R version 3.5.2 (2018-12-20) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 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 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] BiocManager_1.30.4 compiler_3.5.2 tools_3.5.2 > BiocManager::install() Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20) > BiocManager::valid() FALSE antaresViz_0.15.0.tar.gz ./antaresViz.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/antaresViz.Rcheck’ ./antaresViz.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./antaresViz.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./antaresViz.Rcheck/00check.log:* using session charset: UTF-8 ./antaresViz.Rcheck/00check.log:* checking for file ‘antaresViz/DESCRIPTION’ ... OK ./antaresViz.Rcheck/00check.log:* checking extension type ... Package ./antaresViz.Rcheck/00check.log:* this is package ‘antaresViz’ version ‘0.15.0’ ./antaresViz.Rcheck/00check.log:* package encoding: UTF-8 ./antaresViz.Rcheck/00check.log:* checking package namespace information ... OK ./antaresViz.Rcheck/00check.log:* checking package dependencies ... OK ./antaresViz.Rcheck/00check.log:* checking if this is a source package ... OK ./antaresViz.Rcheck/00check.log:* checking if there is a namespace ... OK ./antaresViz.Rcheck/00check.log:* checking for executable files ... OK ./antaresViz.Rcheck/00check.log:* checking for hidden files and directories ... OK ./antaresViz.Rcheck/00check.log:* checking for portable file names ... OK ./antaresViz.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./antaresViz.Rcheck/00check.log:* checking whether package ‘antaresViz’ can be installed ... OK ./antaresViz.Rcheck/00check.log:* checking installed package size ... OK ./antaresViz.Rcheck/00check.log:* checking package directory ... OK ./antaresViz.Rcheck/00check.log:* checking ‘build’ directory ... OK ./antaresViz.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./antaresViz.Rcheck/00check.log:* checking top-level files ... OK ./antaresViz.Rcheck/00check.log:* checking for left-over files ... OK ./antaresViz.Rcheck/00check.log:* checking index information ... OK ./antaresViz.Rcheck/00check.log:* checking package subdirectories ... OK ./antaresViz.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./antaresViz.Rcheck/00check.log:* checking R files for syntax errors ... OK ./antaresViz.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./antaresViz.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./antaresViz.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./antaresViz.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./antaresViz.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./antaresViz.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./antaresViz.Rcheck/00check.log:* checking dependencies in R code ... OK ./antaresViz.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./antaresViz.Rcheck/00check.log:* checking replacement functions ... OK ./antaresViz.Rcheck/00check.log:* checking foreign function calls ... OK ./antaresViz.Rcheck/00check.log:* checking R code for possible problems ... OK ./antaresViz.Rcheck/00check.log:* checking Rd files ... OK ./antaresViz.Rcheck/00check.log:* checking Rd metadata ... OK ./antaresViz.Rcheck/00check.log:* checking Rd cross-references ... OK ./antaresViz.Rcheck/00check.log:* checking for missing documentation entries ... OK ./antaresViz.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./antaresViz.Rcheck/00check.log:* checking Rd \usage sections ... OK ./antaresViz.Rcheck/00check.log:* checking Rd contents ... OK ./antaresViz.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./antaresViz.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./antaresViz.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./antaresViz.Rcheck/00check.log:* checking examples ... OK ./antaresViz.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./antaresViz.Rcheck/00check.log:* checking tests ... ERROR ./antaresViz.Rcheck/00check.log: Running ‘testthat.R’ ./antaresViz.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./antaresViz.Rcheck/00check.log:Last 13 lines of output: ./antaresViz.Rcheck/00check.log: hydroStorage = hydroStorage, hydroStorageMaxPower = hydroStorageMaxPower, reserve = reserve, ./antaresViz.Rcheck/00check.log: linkCapacity = linkCapacity, mustRun = mustRun, thermalModulation = thermalModulation, ./antaresViz.Rcheck/00check.log: select = select, mcYears = mcYears, timeStep = timeStep[1], showProgress = showProgress, ./antaresViz.Rcheck/00check.log: simplify = simplify) ./antaresViz.Rcheck/00check.log: 6: .loadAreas(areas = areas, fid = fid, select = select$areas, mcYears = mcYears, GP = GP, ./antaresViz.Rcheck/00check.log: mcType = mcType, synthesis = synthesis, simplify = simplify, attrib = attrib) ./antaresViz.Rcheck/00check.log: 7: areas[, `:=`(c(names(tim)), tim)] ./antaresViz.Rcheck/00check.log: 8: `[.data.table`(areas, , `:=`(c(names(tim)), tim)) ./antaresViz.Rcheck/00check.log: ./antaresViz.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./antaresViz.Rcheck/00check.log: OK: 243 SKIPPED: 3 FAILED: 1 ./antaresViz.Rcheck/00check.log: 1. Error: (unknown) (@test-plotMap.R#3) ./antaresViz.Rcheck/00check.log: ./antaresViz.Rcheck/00check.log: Error: testthat unit tests failed ./antaresViz.Rcheck/00check.log: Execution halted ./antaresViz.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./antaresViz.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./antaresViz.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./antaresViz.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./antaresViz.Rcheck/00check.log:* checking PDF version of manual ... OK ./antaresViz.Rcheck/00check.log:* DONE ./antaresViz.Rcheck/00check.log:Status: 1 ERROR expss_0.8.10.tar.gz ./expss.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/expss.Rcheck’ ./expss.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./expss.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./expss.Rcheck/00check.log:* using session charset: UTF-8 ./expss.Rcheck/00check.log:* checking for file ‘expss/DESCRIPTION’ ... OK ./expss.Rcheck/00check.log:* checking extension type ... Package ./expss.Rcheck/00check.log:* this is package ‘expss’ version ‘0.8.10’ ./expss.Rcheck/00check.log:* checking package namespace information ... OK ./expss.Rcheck/00check.log:* checking package dependencies ... OK ./expss.Rcheck/00check.log:* checking if this is a source package ... OK ./expss.Rcheck/00check.log:* checking if there is a namespace ... OK ./expss.Rcheck/00check.log:* checking for executable files ... OK ./expss.Rcheck/00check.log:* checking for hidden files and directories ... OK ./expss.Rcheck/00check.log:* checking for portable file names ... OK ./expss.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./expss.Rcheck/00check.log:* checking whether package ‘expss’ can be installed ... OK ./expss.Rcheck/00check.log:* checking installed package size ... OK ./expss.Rcheck/00check.log:* checking package directory ... OK ./expss.Rcheck/00check.log:* checking ‘build’ directory ... OK ./expss.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./expss.Rcheck/00check.log:* checking top-level files ... OK ./expss.Rcheck/00check.log:* checking for left-over files ... OK ./expss.Rcheck/00check.log:* checking index information ... OK ./expss.Rcheck/00check.log:* checking package subdirectories ... OK ./expss.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./expss.Rcheck/00check.log:* checking R files for syntax errors ... OK ./expss.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./expss.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./expss.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./expss.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./expss.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./expss.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./expss.Rcheck/00check.log:* checking dependencies in R code ... OK ./expss.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./expss.Rcheck/00check.log:* checking replacement functions ... OK ./expss.Rcheck/00check.log:* checking foreign function calls ... OK ./expss.Rcheck/00check.log:* checking R code for possible problems ... OK ./expss.Rcheck/00check.log:* checking Rd files ... OK ./expss.Rcheck/00check.log:* checking Rd metadata ... OK ./expss.Rcheck/00check.log:* checking Rd cross-references ... OK ./expss.Rcheck/00check.log:* checking for missing documentation entries ... OK ./expss.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./expss.Rcheck/00check.log:* checking Rd \usage sections ... OK ./expss.Rcheck/00check.log:* checking Rd contents ... OK ./expss.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./expss.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./expss.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./expss.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./expss.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./expss.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./expss.Rcheck/00check.log:* checking examples ... OK ./expss.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./expss.Rcheck/00check.log:* checking tests ... ERROR ./expss.Rcheck/00check.log: Running ‘testthat.R’ ./expss.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./expss.Rcheck/00check.log:Last 13 lines of output: ./expss.Rcheck/00check.log: Set default dataset to 'mtcars' ./expss.Rcheck/00check.log: Set default dataset to 'ir' ./expss.Rcheck/00check.log: Set default dataset to 'def' ./expss.Rcheck/00check.log: Set default dataset to 'dfs' ./expss.Rcheck/00check.log: Default dataset disabled. ./expss.Rcheck/00check.log: Set default dataset to 'sh1' ./expss.Rcheck/00check.log: Set default dataset to 'd_iris' ./expss.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════ ./expss.Rcheck/00check.log: OK: 2542 SKIPPED: 1 FAILED: 2 ./expss.Rcheck/00check.log: 1. Error: (unknown) (@test_cro_fun_df_extended.R#151) ./expss.Rcheck/00check.log: 2. Error: (unknown) (@test_cro_fun_extended.R#267) ./expss.Rcheck/00check.log: ./expss.Rcheck/00check.log: Error: testthat unit tests failed ./expss.Rcheck/00check.log: In addition: There were 44 warnings (use warnings() to see them) ./expss.Rcheck/00check.log: Execution halted ./expss.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./expss.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./expss.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./expss.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./expss.Rcheck/00check.log:* checking PDF version of manual ... OK ./expss.Rcheck/00check.log:* DONE ./expss.Rcheck/00check.log:Status: 1 ERROR iml_0.8.1.tar.gz ./iml.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/iml.Rcheck’ ./iml.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./iml.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./iml.Rcheck/00check.log:* using session charset: UTF-8 ./iml.Rcheck/00check.log:* checking for file ‘iml/DESCRIPTION’ ... OK ./iml.Rcheck/00check.log:* checking extension type ... Package ./iml.Rcheck/00check.log:* this is package ‘iml’ version ‘0.8.1’ ./iml.Rcheck/00check.log:* checking package namespace information ... OK ./iml.Rcheck/00check.log:* checking package dependencies ... OK ./iml.Rcheck/00check.log:* checking if this is a source package ... OK ./iml.Rcheck/00check.log:* checking if there is a namespace ... OK ./iml.Rcheck/00check.log:* checking for executable files ... OK ./iml.Rcheck/00check.log:* checking for hidden files and directories ... OK ./iml.Rcheck/00check.log:* checking for portable file names ... OK ./iml.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./iml.Rcheck/00check.log:* checking whether package ‘iml’ can be installed ... OK ./iml.Rcheck/00check.log:* checking installed package size ... OK ./iml.Rcheck/00check.log:* checking package directory ... OK ./iml.Rcheck/00check.log:* checking ‘build’ directory ... OK ./iml.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./iml.Rcheck/00check.log:* checking top-level files ... OK ./iml.Rcheck/00check.log:* checking for left-over files ... OK ./iml.Rcheck/00check.log:* checking index information ... OK ./iml.Rcheck/00check.log:* checking package subdirectories ... OK ./iml.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./iml.Rcheck/00check.log:* checking R files for syntax errors ... OK ./iml.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./iml.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./iml.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./iml.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./iml.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./iml.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./iml.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./iml.Rcheck/00check.log:Namespace in Imports field not imported from: ‘prediction’ ./iml.Rcheck/00check.log: All declared Imports should be used. ./iml.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./iml.Rcheck/00check.log:* checking replacement functions ... OK ./iml.Rcheck/00check.log:* checking foreign function calls ... OK ./iml.Rcheck/00check.log:* checking R code for possible problems ... OK ./iml.Rcheck/00check.log:* checking Rd files ... OK ./iml.Rcheck/00check.log:* checking Rd metadata ... OK ./iml.Rcheck/00check.log:* checking Rd cross-references ... OK ./iml.Rcheck/00check.log:* checking for missing documentation entries ... OK ./iml.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./iml.Rcheck/00check.log:* checking Rd \usage sections ... OK ./iml.Rcheck/00check.log:* checking Rd contents ... OK ./iml.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./iml.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./iml.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./iml.Rcheck/00check.log:* checking examples ... OK ./iml.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./iml.Rcheck/00check.log:* checking tests ... ERROR ./iml.Rcheck/00check.log: Running ‘testthat.R’ ./iml.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./iml.Rcheck/00check.log:Last 13 lines of output: ./iml.Rcheck/00check.log: 1: Shapley$new(predictor2, x.interest, sample.size = 400) at testthat/test-Shapley.R:37 ./iml.Rcheck/00check.log: 2: .subset2(public_bind_env, "initialize")(...) ./iml.Rcheck/00check.log: 3: self$run() ./iml.Rcheck/00check.log: 4: data.frame(private$aggregate()) ./iml.Rcheck/00check.log: 5: private$aggregate() ./iml.Rcheck/00check.log: 6: `$<-`(`*tmp*`, feature.value, value = c("a=1", "b=10", "c=a", "d=A")) ./iml.Rcheck/00check.log: 7: `$<-.data.table`(`*tmp*`, feature.value, value = c("a=1", "b=10", "c=a", "d=A")) ./iml.Rcheck/00check.log: 8: `[<-.data.table`(x, j = name, value = value) ./iml.Rcheck/00check.log: ./iml.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./iml.Rcheck/00check.log: OK: 474 SKIPPED: 0 FAILED: 1 ./iml.Rcheck/00check.log: 1. Error: Shapley works for multiple output (@test-Shapley.R#37) ./iml.Rcheck/00check.log: ./iml.Rcheck/00check.log: Error: testthat unit tests failed ./iml.Rcheck/00check.log: Execution halted ./iml.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./iml.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./iml.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./iml.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./iml.Rcheck/00check.log:* checking PDF version of manual ... OK ./iml.Rcheck/00check.log:* DONE ./iml.Rcheck/00check.log:Status: 1 ERROR, 1 NOTE irg_0.1.0.tar.gz ./irg.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/irg.Rcheck’ ./irg.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./irg.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./irg.Rcheck/00check.log:* using session charset: UTF-8 ./irg.Rcheck/00check.log:* checking for file ‘irg/DESCRIPTION’ ... OK ./irg.Rcheck/00check.log:* this is package ‘irg’ version ‘0.1.0’ ./irg.Rcheck/00check.log:* package encoding: UTF-8 ./irg.Rcheck/00check.log:* checking package namespace information ... OK ./irg.Rcheck/00check.log:* checking package dependencies ... OK ./irg.Rcheck/00check.log:* checking if this is a source package ... OK ./irg.Rcheck/00check.log:* checking if there is a namespace ... OK ./irg.Rcheck/00check.log:* checking for executable files ... OK ./irg.Rcheck/00check.log:* checking for hidden files and directories ... OK ./irg.Rcheck/00check.log:* checking for portable file names ... OK ./irg.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./irg.Rcheck/00check.log:* checking whether package ‘irg’ can be installed ... OK ./irg.Rcheck/00check.log:* checking installed package size ... OK ./irg.Rcheck/00check.log:* checking package directory ... OK ./irg.Rcheck/00check.log:* checking ‘build’ directory ... OK ./irg.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./irg.Rcheck/00check.log:* checking top-level files ... OK ./irg.Rcheck/00check.log:* checking for left-over files ... OK ./irg.Rcheck/00check.log:* checking index information ... OK ./irg.Rcheck/00check.log:* checking package subdirectories ... OK ./irg.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./irg.Rcheck/00check.log:* checking R files for syntax errors ... OK ./irg.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./irg.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./irg.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./irg.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./irg.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./irg.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./irg.Rcheck/00check.log:* checking dependencies in R code ... OK ./irg.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./irg.Rcheck/00check.log:* checking replacement functions ... OK ./irg.Rcheck/00check.log:* checking foreign function calls ... OK ./irg.Rcheck/00check.log:* checking R code for possible problems ... OK ./irg.Rcheck/00check.log:* checking Rd files ... OK ./irg.Rcheck/00check.log:* checking Rd metadata ... OK ./irg.Rcheck/00check.log:* checking Rd cross-references ... OK ./irg.Rcheck/00check.log:* checking for missing documentation entries ... OK ./irg.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./irg.Rcheck/00check.log:* checking Rd \usage sections ... OK ./irg.Rcheck/00check.log:* checking Rd contents ... OK ./irg.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./irg.Rcheck/00check.log:* checking R/sysdata.rda ... OK ./irg.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./irg.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./irg.Rcheck/00check.log:* checking examples ... ERROR ./irg.Rcheck/00check.log:Running examples in ‘irg-Ex.R’ failed ./irg.Rcheck/00check.log:The error most likely occurred in: ./irg.Rcheck/00check.log:> ### Name: calc_irg ./irg.Rcheck/00check.log:> ### Title: IRG ./irg.Rcheck/00check.log:> ### Aliases: calc_irg ./irg.Rcheck/00check.log:> ./irg.Rcheck/00check.log:> ### ** Examples ./irg.Rcheck/00check.log:> ./irg.Rcheck/00check.log:> # Load data.table ./irg.Rcheck/00check.log:> library(data.table) ./irg.Rcheck/00check.log:> ./irg.Rcheck/00check.log:> # Read in example data ./irg.Rcheck/00check.log:> ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg")) ./irg.Rcheck/00check.log:> ./irg.Rcheck/00check.log:> # Filter and scale NDVI time series ./irg.Rcheck/00check.log:> filter_ndvi(ndvi) ./irg.Rcheck/00check.log:> scale_doy(ndvi) ./irg.Rcheck/00check.log:> scale_ndvi(ndvi) ./irg.Rcheck/00check.log:> ./irg.Rcheck/00check.log:> # Guess starting parameters ./irg.Rcheck/00check.log:> model_start(ndvi) ./irg.Rcheck/00check.log:> ./irg.Rcheck/00check.log:> # Double logistic model parameters given starting parameters for nls ./irg.Rcheck/00check.log:> mods <- model_params( ./irg.Rcheck/00check.log:+ ndvi, ./irg.Rcheck/00check.log:+ return = 'models', ./irg.Rcheck/00check.log:+ xmidS = 'xmidS_start', ./irg.Rcheck/00check.log:+ xmidA = 'xmidA_start', ./irg.Rcheck/00check.log:+ scalS = 0.05, ./irg.Rcheck/00check.log:+ scalA = 0.01 ./irg.Rcheck/00check.log:+ ) ./irg.Rcheck/00check.log:> ./irg.Rcheck/00check.log:> # Fit double logistic curve to NDVI time series ./irg.Rcheck/00check.log:> fit <- model_ndvi(mods, observed = FALSE) ./irg.Rcheck/00check.log:Error in `[.data.table`(DT[rep(1:.N, each = 366)], , `:=`(t, julseq$t)) : ./irg.Rcheck/00check.log: Supplied 366 items to be assigned to 40260 items of column 't'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./irg.Rcheck/00check.log:Calls: model_ndvi -> [ -> [.data.table ./irg.Rcheck/00check.log:Execution halted ./irg.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./irg.Rcheck/00check.log:* checking tests ... ERROR ./irg.Rcheck/00check.log: Running ‘testthat.R’ ./irg.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./irg.Rcheck/00check.log:Last 13 lines of output: ./irg.Rcheck/00check.log: > library(irg) ./irg.Rcheck/00check.log: > ./irg.Rcheck/00check.log: > test_check("irg") ./irg.Rcheck/00check.log: ── 1. Error: model_ndvi works (@test-model.R#140) ───────────────────────────── ./irg.Rcheck/00check.log: Supplied 366 items to be assigned to 420900 items of column 't'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./irg.Rcheck/00check.log: 1: model_ndvi(ndvi, observed = FALSE) at testthat/test-model.R:140 ./irg.Rcheck/00check.log: 2: DT[rep(1:.N, each = 366)][, `:=`(t, julseq$t)] ./irg.Rcheck/00check.log: 3: `[.data.table`(DT[rep(1:.N, each = 366)], , `:=`(t, julseq$t)) ./irg.Rcheck/00check.log: ./irg.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./irg.Rcheck/00check.log: OK: 57 SKIPPED: 0 FAILED: 1 ./irg.Rcheck/00check.log: 1. Error: model_ndvi works (@test-model.R#140) ./irg.Rcheck/00check.log: ./irg.Rcheck/00check.log: Error: testthat unit tests failed ./irg.Rcheck/00check.log: Execution halted ./irg.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./irg.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./irg.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./irg.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./irg.Rcheck/00check.log:Error in re-building vignettes: ./irg.Rcheck/00check.log: ... ./irg.Rcheck/00check.log: SummaryQA details: ./irg.Rcheck/00check.log: • 0 - Good data, use with confidence ./irg.Rcheck/00check.log: • 1 - Marginal data, useful but look at detailed QA for more ./irg.Rcheck/00check.log: information ./irg.Rcheck/00check.log: • 2 - Pixel covered with snow/ice ./irg.Rcheck/00check.log: • 3 - Pixel is cloudy ./irg.Rcheck/00check.log:_E_x_a_m_p_l_e_s: ./irg.Rcheck/00check.log: # Load data.table ./irg.Rcheck/00check.log: library(data.table) ./irg.Rcheck/00check.log: ./irg.Rcheck/00check.log: # Read example data ./irg.Rcheck/00check.log: ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg")) ./irg.Rcheck/00check.log: ./irg.Rcheck/00check.log:Quitting from lines 173-174 (getting-started-with-irg.Rmd) ./irg.Rcheck/00check.log:Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics: ./irg.Rcheck/00check.log:Supplied 366 items to be assigned to 925980 items of column 't'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./irg.Rcheck/00check.log:Execution halted ./irg.Rcheck/00check.log:* checking PDF version of manual ... OK ./irg.Rcheck/00check.log:* DONE ./irg.Rcheck/00check.log:Status: 2 ERRORs, 1 WARNING popEpi_0.4.5.tar.gz ./popEpi.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/popEpi.Rcheck’ ./popEpi.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./popEpi.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./popEpi.Rcheck/00check.log:* using session charset: UTF-8 ./popEpi.Rcheck/00check.log:* checking for file ‘popEpi/DESCRIPTION’ ... OK ./popEpi.Rcheck/00check.log:* this is package ‘popEpi’ version ‘0.4.5’ ./popEpi.Rcheck/00check.log:* package encoding: UTF-8 ./popEpi.Rcheck/00check.log:* checking package namespace information ... OK ./popEpi.Rcheck/00check.log:* checking package dependencies ... OK ./popEpi.Rcheck/00check.log:* checking if this is a source package ... OK ./popEpi.Rcheck/00check.log:* checking if there is a namespace ... OK ./popEpi.Rcheck/00check.log:* checking for executable files ... OK ./popEpi.Rcheck/00check.log:* checking for hidden files and directories ... OK ./popEpi.Rcheck/00check.log:* checking for portable file names ... OK ./popEpi.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./popEpi.Rcheck/00check.log:* checking whether package ‘popEpi’ can be installed ... OK ./popEpi.Rcheck/00check.log:* checking installed package size ... OK ./popEpi.Rcheck/00check.log:* checking package directory ... OK ./popEpi.Rcheck/00check.log:* checking ‘build’ directory ... OK ./popEpi.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./popEpi.Rcheck/00check.log:* checking top-level files ... OK ./popEpi.Rcheck/00check.log:* checking for left-over files ... OK ./popEpi.Rcheck/00check.log:* checking index information ... OK ./popEpi.Rcheck/00check.log:* checking package subdirectories ... OK ./popEpi.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./popEpi.Rcheck/00check.log:* checking R files for syntax errors ... OK ./popEpi.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./popEpi.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./popEpi.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./popEpi.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./popEpi.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./popEpi.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./popEpi.Rcheck/00check.log:* checking dependencies in R code ... OK ./popEpi.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./popEpi.Rcheck/00check.log:* checking replacement functions ... OK ./popEpi.Rcheck/00check.log:* checking foreign function calls ... OK ./popEpi.Rcheck/00check.log:* checking R code for possible problems ... OK ./popEpi.Rcheck/00check.log:* checking Rd files ... OK ./popEpi.Rcheck/00check.log:* checking Rd metadata ... OK ./popEpi.Rcheck/00check.log:* checking Rd cross-references ... OK ./popEpi.Rcheck/00check.log:* checking for missing documentation entries ... OK ./popEpi.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./popEpi.Rcheck/00check.log:* checking Rd \usage sections ... OK ./popEpi.Rcheck/00check.log:* checking Rd contents ... OK ./popEpi.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./popEpi.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./popEpi.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./popEpi.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./popEpi.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./popEpi.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./popEpi.Rcheck/00check.log:* checking examples ... ERROR ./popEpi.Rcheck/00check.log:Running examples in ‘popEpi-Ex.R’ failed ./popEpi.Rcheck/00check.log:The error most likely occurred in: ./popEpi.Rcheck/00check.log:> ### Name: lines.survtab ./popEpi.Rcheck/00check.log:> ### Title: 'lines' method for survtab objects ./popEpi.Rcheck/00check.log:> ### Aliases: lines.survtab ./popEpi.Rcheck/00check.log:> ./popEpi.Rcheck/00check.log:> ### ** Examples ./popEpi.Rcheck/00check.log:> ./popEpi.Rcheck/00check.log:> data(sire) ./popEpi.Rcheck/00check.log:> data(sibr) ./popEpi.Rcheck/00check.log:> si <- rbind(sire, sibr) ./popEpi.Rcheck/00check.log:> si$period <- cut(si$dg_date, as.Date(c("1993-01-01", "2004-01-01", "2013-01-01")), right = FALSE) ./popEpi.Rcheck/00check.log:> si$cancer <- c(rep("rectal", nrow(sire)), rep("breast", nrow(sibr))) ./popEpi.Rcheck/00check.log:> x <- lexpand(si, birth = bi_date, entry = dg_date, exit = ex_date, ./popEpi.Rcheck/00check.log:+ status = status %in% 1:2, ./popEpi.Rcheck/00check.log:+ fot = 0:5, aggre = list(cancer, period, fot)) ./popEpi.Rcheck/00check.log:dropped 17 rows where entry == exit ./popEpi.Rcheck/00check.log:> st <- survtab_ag(fot ~ cancer + period, data = x, ./popEpi.Rcheck/00check.log:+ surv.method = "lifetable", surv.type = "surv.obs") ./popEpi.Rcheck/00check.log:Error in `[.data.table`(data, , `:=`("Tstop", surv.breaks[-1])) : ./popEpi.Rcheck/00check.log: Supplied 5 items to be assigned to 20 items of column 'Tstop'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./popEpi.Rcheck/00check.log:Calls: survtab_ag -> [ -> [.data.table ./popEpi.Rcheck/00check.log:Execution halted ./popEpi.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./popEpi.Rcheck/00check.log:* checking tests ... ERROR ./popEpi.Rcheck/00check.log: Running ‘testthat.R’ ./popEpi.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./popEpi.Rcheck/00check.log:Last 13 lines of output: ./popEpi.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./popEpi.Rcheck/00check.log: OK: 218 SKIPPED: 41 FAILED: 10 ./popEpi.Rcheck/00check.log: 1. Error: sir_exp and sir_ag and sir_lexis are working (@test_sir.R#324) ./popEpi.Rcheck/00check.log: 2. Error: removing consecutively bad surv.ints is logical w/ & w/out adjusting (@test_survtab_bad_surv_ints.R#16) ./popEpi.Rcheck/00check.log: 3. Error: survtab_ag messages & results due to non-consecutively bad surv.ints are OK (@test_survtab_bad_surv_ints.R#85) ./popEpi.Rcheck/00check.log: 4. Error: survtab works with more complicated estimation (@test_survtab_observed.R#121) ./popEpi.Rcheck/00check.log: 5. Error: relative survivals about the same as relsurv's (@test_survtab_relative.R#59) ./popEpi.Rcheck/00check.log: 6. Error: getCall & formula methods for survtab work (@test_survtab_usage.R#259) ./popEpi.Rcheck/00check.log: 7. Error: survtab_ag allows for certain arguments to be length > 1 (@test_survtab_usage.R#284) ./popEpi.Rcheck/00check.log: 8. Error: update() works with survtab objects (@test_survtab_usage.R#325) ./popEpi.Rcheck/00check.log: 9. Error: internal weights work as intended (@test_survtab_usage.R#373) ./popEpi.Rcheck/00check.log: 10. Error: comp_pp_weighted_figures produces intended results (@test_utils.R#209) ./popEpi.Rcheck/00check.log: ./popEpi.Rcheck/00check.log: Error: testthat unit tests failed ./popEpi.Rcheck/00check.log: Execution halted ./popEpi.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./popEpi.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./popEpi.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./popEpi.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./popEpi.Rcheck/00check.log:Error in re-building vignettes: ./popEpi.Rcheck/00check.log: ... ./popEpi.Rcheck/00check.log:Quitting from lines 38-67 (survtab_examples.Rmd) ./popEpi.Rcheck/00check.log:Error: processing vignette 'survtab_examples.Rmd' failed with diagnostics: ./popEpi.Rcheck/00check.log:Supplied 60 items to be assigned to 120 items of column 'Tstop'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./popEpi.Rcheck/00check.log:Execution halted ./popEpi.Rcheck/00check.log:* checking PDF version of manual ... OK ./popEpi.Rcheck/00check.log:* DONE ./popEpi.Rcheck/00check.log:Status: 2 ERRORs, 1 WARNING rAmCharts_2.1.9.tar.gz ./rAmCharts.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/rAmCharts.Rcheck’ ./rAmCharts.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./rAmCharts.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./rAmCharts.Rcheck/00check.log:* using session charset: UTF-8 ./rAmCharts.Rcheck/00check.log:* checking for file ‘rAmCharts/DESCRIPTION’ ... OK ./rAmCharts.Rcheck/00check.log:* this is package ‘rAmCharts’ version ‘2.1.9’ ./rAmCharts.Rcheck/00check.log:* checking package namespace information ... OK ./rAmCharts.Rcheck/00check.log:* checking package dependencies ... OK ./rAmCharts.Rcheck/00check.log:* checking if this is a source package ... OK ./rAmCharts.Rcheck/00check.log:* checking if there is a namespace ... OK ./rAmCharts.Rcheck/00check.log:* checking for executable files ... OK ./rAmCharts.Rcheck/00check.log:* checking for hidden files and directories ... OK ./rAmCharts.Rcheck/00check.log:* checking for portable file names ... OK ./rAmCharts.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./rAmCharts.Rcheck/00check.log:* checking whether package ‘rAmCharts’ can be installed ... OK ./rAmCharts.Rcheck/00check.log:* checking installed package size ... NOTE ./rAmCharts.Rcheck/00check.log: installed size is 14.3Mb ./rAmCharts.Rcheck/00check.log: sub-directories of 1Mb or more: ./rAmCharts.Rcheck/00check.log: api 3.2Mb ./rAmCharts.Rcheck/00check.log: htmlwidgets 9.3Mb ./rAmCharts.Rcheck/00check.log:* checking package directory ... OK ./rAmCharts.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./rAmCharts.Rcheck/00check.log:* checking top-level files ... OK ./rAmCharts.Rcheck/00check.log:* checking for left-over files ... OK ./rAmCharts.Rcheck/00check.log:* checking index information ... OK ./rAmCharts.Rcheck/00check.log:* checking package subdirectories ... OK ./rAmCharts.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./rAmCharts.Rcheck/00check.log:* checking R files for syntax errors ... OK ./rAmCharts.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./rAmCharts.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./rAmCharts.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./rAmCharts.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./rAmCharts.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./rAmCharts.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./rAmCharts.Rcheck/00check.log:* checking dependencies in R code ... OK ./rAmCharts.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./rAmCharts.Rcheck/00check.log:* checking replacement functions ... OK ./rAmCharts.Rcheck/00check.log:* checking foreign function calls ... OK ./rAmCharts.Rcheck/00check.log:* checking R code for possible problems ... OK ./rAmCharts.Rcheck/00check.log:* checking Rd files ... OK ./rAmCharts.Rcheck/00check.log:* checking Rd metadata ... OK ./rAmCharts.Rcheck/00check.log:* checking Rd cross-references ... OK ./rAmCharts.Rcheck/00check.log:* checking for missing documentation entries ... OK ./rAmCharts.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./rAmCharts.Rcheck/00check.log:* checking Rd \usage sections ... OK ./rAmCharts.Rcheck/00check.log:* checking Rd contents ... OK ./rAmCharts.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./rAmCharts.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./rAmCharts.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./rAmCharts.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./rAmCharts.Rcheck/00check.log:* checking examples ... OK ./rAmCharts.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./rAmCharts.Rcheck/00check.log:* checking tests ... ERROR ./rAmCharts.Rcheck/00check.log: Running ‘testthat.R’ ./rAmCharts.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./rAmCharts.Rcheck/00check.log:Last 13 lines of output: ./rAmCharts.Rcheck/00check.log: 8: eval_bare(get_expr(quo), get_env(quo)) ./rAmCharts.Rcheck/00check.log: 9: amBoxplot(x, use.cols = FALSE, col = c("blue", "red")) at testthat/test_amBoxplot.R:42 ./rAmCharts.Rcheck/00check.log: 10: amBoxplot.matrix(x, use.cols = FALSE, col = c("blue", "red")) ./rAmCharts.Rcheck/00check.log: 11: .finalDataBoxplot(res, col = col, precision = precision) ./rAmCharts.Rcheck/00check.log: 12: `$<-`(`*tmp*`, "color", value = c("blue", "red")) ./rAmCharts.Rcheck/00check.log: 13: `$<-.data.table`(`*tmp*`, "color", value = c("blue", "red")) ./rAmCharts.Rcheck/00check.log: 14: `[<-.data.table`(x, j = name, value = value) ./rAmCharts.Rcheck/00check.log: ./rAmCharts.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./rAmCharts.Rcheck/00check.log: OK: 267 SKIPPED: 0 FAILED: 2 ./rAmCharts.Rcheck/00check.log: 1. Error: Formula (@test_amBoxplot.R#5) ./rAmCharts.Rcheck/00check.log: 2. Error: matrix (@test_amBoxplot.R#36) ./rAmCharts.Rcheck/00check.log: ./rAmCharts.Rcheck/00check.log: Error: testthat unit tests failed ./rAmCharts.Rcheck/00check.log: Execution halted ./rAmCharts.Rcheck/00check.log:* checking PDF version of manual ... OK ./rAmCharts.Rcheck/00check.log:* DONE ./rAmCharts.Rcheck/00check.log:Status: 1 ERROR, 1 NOTE riskRegression_2018.10.03.tar.gz ./riskRegression.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/riskRegression.Rcheck’ ./riskRegression.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./riskRegression.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./riskRegression.Rcheck/00check.log:* using session charset: UTF-8 ./riskRegression.Rcheck/00check.log:* checking for file ‘riskRegression/DESCRIPTION’ ... OK ./riskRegression.Rcheck/00check.log:* checking extension type ... Package ./riskRegression.Rcheck/00check.log:* this is package ‘riskRegression’ version ‘2018.10.03’ ./riskRegression.Rcheck/00check.log:* checking package namespace information ... OK ./riskRegression.Rcheck/00check.log:* checking package dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking if this is a source package ... OK ./riskRegression.Rcheck/00check.log:* checking if there is a namespace ... OK ./riskRegression.Rcheck/00check.log:* checking for executable files ... OK ./riskRegression.Rcheck/00check.log:* checking for hidden files and directories ... OK ./riskRegression.Rcheck/00check.log:* checking for portable file names ... OK ./riskRegression.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./riskRegression.Rcheck/00check.log:* checking whether package ‘riskRegression’ can be installed ... OK ./riskRegression.Rcheck/00check.log:* checking installed package size ... OK ./riskRegression.Rcheck/00check.log:* checking package directory ... OK ./riskRegression.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./riskRegression.Rcheck/00check.log:* checking top-level files ... OK ./riskRegression.Rcheck/00check.log:* checking for left-over files ... OK ./riskRegression.Rcheck/00check.log:* checking index information ... OK ./riskRegression.Rcheck/00check.log:* checking package subdirectories ... OK ./riskRegression.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./riskRegression.Rcheck/00check.log:* checking R files for syntax errors ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./riskRegression.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./riskRegression.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./riskRegression.Rcheck/00check.log:* checking dependencies in R code ... OK ./riskRegression.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./riskRegression.Rcheck/00check.log:* checking replacement functions ... OK ./riskRegression.Rcheck/00check.log:* checking foreign function calls ... OK ./riskRegression.Rcheck/00check.log:* checking R code for possible problems ... OK ./riskRegression.Rcheck/00check.log:* checking Rd files ... OK ./riskRegression.Rcheck/00check.log:* checking Rd metadata ... OK ./riskRegression.Rcheck/00check.log:* checking Rd cross-references ... OK ./riskRegression.Rcheck/00check.log:* checking for missing documentation entries ... OK ./riskRegression.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./riskRegression.Rcheck/00check.log:* checking Rd \usage sections ... OK ./riskRegression.Rcheck/00check.log:* checking Rd contents ... OK ./riskRegression.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./riskRegression.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./riskRegression.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./riskRegression.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./riskRegression.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./riskRegression.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./riskRegression.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./riskRegression.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./riskRegression.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./riskRegression.Rcheck/00check.log:* checking compiled code ... OK ./riskRegression.Rcheck/00check.log:* checking examples ... ERROR ./riskRegression.Rcheck/00check.log:Running examples in ‘riskRegression-Ex.R’ failed ./riskRegression.Rcheck/00check.log:The error most likely occurred in: ./riskRegression.Rcheck/00check.log:> ### Name: autoplot.ate ./riskRegression.Rcheck/00check.log:> ### Title: Plot Average Risks ./riskRegression.Rcheck/00check.log:> ### Aliases: autoplot.ate ./riskRegression.Rcheck/00check.log:> ./riskRegression.Rcheck/00check.log:> ### ** Examples ./riskRegression.Rcheck/00check.log:> ./riskRegression.Rcheck/00check.log:> library(survival) ./riskRegression.Rcheck/00check.log:> library(rms) ./riskRegression.Rcheck/00check.log:Loading required package: Hmisc ./riskRegression.Rcheck/00check.log:Loading required package: lattice ./riskRegression.Rcheck/00check.log:Loading required package: Formula ./riskRegression.Rcheck/00check.log:Attaching package: ‘Hmisc’ ./riskRegression.Rcheck/00check.log:The following objects are masked from ‘package:base’: ./riskRegression.Rcheck/00check.log: format.pval, units ./riskRegression.Rcheck/00check.log:Loading required package: SparseM ./riskRegression.Rcheck/00check.log:Attaching package: ‘SparseM’ ./riskRegression.Rcheck/00check.log:The following object is masked from ‘package:base’: ./riskRegression.Rcheck/00check.log: backsolve ./riskRegression.Rcheck/00check.log:> ./riskRegression.Rcheck/00check.log:> #### simulate data #### ./riskRegression.Rcheck/00check.log:> n <- 1e2 ./riskRegression.Rcheck/00check.log:> set.seed(10) ./riskRegression.Rcheck/00check.log:> dtS <- sampleData(n,outcome="survival") ./riskRegression.Rcheck/00check.log:> ./riskRegression.Rcheck/00check.log:> ./riskRegression.Rcheck/00check.log:> #### Cox model #### ./riskRegression.Rcheck/00check.log:> fit <- cph(formula = Surv(time,event)~ X1+X2,data=dtS,y=TRUE,x=TRUE) ./riskRegression.Rcheck/00check.log:> ./riskRegression.Rcheck/00check.log:> #### Average treatment effect #### ./riskRegression.Rcheck/00check.log:> seqTimes <- sort(unique(fit$y[,1])) ./riskRegression.Rcheck/00check.log:> seqTimes5 <- seqTimes[seqTimes>5 & seqTimes<10] ./riskRegression.Rcheck/00check.log:> ateFit <- ate(fit, data = dtS, treatment = "X1", contrasts = NULL, ./riskRegression.Rcheck/00check.log:+ times = seqTimes, B = 0, band = TRUE, nsim.band = 500, y = TRUE, ./riskRegression.Rcheck/00check.log:+ mc.cores=1) ./riskRegression.Rcheck/00check.log:Error in `[.data.table`(object$meanRisk, vec.index.tempo, `:=`(c("meanRisk.quantileBand"), : ./riskRegression.Rcheck/00check.log: Supplied 2 items to be assigned to 200 items of column 'meanRisk.quantileBand'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./riskRegression.Rcheck/00check.log:Calls: ate ... -> confint.ate -> confintIID.ate -> [ -> [.data.table ./riskRegression.Rcheck/00check.log:Execution halted ./riskRegression.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./riskRegression.Rcheck/00check.log:* checking tests ... ERROR ./riskRegression.Rcheck/00check.log: Running ‘test-AUC.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-BinomialRegression.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-BrierScore.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-CauseSpecificCoxRegression.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-FineGrayRegression.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-ate.R’ ./riskRegression.Rcheck/00check.log:Running the tests in ‘tests/test-ate.R’ failed. ./riskRegression.Rcheck/00check.log:Last 13 lines of output: ./riskRegression.Rcheck/00check.log: + res <- ate(fit, data = df, treatment = "X1", contrasts = NULL, ./riskRegression.Rcheck/00check.log: + times = 7, cause = 1, B = 0, mc.cores=1) ./riskRegression.Rcheck/00check.log: + }) ./riskRegression.Rcheck/00check.log: Error: Test failed: 'CSC model bootstrap' ./riskRegression.Rcheck/00check.log: * Supplied 100 items to be assigned to 101 items of column 'X1'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./riskRegression.Rcheck/00check.log: 1: `$<-`(`*tmp*`, X1, value = structure(c(1L, 1L, 2L, 3L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, ./riskRegression.Rcheck/00check.log: 2L, 3L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 3L, 2L, ./riskRegression.Rcheck/00check.log: 1L, 2L, 1L, 2L, 3L, 2L, 3L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 1L, 1L, 1L, 2L, ./riskRegression.Rcheck/00check.log: 2L, 2L, 1L, 2L, 3L, 3L, 1L, 2L, 3L, 2L, 1L, 2L, 2L, 3L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, ./riskRegression.Rcheck/00check.log: 1L, 1L, 1L, 1L, 2L, 3L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, ./riskRegression.Rcheck/00check.log: 1L, 1L, 2L, 1L, 1L), .Label = c("T0", "T1", "T2"), class = "factor")) ./riskRegression.Rcheck/00check.log: 2: `$<-.data.table`(`*tmp*`, X1, value = structure(c(1L, 1L, 2L, 3L, 2L, 2L, 1L, 1L, ./riskRegression.Rcheck/00check.log: 2L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, ./riskRegression.Rcheck/00check.log: 1L, ./riskRegression.Rcheck/00check.log: Execution halted ./riskRegression.Rcheck/00check.log:* checking PDF version of manual ... OK ./riskRegression.Rcheck/00check.log:* DONE ./riskRegression.Rcheck/00check.log:Status: 2 ERRORs scopr_0.3.2.tar.gz ./scopr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/scopr.Rcheck’ ./scopr.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./scopr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./scopr.Rcheck/00check.log:* using session charset: UTF-8 ./scopr.Rcheck/00check.log:* checking for file ‘scopr/DESCRIPTION’ ... OK ./scopr.Rcheck/00check.log:* this is package ‘scopr’ version ‘0.3.2’ ./scopr.Rcheck/00check.log:* package encoding: UTF-8 ./scopr.Rcheck/00check.log:* checking package namespace information ... OK ./scopr.Rcheck/00check.log:* checking package dependencies ... OK ./scopr.Rcheck/00check.log:* checking if this is a source package ... OK ./scopr.Rcheck/00check.log:* checking if there is a namespace ... OK ./scopr.Rcheck/00check.log:* checking for executable files ... OK ./scopr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./scopr.Rcheck/00check.log:* checking for portable file names ... OK ./scopr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./scopr.Rcheck/00check.log:* checking whether package ‘scopr’ can be installed ... OK ./scopr.Rcheck/00check.log:* checking installed package size ... OK ./scopr.Rcheck/00check.log:* checking package directory ... OK ./scopr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./scopr.Rcheck/00check.log:* checking top-level files ... OK ./scopr.Rcheck/00check.log:* checking for left-over files ... OK ./scopr.Rcheck/00check.log:* checking index information ... OK ./scopr.Rcheck/00check.log:* checking package subdirectories ... OK ./scopr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./scopr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./scopr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./scopr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./scopr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./scopr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./scopr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./scopr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./scopr.Rcheck/00check.log:* checking dependencies in R code ... OK ./scopr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./scopr.Rcheck/00check.log:* checking replacement functions ... OK ./scopr.Rcheck/00check.log:* checking foreign function calls ... OK ./scopr.Rcheck/00check.log:* checking R code for possible problems ... OK ./scopr.Rcheck/00check.log:* checking Rd files ... OK ./scopr.Rcheck/00check.log:* checking Rd metadata ... OK ./scopr.Rcheck/00check.log:* checking Rd cross-references ... OK ./scopr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./scopr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./scopr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./scopr.Rcheck/00check.log:* checking Rd contents ... OK ./scopr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./scopr.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./scopr.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./scopr.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./scopr.Rcheck/00check.log:* checking examples ... OK ./scopr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./scopr.Rcheck/00check.log:* checking tests ... ERROR ./scopr.Rcheck/00check.log: Running ‘testthat.R’ ./scopr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./scopr.Rcheck/00check.log:Last 13 lines of output: ./scopr.Rcheck/00check.log: 1: query[, `:=`(treatment, 1:3)] at testthat/test-link_ethocope_metadata.R:58 ./scopr.Rcheck/00check.log: 2: `[.data.table`(query, , `:=`(treatment, 1:3)) at testthat/test-link_ethocope_metadata.R:58 ./scopr.Rcheck/00check.log: ./scopr.Rcheck/00check.log: ── 2. Error: parse_query with date, machine name, and ROIs (@test-link_ethoscope ./scopr.Rcheck/00check.log: Supplied 3 items to be assigned to 15 items of column 'treatment'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./scopr.Rcheck/00check.log: 1: query[, `:=`(treatment, 1:3)] at testthat/test-link_ethoscope_metadata_remote.R:48 ./scopr.Rcheck/00check.log: 2: `[.data.table`(query, , `:=`(treatment, 1:3)) at testthat/test-link_ethoscope_metadata_remote.R:48 ./scopr.Rcheck/00check.log: ./scopr.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./scopr.Rcheck/00check.log: OK: 45 SKIPPED: 0 FAILED: 2 ./scopr.Rcheck/00check.log: 1. Error: link_ethoscope_metadata with date, machine name, and ROIs (@test-link_ethocope_metadata.R#58) ./scopr.Rcheck/00check.log: 2. Error: parse_query with date, machine name, and ROIs (@test-link_ethoscope_metadata_remote.R#48) ./scopr.Rcheck/00check.log: ./scopr.Rcheck/00check.log: Error: testthat unit tests failed ./scopr.Rcheck/00check.log: Execution halted ./scopr.Rcheck/00check.log:* checking PDF version of manual ... OK ./scopr.Rcheck/00check.log:* DONE ./scopr.Rcheck/00check.log:Status: 1 ERROR sdcTable_0.26.tar.gz ./sdcTable.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/sdcTable.Rcheck’ ./sdcTable.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./sdcTable.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./sdcTable.Rcheck/00check.log:* using session charset: UTF-8 ./sdcTable.Rcheck/00check.log:* checking for file ‘sdcTable/DESCRIPTION’ ... OK ./sdcTable.Rcheck/00check.log:* this is package ‘sdcTable’ version ‘0.26’ ./sdcTable.Rcheck/00check.log:* package encoding: UTF-8 ./sdcTable.Rcheck/00check.log:* checking package namespace information ... OK ./sdcTable.Rcheck/00check.log:* checking package dependencies ... OK ./sdcTable.Rcheck/00check.log:* checking if this is a source package ... OK ./sdcTable.Rcheck/00check.log:* checking if there is a namespace ... OK ./sdcTable.Rcheck/00check.log:* checking for executable files ... OK ./sdcTable.Rcheck/00check.log:* checking for hidden files and directories ... OK ./sdcTable.Rcheck/00check.log:* checking for portable file names ... OK ./sdcTable.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./sdcTable.Rcheck/00check.log:* checking whether package ‘sdcTable’ can be installed ... OK ./sdcTable.Rcheck/00check.log:* checking installed package size ... NOTE ./sdcTable.Rcheck/00check.log: installed size is 5.5Mb ./sdcTable.Rcheck/00check.log: sub-directories of 1Mb or more: ./sdcTable.Rcheck/00check.log: R 1.3Mb ./sdcTable.Rcheck/00check.log: doc 3.2Mb ./sdcTable.Rcheck/00check.log:* checking package directory ... OK ./sdcTable.Rcheck/00check.log:* checking ‘build’ directory ... OK ./sdcTable.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./sdcTable.Rcheck/00check.log:* checking top-level files ... OK ./sdcTable.Rcheck/00check.log:* checking for left-over files ... OK ./sdcTable.Rcheck/00check.log:* checking index information ... OK ./sdcTable.Rcheck/00check.log:* checking package subdirectories ... OK ./sdcTable.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./sdcTable.Rcheck/00check.log:* checking R files for syntax errors ... OK ./sdcTable.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./sdcTable.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./sdcTable.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./sdcTable.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./sdcTable.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./sdcTable.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./sdcTable.Rcheck/00check.log:* checking dependencies in R code ... OK ./sdcTable.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./sdcTable.Rcheck/00check.log:* checking replacement functions ... OK ./sdcTable.Rcheck/00check.log:* checking foreign function calls ... OK ./sdcTable.Rcheck/00check.log:* checking R code for possible problems ... OK ./sdcTable.Rcheck/00check.log:* checking Rd files ... OK ./sdcTable.Rcheck/00check.log:* checking Rd metadata ... OK ./sdcTable.Rcheck/00check.log:* checking Rd cross-references ... OK ./sdcTable.Rcheck/00check.log:* checking for missing documentation entries ... OK ./sdcTable.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./sdcTable.Rcheck/00check.log:* checking Rd \usage sections ... OK ./sdcTable.Rcheck/00check.log:* checking Rd contents ... OK ./sdcTable.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./sdcTable.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./sdcTable.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./sdcTable.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./sdcTable.Rcheck/00check.log:* checking line endings in shell scripts ... OK ./sdcTable.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./sdcTable.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./sdcTable.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./sdcTable.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./sdcTable.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./sdcTable.Rcheck/00check.log:* checking compiled code ... OK ./sdcTable.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./sdcTable.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./sdcTable.Rcheck/00check.log:* checking examples ... ERROR ./sdcTable.Rcheck/00check.log:Running examples in ‘sdcTable-Ex.R’ failed ./sdcTable.Rcheck/00check.log:The error most likely occurred in: ./sdcTable.Rcheck/00check.log:> ### Name: createArgusInput ./sdcTable.Rcheck/00check.log:> ### Title: createArgusInput ./sdcTable.Rcheck/00check.log:> ### Aliases: createArgusInput ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> ### ** Examples ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> # loading micro data from sdcTable ./sdcTable.Rcheck/00check.log:> data("microData1", package="sdcTable") ./sdcTable.Rcheck/00check.log:> microData1$num1 <- rnorm(mean=100, sd=25, nrow(microData1)) ./sdcTable.Rcheck/00check.log:> microData1$num2 <- round(rnorm(mean=500, sd=125, nrow(microData1)),2) ./sdcTable.Rcheck/00check.log:> microData1$weight <- sample(10:100, nrow(microData1), replace=TRUE) ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> dim.region <- data.frame( ./sdcTable.Rcheck/00check.log:+ levels=c('@','@@','@@','@@','@@'), ./sdcTable.Rcheck/00check.log:+ codes=c('Total', 'A','B','C','D'), ./sdcTable.Rcheck/00check.log:+ stringsAsFactors=FALSE) ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> dim.region_dupl <- data.frame( ./sdcTable.Rcheck/00check.log:+ levels=c('@','@@','@@','@@@','@@','@@','@@@'), ./sdcTable.Rcheck/00check.log:+ codes=c('Total', 'A','B','b1','C','D','d1'), ./sdcTable.Rcheck/00check.log:+ stringsAsFactors=FALSE) ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> dim.gender <- data.frame( ./sdcTable.Rcheck/00check.log:+ levels=c('@','@@','@@'), ./sdcTable.Rcheck/00check.log:+ codes=c('Total', 'male','female'), ./sdcTable.Rcheck/00check.log:+ stringsAsFactors=FALSE) ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> dimList <- list(region=dim.region, gender=dim.gender) ./sdcTable.Rcheck/00check.log:> dimList_dupl <- list(region=dim.region_dupl, gender=dim.gender) ./sdcTable.Rcheck/00check.log:> dimVarInd <- c(1,2) ./sdcTable.Rcheck/00check.log:> numVarInd <- 3:5 ./sdcTable.Rcheck/00check.log:> sampWeightInd <- 6 ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> freqVarInd <- weightInd <- NULL ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> ## creating an object of class \code{sdcProblem-class} ./sdcTable.Rcheck/00check.log:> obj <- makeProblem( ./sdcTable.Rcheck/00check.log:+ data=microData1, ./sdcTable.Rcheck/00check.log:+ dimList=dimList, ./sdcTable.Rcheck/00check.log:+ dimVarInd=dimVarInd, ./sdcTable.Rcheck/00check.log:+ freqVarInd=freqVarInd, ./sdcTable.Rcheck/00check.log:+ numVarInd=numVarInd, ./sdcTable.Rcheck/00check.log:+ weightInd=weightInd, ./sdcTable.Rcheck/00check.log:+ sampWeightInd=sampWeightInd) ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> ## creating an object of class \code{sdcProblem-class} containing "duplicated" codes ./sdcTable.Rcheck/00check.log:> obj_dupl <- makeProblem( ./sdcTable.Rcheck/00check.log:+ data=microData1, ./sdcTable.Rcheck/00check.log:+ dimList=dimList_dupl, ./sdcTable.Rcheck/00check.log:+ dimVarInd=dimVarInd, ./sdcTable.Rcheck/00check.log:+ freqVarInd=freqVarInd, ./sdcTable.Rcheck/00check.log:+ numVarInd=numVarInd, ./sdcTable.Rcheck/00check.log:+ weightInd=weightInd, ./sdcTable.Rcheck/00check.log:+ sampWeightInd=sampWeightInd) ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> ## create primary suppression rules ./sdcTable.Rcheck/00check.log:> primSuppRules <- list() ./sdcTable.Rcheck/00check.log:> primSuppRules[[1]] <- list(type="freq", n=5, rg=20) ./sdcTable.Rcheck/00check.log:> primSuppRules[[2]] <- list(type="p", n=5, p=20) ./sdcTable.Rcheck/00check.log:> # other supported formats are: ./sdcTable.Rcheck/00check.log:> # list(type="nk", n=5, k=20) ./sdcTable.Rcheck/00check.log:> # list(type="zero", rg=5) ./sdcTable.Rcheck/00check.log:> # list(type="mis", val=1) ./sdcTable.Rcheck/00check.log:> # list(type="wgt", val=1) ./sdcTable.Rcheck/00check.log:> # list(type="man", val=20) ./sdcTable.Rcheck/00check.log:> ./sdcTable.Rcheck/00check.log:> ## create batchInput object ./sdcTable.Rcheck/00check.log:> bO_md1 <- createArgusInput(obj, typ="microdata", path=getwd(), solver="FREE", method="OPT", ./sdcTable.Rcheck/00check.log:+ primSuppRules=primSuppRules, responsevar="num1") ./sdcTable.Rcheck/00check.log:> bO_td1 <- createArgusInput(obj, typ="tabular", path=getwd(), solver="FREE", method="OPT") ./sdcTable.Rcheck/00check.log:> bO_td2 <- createArgusInput(obj_dupl, typ="tabular", path=getwd(), solver="FREE", method="OPT") ./sdcTable.Rcheck/00check.log:Error in `[.data.table`(mdat, , `:=`(lpl, get.problemInstance(pI, "LPL"))) : ./sdcTable.Rcheck/00check.log: Supplied 15 items to be assigned to 21 items of column 'lpl'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./sdcTable.Rcheck/00check.log:Calls: createArgusInput ... tauBatchInput_table -> create_tabdata_and_metadata -> [ -> [.data.table ./sdcTable.Rcheck/00check.log:Execution halted ./sdcTable.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./sdcTable.Rcheck/00check.log:* checking tests ... OK ./sdcTable.Rcheck/00check.log: Running ‘testthat.R’ ./sdcTable.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./sdcTable.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./sdcTable.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./sdcTable.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./sdcTable.Rcheck/00check.log:* checking PDF version of manual ... OK ./sdcTable.Rcheck/00check.log:* DONE ./sdcTable.Rcheck/00check.log:Status: 1 ERROR, 1 NOTE simstudy_0.1.10.tar.gz ./simstudy.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/simstudy.Rcheck’ ./simstudy.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./simstudy.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./simstudy.Rcheck/00check.log:* using session charset: UTF-8 ./simstudy.Rcheck/00check.log:* checking for file ‘simstudy/DESCRIPTION’ ... OK ./simstudy.Rcheck/00check.log:* checking extension type ... Package ./simstudy.Rcheck/00check.log:* this is package ‘simstudy’ version ‘0.1.10’ ./simstudy.Rcheck/00check.log:* package encoding: UTF-8 ./simstudy.Rcheck/00check.log:* checking package namespace information ... OK ./simstudy.Rcheck/00check.log:* checking package dependencies ... OK ./simstudy.Rcheck/00check.log:* checking if this is a source package ... OK ./simstudy.Rcheck/00check.log:* checking if there is a namespace ... OK ./simstudy.Rcheck/00check.log:* checking for executable files ... OK ./simstudy.Rcheck/00check.log:* checking for hidden files and directories ... OK ./simstudy.Rcheck/00check.log:* checking for portable file names ... OK ./simstudy.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./simstudy.Rcheck/00check.log:* checking whether package ‘simstudy’ can be installed ... OK ./simstudy.Rcheck/00check.log:* checking installed package size ... OK ./simstudy.Rcheck/00check.log:* checking package directory ... OK ./simstudy.Rcheck/00check.log:* checking ‘build’ directory ... OK ./simstudy.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./simstudy.Rcheck/00check.log:* checking top-level files ... OK ./simstudy.Rcheck/00check.log:* checking for left-over files ... OK ./simstudy.Rcheck/00check.log:* checking index information ... OK ./simstudy.Rcheck/00check.log:* checking package subdirectories ... OK ./simstudy.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./simstudy.Rcheck/00check.log:* checking R files for syntax errors ... OK ./simstudy.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./simstudy.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./simstudy.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./simstudy.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./simstudy.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./simstudy.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./simstudy.Rcheck/00check.log:* checking dependencies in R code ... OK ./simstudy.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./simstudy.Rcheck/00check.log:* checking replacement functions ... OK ./simstudy.Rcheck/00check.log:* checking foreign function calls ... OK ./simstudy.Rcheck/00check.log:* checking R code for possible problems ... OK ./simstudy.Rcheck/00check.log:* checking Rd files ... OK ./simstudy.Rcheck/00check.log:* checking Rd metadata ... OK ./simstudy.Rcheck/00check.log:* checking Rd cross-references ... OK ./simstudy.Rcheck/00check.log:* checking for missing documentation entries ... OK ./simstudy.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./simstudy.Rcheck/00check.log:* checking Rd \usage sections ... OK ./simstudy.Rcheck/00check.log:* checking Rd contents ... OK ./simstudy.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./simstudy.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./simstudy.Rcheck/00check.log:* checking compiled code ... OK ./simstudy.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./simstudy.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./simstudy.Rcheck/00check.log:* checking examples ... ERROR ./simstudy.Rcheck/00check.log:Running examples in ‘simstudy-Ex.R’ failed ./simstudy.Rcheck/00check.log:The error most likely occurred in: ./simstudy.Rcheck/00check.log:> ### Name: addMultiFac ./simstudy.Rcheck/00check.log:> ### Title: Add multi-factorial data ./simstudy.Rcheck/00check.log:> ### Aliases: addMultiFac ./simstudy.Rcheck/00check.log:> ./simstudy.Rcheck/00check.log:> ### ** Examples ./simstudy.Rcheck/00check.log:> ./simstudy.Rcheck/00check.log:> defD <-defData(varname = "x", formula = 0, variance = 1) ./simstudy.Rcheck/00check.log:> ./simstudy.Rcheck/00check.log:> DT <- genData(360, defD) ./simstudy.Rcheck/00check.log:> DT <- addMultiFac(DT, nFactors = 3, levels = c(2, 3, 3), colNames = c("A", "B", "C")) ./simstudy.Rcheck/00check.log:Error in `[.data.table`(dnew, , `:=`(count, c(1:each))) : ./simstudy.Rcheck/00check.log: Supplied 20 items to be assigned to 360 items of column 'count'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./simstudy.Rcheck/00check.log:Calls: addMultiFac -> [ -> [.data.table ./simstudy.Rcheck/00check.log:Execution halted ./simstudy.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./simstudy.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./simstudy.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./simstudy.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./simstudy.Rcheck/00check.log:* checking PDF version of manual ... OK ./simstudy.Rcheck/00check.log:* DONE ./simstudy.Rcheck/00check.log:Status: 1 ERROR vardpoor_0.12.0.tar.gz ./vardpoor.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/vardpoor.Rcheck’ ./vardpoor.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./vardpoor.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./vardpoor.Rcheck/00check.log:* using session charset: UTF-8 ./vardpoor.Rcheck/00check.log:* checking for file ‘vardpoor/DESCRIPTION’ ... OK ./vardpoor.Rcheck/00check.log:* checking extension type ... Package ./vardpoor.Rcheck/00check.log:* this is package ‘vardpoor’ version ‘0.12.0’ ./vardpoor.Rcheck/00check.log:* package encoding: latin1 ./vardpoor.Rcheck/00check.log:* checking package namespace information ... OK ./vardpoor.Rcheck/00check.log:* checking package dependencies ... OK ./vardpoor.Rcheck/00check.log:* checking if this is a source package ... OK ./vardpoor.Rcheck/00check.log:* checking if there is a namespace ... OK ./vardpoor.Rcheck/00check.log:* checking for executable files ... OK ./vardpoor.Rcheck/00check.log:* checking for hidden files and directories ... OK ./vardpoor.Rcheck/00check.log:* checking for portable file names ... OK ./vardpoor.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./vardpoor.Rcheck/00check.log:* checking whether package ‘vardpoor’ can be installed ... OK ./vardpoor.Rcheck/00check.log:* checking installed package size ... OK ./vardpoor.Rcheck/00check.log:* checking package directory ... OK ./vardpoor.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./vardpoor.Rcheck/00check.log:* checking top-level files ... OK ./vardpoor.Rcheck/00check.log:* checking for left-over files ... OK ./vardpoor.Rcheck/00check.log:* checking index information ... OK ./vardpoor.Rcheck/00check.log:* checking package subdirectories ... OK ./vardpoor.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./vardpoor.Rcheck/00check.log:* checking R files for syntax errors ... OK ./vardpoor.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./vardpoor.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./vardpoor.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./vardpoor.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./vardpoor.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./vardpoor.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./vardpoor.Rcheck/00check.log:* checking dependencies in R code ... OK ./vardpoor.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./vardpoor.Rcheck/00check.log:* checking replacement functions ... OK ./vardpoor.Rcheck/00check.log:* checking foreign function calls ... OK ./vardpoor.Rcheck/00check.log:* checking R code for possible problems ... OK ./vardpoor.Rcheck/00check.log:* checking Rd files ... OK ./vardpoor.Rcheck/00check.log:* checking Rd metadata ... OK ./vardpoor.Rcheck/00check.log:* checking Rd cross-references ... OK ./vardpoor.Rcheck/00check.log:* checking for missing documentation entries ... OK ./vardpoor.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./vardpoor.Rcheck/00check.log:* checking Rd \usage sections ... OK ./vardpoor.Rcheck/00check.log:* checking Rd contents ... OK ./vardpoor.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./vardpoor.Rcheck/00check.log:* checking examples ... ERROR ./vardpoor.Rcheck/00check.log:Running examples in ‘vardpoor-Ex.R’ failed ./vardpoor.Rcheck/00check.log:The error most likely occurred in: ./vardpoor.Rcheck/00check.log:> ### Name: vardannual ./vardpoor.Rcheck/00check.log:> ### Title: Variance estimation for measures of annual net change or annual ./vardpoor.Rcheck/00check.log:> ### for single and multistage stage cluster sampling designs ./vardpoor.Rcheck/00check.log:> ### Aliases: vardannual ./vardpoor.Rcheck/00check.log:> ### Keywords: vardchangannual ./vardpoor.Rcheck/00check.log:> ./vardpoor.Rcheck/00check.log:> ### ** Examples ./vardpoor.Rcheck/00check.log:> ./vardpoor.Rcheck/00check.log:> ./vardpoor.Rcheck/00check.log:> ### Example ./vardpoor.Rcheck/00check.log:> data("eusilc") ./vardpoor.Rcheck/00check.log:> set.seed(1) ./vardpoor.Rcheck/00check.log:> eusilc1 <- eusilc[1 : 100,] ./vardpoor.Rcheck/00check.log:> set.seed(1) ./vardpoor.Rcheck/00check.log:> data <- data.table(rbind(eusilc1, eusilc1), ./vardpoor.Rcheck/00check.log:+ year = c(rep(2010, nrow(eusilc1)), ./vardpoor.Rcheck/00check.log:+ rep(2011, nrow(eusilc1)))) ./vardpoor.Rcheck/00check.log:> data[, country := "AT"] ./vardpoor.Rcheck/00check.log:> data[, quarter:= .I - 4 * trunc((.I - 1) / 4)] ./vardpoor.Rcheck/00check.log:> data[age < 0, age:= 0] ./vardpoor.Rcheck/00check.log:> PSU <- data[, .N, keyby = "db030"][, N:= NULL] ./vardpoor.Rcheck/00check.log:> PSU[, PSU:= trunc(runif(nrow(PSU), 0, 5))] ./vardpoor.Rcheck/00check.log:> data <- merge(data, PSU, all = TRUE, by = "db030") ./vardpoor.Rcheck/00check.log:> PSU <- eusilc <- NULL ./vardpoor.Rcheck/00check.log:> data[, strata := c("XXXX")] ./vardpoor.Rcheck/00check.log:> ./vardpoor.Rcheck/00check.log:> data[, employed := trunc(runif(nrow(data), 0, 2))] ./vardpoor.Rcheck/00check.log:> data[, unemployed := trunc(runif(nrow(data), 0, 2))] ./vardpoor.Rcheck/00check.log:> data[, labour_force := employed + unemployed] ./vardpoor.Rcheck/00check.log:> data[, id_lv2 := paste0("V", .I)] ./vardpoor.Rcheck/00check.log:> ./vardpoor.Rcheck/00check.log:> result <- vardannual(Y = "employed", H = "strata", ./vardpoor.Rcheck/00check.log:+ PSU = "PSU", w_final = "rb050", ./vardpoor.Rcheck/00check.log:+ ID_level1 = "db030", ID_level2 = "id_lv2", ./vardpoor.Rcheck/00check.log:+ Dom = NULL, Z = NULL, country = "country", ./vardpoor.Rcheck/00check.log:+ years = "year", subperiods = "quarter", ./vardpoor.Rcheck/00check.log:+ dataset = data, percentratio = 100, ./vardpoor.Rcheck/00check.log:+ confidence = 0.95, method = "cros") ./vardpoor.Rcheck/00check.log:Error in get("V1") : object 'V1' not found ./vardpoor.Rcheck/00check.log:Calls: vardannual ... vardchanges_calculation -> [ -> [.data.table -> eval -> eval -> paste0 -> get ./vardpoor.Rcheck/00check.log:Execution halted ./vardpoor.Rcheck/00check.log:* checking PDF version of manual ... OK ./vardpoor.Rcheck/00check.log:* DONE ./vardpoor.Rcheck/00check.log:Status: 1 ERROR multistateutils_1.2.0.tar.gz ./multistateutils.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/multistateutils.Rcheck’ ./multistateutils.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./multistateutils.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./multistateutils.Rcheck/00check.log:* using session charset: UTF-8 ./multistateutils.Rcheck/00check.log:* checking for file ‘multistateutils/DESCRIPTION’ ... OK ./multistateutils.Rcheck/00check.log:* checking extension type ... Package ./multistateutils.Rcheck/00check.log:* this is package ‘multistateutils’ version ‘1.2.0’ ./multistateutils.Rcheck/00check.log:* checking package namespace information ... OK ./multistateutils.Rcheck/00check.log:* checking package dependencies ... OK ./multistateutils.Rcheck/00check.log:* checking if this is a source package ... OK ./multistateutils.Rcheck/00check.log:* checking if there is a namespace ... OK ./multistateutils.Rcheck/00check.log:* checking for executable files ... OK ./multistateutils.Rcheck/00check.log:* checking for hidden files and directories ... OK ./multistateutils.Rcheck/00check.log:* checking for portable file names ... OK ./multistateutils.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./multistateutils.Rcheck/00check.log:* checking whether package ‘multistateutils’ can be installed ... OK ./multistateutils.Rcheck/00check.log:* checking installed package size ... OK ./multistateutils.Rcheck/00check.log:* checking package directory ... OK ./multistateutils.Rcheck/00check.log:* checking ‘build’ directory ... OK ./multistateutils.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./multistateutils.Rcheck/00check.log:* checking top-level files ... OK ./multistateutils.Rcheck/00check.log:* checking for left-over files ... OK ./multistateutils.Rcheck/00check.log:* checking index information ... OK ./multistateutils.Rcheck/00check.log:* checking package subdirectories ... OK ./multistateutils.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./multistateutils.Rcheck/00check.log:* checking R files for syntax errors ... OK ./multistateutils.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./multistateutils.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./multistateutils.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./multistateutils.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./multistateutils.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./multistateutils.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./multistateutils.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./multistateutils.Rcheck/00check.log:Namespaces in Imports field not imported from: ./multistateutils.Rcheck/00check.log: ‘Rcpp’ ‘survival’ ./multistateutils.Rcheck/00check.log: All declared Imports should be used. ./multistateutils.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./multistateutils.Rcheck/00check.log:* checking replacement functions ... OK ./multistateutils.Rcheck/00check.log:* checking foreign function calls ... OK ./multistateutils.Rcheck/00check.log:* checking R code for possible problems ... OK ./multistateutils.Rcheck/00check.log:* checking Rd files ... OK ./multistateutils.Rcheck/00check.log:* checking Rd metadata ... OK ./multistateutils.Rcheck/00check.log:* checking Rd cross-references ... OK ./multistateutils.Rcheck/00check.log:* checking for missing documentation entries ... OK ./multistateutils.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./multistateutils.Rcheck/00check.log:* checking Rd \usage sections ... OK ./multistateutils.Rcheck/00check.log:* checking Rd contents ... OK ./multistateutils.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./multistateutils.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./multistateutils.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./multistateutils.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./multistateutils.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./multistateutils.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./multistateutils.Rcheck/00check.log:* checking compiled code ... OK ./multistateutils.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./multistateutils.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./multistateutils.Rcheck/00check.log:* checking examples ... OK ./multistateutils.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./multistateutils.Rcheck/00check.log:* checking tests ... OK ./multistateutils.Rcheck/00check.log: Running ‘testthat.R’ ./multistateutils.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./multistateutils.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./multistateutils.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./multistateutils.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./multistateutils.Rcheck/00check.log:Error in re-building vignettes: ./multistateutils.Rcheck/00check.log: ... ./multistateutils.Rcheck/00check.log:Quitting from lines 147-148 (Examples.Rmd) ./multistateutils.Rcheck/00check.log:Error: processing vignette 'Examples.Rmd' failed with diagnostics: ./multistateutils.Rcheck/00check.log:Supplied 9 items to be assigned to 900000 items of column 'end_time'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./multistateutils.Rcheck/00check.log:Execution halted ./multistateutils.Rcheck/00check.log:* checking PDF version of manual ... OK ./multistateutils.Rcheck/00check.log:* DONE ./multistateutils.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE POUMM_2.1.2.tar.gz ./POUMM.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/POUMM.Rcheck’ ./POUMM.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./POUMM.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./POUMM.Rcheck/00check.log:* using session charset: UTF-8 ./POUMM.Rcheck/00check.log:* checking for file ‘POUMM/DESCRIPTION’ ... OK ./POUMM.Rcheck/00check.log:* checking extension type ... Package ./POUMM.Rcheck/00check.log:* this is package ‘POUMM’ version ‘2.1.2’ ./POUMM.Rcheck/00check.log:* package encoding: UTF-8 ./POUMM.Rcheck/00check.log:* checking package namespace information ... OK ./POUMM.Rcheck/00check.log:* checking package dependencies ... OK ./POUMM.Rcheck/00check.log:* checking if this is a source package ... OK ./POUMM.Rcheck/00check.log:* checking if there is a namespace ... OK ./POUMM.Rcheck/00check.log:* checking for executable files ... OK ./POUMM.Rcheck/00check.log:* checking for hidden files and directories ... OK ./POUMM.Rcheck/00check.log:* checking for portable file names ... OK ./POUMM.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./POUMM.Rcheck/00check.log:* checking whether package ‘POUMM’ can be installed ... OK ./POUMM.Rcheck/00check.log:* checking installed package size ... NOTE ./POUMM.Rcheck/00check.log: installed size is 6.8Mb ./POUMM.Rcheck/00check.log: sub-directories of 1Mb or more: ./POUMM.Rcheck/00check.log: libs 5.6Mb ./POUMM.Rcheck/00check.log:* checking package directory ... OK ./POUMM.Rcheck/00check.log:* checking ‘build’ directory ... OK ./POUMM.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./POUMM.Rcheck/00check.log:* checking top-level files ... OK ./POUMM.Rcheck/00check.log:* checking for left-over files ... OK ./POUMM.Rcheck/00check.log:* checking index information ... OK ./POUMM.Rcheck/00check.log:* checking package subdirectories ... OK ./POUMM.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./POUMM.Rcheck/00check.log:* checking R files for syntax errors ... OK ./POUMM.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./POUMM.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./POUMM.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./POUMM.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./POUMM.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./POUMM.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./POUMM.Rcheck/00check.log:* checking dependencies in R code ... OK ./POUMM.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./POUMM.Rcheck/00check.log:* checking replacement functions ... OK ./POUMM.Rcheck/00check.log:* checking foreign function calls ... OK ./POUMM.Rcheck/00check.log:* checking R code for possible problems ... OK ./POUMM.Rcheck/00check.log:* checking Rd files ... OK ./POUMM.Rcheck/00check.log:* checking Rd metadata ... OK ./POUMM.Rcheck/00check.log:* checking Rd cross-references ... OK ./POUMM.Rcheck/00check.log:* checking for missing documentation entries ... OK ./POUMM.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./POUMM.Rcheck/00check.log:* checking Rd \usage sections ... OK ./POUMM.Rcheck/00check.log:* checking Rd contents ... OK ./POUMM.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./POUMM.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./POUMM.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./POUMM.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./POUMM.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./POUMM.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./POUMM.Rcheck/00check.log:* checking compiled code ... OK ./POUMM.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./POUMM.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./POUMM.Rcheck/00check.log:* checking examples ... OK ./POUMM.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./POUMM.Rcheck/00check.log:* checking tests ... OK ./POUMM.Rcheck/00check.log: Running ‘test-all.R’ ./POUMM.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./POUMM.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./POUMM.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./POUMM.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./POUMM.Rcheck/00check.log:Error in re-building vignettes: ./POUMM.Rcheck/00check.log: ... ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "loglik", : ./POUMM.Rcheck/00check.log: For loglik calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : ./POUMM.Rcheck/00check.log: 0 (non-NA) cases ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AIC", : ./POUMM.Rcheck/00check.log: For AIC calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : ./POUMM.Rcheck/00check.log: 0 (non-NA) cases ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in FUN(X[[i]], ...) : end value not changed ./POUMM.Rcheck/00check.log:Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AICc", : ./POUMM.Rcheck/00check.log: For AICc calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : ./POUMM.Rcheck/00check.log: 0 (non-NA) cases ./POUMM.Rcheck/00check.log:Quitting from lines 197-199 (InterpretingPOUMM.Rmd) ./POUMM.Rcheck/00check.log:Error: processing vignette 'InterpretingPOUMM.Rmd' failed with diagnostics: ./POUMM.Rcheck/00check.log:Supplied 3 items to be assigned to 48 items of column 'samplePriorMCMC'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./POUMM.Rcheck/00check.log:Execution halted ./POUMM.Rcheck/00check.log:* checking PDF version of manual ... OK ./POUMM.Rcheck/00check.log:* DONE ./POUMM.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE dada2_1.10.1.tar.gz ./dada2.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/dada2.Rcheck’ ./dada2.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./dada2.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./dada2.Rcheck/00check.log:* using session charset: UTF-8 ./dada2.Rcheck/00check.log:* checking for file ‘dada2/DESCRIPTION’ ... OK ./dada2.Rcheck/00check.log:* checking extension type ... Package ./dada2.Rcheck/00check.log:* this is package ‘dada2’ version ‘1.10.1’ ./dada2.Rcheck/00check.log:* checking package namespace information ... OK ./dada2.Rcheck/00check.log:* checking package dependencies ... OK ./dada2.Rcheck/00check.log:* checking if this is a source package ... OK ./dada2.Rcheck/00check.log:* checking if there is a namespace ... OK ./dada2.Rcheck/00check.log:* checking for executable files ... OK ./dada2.Rcheck/00check.log:* checking for hidden files and directories ... NOTE ./dada2.Rcheck/00check.log:Found the following hidden files and directories: ./dada2.Rcheck/00check.log: .travis.yml ./dada2.Rcheck/00check.log:These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ./dada2.Rcheck/00check.log:* checking for portable file names ... OK ./dada2.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./dada2.Rcheck/00check.log:* checking whether package ‘dada2’ can be installed ... OK ./dada2.Rcheck/00check.log:* checking installed package size ... NOTE ./dada2.Rcheck/00check.log: installed size is 9.0Mb ./dada2.Rcheck/00check.log: sub-directories of 1Mb or more: ./dada2.Rcheck/00check.log: doc 1.1Mb ./dada2.Rcheck/00check.log: extdata 1.1Mb ./dada2.Rcheck/00check.log: libs 6.0Mb ./dada2.Rcheck/00check.log:* checking package directory ... OK ./dada2.Rcheck/00check.log:* checking ‘build’ directory ... OK ./dada2.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./dada2.Rcheck/00check.log:* checking top-level files ... OK ./dada2.Rcheck/00check.log:* checking for left-over files ... OK ./dada2.Rcheck/00check.log:* checking index information ... OK ./dada2.Rcheck/00check.log:* checking package subdirectories ... OK ./dada2.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./dada2.Rcheck/00check.log:* checking R files for syntax errors ... OK ./dada2.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./dada2.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./dada2.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./dada2.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./dada2.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./dada2.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./dada2.Rcheck/00check.log:* checking dependencies in R code ... WARNING ./dada2.Rcheck/00check.log:'::' or ':::' import not declared from: ‘BiocManager’ ./dada2.Rcheck/00check.log:'loadNamespace' or 'requireNamespace' call not declared from: ‘BiocManager’ ./dada2.Rcheck/00check.log:Unexported object imported by a ':::' call: ‘ShortRead:::.set_omp_threads’ ./dada2.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./dada2.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./dada2.Rcheck/00check.log:* checking replacement functions ... OK ./dada2.Rcheck/00check.log:* checking foreign function calls ... NOTE ./dada2.Rcheck/00check.log:Foreign function call to a different package: ./dada2.Rcheck/00check.log: .Call(ShortRead:::.set_omp_threads, ...) ./dada2.Rcheck/00check.log:See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. ./dada2.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./dada2.Rcheck/00check.log:bcinstall: no visible global function definition for ‘install.packages’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible global function definition for ‘:=’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘seqF’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘seqR’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘abundance’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘accept’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘als1’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘als2’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘prefer’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘n0R’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘n0F’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘allMismatch’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘mismatch’ ./dada2.Rcheck/00check.log:mergePairsByID: no visible binding for global variable ‘indel’ ./dada2.Rcheck/00check.log:plotErrors: no visible binding for global variable ‘Qual’ ./dada2.Rcheck/00check.log:plotErrors: no visible binding for global variable ‘Observed’ ./dada2.Rcheck/00check.log:plotErrors: no visible binding for global variable ‘Input’ ./dada2.Rcheck/00check.log:plotErrors: no visible binding for global variable ‘Estimated’ ./dada2.Rcheck/00check.log:plotErrors: no visible binding for global variable ‘Nominal’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Cycle’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Score’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Count’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Mean’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Q25’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Q50’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Q75’ ./dada2.Rcheck/00check.log:plotQualityProfile: no visible binding for global variable ‘Cum’ ./dada2.Rcheck/00check.log:samdf_to_qiime2: no visible global function definition for ./dada2.Rcheck/00check.log: ‘write.table’ ./dada2.Rcheck/00check.log:seqtab_to_mothur: no visible global function definition for ./dada2.Rcheck/00check.log: ‘write.table’ ./dada2.Rcheck/00check.log:seqtab_to_mothur: no visible binding for global variable ‘four’ ./dada2.Rcheck/00check.log:seqtab_to_qiime: no visible global function definition for ./dada2.Rcheck/00check.log: ‘write.table’ ./dada2.Rcheck/00check.log:Undefined global functions or variables: ./dada2.Rcheck/00check.log: := Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75 ./dada2.Rcheck/00check.log: Qual Score abundance accept allMismatch als1 als2 four indel ./dada2.Rcheck/00check.log: install.packages mismatch n0F n0R prefer seqF seqR write.table ./dada2.Rcheck/00check.log:Consider adding ./dada2.Rcheck/00check.log: importFrom("utils", "install.packages", "write.table") ./dada2.Rcheck/00check.log:to your NAMESPACE file. ./dada2.Rcheck/00check.log:* checking Rd files ... OK ./dada2.Rcheck/00check.log:* checking Rd metadata ... OK ./dada2.Rcheck/00check.log:* checking Rd cross-references ... OK ./dada2.Rcheck/00check.log:* checking for missing documentation entries ... OK ./dada2.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./dada2.Rcheck/00check.log:* checking Rd \usage sections ... OK ./dada2.Rcheck/00check.log:* checking Rd contents ... OK ./dada2.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./dada2.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./dada2.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./dada2.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./dada2.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./dada2.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./dada2.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./dada2.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... NOTE ./dada2.Rcheck/00check.log:GNU make is a SystemRequirements. ./dada2.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./dada2.Rcheck/00check.log:* checking compiled code ... OK ./dada2.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./dada2.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./dada2.Rcheck/00check.log:* checking examples ... ERROR ./dada2.Rcheck/00check.log:Running examples in ‘dada2-Ex.R’ failed ./dada2.Rcheck/00check.log:The error most likely occurred in: ./dada2.Rcheck/00check.log:> ### Name: mergePairsByID ./dada2.Rcheck/00check.log:> ### Title: Merge forward and reverse reads after DADA denoising, even if ./dada2.Rcheck/00check.log:> ### reads were not originally ordered together. ./dada2.Rcheck/00check.log:> ### Aliases: mergePairsByID ./dada2.Rcheck/00check.log:> ./dada2.Rcheck/00check.log:> ### ** Examples ./dada2.Rcheck/00check.log:> ./dada2.Rcheck/00check.log:> # For the following example files, there are two ways to merge denoised directions. ./dada2.Rcheck/00check.log:> # Because the read sequences are in order, `mergePairs()` works. ./dada2.Rcheck/00check.log:> # `mergePairsByID` always works, ./dada2.Rcheck/00check.log:> # because it uses the read IDs to match denoised pairs. ./dada2.Rcheck/00check.log:> exFileF = system.file("extdata", "sam1F.fastq.gz", package="dada2") ./dada2.Rcheck/00check.log:> exFileR = system.file("extdata", "sam1R.fastq.gz", package="dada2") ./dada2.Rcheck/00check.log:> srF = ShortRead::readFastq(exFileF) ./dada2.Rcheck/00check.log:> srR = ShortRead::readFastq(exFileR) ./dada2.Rcheck/00check.log:> derepF = derepFastq(exFileF) ./dada2.Rcheck/00check.log:> derepR = derepFastq(exFileR) ./dada2.Rcheck/00check.log:> dadaF <- dada(derepF, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE) ./dada2.Rcheck/00check.log:selfConsist step 1 . ./dada2.Rcheck/00check.log: selfConsist step 2 ./dada2.Rcheck/00check.log: selfConsist step 3 ./dada2.Rcheck/00check.log: selfConsist step 4 ./dada2.Rcheck/00check.log:Convergence after 4 rounds. ./dada2.Rcheck/00check.log:> dadaR <- dada(derepR, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE) ./dada2.Rcheck/00check.log:selfConsist step 1 . ./dada2.Rcheck/00check.log: selfConsist step 2 ./dada2.Rcheck/00check.log: selfConsist step 3 ./dada2.Rcheck/00check.log: selfConsist step 4 ./dada2.Rcheck/00check.log:Convergence after 4 rounds. ./dada2.Rcheck/00check.log:> # Run and compare ./dada2.Rcheck/00check.log:> ex1time = system.time({ ./dada2.Rcheck/00check.log:+ ex1 <- mergePairs(dadaF, derepF, dadaR, derepR, verbose = TRUE) ./dada2.Rcheck/00check.log:+ ex1 <- data.table::data.table(ex1) ./dada2.Rcheck/00check.log:+ }) ./dada2.Rcheck/00check.log:1213 paired-reads (in 5 unique pairings) successfully merged out of 1315 (in 13 pairings) input. ./dada2.Rcheck/00check.log:> ex1time ./dada2.Rcheck/00check.log: user system elapsed ./dada2.Rcheck/00check.log: 0.036 0.000 0.035 ./dada2.Rcheck/00check.log:> # The new function, based on read IDs. ./dada2.Rcheck/00check.log:> ex2time = system.time({ ./dada2.Rcheck/00check.log:+ ex2 = dada2:::mergePairsByID(dadaF = dadaF, derepF = derepF, srF = srF, ./dada2.Rcheck/00check.log:+ dadaR = dadaR, derepR = derepR, srR = srR, verbose = TRUE) ./dada2.Rcheck/00check.log:+ }) ./dada2.Rcheck/00check.log:1434 unique forward read IDs. ./dada2.Rcheck/00check.log:1343 unique reverse read IDs. ./dada2.Rcheck/00check.log:1315 paired reads, corresponding to 13 unique pairs that must be assessed for overlap merge ./dada2.Rcheck/00check.log:1213 paired-reads (in 5 unique pairings) successfully merged ./dada2.Rcheck/00check.log:from 1315 read pairs. ./dada2.Rcheck/00check.log:> ex2time ./dada2.Rcheck/00check.log: user system elapsed ./dada2.Rcheck/00check.log: 3.805 0.026 1.842 ./dada2.Rcheck/00check.log:> # Compare results (should be identical) ./dada2.Rcheck/00check.log:> ex2[(accept)] ./dada2.Rcheck/00check.log: seqF ./dada2.Rcheck/00check.log:1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAAC ./dada2.Rcheck/00check.log:2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAAC ./dada2.Rcheck/00check.log:3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC ./dada2.Rcheck/00check.log:4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC ./dada2.Rcheck/00check.log:5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC ./dada2.Rcheck/00check.log: seqR ./dada2.Rcheck/00check.log:1: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:2: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:3: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:4: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:5: GTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG ./dada2.Rcheck/00check.log: n0F n0R abundance ./dada2.Rcheck/00check.log:1: 164 27 424 ./dada2.Rcheck/00check.log:2: 27 6 61 ./dada2.Rcheck/00check.log:3: 57 11 156 ./dada2.Rcheck/00check.log:4: 206 31 526 ./dada2.Rcheck/00check.log:5: 17 2 46 ./dada2.Rcheck/00check.log: als1 ./dada2.Rcheck/00check.log:1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAAC--- ./dada2.Rcheck/00check.log:2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAAC--- ./dada2.Rcheck/00check.log:3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC--- ./dada2.Rcheck/00check.log:4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC--- ./dada2.Rcheck/00check.log:5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC--- ./dada2.Rcheck/00check.log: als2 ./dada2.Rcheck/00check.log:1: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:2: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:3: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:4: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:5: ---GTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG ./dada2.Rcheck/00check.log: match mismatch indel prefer allMismatch accept ./dada2.Rcheck/00check.log:1: 247 0 0 1 0 TRUE ./dada2.Rcheck/00check.log:2: 247 0 0 1 0 TRUE ./dada2.Rcheck/00check.log:3: 247 0 0 1 0 TRUE ./dada2.Rcheck/00check.log:4: 247 0 0 1 0 TRUE ./dada2.Rcheck/00check.log:5: 247 0 0 1 0 TRUE ./dada2.Rcheck/00check.log: sequence ./dada2.Rcheck/00check.log:1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG ./dada2.Rcheck/00check.log:> data.table::setkey(ex2, sequence) ./dada2.Rcheck/00check.log:> ex2[(accept), list(abundance = sum(abundance)), by = sequence] ./dada2.Rcheck/00check.log: sequence ./dada2.Rcheck/00check.log:1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG ./dada2.Rcheck/00check.log:5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG ./dada2.Rcheck/00check.log: abundance ./dada2.Rcheck/00check.log:1: 424 ./dada2.Rcheck/00check.log:2: 61 ./dada2.Rcheck/00check.log:3: 156 ./dada2.Rcheck/00check.log:4: 526 ./dada2.Rcheck/00check.log:5: 46 ./dada2.Rcheck/00check.log:> # Same sequence set (exactly) ./dada2.Rcheck/00check.log:> setequal(x = ex1$sequence, ./dada2.Rcheck/00check.log:+ y = ex2[(accept)]$sequence) ./dada2.Rcheck/00check.log:[1] TRUE ./dada2.Rcheck/00check.log:> # Test concatenation functionality ./dada2.Rcheck/00check.log:> ex1cattime = system.time({ ./dada2.Rcheck/00check.log:+ ex1cat <- mergePairs(dadaF, derepF, dadaR, derepR, justConcatenate = TRUE, verbose = TRUE) ./dada2.Rcheck/00check.log:+ sapply(ex1cat, class) ./dada2.Rcheck/00check.log:+ # need to convert to a character ./dada2.Rcheck/00check.log:+ ex1cat$sequence <- unlist(ex1cat$sequence) ./dada2.Rcheck/00check.log:+ ex1cat <- data.table::data.table(ex1cat) ./dada2.Rcheck/00check.log:+ }) ./dada2.Rcheck/00check.log:1315 paired-reads (in 13 unique pairings) successfully merged out of 1315 (in 13 pairings) input. ./dada2.Rcheck/00check.log:> ex1cattime ./dada2.Rcheck/00check.log: user system elapsed ./dada2.Rcheck/00check.log: 0.027 0.000 0.027 ./dada2.Rcheck/00check.log:> ex2cattime = system.time({ ./dada2.Rcheck/00check.log:+ ex2cat <- dada2:::mergePairsByID(dadaF = dadaF, derepF = derepF, srF = srF, ./dada2.Rcheck/00check.log:+ dadaR = dadaR, derepR = derepR, srR = srR, ./dada2.Rcheck/00check.log:+ justConcatenate = TRUE, verbose = TRUE) ./dada2.Rcheck/00check.log:+ }) ./dada2.Rcheck/00check.log:1434 unique forward read IDs. ./dada2.Rcheck/00check.log:1343 unique reverse read IDs. ./dada2.Rcheck/00check.log:1315 paired reads, corresponding to 13 unique pairs that must be assessed for overlap merge ./dada2.Rcheck/00check.log:Error in `[.data.table`(upiddt, , `:=`(sequence, paste0(seqF, rep("N", : ./dada2.Rcheck/00check.log: Supplied 10 items to be assigned to group 1 of size 1 in column 'sequence'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./dada2.Rcheck/00check.log:Calls: system.time -> -> [ -> [.data.table ./dada2.Rcheck/00check.log:Timing stopped at: 3.123 0.009 1.442 ./dada2.Rcheck/00check.log:Execution halted ./dada2.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./dada2.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./dada2.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./dada2.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./dada2.Rcheck/00check.log:* checking PDF version of manual ... OK ./dada2.Rcheck/00check.log:* DONE ./dada2.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 5 NOTEs maftools_1.8.0.tar.gz ./maftools.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/maftools.Rcheck’ ./maftools.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./maftools.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./maftools.Rcheck/00check.log:* using session charset: UTF-8 ./maftools.Rcheck/00check.log:* checking for file ‘maftools/DESCRIPTION’ ... OK ./maftools.Rcheck/00check.log:* checking extension type ... Package ./maftools.Rcheck/00check.log:* this is package ‘maftools’ version ‘1.8.0’ ./maftools.Rcheck/00check.log:* package encoding: UTF-8 ./maftools.Rcheck/00check.log:* checking package namespace information ... OK ./maftools.Rcheck/00check.log:* checking package dependencies ... OK ./maftools.Rcheck/00check.log:* checking if this is a source package ... OK ./maftools.Rcheck/00check.log:* checking if there is a namespace ... OK ./maftools.Rcheck/00check.log:* checking for executable files ... OK ./maftools.Rcheck/00check.log:* checking for hidden files and directories ... OK ./maftools.Rcheck/00check.log:* checking for portable file names ... OK ./maftools.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./maftools.Rcheck/00check.log:* checking whether package ‘maftools’ can be installed ... OK ./maftools.Rcheck/00check.log:* checking installed package size ... NOTE ./maftools.Rcheck/00check.log: installed size is 12.0Mb ./maftools.Rcheck/00check.log: sub-directories of 1Mb or more: ./maftools.Rcheck/00check.log: doc 5.1Mb ./maftools.Rcheck/00check.log: extdata 6.0Mb ./maftools.Rcheck/00check.log:* checking package directory ... OK ./maftools.Rcheck/00check.log:* checking ‘build’ directory ... OK ./maftools.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./maftools.Rcheck/00check.log:* checking top-level files ... OK ./maftools.Rcheck/00check.log:* checking for left-over files ... OK ./maftools.Rcheck/00check.log:* checking index information ... OK ./maftools.Rcheck/00check.log:* checking package subdirectories ... OK ./maftools.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./maftools.Rcheck/00check.log:* checking R files for syntax errors ... OK ./maftools.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./maftools.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./maftools.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./maftools.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./maftools.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./maftools.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./maftools.Rcheck/00check.log:* checking dependencies in R code ... OK ./maftools.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./maftools.Rcheck/00check.log:* checking replacement functions ... OK ./maftools.Rcheck/00check.log:* checking foreign function calls ... OK ./maftools.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./maftools.Rcheck/00check.log:OncogenicPathways: no visible binding for global variable ‘Pathway’ ./maftools.Rcheck/00check.log:OncogenicPathways: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘fraction_affected’ ./maftools.Rcheck/00check.log:OncogenicPathways: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘n_affected_genes’ ./maftools.Rcheck/00check.log:OncogenicPathways: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:PlotOncogenicPathways: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:add_oncoprint: no visible binding for global variable ‘bg’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘ExonicFunc.refGene’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ‘uid’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ‘ens_id’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ‘hgnc_symbol’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ‘Entrez_Gene_Id’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ‘Entrez’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:annovarToMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘AlteredSamples’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘MutatedSamples’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : : no visible binding for ./maftools.Rcheck/00check.log: global variable ‘Group’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : : no visible binding for ./maftools.Rcheck/00check.log: global variable ‘Genotype’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Analysis’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible global function definition ./maftools.Rcheck/00check.log: for ‘.’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Var1’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Var2’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘value’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘fdr’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘cf’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Genotype’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘N’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘n_mutated_Feature’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘N.x’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘N.y’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Feature_1’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Feature_2’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘n_mutated_Feature1’ ./maftools.Rcheck/00check.log:clinicalEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘n_mutated_Feature2’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘Analysis’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘Feature_1’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘Feature_2’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘n_mutated_Feature1’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘n_mutated_Feature2’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘fdr’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘Group1’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘Group2’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘n_mutated_group1’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘n_mutated_group2’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘p_value’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘OR_low’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘OR_high’ ./maftools.Rcheck/00check.log:clinicalEnrichment: no visible binding for global variable ‘cf’ ./maftools.Rcheck/00check.log:cluster_prot: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:cluster_prot: no visible binding for global variable ‘distance’ ./maftools.Rcheck/00check.log:cluster_prot: no visible binding for global variable ‘startDist’ ./maftools.Rcheck/00check.log:cluster_prot: no visible binding for global variable ‘endDist’ ./maftools.Rcheck/00check.log:cluster_prot: no visible binding for global variable ‘fraction’ ./maftools.Rcheck/00check.log:cluster_prot : : no visible binding for global variable ./maftools.Rcheck/00check.log: ‘fraction’ ./maftools.Rcheck/00check.log:coOncoplot: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:coOncoplot: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:coOncoplot: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:coOncoplot: no visible binding for global variable ‘MutatedSamples.x’ ./maftools.Rcheck/00check.log:coOncoplot: no visible binding for global variable ‘MutatedSamples.y’ ./maftools.Rcheck/00check.log:createOncoMatrix: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:createOncoMatrix: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:createOncoMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:createOncoMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:createOncoMatrix: no visible binding for global variable ‘sampleId’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘statFontSize’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘fs’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘value’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘variable’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘ID’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘Mean’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘Median’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:dashboard: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘boxStat’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:dashboard: no visible binding for global variable ‘AlteredSamples’ ./maftools.Rcheck/00check.log:detect_kataegis: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible binding for global variable ‘row_idx’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Chromosome’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible binding for global variable ‘Size’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘End_Position’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible binding for global variable ‘con.class’ ./maftools.Rcheck/00check.log:detect_kataegis_chr: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:dirichletClusters: no visible binding for global variable ‘dp’ ./maftools.Rcheck/00check.log:drugInteractions: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:drugInteractions: no visible binding for global variable ‘Gene’ ./maftools.Rcheck/00check.log:drugInteractions: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:drugInteractions: no visible binding for global variable ‘category’ ./maftools.Rcheck/00check.log:drugInteractions: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:drugInteractions: no visible binding for global variable ‘V1’ ./maftools.Rcheck/00check.log:drugInteractions: no visible binding for global variable ‘label’ ./maftools.Rcheck/00check.log:drugInteractions: no visible global function definition for ./maftools.Rcheck/00check.log: ‘heat.colors’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘i.Start_Position’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘i.End_Position’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ‘t_vaf’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ‘Segment_Mean’ ./maftools.Rcheck/00check.log:filterCopyNumber: no visible binding for global variable ‘CN’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘pval’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘adjPval’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘Cohort’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘SampleSize’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘log10OR’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘or’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘log10OR_high’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘ci.up’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘log10OR_low’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘ci.low’ ./maftools.Rcheck/00check.log:forestPlot: no visible binding for global variable ‘gg.fp’ ./maftools.Rcheck/00check.log:geneCloud: no visible binding for global variable ‘Cytoband’ ./maftools.Rcheck/00check.log:geneCloud: no visible binding for global variable ‘qvalues’ ./maftools.Rcheck/00check.log:geneCloud: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:geneCloud: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:genesToBarcodes: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:genesToBarcodes : : no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:genotypeMatrix: no visible binding for global variable ‘id’ ./maftools.Rcheck/00check.log:genotypeMatrix: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:genotypeMatrix: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:genotypeMatrix: no visible binding for global variable ‘t_vaf’ ./maftools.Rcheck/00check.log:getOncoPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:getOncoPlot: no visible binding for global variable ‘ID’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:get_lp_data: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘AAChange’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘HGNC’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘refseq.ID’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘protein.ID’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘aa.length’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘Label’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘domain_lenght’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘End’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘Start’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘ID’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘conv’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘count2’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘count’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘posRounded’ ./maftools.Rcheck/00check.log:get_lp_data: no visible binding for global variable ‘lab’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ‘qvalues’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ‘loc’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ‘Cytoband’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ‘nSamples’ ./maftools.Rcheck/00check.log:gisticBubblePlot: no visible binding for global variable ‘lab’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘qvalues’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘loc’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘Cytoband’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position_updated’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘End_Position_updated’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘ystart’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘amp’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘ysmall’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘ybig’ ./maftools.Rcheck/00check.log:gisticChromPlot: no visible binding for global variable ‘labPos’ ./maftools.Rcheck/00check.log:gisticMap: no visible binding for global variable ‘Cytoband’ ./maftools.Rcheck/00check.log:gisticMap: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘consequence_type’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘gene_affected’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘assembly_version’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘chromosome’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘chromosome_start’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘chromosome_end’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Type’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘reference_genome_allele’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘mutated_from_allele’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘mutated_to_allele’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘icgc_sample_id’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘verification_status’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘sequencing_strategy’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘verification_platform’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘ens_id’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘hgnc_symbol’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Entrez_Gene_Id’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Entrez’ ./maftools.Rcheck/00check.log:icgcSimpleMutationToMAF: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ‘t_vaf’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘t_alt_count’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘t_ref_count’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘End_Position’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ‘Sample’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:inferHeterogeneity: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:label_pos: no visible binding for global variable ‘labThis’ ./maftools.Rcheck/00check.log:label_pos: no visible binding for global variable ‘pos2’ ./maftools.Rcheck/00check.log:label_pos: no visible binding for global variable ‘count2’ ./maftools.Rcheck/00check.log:label_pos: no visible binding for global variable ‘conv’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘AAChange’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘HGNC’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘refseq.ID’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘protein.ID’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘aa.length’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘Label’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘ID’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘conv’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘count2’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘count’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘posRounded’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘lab’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘pos2’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘Start’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘End’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘labThis’ ./maftools.Rcheck/00check.log:lollipopPlot: no visible binding for global variable ‘mutations’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ‘Label’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ‘pos2’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ‘count2’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ‘Start’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ‘End’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ‘refseq.ID’ ./maftools.Rcheck/00check.log:lollipopPlot2: no visible binding for global variable ‘conv’ ./maftools.Rcheck/00check.log:mafCompare: no visible binding for global variable ‘AlteredSamples’ ./maftools.Rcheck/00check.log:mafCompare: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:mafCompare: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:mafCompare: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:mafCompare: no visible binding for global variable ‘adjPval’ ./maftools.Rcheck/00check.log:mafSurvival: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:mafSurvival: no visible binding for global variable ‘Time’ ./maftools.Rcheck/00check.log:mafSurvival: no visible binding for global variable ‘Group’ ./maftools.Rcheck/00check.log:mafSurvival: no visible binding for global variable ‘survProb’ ./maftools.Rcheck/00check.log:mafSurvival: no visible binding for global variable ‘survLower’ ./maftools.Rcheck/00check.log:mafSurvival: no visible binding for global variable ‘survUp’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘Sample’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘i.Start_Position’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘i.End_Position’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘Segment_Mean’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position_updated’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘End_Position_updated’ ./maftools.Rcheck/00check.log:mapMutsToSegs: no visible binding for global variable ‘CN’ ./maftools.Rcheck/00check.log:math.score: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:math.score: no visible binding for global variable ‘t_vaf’ ./maftools.Rcheck/00check.log:math.score: no visible binding for global variable ‘t_alt_count’ ./maftools.Rcheck/00check.log:math.score: no visible binding for global variable ‘t_ref_count’ ./maftools.Rcheck/00check.log:math.score: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:math.score: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:math.score : : no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:mutCountMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:mutCountMatrix: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:mutCountMatrix: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:mutCountMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:mutCountMatrix: no visible binding for global variable ‘tot’ ./maftools.Rcheck/00check.log:oncodrive: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:oncodrive: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘fract_muts_in_clusters’ ./maftools.Rcheck/00check.log:oncodrive: no visible binding for global variable ‘muts_in_clusters’ ./maftools.Rcheck/00check.log:oncodrive: no visible binding for global variable ‘total’ ./maftools.Rcheck/00check.log:oncodrive: no visible binding for global variable ‘poissonFdr’ ./maftools.Rcheck/00check.log:oncodrive: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:oncodrive: no visible binding for global variable ‘tFdr’ ./maftools.Rcheck/00check.log:oncodrive: no visible binding for global variable ‘fdr’ ./maftools.Rcheck/00check.log:oncoplot: no visible binding for global variable ‘FDR’ ./maftools.Rcheck/00check.log:oncoplot: no visible binding for global variable ‘gene’ ./maftools.Rcheck/00check.log:oncoplot: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:oncoplot: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:oncoplot: no visible binding for global variable ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:oncoplot : anno_column_bar: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:oncostrip: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:oncostrip: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:oncostrip : anno_pct: no visible binding for global variable ‘numMat’ ./maftools.Rcheck/00check.log:oncotate: no visible binding for global variable ‘anno.df’ ./maftools.Rcheck/00check.log:pancanComparison: no visible binding for global variable ‘gene’ ./maftools.Rcheck/00check.log:pancanComparison: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:pancanComparison: no visible binding for global variable ‘nMut’ ./maftools.Rcheck/00check.log:pancanComparison: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘SampleFraction’ ./maftools.Rcheck/00check.log:parse_prot: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:parse_prot: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:parse_prot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:parse_prot: no visible binding for global variable ‘AAChange’ ./maftools.Rcheck/00check.log:parse_prot: no visible binding for global variable ‘conv’ ./maftools.Rcheck/00check.log:parse_prot: no visible binding for global variable ‘aa.length’ ./maftools.Rcheck/00check.log:parse_prot: no visible binding for global variable ‘total’ ./maftools.Rcheck/00check.log:parse_prot: no visible binding for global variable ‘th’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:pfamDomains: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘AAChange’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘conv’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘total’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘fraction’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘HGNC’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘Start’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘End’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘Label’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘pfam’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘Description’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘idx’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘DomainLabel’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘nMut’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘nGenes’ ./maftools.Rcheck/00check.log:pfamDomains: no visible binding for global variable ‘nMuts’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘n_mutations’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘APOBEC_Enriched’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘fraction_APOBEC_mutations’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘ID’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘Mean’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘Median’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘Cohort’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘pval’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘SampleSize’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘nonApobec’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘V1’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘variable’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘value’ ./maftools.Rcheck/00check.log:plotApobecDiff: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:plotCBS: no visible binding for global variable ‘Sample’ ./maftools.Rcheck/00check.log:plotCBS: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:plotCBS: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:plotCBS: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position_updated’ ./maftools.Rcheck/00check.log:plotCBS: no visible binding for global variable ‘End_Position_updated’ ./maftools.Rcheck/00check.log:plotCBS: no visible binding for global variable ‘Segment_Mean’ ./maftools.Rcheck/00check.log:plotCBSchr: no visible binding for global variable ‘Sample’ ./maftools.Rcheck/00check.log:plotCBSchr: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:plotCBSchr: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:plotCBSchr: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:plotCBSchr: no visible binding for global variable ‘Segment_Mean’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘Sample’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘CN’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘Segment_Mean’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position_updated’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘Segment_Start’ ./maftools.Rcheck/00check.log:plotCBSsegments: no visible binding for global variable ‘Segment_End’ ./maftools.Rcheck/00check.log:plotClusters: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:plotClusters: no visible binding for global variable ‘t_vaf’ ./maftools.Rcheck/00check.log:plotClusters: no visible binding for global variable ‘MATH’ ./maftools.Rcheck/00check.log:plotClusters: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ‘P_value’ ./maftools.Rcheck/00check.log:plotEnrichmentResults : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘g1_muts’ ./maftools.Rcheck/00check.log:plotEnrichmentResults : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘g1_tot’ ./maftools.Rcheck/00check.log:plotEnrichmentResults : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘g2_muts’ ./maftools.Rcheck/00check.log:plotEnrichmentResults : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘g2_tot’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘g1_title’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ‘g1_muts’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ‘g1_tot’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘g2_title’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ‘g2_muts’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ‘g2_tot’ ./maftools.Rcheck/00check.log:plotEnrichmentResults: no visible binding for global variable ‘Group1’ ./maftools.Rcheck/00check.log:plotOncodrive: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘fract_muts_in_clusters’ ./maftools.Rcheck/00check.log:plotOncodrive: no visible binding for global variable ‘fdr’ ./maftools.Rcheck/00check.log:plotOncodrive: no visible binding for global variable ‘clusters’ ./maftools.Rcheck/00check.log:plotOncodrive: no visible binding for global variable ‘significant’ ./maftools.Rcheck/00check.log:plotOncodrive: no visible binding for global variable ‘label’ ./maftools.Rcheck/00check.log:plotOncodrive: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘muts_in_clusters’ ./maftools.Rcheck/00check.log:plotTiTv: no visible binding for global variable ‘value’ ./maftools.Rcheck/00check.log:plotTiTv: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:plotTiTv: no visible binding for global variable ‘variable’ ./maftools.Rcheck/00check.log:plotTiTv: no visible binding for global variable ‘V1’ ./maftools.Rcheck/00check.log:plotVaf: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:plotVaf: no visible binding for global variable ‘t_vaf’ ./maftools.Rcheck/00check.log:plotVaf: no visible binding for global variable ‘t_alt_count’ ./maftools.Rcheck/00check.log:plotVaf: no visible binding for global variable ‘t_ref_count’ ./maftools.Rcheck/00check.log:plotVaf: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:plotVaf: no visible binding for global variable ‘value’ ./maftools.Rcheck/00check.log:plotVaf: no visible binding for global variable ‘V1’ ./maftools.Rcheck/00check.log:plotmafSummary: no visible binding for global variable ‘statFontSize’ ./maftools.Rcheck/00check.log:plotmafSummary: no visible binding for global variable ‘Mean’ ./maftools.Rcheck/00check.log:plotmafSummary: no visible binding for global variable ‘Median’ ./maftools.Rcheck/00check.log:plotmafSummary: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:plotmafSummary: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:plotmafSummary: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:plotmafSummary: no visible binding for global variable ‘boxStat’ ./maftools.Rcheck/00check.log:prepareMutSig: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:prepareMutSig: no visible binding for global variable ‘OG_Hugo_Symbol’ ./maftools.Rcheck/00check.log:prepareMutSig: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:prepareMutSig: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:prepareMutSig: no visible binding for global variable ‘MutSig_Synonym’ ./maftools.Rcheck/00check.log:prepareMutSig: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘Reference_Allele’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Seq_Allele2’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position_updated’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘con.class’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘id’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ‘minDiff’ ./maftools.Rcheck/00check.log:rainfallPlot: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘End_Position_updated’ ./maftools.Rcheck/00check.log:read.maf: no visible binding for global variable ‘Mutation_Status’ ./maftools.Rcheck/00check.log:read.maf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:read.maf: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:read.maf: no visible binding for global variable ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:read.maf: no visible binding for global variable ‘id’ ./maftools.Rcheck/00check.log:read.maf: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘Unique_Name’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘Wide_Peak_Limits’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘cytoband’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘value’ ./maftools.Rcheck/00check.log:readGistic: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘variable’ ./maftools.Rcheck/00check.log:readGistic : : no visible binding for global variable ./maftools.Rcheck/00check.log: ‘variable’ ./maftools.Rcheck/00check.log:readGistic : : no visible binding for global variable ./maftools.Rcheck/00check.log: ‘cytoband’ ./maftools.Rcheck/00check.log:readGistic : : no visible binding for global variable ./maftools.Rcheck/00check.log: ‘TumorSampleBarcode’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘CN’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘TumorSampleBarcode’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘Cytoband’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘peakID’ ./maftools.Rcheck/00check.log:readGistic: no visible binding for global variable ‘qvalues’ ./maftools.Rcheck/00check.log:readSegs: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:readSegs: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:readSegs: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:refineClusters: no visible binding for global variable ‘t_vaf’ ./maftools.Rcheck/00check.log:repelPoints: no visible binding for global variable ‘distance’ ./maftools.Rcheck/00check.log:repelPoints: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:signatureEnrichment: no visible binding for global variable ‘Cluster’ ./maftools.Rcheck/00check.log:signatureEnrichment: no visible binding for global variable ‘Signature’ ./maftools.Rcheck/00check.log:signatureEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Signature’ ./maftools.Rcheck/00check.log:signatureEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:signatureEnrichment : : no visible binding for global ./maftools.Rcheck/00check.log: variable ‘N’ ./maftools.Rcheck/00check.log:signatureEnrichment: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:signatureEnrichment: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:signatureEnrichment: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘mut.load.p’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible binding for global variable ‘gene1’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible binding for global variable ‘gene2’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible binding for global variable ‘pValue’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible binding for global variable ‘pair’ ./maftools.Rcheck/00check.log:somaticInteractions: no visible binding for global variable ‘Event’ ./maftools.Rcheck/00check.log:sortByMutation: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:sortByMutation: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:subsetMaf: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:subsetMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:subsetMaf: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:summarizeGistic: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:summarizeGistic: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:summarizeGistic: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:summarizeGistic: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:summarizeGistic: no visible binding for global variable ‘total’ ./maftools.Rcheck/00check.log:summarizeGistic: no visible binding for global variable ‘Cytoband’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘total’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘CNV_total’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘CNV’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘MutatedSamples’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘Mean’ ./maftools.Rcheck/00check.log:summarizeMaf: no visible binding for global variable ‘Median’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ‘total’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ‘site’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ‘cohort’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ‘V2’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ‘TCGA’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ‘Median_Mutations’ ./maftools.Rcheck/00check.log:tcgaCompare: no visible binding for global variable ‘Cohort’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:titv: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘End_Position’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘Reference_Allele’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘Tumor_Seq_Allele2’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘con’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘con.class’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘fract’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘nVars’ ./maftools.Rcheck/00check.log:titv: no visible binding for global variable ‘TiTv’ ./maftools.Rcheck/00check.log:transformSegments: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:transformSegments: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘End_Position’ ./maftools.Rcheck/00check.log:transformSegments: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘pkgname’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Chromosome’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Start_Position’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘N’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘Start’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘End’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘upstream’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘downstream’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible global function definition for ‘.’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘G’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘trinucleotide’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘updown’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘TCA’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘TCT’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘AGA’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘TGA’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘tcw’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘wga’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Substitution’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘SubstitutionType’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘n_A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘A>C’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘A>G’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘A>T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘n_T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T>A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T>C’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T>G’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘n_G’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘G>A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘G>C’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘G>T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘n_C’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘C>A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘C>G’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘C>T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘n_mutations’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘SubstitutionMotif’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘tCw_to_A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[C>A]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[C>A]T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘tCw_to_G’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[C>G]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[C>G]T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘tCw_to_T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[C>T]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[C>T]T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘tCw’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘wGa_to_C’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘A[G>C]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[G>C]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘wGa_to_T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘A[G>T]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[G>T]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘wGa_to_A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘A[G>A]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘T[G>A]A’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘wGa’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘tCw_to_G+tCw_to_T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘APOBEC_Enrichment’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘n_C>G_and_C>T’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘non_APOBEC_mutations’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘fraction_APOBEC_mutations’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘fisher_pvalue’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ‘fdr’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘APOBEC_Enriched’ ./maftools.Rcheck/00check.log:trinucleotideMatrix: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘SubstitutionTypeMotif’ ./maftools.Rcheck/00check.log:validateMaf: no visible binding for global variable ‘variantId’ ./maftools.Rcheck/00check.log:validateMaf: no visible binding for global variable ‘Chromosome’ ./maftools.Rcheck/00check.log:validateMaf: no visible binding for global variable ‘Start_Position’ ./maftools.Rcheck/00check.log:validateMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./maftools.Rcheck/00check.log:validateMaf: no visible binding for global variable ‘Hugo_Symbol’ ./maftools.Rcheck/00check.log:validateMaf: no visible binding for global variable ./maftools.Rcheck/00check.log: ‘Variant_Classification’ ./maftools.Rcheck/00check.log:validateMaf: no visible binding for global variable ‘Variant_Type’ ./maftools.Rcheck/00check.log:Undefined global functions or variables: ./maftools.Rcheck/00check.log: . A A>C A>G A>T AAChange AGA APOBEC_Enriched APOBEC_Enrichment ./maftools.Rcheck/00check.log: A[G>A]A A[G>C]A A[G>T]A AlteredSamples Analysis C>A C>G C>T CN CNV ./maftools.Rcheck/00check.log: CNV_total Chromosome Cluster Cohort Cytoband Description DomainLabel ./maftools.Rcheck/00check.log: End End_Position End_Position_updated Entrez Entrez_Gene_Id Event ./maftools.Rcheck/00check.log: ExonicFunc.refGene FDR Feature_1 Feature_2 G G>A G>C G>T Gene ./maftools.Rcheck/00check.log: Genotype Group Group1 Group2 HGNC Hugo_Symbol ID Label MATH Mean ./maftools.Rcheck/00check.log: Median Median_Mutations MutSig_Synonym MutatedSamples ./maftools.Rcheck/00check.log: MutatedSamples.x MutatedSamples.y Mutation_Status N N.x N.y ./maftools.Rcheck/00check.log: OG_Hugo_Symbol OR_high OR_low P_value Pathway Reference_Allele Sample ./maftools.Rcheck/00check.log: SampleFraction SampleSize Segment_End Segment_Mean Segment_Start ./maftools.Rcheck/00check.log: Signature Size Start Start_Position Start_Position_updated ./maftools.Rcheck/00check.log: Substitution SubstitutionMotif SubstitutionType SubstitutionTypeMotif ./maftools.Rcheck/00check.log: T>A T>C T>G TCA TCGA TCT TGA T[C>A]A T[C>A]T T[C>G]A T[C>G]T T[C>T]A ./maftools.Rcheck/00check.log: T[C>T]T T[G>A]A T[G>C]A T[G>T]A TiTv Time TumorSampleBarcode ./maftools.Rcheck/00check.log: Tumor_Sample_Barcode Tumor_Seq_Allele2 Unique_Name V1 V2 Var1 Var2 ./maftools.Rcheck/00check.log: Variant_Classification Variant_Type Wide_Peak_Limits aa.length ./maftools.Rcheck/00check.log: adjPval amp anno.df assembly_version bg boxStat category cf ./maftools.Rcheck/00check.log: chromosome chromosome_end chromosome_start ci.low ci.up clusters ./maftools.Rcheck/00check.log: cohort con con.class consequence_type conv count count2 cytoband ./maftools.Rcheck/00check.log: distance domain_lenght downstream dp endDist ens_id fdr fisher_pvalue ./maftools.Rcheck/00check.log: fract fract_muts_in_clusters fraction fraction_APOBEC_mutations ./maftools.Rcheck/00check.log: fraction_affected fs g1_muts g1_title g1_tot g2_muts g2_title g2_tot ./maftools.Rcheck/00check.log: gene gene1 gene2 gene_affected gg.fp heat.colors hgnc_symbol ./maftools.Rcheck/00check.log: i.End_Position i.Start_Position icgc_sample_id id idx lab labPos ./maftools.Rcheck/00check.log: labThis label loc log10OR log10OR_high log10OR_low minDiff mut.load.p ./maftools.Rcheck/00check.log: mutated_from_allele mutated_to_allele mutations muts_in_clusters ./maftools.Rcheck/00check.log: nGenes nMut nMuts nSamples nVars n_A n_C n_C>G_and_C>T n_G n_T ./maftools.Rcheck/00check.log: n_affected_genes n_mutated_Feature n_mutated_Feature1 ./maftools.Rcheck/00check.log: n_mutated_Feature2 n_mutated_group1 n_mutated_group2 n_mutations ./maftools.Rcheck/00check.log: nonApobec non_APOBEC_mutations numMat or pValue p_value pair peakID ./maftools.Rcheck/00check.log: pfam pkgname poissonFdr pos2 posRounded protein.ID pval qvalues ./maftools.Rcheck/00check.log: reference_genome_allele refseq.ID row_idx sampleId ./maftools.Rcheck/00check.log: sequencing_strategy significant site startDist statFontSize survLower ./maftools.Rcheck/00check.log: survProb survUp tCw tCw_to_A tCw_to_G tCw_to_G+tCw_to_T tCw_to_T tFdr ./maftools.Rcheck/00check.log: t_alt_count t_ref_count t_vaf tcw th tot total trinucleotide uid ./maftools.Rcheck/00check.log: updown upstream value variable variantId verification_platform ./maftools.Rcheck/00check.log: verification_status wGa wGa_to_A wGa_to_C wGa_to_T wga ybig ysmall ./maftools.Rcheck/00check.log: ystart ./maftools.Rcheck/00check.log:Consider adding ./maftools.Rcheck/00check.log: importFrom("grDevices", "heat.colors") ./maftools.Rcheck/00check.log:to your NAMESPACE file. ./maftools.Rcheck/00check.log:* checking Rd files ... OK ./maftools.Rcheck/00check.log:* checking Rd metadata ... OK ./maftools.Rcheck/00check.log:* checking Rd cross-references ... OK ./maftools.Rcheck/00check.log:* checking for missing documentation entries ... OK ./maftools.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./maftools.Rcheck/00check.log:* checking Rd \usage sections ... OK ./maftools.Rcheck/00check.log:* checking Rd contents ... OK ./maftools.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./maftools.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./maftools.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./maftools.Rcheck/00check.log:* checking examples ... ERROR ./maftools.Rcheck/00check.log:Running examples in ‘maftools-Ex.R’ failed ./maftools.Rcheck/00check.log:The error most likely occurred in: ./maftools.Rcheck/00check.log:> ### Name: gisticChromPlot ./maftools.Rcheck/00check.log:> ### Title: Plot gistic results along linearized chromosome ./maftools.Rcheck/00check.log:> ### Aliases: gisticChromPlot ./maftools.Rcheck/00check.log:> ./maftools.Rcheck/00check.log:> ### ** Examples ./maftools.Rcheck/00check.log:> ./maftools.Rcheck/00check.log:> all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools") ./maftools.Rcheck/00check.log:> amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools") ./maftools.Rcheck/00check.log:> del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools") ./maftools.Rcheck/00check.log:> scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools") ./maftools.Rcheck/00check.log:> laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic) ./maftools.Rcheck/00check.log:Processing Gistic files.. ./maftools.Rcheck/00check.log:Processing amp_genes.conf_99.txt.. ./maftools.Rcheck/00check.log:Processing del_genes.conf_99.txt.. ./maftools.Rcheck/00check.log:Processing scores.gistic.. ./maftools.Rcheck/00check.log:Summarizing samples.. ./maftools.Rcheck/00check.log:> gisticChromPlot(laml.gistic) ./maftools.Rcheck/00check.log:Error in `[<-.data.table`(x, j = name, value = value) : ./maftools.Rcheck/00check.log: Supplied 2 items to be assigned to 24 items of column 'color'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./maftools.Rcheck/00check.log:Calls: gisticChromPlot -> $<- -> $<-.data.table -> [<-.data.table ./maftools.Rcheck/00check.log:Execution halted ./maftools.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... NOTE ./maftools.Rcheck/00check.log:'::' or ':::' import not declared from: ‘pheatmap’ ./maftools.Rcheck/00check.log:'library' or 'require' calls not declared from: ./maftools.Rcheck/00check.log: ‘BSgenome.Hsapiens.UCSC.hg19’ ‘pheatmap’ ./maftools.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./maftools.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./maftools.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./maftools.Rcheck/00check.log:Error in re-building vignettes: ./maftools.Rcheck/00check.log: ... ./maftools.Rcheck/00check.log:Loading required package: maftools ./maftools.Rcheck/00check.log:reading maf.. ./maftools.Rcheck/00check.log:silent variants: 475 ./maftools.Rcheck/00check.log:Summarizing.. ./maftools.Rcheck/00check.log:Gene Summary.. ./maftools.Rcheck/00check.log:Checking clinical data.. ./maftools.Rcheck/00check.log:Done ! ./maftools.Rcheck/00check.log:reading maf.. ./maftools.Rcheck/00check.log:silent variants: 475 ./maftools.Rcheck/00check.log:Processing Gistic files.. ./maftools.Rcheck/00check.log:Processing amp_genes.conf_99.txt.. ./maftools.Rcheck/00check.log:Processing del_genes.conf_99.txt.. ./maftools.Rcheck/00check.log:Processing scores.gistic.. ./maftools.Rcheck/00check.log:Summarizing samples.. ./maftools.Rcheck/00check.log:Summarizing.. ./maftools.Rcheck/00check.log:Gene Summary.. ./maftools.Rcheck/00check.log:Checking clinical data.. ./maftools.Rcheck/00check.log:NOTE: Missing clinical data! It is strongly recommended to provide clinical data associated with samples if available. ./maftools.Rcheck/00check.log:Done ! ./maftools.Rcheck/00check.log:Removed 3 mutations for which AA position was not available ./maftools.Rcheck/00check.log:Summary.. ./maftools.Rcheck/00check.log:Quitting from lines 269-270 (maftools.Rmd) ./maftools.Rcheck/00check.log:Error: processing vignette 'maftools.Rmd' failed with diagnostics: ./maftools.Rcheck/00check.log:Supplied 2 items to be assigned to 24 items of column 'color'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./maftools.Rcheck/00check.log:Execution halted ./maftools.Rcheck/00check.log:* checking PDF version of manual ... OK ./maftools.Rcheck/00check.log:* DONE ./maftools.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 3 NOTEs metagene_2.14.0.tar.gz ./metagene.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/metagene.Rcheck’ ./metagene.Rcheck/00check.log:* using R version 3.5.2 (2018-12-20) ./metagene.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./metagene.Rcheck/00check.log:* using session charset: UTF-8 ./metagene.Rcheck/00check.log:* checking for file ‘metagene/DESCRIPTION’ ... OK ./metagene.Rcheck/00check.log:* this is package ‘metagene’ version ‘2.14.0’ ./metagene.Rcheck/00check.log:* checking package namespace information ... OK ./metagene.Rcheck/00check.log:* checking package dependencies ... OK ./metagene.Rcheck/00check.log:* checking if this is a source package ... OK ./metagene.Rcheck/00check.log:* checking if there is a namespace ... OK ./metagene.Rcheck/00check.log:* checking for executable files ... OK ./metagene.Rcheck/00check.log:* checking for hidden files and directories ... OK ./metagene.Rcheck/00check.log:* checking for portable file names ... OK ./metagene.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./metagene.Rcheck/00check.log:* checking whether package ‘metagene’ can be installed ... OK ./metagene.Rcheck/00check.log:* checking installed package size ... NOTE ./metagene.Rcheck/00check.log: installed size is 10.1Mb ./metagene.Rcheck/00check.log: sub-directories of 1Mb or more: ./metagene.Rcheck/00check.log: doc 3.2Mb ./metagene.Rcheck/00check.log: extdata 5.4Mb ./metagene.Rcheck/00check.log:* checking package directory ... OK ./metagene.Rcheck/00check.log:* checking ‘build’ directory ... OK ./metagene.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./metagene.Rcheck/00check.log:Package listed in more than one of Depends, Imports, Suggests, Enhances: ./metagene.Rcheck/00check.log: ‘similaRpeak’ ./metagene.Rcheck/00check.log:A package should be listed in only one of these fields. ./metagene.Rcheck/00check.log:* checking top-level files ... OK ./metagene.Rcheck/00check.log:* checking for left-over files ... OK ./metagene.Rcheck/00check.log:* checking index information ... OK ./metagene.Rcheck/00check.log:* checking package subdirectories ... OK ./metagene.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./metagene.Rcheck/00check.log:* checking R files for syntax errors ... OK ./metagene.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./metagene.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./metagene.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./metagene.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./metagene.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./metagene.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./metagene.Rcheck/00check.log:* checking dependencies in R code ... OK ./metagene.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./metagene.Rcheck/00check.log:* checking replacement functions ... OK ./metagene.Rcheck/00check.log:* checking foreign function calls ... OK ./metagene.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./metagene.Rcheck/00check.log:avoid_gaps_update: no visible binding for global variable 'value' ./metagene.Rcheck/00check.log:avoid_gaps_update: no visible binding for global variable 'bam' ./metagene.Rcheck/00check.log:avoid_gaps_update: no visible binding for global variable 'tab' ./metagene.Rcheck/00check.log:avoid_gaps_update: no visible binding for global variable 'nuc' ./metagene.Rcheck/00check.log:permutation_test: no visible global function definition for '.' ./metagene.Rcheck/00check.log:permutation_test: no visible binding for global variable 'value' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'bin' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'value' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'qinf' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'qsup' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'group' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'nuc' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'design' ./metagene.Rcheck/00check.log:plot_metagene: no visible binding for global variable 'nuctot' ./metagene.Rcheck/00check.log:Undefined global functions or variables: ./metagene.Rcheck/00check.log: . bam bin design group nuc nuctot qinf qsup tab value ./metagene.Rcheck/00check.log:* checking Rd files ... OK ./metagene.Rcheck/00check.log:* checking Rd metadata ... OK ./metagene.Rcheck/00check.log:* checking Rd cross-references ... OK ./metagene.Rcheck/00check.log:* checking for missing documentation entries ... OK ./metagene.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./metagene.Rcheck/00check.log:* checking Rd \usage sections ... OK ./metagene.Rcheck/00check.log:* checking Rd contents ... OK ./metagene.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./metagene.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./metagene.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./metagene.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./metagene.Rcheck/00check.log:* checking R/sysdata.rda ... OK ./metagene.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./metagene.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./metagene.Rcheck/00check.log:* checking include directives in Makefiles ... OK ./metagene.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./metagene.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./metagene.Rcheck/00check.log:* checking examples ... OK ./metagene.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./metagene.Rcheck/00check.log:* checking tests ... ERROR ./metagene.Rcheck/00check.log: Running ‘runTests.R’ ./metagene.Rcheck/00check.log:Running the tests in ‘tests/runTests.R’ failed. ./metagene.Rcheck/00check.log:Last 13 lines of output: ./metagene.Rcheck/00check.log: ERROR in test.metagene_get_table_check_copy_of_table: Error in `[.data.table`(tab, , `:=`(c, 1:5)) : ./metagene.Rcheck/00check.log: Supplied 5 items to be assigned to 50000 items of column 'c'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code. ./metagene.Rcheck/00check.log: ./metagene.Rcheck/00check.log: Test files with failing tests ./metagene.Rcheck/00check.log: ./metagene.Rcheck/00check.log: test_metagene.R ./metagene.Rcheck/00check.log: test.metagene_get_table_check_copy_of_table ./metagene.Rcheck/00check.log: ./metagene.Rcheck/00check.log: ./metagene.Rcheck/00check.log: Error in BiocGenerics:::testPackage("metagene") : ./metagene.Rcheck/00check.log: unit tests failed for package metagene ./metagene.Rcheck/00check.log: In addition: Warning message: ./metagene.Rcheck/00check.log: In `[<-`(`*tmp*`, design_name, value = new("SimpleRleList", elementType = "Rle", : ./metagene.Rcheck/00check.log: implicit list embedding of S4 objects is deprecated ./metagene.Rcheck/00check.log: Execution halted ./metagene.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./metagene.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./metagene.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./metagene.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./metagene.Rcheck/00check.log:* checking PDF version of manual ... OK ./metagene.Rcheck/00check.log:* DONE ./metagene.Rcheck/00check.log:Status: 1 ERROR, 3 NOTEs