck/00check.log: ‘GeneName’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘as.data.table’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘getSeq’ ./Ularcirc.Rcheck/00check.log:BSJ_to_circRNA_sequence: no visible global function definition for ./Ularcirc.Rcheck/00check.log: ‘DNAString’ ./Ularcirc.Rcheck/00check.log:Undefined global functions or variables: ./Ularcirc.Rcheck/00check.log: DNAString GRanges GeneList GeneName as.data.table findOverlaps genes ./Ularcirc.Rcheck/00check.log: getSeq invertStrand select strand subjectHits ./Ularcirc.Rcheck/00check.log:* checking Rd files ... OK ./Ularcirc.Rcheck/00check.log:* checking Rd metadata ... OK ./Ularcirc.Rcheck/00check.log:* checking Rd cross-references ... OK ./Ularcirc.Rcheck/00check.log:* checking for missing documentation entries ... OK ./Ularcirc.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./Ularcirc.Rcheck/00check.log:* checking Rd \usage sections ... OK ./Ularcirc.Rcheck/00check.log:* checking Rd contents ... OK ./Ularcirc.Rcheck/00check.log:* checking for unstated dependencies in examples ... WARNING ./Ularcirc.Rcheck/00check.log:'::' or ':::' import not declared from: ‘BiocManager’ ./Ularcirc.Rcheck/00check.log:'library' or 'require' call not declared from: ‘BiocManager’ ./Ularcirc.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./Ularcirc.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./Ularcirc.Rcheck/00check.log:* checking examples ... OK ./Ularcirc.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... NOTE ./Ularcirc.Rcheck/00check.log:'library' or 'require' call not declared from: ‘BiocStyle’ ./Ularcirc.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./Ularcirc.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./Ularcirc.Rcheck/00check.log: ‘Ularcirc.rmd’using ‘UTF-8’... OK ./Ularcirc.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./Ularcirc.Rcheck/00check.log:* checking PDF version of manual ... OK ./Ularcirc.Rcheck/00check.log:* DONE ./Ularcirc.Rcheck/00check.log:Status: 1 WARNING, 4 NOTEs