R version 3.5.1 (2018-07-02) 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 other attached packages: [1] BiocInstaller_1.30.0 loaded via a namespace (and not attached): [1] compiler_3.5.1 tools_3.5.1 ./antaresRead.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/antaresRead.Rcheck’ ./antaresRead.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./antaresRead.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./antaresRead.Rcheck/00check.log:* using session charset: UTF-8 ./antaresRead.Rcheck/00check.log:* checking for file ‘antaresRead/DESCRIPTION’ ... OK ./antaresRead.Rcheck/00check.log:* checking extension type ... Package ./antaresRead.Rcheck/00check.log:* this is package ‘antaresRead’ version ‘2.2.1’ ./antaresRead.Rcheck/00check.log:* package encoding: UTF-8 ./antaresRead.Rcheck/00check.log:* checking package namespace information ... OK ./antaresRead.Rcheck/00check.log:* checking package dependencies ... OK ./antaresRead.Rcheck/00check.log:* checking if this is a source package ... OK ./antaresRead.Rcheck/00check.log:* checking if there is a namespace ... OK ./antaresRead.Rcheck/00check.log:* checking for executable files ... OK ./antaresRead.Rcheck/00check.log:* checking for hidden files and directories ... OK ./antaresRead.Rcheck/00check.log:* checking for portable file names ... OK ./antaresRead.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./antaresRead.Rcheck/00check.log:* checking whether package ‘antaresRead’ can be installed ... OK ./antaresRead.Rcheck/00check.log:* checking installed package size ... OK ./antaresRead.Rcheck/00check.log:* checking package directory ... OK ./antaresRead.Rcheck/00check.log:* checking ‘build’ directory ... OK ./antaresRead.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./antaresRead.Rcheck/00check.log:* checking top-level files ... OK ./antaresRead.Rcheck/00check.log:* checking for left-over files ... OK ./antaresRead.Rcheck/00check.log:* checking index information ... OK ./antaresRead.Rcheck/00check.log:* checking package subdirectories ... OK ./antaresRead.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./antaresRead.Rcheck/00check.log:* checking R files for syntax errors ... OK ./antaresRead.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./antaresRead.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./antaresRead.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./antaresRead.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./antaresRead.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./antaresRead.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./antaresRead.Rcheck/00check.log:* checking dependencies in R code ... OK ./antaresRead.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./antaresRead.Rcheck/00check.log:* checking replacement functions ... OK ./antaresRead.Rcheck/00check.log:* checking foreign function calls ... OK ./antaresRead.Rcheck/00check.log:* checking R code for possible problems ... OK ./antaresRead.Rcheck/00check.log:* checking Rd files ... OK ./antaresRead.Rcheck/00check.log:* checking Rd metadata ... OK ./antaresRead.Rcheck/00check.log:* checking Rd cross-references ... OK ./antaresRead.Rcheck/00check.log:* checking for missing documentation entries ... OK ./antaresRead.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./antaresRead.Rcheck/00check.log:* checking Rd \usage sections ... OK ./antaresRead.Rcheck/00check.log:* checking Rd contents ... OK ./antaresRead.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./antaresRead.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./antaresRead.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./antaresRead.Rcheck/00check.log:* checking examples ... OK ./antaresRead.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./antaresRead.Rcheck/00check.log:* checking tests ... ERROR ./antaresRead.Rcheck/00check.log: Running ‘testthat.R’ ./antaresRead.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./antaresRead.Rcheck/00check.log:Last 13 lines of output: ./antaresRead.Rcheck/00check.log: 1: suppressWarnings(removeVirtualAreas(x = data, storageFlexibility = c("psp out"), ./antaresRead.Rcheck/00check.log: reassignCosts = TRUE)) at testthat/test-removeVirtualAreas.R:101 ./antaresRead.Rcheck/00check.log: 2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) ./antaresRead.Rcheck/00check.log: 3: removeVirtualAreas(x = data, storageFlexibility = c("psp out"), reassignCosts = TRUE) ./antaresRead.Rcheck/00check.log: 4: costs[flows, c(byarea, varCost, "flow", "rarea"), with = FALSE] ./antaresRead.Rcheck/00check.log: 5: `[.data.table`(costs, flows, c(byarea, varCost, "flow", "rarea"), with = FALSE) ./antaresRead.Rcheck/00check.log: 6: stop("column(s) not found: ", paste(ansvars[is.na(ansvals)], collapse = ", ")) ./antaresRead.Rcheck/00check.log: ./antaresRead.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./antaresRead.Rcheck/00check.log: OK: 728 SKIPPED: 0 FAILED: 2 ./antaresRead.Rcheck/00check.log: 1. Error: RemoveVirtualAreas removes production areas (@test-removeVirtualAreas.R#49) ./antaresRead.Rcheck/00check.log: 2. Error: reassignCosts works correctly (@test-removeVirtualAreas.R#101) ./antaresRead.Rcheck/00check.log: ./antaresRead.Rcheck/00check.log: Error: testthat unit tests failed ./antaresRead.Rcheck/00check.log: Execution halted ./antaresRead.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./antaresRead.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./antaresRead.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./antaresRead.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./antaresRead.Rcheck/00check.log:* checking PDF version of manual ... OK ./antaresRead.Rcheck/00check.log:* DONE ./antaresRead.Rcheck/00check.log:Status: 1 ERROR ./batchtools.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/batchtools.Rcheck’ ./batchtools.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./batchtools.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./batchtools.Rcheck/00check.log:* using session charset: UTF-8 ./batchtools.Rcheck/00check.log:* checking for file ‘batchtools/DESCRIPTION’ ... OK ./batchtools.Rcheck/00check.log:* this is package ‘batchtools’ version ‘0.9.11’ ./batchtools.Rcheck/00check.log:* package encoding: UTF-8 ./batchtools.Rcheck/00check.log:* checking package namespace information ... OK ./batchtools.Rcheck/00check.log:* checking package dependencies ... OK ./batchtools.Rcheck/00check.log:* checking if this is a source package ... OK ./batchtools.Rcheck/00check.log:* checking if there is a namespace ... OK ./batchtools.Rcheck/00check.log:* checking for executable files ... OK ./batchtools.Rcheck/00check.log:* checking for hidden files and directories ... OK ./batchtools.Rcheck/00check.log:* checking for portable file names ... OK ./batchtools.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./batchtools.Rcheck/00check.log:* checking whether package ‘batchtools’ can be installed ... OK ./batchtools.Rcheck/00check.log:* checking installed package size ... OK ./batchtools.Rcheck/00check.log:* checking package directory ... OK ./batchtools.Rcheck/00check.log:* checking ‘build’ directory ... OK ./batchtools.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./batchtools.Rcheck/00check.log:* checking top-level files ... OK ./batchtools.Rcheck/00check.log:* checking for left-over files ... OK ./batchtools.Rcheck/00check.log:* checking index information ... OK ./batchtools.Rcheck/00check.log:* checking package subdirectories ... OK ./batchtools.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./batchtools.Rcheck/00check.log:* checking R files for syntax errors ... OK ./batchtools.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./batchtools.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./batchtools.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./batchtools.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./batchtools.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./batchtools.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./batchtools.Rcheck/00check.log:* checking dependencies in R code ... OK ./batchtools.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./batchtools.Rcheck/00check.log:* checking replacement functions ... OK ./batchtools.Rcheck/00check.log:* checking foreign function calls ... OK ./batchtools.Rcheck/00check.log:* checking R code for possible problems ... OK ./batchtools.Rcheck/00check.log:* checking Rd files ... OK ./batchtools.Rcheck/00check.log:* checking Rd metadata ... OK ./batchtools.Rcheck/00check.log:* checking Rd cross-references ... OK ./batchtools.Rcheck/00check.log:* checking for missing documentation entries ... OK ./batchtools.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./batchtools.Rcheck/00check.log:* checking Rd \usage sections ... OK ./batchtools.Rcheck/00check.log:* checking Rd contents ... OK ./batchtools.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./batchtools.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./batchtools.Rcheck/00check.log:* checking compiled code ... OK ./batchtools.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./batchtools.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./batchtools.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./batchtools.Rcheck/00check.log:* checking examples ... ERROR ./batchtools.Rcheck/00check.log:Running examples in ‘batchtools-Ex.R’ failed ./batchtools.Rcheck/00check.log:The error most likely occurred in: ./batchtools.Rcheck/00check.log:> ### Name: makeJobCollection ./batchtools.Rcheck/00check.log:> ### Title: JobCollection Constructor ./batchtools.Rcheck/00check.log:> ### Aliases: makeJobCollection JobCollection ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> ### ** Examples ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> ## Don't show: ./batchtools.Rcheck/00check.log:> batchtools:::example_push_temp(1) ./batchtools.Rcheck/00check.log:> ## End(Don't show) ./batchtools.Rcheck/00check.log:> tmp = makeRegistry(file.dir = NA, make.default = FALSE, packages = "methods") ./batchtools.Rcheck/00check.log:No readable configuration file found ./batchtools.Rcheck/00check.log:Created registry in '/tmp/Rtmp4fBkEC/registry859721d22e1' using cluster functions 'Interactive' ./batchtools.Rcheck/00check.log:> batchMap(identity, 1:5, reg = tmp) ./batchtools.Rcheck/00check.log:Adding 5 jobs ... ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> # resources are usually set in submitJobs() ./batchtools.Rcheck/00check.log:> jc = makeJobCollection(1:3, resources = list(foo = "bar"), reg = tmp) ./batchtools.Rcheck/00check.log:Error in `[.data.table`(reg$defs, reg$status[ids, nomatch = 0L, on = "job.id"], : ./batchtools.Rcheck/00check.log: column(s) not found: job.id, job.name ./batchtools.Rcheck/00check.log:Calls: makeJobCollection ... setkeyv -> is.data.table -> mergedJobs -> [ -> [.data.table ./batchtools.Rcheck/00check.log:Execution halted ./batchtools.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./batchtools.Rcheck/00check.log:* checking tests ... ERROR ./batchtools.Rcheck/00check.log: Running ‘testthat.R’ ./batchtools.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./batchtools.Rcheck/00check.log:Last 13 lines of output: ./batchtools.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./batchtools.Rcheck/00check.log: OK: 566 SKIPPED: 7 FAILED: 74 ./batchtools.Rcheck/00check.log: 1. Error: addAlgorithm (@test_Algorithm.R#16) ./batchtools.Rcheck/00check.log: 2. Error: addAlgorithm overwrites old algo (@test_Algorithm.R#34) ./batchtools.Rcheck/00check.log: 3. Error: brew (@test_ClusterFunctions.R#67) ./batchtools.Rcheck/00check.log: 4. Error: Special chars in directory names (@test_ClusterFunctions.R#85) ./batchtools.Rcheck/00check.log: 5. Error: Export of environment variable DEBUGME (@test_ClusterFunctions.R#98) ./batchtools.Rcheck/00check.log: 6. Error: cf multicore (@test_ClusterFunctionsMulticore.R#9) ./batchtools.Rcheck/00check.log: 7. Error: cf socket (@test_ClusterFunctionsSocket.R#10) ./batchtools.Rcheck/00check.log: 8. Error: Job (@test_Job.R#7) ./batchtools.Rcheck/00check.log: 9. Error: Experiment (@test_Job.R#35) ./batchtools.Rcheck/00check.log: 1. ... ./batchtools.Rcheck/00check.log: ./batchtools.Rcheck/00check.log: Error: testthat unit tests failed ./batchtools.Rcheck/00check.log: Execution halted ./batchtools.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./batchtools.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./batchtools.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./batchtools.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./batchtools.Rcheck/00check.log:Error in re-building vignettes: ./batchtools.Rcheck/00check.log: ... ./batchtools.Rcheck/00check.log:No readable configuration file found ./batchtools.Rcheck/00check.log:Created registry in '/tmp/RtmpaHpeew/registrye8d7a84d4c5' using cluster functions 'Interactive' ./batchtools.Rcheck/00check.log:No readable configuration file found ./batchtools.Rcheck/00check.log:Created registry in '/tmp/RtmpaHpeew/registrye8d654b7bb9' using cluster functions 'Interactive' ./batchtools.Rcheck/00check.log:Quitting from lines 220-221 (batchtools.Rmd) ./batchtools.Rcheck/00check.log:Error: processing vignette 'batchtools.Rmd' failed with diagnostics: ./batchtools.Rcheck/00check.log:column(s) not found: job.id ./batchtools.Rcheck/00check.log:Execution halted ./batchtools.Rcheck/00check.log:* checking PDF version of manual ... OK ./batchtools.Rcheck/00check.log:* DONE ./batchtools.Rcheck/00check.log:Status: 2 ERRORs, 1 WARNING ./behavr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/behavr.Rcheck’ ./behavr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./behavr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./behavr.Rcheck/00check.log:* using session charset: UTF-8 ./behavr.Rcheck/00check.log:* checking for file ‘behavr/DESCRIPTION’ ... OK ./behavr.Rcheck/00check.log:* this is package ‘behavr’ version ‘0.3.1’ ./behavr.Rcheck/00check.log:* package encoding: UTF-8 ./behavr.Rcheck/00check.log:* checking package namespace information ... OK ./behavr.Rcheck/00check.log:* checking package dependencies ... OK ./behavr.Rcheck/00check.log:* checking if this is a source package ... OK ./behavr.Rcheck/00check.log:* checking if there is a namespace ... OK ./behavr.Rcheck/00check.log:* checking for executable files ... OK ./behavr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./behavr.Rcheck/00check.log:* checking for portable file names ... OK ./behavr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./behavr.Rcheck/00check.log:* checking whether package ‘behavr’ can be installed ... OK ./behavr.Rcheck/00check.log:* checking installed package size ... OK ./behavr.Rcheck/00check.log:* checking package directory ... OK ./behavr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./behavr.Rcheck/00check.log:* checking top-level files ... OK ./behavr.Rcheck/00check.log:* checking for left-over files ... OK ./behavr.Rcheck/00check.log:* checking index information ... OK ./behavr.Rcheck/00check.log:* checking package subdirectories ... OK ./behavr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./behavr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./behavr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./behavr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./behavr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./behavr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./behavr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./behavr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./behavr.Rcheck/00check.log:* checking dependencies in R code ... OK ./behavr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./behavr.Rcheck/00check.log:* checking replacement functions ... OK ./behavr.Rcheck/00check.log:* checking foreign function calls ... OK ./behavr.Rcheck/00check.log:* checking R code for possible problems ... OK ./behavr.Rcheck/00check.log:* checking Rd files ... OK ./behavr.Rcheck/00check.log:* checking Rd metadata ... OK ./behavr.Rcheck/00check.log:* checking Rd cross-references ... OK ./behavr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./behavr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./behavr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./behavr.Rcheck/00check.log:* checking Rd contents ... OK ./behavr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./behavr.Rcheck/00check.log:* checking examples ... ERROR ./behavr.Rcheck/00check.log:Running examples in ‘behavr-Ex.R’ failed ./behavr.Rcheck/00check.log:The error most likely occurred in: ./behavr.Rcheck/00check.log:> ### Name: behavr ./behavr.Rcheck/00check.log:> ### Title: An S3 class, based on data.table, to store ethomics data ./behavr.Rcheck/00check.log:> ### Aliases: behavr behavr setbehavr is.behavr ./behavr.Rcheck/00check.log:> ./behavr.Rcheck/00check.log:> ### ** Examples ./behavr.Rcheck/00check.log:> ./behavr.Rcheck/00check.log:> # We generate some metadata and data ./behavr.Rcheck/00check.log:> set.seed(1) ./behavr.Rcheck/00check.log:> met <- data.table::data.table(id = 1:5, ./behavr.Rcheck/00check.log:+ condition = letters[1:5], ./behavr.Rcheck/00check.log:+ sex = c("M", "M", "M", "F", "F"), ./behavr.Rcheck/00check.log:+ key = "id") ./behavr.Rcheck/00check.log:> data <- met[ , ./behavr.Rcheck/00check.log:+ list(t = 1L:100L, ./behavr.Rcheck/00check.log:+ x = rnorm(100), ./behavr.Rcheck/00check.log:+ y = rnorm(100), ./behavr.Rcheck/00check.log:+ eating = runif(100) > .5 ), ./behavr.Rcheck/00check.log:+ by = "id"] ./behavr.Rcheck/00check.log:> # we store them together in a behavr object d ./behavr.Rcheck/00check.log:> # d is a copy of the data ./behavr.Rcheck/00check.log:> d <- behavr(data, met) ./behavr.Rcheck/00check.log:> print(d) ./behavr.Rcheck/00check.log: ==== METADATA ==== ./behavr.Rcheck/00check.log: id condition sex ./behavr.Rcheck/00check.log: ./behavr.Rcheck/00check.log:1: 1 a M ./behavr.Rcheck/00check.log:2: 2 b M ./behavr.Rcheck/00check.log:3: 3 c M ./behavr.Rcheck/00check.log:4: 4 d F ./behavr.Rcheck/00check.log:5: 5 e F ./behavr.Rcheck/00check.log: ====== DATA ====== ./behavr.Rcheck/00check.log:Error: C stack usage 7969636 is too close to the limit ./behavr.Rcheck/00check.log:Execution halted ./behavr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./behavr.Rcheck/00check.log:* checking tests ... ERROR ./behavr.Rcheck/00check.log: Running ‘testthat.R’ ./behavr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./behavr.Rcheck/00check.log:Complete output: ./behavr.Rcheck/00check.log: > library(testthat) ./behavr.Rcheck/00check.log: > library(behavr) ./behavr.Rcheck/00check.log: Loading required package: data.table ./behavr.Rcheck/00check.log: > ./behavr.Rcheck/00check.log: > test_check("behavr") ./behavr.Rcheck/00check.log: Error: C stack usage 7970900 is too close to the limit ./behavr.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./behavr.Rcheck/00check.log: OK: 2 SKIPPED: 0 FAILED: 0 ./behavr.Rcheck/00check.log: Execution halted ./behavr.Rcheck/00check.log:* checking PDF version of manual ... OK ./behavr.Rcheck/00check.log:* DONE ./behavr.Rcheck/00check.log:Status: 2 ERRORs ./damr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/damr.Rcheck’ ./damr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./damr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./damr.Rcheck/00check.log:* using session charset: UTF-8 ./damr.Rcheck/00check.log:* checking for file ‘damr/DESCRIPTION’ ... OK ./damr.Rcheck/00check.log:* this is package ‘damr’ version ‘0.3.1’ ./damr.Rcheck/00check.log:* package encoding: UTF-8 ./damr.Rcheck/00check.log:* checking package namespace information ... OK ./damr.Rcheck/00check.log:* checking package dependencies ... OK ./damr.Rcheck/00check.log:* checking if this is a source package ... OK ./damr.Rcheck/00check.log:* checking if there is a namespace ... OK ./damr.Rcheck/00check.log:* checking for executable files ... OK ./damr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./damr.Rcheck/00check.log:* checking for portable file names ... OK ./damr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./damr.Rcheck/00check.log:* checking whether package ‘damr’ can be installed ... OK ./damr.Rcheck/00check.log:* checking installed package size ... OK ./damr.Rcheck/00check.log:* checking package directory ... OK ./damr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./damr.Rcheck/00check.log:* checking top-level files ... OK ./damr.Rcheck/00check.log:* checking for left-over files ... OK ./damr.Rcheck/00check.log:* checking index information ... OK ./damr.Rcheck/00check.log:* checking package subdirectories ... OK ./damr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./damr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./damr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./damr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./damr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./damr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./damr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./damr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./damr.Rcheck/00check.log:* checking dependencies in R code ... OK ./damr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./damr.Rcheck/00check.log:* checking replacement functions ... OK ./damr.Rcheck/00check.log:* checking foreign function calls ... OK ./damr.Rcheck/00check.log:* checking R code for possible problems ... OK ./damr.Rcheck/00check.log:* checking Rd files ... OK ./damr.Rcheck/00check.log:* checking Rd metadata ... OK ./damr.Rcheck/00check.log:* checking Rd cross-references ... OK ./damr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./damr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./damr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./damr.Rcheck/00check.log:* checking Rd contents ... OK ./damr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./damr.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./damr.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./damr.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./damr.Rcheck/00check.log:* checking examples ... ERROR ./damr.Rcheck/00check.log:Running examples in ‘damr-Ex.R’ failed ./damr.Rcheck/00check.log:The error most likely occurred in: ./damr.Rcheck/00check.log:> ### Name: load_dam ./damr.Rcheck/00check.log:> ### Title: Load DAMS data from one or several continuous text files ./damr.Rcheck/00check.log:> ### Aliases: load_dam load_dam2 ./damr.Rcheck/00check.log:> ./damr.Rcheck/00check.log:> ### ** Examples ./damr.Rcheck/00check.log:> ./damr.Rcheck/00check.log:> # This is where our toy data lives ./damr.Rcheck/00check.log:> root_dir <- damr_example_dir() ./damr.Rcheck/00check.log:> ./damr.Rcheck/00check.log:> # Metadata already made for us. ./damr.Rcheck/00check.log:> # It defines condition and genotype of each animal ./damr.Rcheck/00check.log:> data(single_file_metadata) ./damr.Rcheck/00check.log:> print(single_file_metadata) ./damr.Rcheck/00check.log: file start_datetime stop_datetime region_id condition genotype ./damr.Rcheck/00check.log:1 M064.txt 2017-07-01 10:00:00 2017-07-07 1 a A ./damr.Rcheck/00check.log:2 M064.txt 2017-07-02 10:00:00 2017-07-07 2 a A ./damr.Rcheck/00check.log:3 M064.txt 2017-07-01 10:00:00 2017-07-07 3 a B ./damr.Rcheck/00check.log:4 M064.txt 2017-07-02 10:00:00 2017-07-07 4 a B ./damr.Rcheck/00check.log:5 M064.txt 2017-07-01 10:00:00 2017-07-07 5 a A ./damr.Rcheck/00check.log:6 M064.txt 2017-07-02 10:00:00 2017-07-07 6 a A ./damr.Rcheck/00check.log:7 M064.txt 2017-07-01 10:00:00 2017-07-07 7 a B ./damr.Rcheck/00check.log:8 M064.txt 2017-07-02 10:00:00 2017-07-07 8 a B ./damr.Rcheck/00check.log:9 M064.txt 2017-07-01 10:00:00 2017-07-07 9 a A ./damr.Rcheck/00check.log:10 M064.txt 2017-07-02 10:00:00 2017-07-07 10 a A ./damr.Rcheck/00check.log:11 M064.txt 2017-07-01 10:00:00 2017-07-07 11 a B ./damr.Rcheck/00check.log:12 M064.txt 2017-07-02 10:00:00 2017-07-07 12 a B ./damr.Rcheck/00check.log:13 M064.txt 2017-07-01 10:00:00 2017-07-07 13 a A ./damr.Rcheck/00check.log:14 M064.txt 2017-07-02 10:00:00 2017-07-07 14 a A ./damr.Rcheck/00check.log:15 M064.txt 2017-07-01 10:00:00 2017-07-07 15 a B ./damr.Rcheck/00check.log:16 M064.txt 2017-07-02 10:00:00 2017-07-07 16 a B ./damr.Rcheck/00check.log:17 M064.txt 2017-07-01 10:00:00 2017-07-07 17 b A ./damr.Rcheck/00check.log:18 M064.txt 2017-07-02 10:00:00 2017-07-07 18 b A ./damr.Rcheck/00check.log:19 M064.txt 2017-07-01 10:00:00 2017-07-07 19 b B ./damr.Rcheck/00check.log:20 M064.txt 2017-07-02 10:00:00 2017-07-07 20 b B ./damr.Rcheck/00check.log:21 M064.txt 2017-07-01 10:00:00 2017-07-07 21 b A ./damr.Rcheck/00check.log:22 M064.txt 2017-07-02 10:00:00 2017-07-07 22 b A ./damr.Rcheck/00check.log:23 M064.txt 2017-07-01 10:00:00 2017-07-07 23 b B ./damr.Rcheck/00check.log:24 M064.txt 2017-07-02 10:00:00 2017-07-07 24 b B ./damr.Rcheck/00check.log:25 M064.txt 2017-07-01 10:00:00 2017-07-07 25 b A ./damr.Rcheck/00check.log:26 M064.txt 2017-07-02 10:00:00 2017-07-07 26 b A ./damr.Rcheck/00check.log:27 M064.txt 2017-07-01 10:00:00 2017-07-07 27 b B ./damr.Rcheck/00check.log:28 M064.txt 2017-07-02 10:00:00 2017-07-07 28 b B ./damr.Rcheck/00check.log:29 M064.txt 2017-07-01 10:00:00 2017-07-07 29 b A ./damr.Rcheck/00check.log:30 M064.txt 2017-07-02 10:00:00 2017-07-07 30 b A ./damr.Rcheck/00check.log:31 M064.txt 2017-07-01 10:00:00 2017-07-07 31 b B ./damr.Rcheck/00check.log:32 M064.txt 2017-07-02 10:00:00 2017-07-07 32 b B ./damr.Rcheck/00check.log:> # Linking: ./damr.Rcheck/00check.log:> metadata <- link_dam_metadata(single_file_metadata, root_dir) ./damr.Rcheck/00check.log:> ./damr.Rcheck/00check.log:> # We find and load the matching data ./damr.Rcheck/00check.log:> dt <- load_dam(metadata) ./damr.Rcheck/00check.log:> print(dt) ./damr.Rcheck/00check.log: ==== METADATA ==== ./damr.Rcheck/00check.log: id file_info region_id ./damr.Rcheck/00check.log: ./damr.Rcheck/00check.log: 1: 2017-07-01 10:00:00|M064.txt|01 1 ./damr.Rcheck/00check.log: 2: 2017-07-01 10:00:00|M064.txt|03 3 ./damr.Rcheck/00check.log: 3: 2017-07-01 10:00:00|M064.txt|05 5 ./damr.Rcheck/00check.log: 4: 2017-07-01 10:00:00|M064.txt|07 7 ./damr.Rcheck/00check.log: 5: 2017-07-01 10:00:00|M064.txt|09 9 ./damr.Rcheck/00check.log: 6: 2017-07-01 10:00:00|M064.txt|11 11 ./damr.Rcheck/00check.log: 7: 2017-07-01 10:00:00|M064.txt|13 13 ./damr.Rcheck/00check.log: 8: 2017-07-01 10:00:00|M064.txt|15 15 ./damr.Rcheck/00check.log: 9: 2017-07-01 10:00:00|M064.txt|17 17 ./damr.Rcheck/00check.log:10: 2017-07-01 10:00:00|M064.txt|19 19 ./damr.Rcheck/00check.log:11: 2017-07-01 10:00:00|M064.txt|21 21 ./damr.Rcheck/00check.log:12: 2017-07-01 10:00:00|M064.txt|23 23 ./damr.Rcheck/00check.log:13: 2017-07-01 10:00:00|M064.txt|25 25 ./damr.Rcheck/00check.log:14: 2017-07-01 10:00:00|M064.txt|27 27 ./damr.Rcheck/00check.log:15: 2017-07-01 10:00:00|M064.txt|29 29 ./damr.Rcheck/00check.log:16: 2017-07-01 10:00:00|M064.txt|31 31 ./damr.Rcheck/00check.log:17: 2017-07-02 10:00:00|M064.txt|02 2 ./damr.Rcheck/00check.log:18: 2017-07-02 10:00:00|M064.txt|04 4 ./damr.Rcheck/00check.log:19: 2017-07-02 10:00:00|M064.txt|06 6 ./damr.Rcheck/00check.log:20: 2017-07-02 10:00:00|M064.txt|08 8 ./damr.Rcheck/00check.log:21: 2017-07-02 10:00:00|M064.txt|10 10 ./damr.Rcheck/00check.log:22: 2017-07-02 10:00:00|M064.txt|12 12 ./damr.Rcheck/00check.log:23: 2017-07-02 10:00:00|M064.txt|14 14 ./damr.Rcheck/00check.log:24: 2017-07-02 10:00:00|M064.txt|16 16 ./damr.Rcheck/00check.log:25: 2017-07-02 10:00:00|M064.txt|18 18 ./damr.Rcheck/00check.log:26: 2017-07-02 10:00:00|M064.txt|20 20 ./damr.Rcheck/00check.log:27: 2017-07-02 10:00:00|M064.txt|22 22 ./damr.Rcheck/00check.log:28: 2017-07-02 10:00:00|M064.txt|24 24 ./damr.Rcheck/00check.log:29: 2017-07-02 10:00:00|M064.txt|26 26 ./damr.Rcheck/00check.log:30: 2017-07-02 10:00:00|M064.txt|28 28 ./damr.Rcheck/00check.log:31: 2017-07-02 10:00:00|M064.txt|30 30 ./damr.Rcheck/00check.log:32: 2017-07-02 10:00:00|M064.txt|32 32 ./damr.Rcheck/00check.log: id file_info region_id ./damr.Rcheck/00check.log: experiment_id start_datetime stop_datetime condition ./damr.Rcheck/00check.log: ./damr.Rcheck/00check.log: 1: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 2: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 3: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 4: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 5: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 6: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 7: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 8: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log: 9: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:10: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:11: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:12: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:13: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:14: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:15: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:16: 2017-07-01 10:00:00|M064.txt 2017-07-01 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:17: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:18: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:19: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:20: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:21: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:22: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:23: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:24: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 a ./damr.Rcheck/00check.log:25: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:26: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:27: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:28: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:29: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:30: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:31: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log:32: 2017-07-02 10:00:00|M064.txt 2017-07-02 10:00:00 2017-07-07 b ./damr.Rcheck/00check.log: experiment_id start_datetime stop_datetime condition ./damr.Rcheck/00check.log: genotype ./damr.Rcheck/00check.log: ./damr.Rcheck/00check.log: 1: A ./damr.Rcheck/00check.log: 2: B ./damr.Rcheck/00check.log: 3: A ./damr.Rcheck/00check.log: 4: B ./damr.Rcheck/00check.log: 5: A ./damr.Rcheck/00check.log: 6: B ./damr.Rcheck/00check.log: 7: A ./damr.Rcheck/00check.log: 8: B ./damr.Rcheck/00check.log: 9: A ./damr.Rcheck/00check.log:10: B ./damr.Rcheck/00check.log:11: A ./damr.Rcheck/00check.log:12: B ./damr.Rcheck/00check.log:13: A ./damr.Rcheck/00check.log:14: B ./damr.Rcheck/00check.log:15: A ./damr.Rcheck/00check.log:16: B ./damr.Rcheck/00check.log:17: A ./damr.Rcheck/00check.log:18: B ./damr.Rcheck/00check.log:19: A ./damr.Rcheck/00check.log:20: B ./damr.Rcheck/00check.log:21: A ./damr.Rcheck/00check.log:22: B ./damr.Rcheck/00check.log:23: A ./damr.Rcheck/00check.log:24: B ./damr.Rcheck/00check.log:25: A ./damr.Rcheck/00check.log:26: B ./damr.Rcheck/00check.log:27: A ./damr.Rcheck/00check.log:28: B ./damr.Rcheck/00check.log:29: A ./damr.Rcheck/00check.log:30: B ./damr.Rcheck/00check.log:31: A ./damr.Rcheck/00check.log:32: B ./damr.Rcheck/00check.log: genotype ./damr.Rcheck/00check.log: ====== DATA ====== ./damr.Rcheck/00check.log:Error: C stack usage 7970740 is too close to the limit ./damr.Rcheck/00check.log:Execution halted ./damr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./damr.Rcheck/00check.log:* checking tests ... ERROR ./damr.Rcheck/00check.log: Running ‘testthat.R’ ./damr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./damr.Rcheck/00check.log:Last 13 lines of output: ./damr.Rcheck/00check.log: 4: `[.data.table`(dt, xmv(region_id) == 15 & activity == 10) ./damr.Rcheck/00check.log: 5: tryCatch(eval(.massagei(isub), x, parent.frame()), error = function(e) .checkTypos(e, ./damr.Rcheck/00check.log: names(x))) ./damr.Rcheck/00check.log: 6: tryCatchList(expr, classes, parentenv, handlers) ./damr.Rcheck/00check.log: 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) ./damr.Rcheck/00check.log: 8: value[[3L]](cond) ./damr.Rcheck/00check.log: 9: .checkTypos(e, names(x)) ./damr.Rcheck/00check.log: 10: stop(err$message, call. = FALSE) ./damr.Rcheck/00check.log: ./damr.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./damr.Rcheck/00check.log: OK: 30 SKIPPED: 0 FAILED: 1 ./damr.Rcheck/00check.log: 1. Error: results match text file (@test-read_dam_file.R#6) ./damr.Rcheck/00check.log: ./damr.Rcheck/00check.log: Error: testthat unit tests failed ./damr.Rcheck/00check.log: Execution halted ./damr.Rcheck/00check.log:* checking PDF version of manual ... OK ./damr.Rcheck/00check.log:* DONE ./damr.Rcheck/00check.log:Status: 2 ERRORs ./DeclareDesign.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/DeclareDesign.Rcheck’ ./DeclareDesign.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./DeclareDesign.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./DeclareDesign.Rcheck/00check.log:* using session charset: UTF-8 ./DeclareDesign.Rcheck/00check.log:* checking for file ‘DeclareDesign/DESCRIPTION’ ... OK ./DeclareDesign.Rcheck/00check.log:* this is package ‘DeclareDesign’ version ‘0.12.0’ ./DeclareDesign.Rcheck/00check.log:* package encoding: UTF-8 ./DeclareDesign.Rcheck/00check.log:* checking package namespace information ... OK ./DeclareDesign.Rcheck/00check.log:* checking package dependencies ... OK ./DeclareDesign.Rcheck/00check.log:* checking if this is a source package ... OK ./DeclareDesign.Rcheck/00check.log:* checking if there is a namespace ... OK ./DeclareDesign.Rcheck/00check.log:* checking for executable files ... OK ./DeclareDesign.Rcheck/00check.log:* checking for hidden files and directories ... OK ./DeclareDesign.Rcheck/00check.log:* checking for portable file names ... OK ./DeclareDesign.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./DeclareDesign.Rcheck/00check.log:* checking whether package ‘DeclareDesign’ can be installed ... OK ./DeclareDesign.Rcheck/00check.log:* checking installed package size ... OK ./DeclareDesign.Rcheck/00check.log:* checking package directory ... OK ./DeclareDesign.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./DeclareDesign.Rcheck/00check.log:* checking top-level files ... OK ./DeclareDesign.Rcheck/00check.log:* checking for left-over files ... OK ./DeclareDesign.Rcheck/00check.log:* checking index information ... OK ./DeclareDesign.Rcheck/00check.log:* checking package subdirectories ... OK ./DeclareDesign.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./DeclareDesign.Rcheck/00check.log:* checking R files for syntax errors ... OK ./DeclareDesign.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./DeclareDesign.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./DeclareDesign.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./DeclareDesign.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./DeclareDesign.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./DeclareDesign.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./DeclareDesign.Rcheck/00check.log:* checking dependencies in R code ... OK ./DeclareDesign.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./DeclareDesign.Rcheck/00check.log:* checking replacement functions ... OK ./DeclareDesign.Rcheck/00check.log:* checking foreign function calls ... OK ./DeclareDesign.Rcheck/00check.log:* checking R code for possible problems ... OK ./DeclareDesign.Rcheck/00check.log:* checking Rd files ... OK ./DeclareDesign.Rcheck/00check.log:* checking Rd metadata ... OK ./DeclareDesign.Rcheck/00check.log:* checking Rd cross-references ... OK ./DeclareDesign.Rcheck/00check.log:* checking for missing documentation entries ... OK ./DeclareDesign.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./DeclareDesign.Rcheck/00check.log:* checking Rd \usage sections ... OK ./DeclareDesign.Rcheck/00check.log:* checking Rd contents ... OK ./DeclareDesign.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./DeclareDesign.Rcheck/00check.log:* checking examples ... OK ./DeclareDesign.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./DeclareDesign.Rcheck/00check.log:* checking tests ... ERROR ./DeclareDesign.Rcheck/00check.log: Running ‘testthat.R’ ./DeclareDesign.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./DeclareDesign.Rcheck/00check.log:Last 13 lines of output: ./DeclareDesign.Rcheck/00check.log: > library(DeclareDesign) ./DeclareDesign.Rcheck/00check.log: Loading required package: randomizr ./DeclareDesign.Rcheck/00check.log: Loading required package: fabricatr ./DeclareDesign.Rcheck/00check.log: Loading required package: estimatr ./DeclareDesign.Rcheck/00check.log: > ./DeclareDesign.Rcheck/00check.log: > test_check("DeclareDesign") ./DeclareDesign.Rcheck/00check.log: ── 1. Failure: gam (@test-model.R#247) ──────────────────────────────────────── ./DeclareDesign.Rcheck/00check.log: `expect_equal(ncol(draw_estimates(des)), 7)` did not produce any warnings. ./DeclareDesign.Rcheck/00check.log: ./DeclareDesign.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./DeclareDesign.Rcheck/00check.log: OK: 456 SKIPPED: 5 FAILED: 1 ./DeclareDesign.Rcheck/00check.log: 1. Failure: gam (@test-model.R#247) ./DeclareDesign.Rcheck/00check.log: ./DeclareDesign.Rcheck/00check.log: Error: testthat unit tests failed ./DeclareDesign.Rcheck/00check.log: Execution halted ./DeclareDesign.Rcheck/00check.log:* checking PDF version of manual ... OK ./DeclareDesign.Rcheck/00check.log:* DONE ./DeclareDesign.Rcheck/00check.log:Status: 1 ERROR ./ggetho.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ggetho.Rcheck’ ./ggetho.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./ggetho.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ggetho.Rcheck/00check.log:* using session charset: UTF-8 ./ggetho.Rcheck/00check.log:* checking for file ‘ggetho/DESCRIPTION’ ... OK ./ggetho.Rcheck/00check.log:* this is package ‘ggetho’ version ‘0.3.4’ ./ggetho.Rcheck/00check.log:* package encoding: UTF-8 ./ggetho.Rcheck/00check.log:* checking package namespace information ... OK ./ggetho.Rcheck/00check.log:* checking package dependencies ... OK ./ggetho.Rcheck/00check.log:* checking if this is a source package ... OK ./ggetho.Rcheck/00check.log:* checking if there is a namespace ... OK ./ggetho.Rcheck/00check.log:* checking for executable files ... OK ./ggetho.Rcheck/00check.log:* checking for hidden files and directories ... OK ./ggetho.Rcheck/00check.log:* checking for portable file names ... OK ./ggetho.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ggetho.Rcheck/00check.log:* checking whether package ‘ggetho’ can be installed ... OK ./ggetho.Rcheck/00check.log:* checking installed package size ... OK ./ggetho.Rcheck/00check.log:* checking package directory ... OK ./ggetho.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ggetho.Rcheck/00check.log:* checking top-level files ... OK ./ggetho.Rcheck/00check.log:* checking for left-over files ... OK ./ggetho.Rcheck/00check.log:* checking index information ... OK ./ggetho.Rcheck/00check.log:* checking package subdirectories ... OK ./ggetho.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ggetho.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ggetho.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ggetho.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ggetho.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ggetho.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ggetho.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ggetho.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ggetho.Rcheck/00check.log:* checking dependencies in R code ... OK ./ggetho.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ggetho.Rcheck/00check.log:* checking replacement functions ... OK ./ggetho.Rcheck/00check.log:* checking foreign function calls ... OK ./ggetho.Rcheck/00check.log:* checking R code for possible problems ... OK ./ggetho.Rcheck/00check.log:* checking Rd files ... OK ./ggetho.Rcheck/00check.log:* checking Rd metadata ... OK ./ggetho.Rcheck/00check.log:* checking Rd cross-references ... OK ./ggetho.Rcheck/00check.log:* checking for missing documentation entries ... OK ./ggetho.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ggetho.Rcheck/00check.log:* checking Rd \usage sections ... OK ./ggetho.Rcheck/00check.log:* checking Rd contents ... OK ./ggetho.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ggetho.Rcheck/00check.log:* checking examples ... ERROR ./ggetho.Rcheck/00check.log:Running examples in ‘ggetho-Ex.R’ failed ./ggetho.Rcheck/00check.log:The error most likely occurred in: ./ggetho.Rcheck/00check.log:> ### Name: time_scales ./ggetho.Rcheck/00check.log:> ### Title: Scales for durations ./ggetho.Rcheck/00check.log:> ### Aliases: time_scales scale_x_days scale_y_days scale_x_hours ./ggetho.Rcheck/00check.log:> ### scale_y_hours scale_x_seconds scale_y_seconds ./ggetho.Rcheck/00check.log:> ./ggetho.Rcheck/00check.log:> ### ** Examples ./ggetho.Rcheck/00check.log:> ./ggetho.Rcheck/00check.log:> # We generate some data ./ggetho.Rcheck/00check.log:> metadata <- data.frame(id = sprintf("toy_experiment | %02d", 1:20), ./ggetho.Rcheck/00check.log:+ condition = c("A","B")) ./ggetho.Rcheck/00check.log:> dt <- toy_activity_data(metadata, 3) ./ggetho.Rcheck/00check.log:> # Then, a simple plot ./ggetho.Rcheck/00check.log:> pl <- ggetho(dt, aes(y = asleep)) + stat_pop_etho() ./ggetho.Rcheck/00check.log:> pl + scale_x_hours(breaks = days(c(1, 2))) ./ggetho.Rcheck/00check.log:Scale for 'x' is already present. Adding another scale for 'x', which will ./ggetho.Rcheck/00check.log:replace the existing scale. ./ggetho.Rcheck/00check.log:> pl + scale_x_hours() ./ggetho.Rcheck/00check.log:Scale for 'x' is already present. Adding another scale for 'x', which will ./ggetho.Rcheck/00check.log:replace the existing scale. ./ggetho.Rcheck/00check.log:> pl + scale_x_days(breaks = days(c(1, 2))) ./ggetho.Rcheck/00check.log:Scale for 'x' is already present. Adding another scale for 'x', which will ./ggetho.Rcheck/00check.log:replace the existing scale. ./ggetho.Rcheck/00check.log:> pl + scale_x_days() ./ggetho.Rcheck/00check.log:Scale for 'x' is already present. Adding another scale for 'x', which will ./ggetho.Rcheck/00check.log:replace the existing scale. ./ggetho.Rcheck/00check.log:> ./ggetho.Rcheck/00check.log:> # To express time modulus `time_wrap` ./ggetho.Rcheck/00check.log:> # e.g. time n the day ./ggetho.Rcheck/00check.log:> pl + scale_x_hours(time_wrap = hours(24)) + ./ggetho.Rcheck/00check.log:+ coord_cartesian(xlim=c(0, days(2))) ./ggetho.Rcheck/00check.log:Scale for 'x' is already present. Adding another scale for 'x', which will ./ggetho.Rcheck/00check.log:replace the existing scale. ./ggetho.Rcheck/00check.log:> ./ggetho.Rcheck/00check.log:> # On a shorter time scale ./ggetho.Rcheck/00check.log:> pl <- ggetho(dt[t < hours(5)], aes(z = asleep)) + stat_tile_etho() ./ggetho.Rcheck/00check.log:Error: C stack usage 7969540 is too close to the limit ./ggetho.Rcheck/00check.log:Execution halted ./ggetho.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./ggetho.Rcheck/00check.log:* checking tests ... OK ./ggetho.Rcheck/00check.log: Running ‘testthat.R’ ./ggetho.Rcheck/00check.log:* checking PDF version of manual ... OK ./ggetho.Rcheck/00check.log:* DONE ./ggetho.Rcheck/00check.log:Status: 1 ERROR ./maditr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/maditr.Rcheck’ ./maditr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./maditr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./maditr.Rcheck/00check.log:* using session charset: UTF-8 ./maditr.Rcheck/00check.log:* checking for file ‘maditr/DESCRIPTION’ ... OK ./maditr.Rcheck/00check.log:* checking extension type ... Package ./maditr.Rcheck/00check.log:* this is package ‘maditr’ version ‘0.6.0’ ./maditr.Rcheck/00check.log:* package encoding: UTF-8 ./maditr.Rcheck/00check.log:* checking package namespace information ... OK ./maditr.Rcheck/00check.log:* checking package dependencies ... OK ./maditr.Rcheck/00check.log:* checking if this is a source package ... OK ./maditr.Rcheck/00check.log:* checking if there is a namespace ... OK ./maditr.Rcheck/00check.log:* checking for executable files ... OK ./maditr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./maditr.Rcheck/00check.log:* checking for portable file names ... OK ./maditr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./maditr.Rcheck/00check.log:* checking whether package ‘maditr’ can be installed ... OK ./maditr.Rcheck/00check.log:* checking installed package size ... OK ./maditr.Rcheck/00check.log:* checking package directory ... OK ./maditr.Rcheck/00check.log:* checking ‘build’ directory ... OK ./maditr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./maditr.Rcheck/00check.log:* checking top-level files ... OK ./maditr.Rcheck/00check.log:* checking for left-over files ... OK ./maditr.Rcheck/00check.log:* checking index information ... OK ./maditr.Rcheck/00check.log:* checking package subdirectories ... OK ./maditr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./maditr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./maditr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./maditr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./maditr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./maditr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./maditr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./maditr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./maditr.Rcheck/00check.log:* checking dependencies in R code ... OK ./maditr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./maditr.Rcheck/00check.log:* checking replacement functions ... OK ./maditr.Rcheck/00check.log:* checking foreign function calls ... OK ./maditr.Rcheck/00check.log:* checking R code for possible problems ... OK ./maditr.Rcheck/00check.log:* checking Rd files ... OK ./maditr.Rcheck/00check.log:* checking Rd metadata ... OK ./maditr.Rcheck/00check.log:* checking Rd cross-references ... OK ./maditr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./maditr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./maditr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./maditr.Rcheck/00check.log:* checking Rd contents ... OK ./maditr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./maditr.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./maditr.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./maditr.Rcheck/00check.log:* checking examples ... OK ./maditr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./maditr.Rcheck/00check.log:* checking tests ... ERROR ./maditr.Rcheck/00check.log: Running ‘testthat.R’ ./maditr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./maditr.Rcheck/00check.log:Last 13 lines of output: ./maditr.Rcheck/00check.log: Objects equal but not identical ./maditr.Rcheck/00check.log: ./maditr.Rcheck/00check.log: ── 4. Failure: (unknown) (@tests.R#170) ─────────────────────────────────────── ./maditr.Rcheck/00check.log: `res3` not identical to `res2`. ./maditr.Rcheck/00check.log: Objects equal but not identical ./maditr.Rcheck/00check.log: ./maditr.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./maditr.Rcheck/00check.log: OK: 110 SKIPPED: 0 FAILED: 4 ./maditr.Rcheck/00check.log: 1. Failure: (unknown) (@test_verbs.R#82) ./maditr.Rcheck/00check.log: 2. Failure: (unknown) (@test_verbs.R#83) ./maditr.Rcheck/00check.log: 3. Failure: (unknown) (@tests.R#169) ./maditr.Rcheck/00check.log: 4. Failure: (unknown) (@tests.R#170) ./maditr.Rcheck/00check.log: ./maditr.Rcheck/00check.log: Error: testthat unit tests failed ./maditr.Rcheck/00check.log: Execution halted ./maditr.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./maditr.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./maditr.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./maditr.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./maditr.Rcheck/00check.log:* checking PDF version of manual ... OK ./maditr.Rcheck/00check.log:* DONE ./maditr.Rcheck/00check.log:Status: 1 ERROR ./popEpi.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/popEpi.Rcheck’ ./popEpi.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./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 ... OK ./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: NOTE: entry.status has been set to "DM" for all. ./popEpi.Rcheck/00check.log: first.bad.surv.int last.bad.surv.int surv.obs ./popEpi.Rcheck/00check.log: 1: 61 120 NaN ./popEpi.Rcheck/00check.log: first.bad.surv.int last.bad.surv.int surv.obs ./popEpi.Rcheck/00check.log: 1: 61 120 NaN ./popEpi.Rcheck/00check.log: agegr first.bad.surv.int last.bad.surv.int surv.obs ./popEpi.Rcheck/00check.log: 1: 3 61 120 NaN ./popEpi.Rcheck/00check.log: agegr first.bad.surv.int last.bad.surv.int surv.obs ./popEpi.Rcheck/00check.log: 1: 3 61 120 NaN ./popEpi.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./popEpi.Rcheck/00check.log: OK: 255 SKIPPED: 41 FAILED: 1 ./popEpi.Rcheck/00check.log: 1. Error: rate.plot doesnt throw an error (@test_rate.R#214) ./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 ... OK ./popEpi.Rcheck/00check.log:* checking PDF version of manual ... OK ./popEpi.Rcheck/00check.log:* DONE ./popEpi.Rcheck/00check.log:Status: 1 ERROR ./PROSPER.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/PROSPER.Rcheck’ ./PROSPER.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./PROSPER.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./PROSPER.Rcheck/00check.log:* using session charset: UTF-8 ./PROSPER.Rcheck/00check.log:* checking for file ‘PROSPER/DESCRIPTION’ ... OK ./PROSPER.Rcheck/00check.log:* checking extension type ... Package ./PROSPER.Rcheck/00check.log:* this is package ‘PROSPER’ version ‘0.3.0’ ./PROSPER.Rcheck/00check.log:* checking package namespace information ... OK ./PROSPER.Rcheck/00check.log:* checking package dependencies ... OK ./PROSPER.Rcheck/00check.log:* checking if this is a source package ... OK ./PROSPER.Rcheck/00check.log:* checking if there is a namespace ... OK ./PROSPER.Rcheck/00check.log:* checking for executable files ... OK ./PROSPER.Rcheck/00check.log:* checking for hidden files and directories ... OK ./PROSPER.Rcheck/00check.log:* checking for portable file names ... OK ./PROSPER.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./PROSPER.Rcheck/00check.log:* checking whether package ‘PROSPER’ can be installed ... OK ./PROSPER.Rcheck/00check.log:* checking installed package size ... OK ./PROSPER.Rcheck/00check.log:* checking package directory ... OK ./PROSPER.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./PROSPER.Rcheck/00check.log:* checking top-level files ... OK ./PROSPER.Rcheck/00check.log:* checking for left-over files ... OK ./PROSPER.Rcheck/00check.log:* checking index information ... OK ./PROSPER.Rcheck/00check.log:* checking package subdirectories ... OK ./PROSPER.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./PROSPER.Rcheck/00check.log:* checking R files for syntax errors ... OK ./PROSPER.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./PROSPER.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./PROSPER.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./PROSPER.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./PROSPER.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./PROSPER.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./PROSPER.Rcheck/00check.log:* checking dependencies in R code ... OK ./PROSPER.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./PROSPER.Rcheck/00check.log:* checking replacement functions ... OK ./PROSPER.Rcheck/00check.log:* checking foreign function calls ... OK ./PROSPER.Rcheck/00check.log:* checking R code for possible problems ... OK ./PROSPER.Rcheck/00check.log:* checking Rd files ... OK ./PROSPER.Rcheck/00check.log:* checking Rd metadata ... OK ./PROSPER.Rcheck/00check.log:* checking Rd cross-references ... OK ./PROSPER.Rcheck/00check.log:* checking for missing documentation entries ... OK ./PROSPER.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./PROSPER.Rcheck/00check.log:* checking Rd \usage sections ... OK ./PROSPER.Rcheck/00check.log:* checking Rd contents ... OK ./PROSPER.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./PROSPER.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./PROSPER.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./PROSPER.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./PROSPER.Rcheck/00check.log:* checking examples ... ERROR ./PROSPER.Rcheck/00check.log:Running examples in ‘PROSPER-Ex.R’ failed ./PROSPER.Rcheck/00check.log:The error most likely occurred in: ./PROSPER.Rcheck/00check.log:> ### Name: plot ./PROSPER.Rcheck/00check.log:> ### Title: Simple plot for prosper simulation results ./PROSPER.Rcheck/00check.log:> ### Aliases: plot plot,prosper,missing-method ./PROSPER.Rcheck/00check.log:> ./PROSPER.Rcheck/00check.log:> ### ** Examples ./PROSPER.Rcheck/00check.log:> ./PROSPER.Rcheck/00check.log:> data(param.LOLRI) ./PROSPER.Rcheck/00check.log:> mod_lolri <- prosper.LOLRI(param.weed=param.LOLRI, area=50, ./PROSPER.Rcheck/00check.log:+ duration=3, repetitions=2) ./PROSPER.Rcheck/00check.log:SIMULATION START ./PROSPER.Rcheck/00check.log:struc_preparation starts...finished! ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:--------preparation ready------ ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:starting simulation run 1 ./PROSPER.Rcheck/00check.log:gen_freq starts...finished! ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:starting the timeloop ./PROSPER.Rcheck/00check.log:time step 1 starts ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_germc starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_reprod starts...finished! ./PROSPER.Rcheck/00check.log:gen_diploid starts...Warning in gen_diploid(start = c("survherb1", "survherb2"), start_comb = "weedatharvest", : ./PROSPER.Rcheck/00check.log: gen_diploid: if length(start)>1 'start_comb' should be defined ./PROSPER.Rcheck/00check.log: step 1... step 2... finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:struc_saveSimData starts... step 1a...[1] "1test" ./PROSPER.Rcheck/00check.log: step 2a... step 4...finished! ./PROSPER.Rcheck/00check.log:The simulation cycle ended. ./PROSPER.Rcheck/00check.log:time step 2 starts ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_germc starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_reprod starts...finished! ./PROSPER.Rcheck/00check.log:gen_diploid starts...Warning in gen_diploid(start = c("survherb1", "survherb2"), start_comb = "weedatharvest", : ./PROSPER.Rcheck/00check.log: gen_diploid: if length(start)>1 'start_comb' should be defined ./PROSPER.Rcheck/00check.log: step 1... step 2... finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:struc_saveSimData starts... step 1... step 2... step 3... step 4...finished! ./PROSPER.Rcheck/00check.log:The simulation cycle ended. ./PROSPER.Rcheck/00check.log:time step 3 starts ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_germc starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_reprod starts...finished! ./PROSPER.Rcheck/00check.log:gen_diploid starts...Warning in gen_diploid(start = c("survherb1", "survherb2"), start_comb = "weedatharvest", : ./PROSPER.Rcheck/00check.log: gen_diploid: if length(start)>1 'start_comb' should be defined ./PROSPER.Rcheck/00check.log: step 1... step 2... finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:struc_saveSimData starts... step 1... step 2... step 3... step 4...finished! ./PROSPER.Rcheck/00check.log:The simulation cycle ended. ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:starting simulation run 2 ./PROSPER.Rcheck/00check.log:gen_freq starts...finished! ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:--------------------------------------------- ./PROSPER.Rcheck/00check.log:starting the timeloop ./PROSPER.Rcheck/00check.log:time step 1 starts ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_germc starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_reprod starts...finished! ./PROSPER.Rcheck/00check.log:gen_diploid starts...Warning in gen_diploid(start = c("survherb1", "survherb2"), start_comb = "weedatharvest", : ./PROSPER.Rcheck/00check.log: gen_diploid: if length(start)>1 'start_comb' should be defined ./PROSPER.Rcheck/00check.log: step 1... step 2... finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:struc_saveSimData starts... step 1... step 2... step 3... step 4...finished! ./PROSPER.Rcheck/00check.log:The simulation cycle ended. ./PROSPER.Rcheck/00check.log:time step 2 starts ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_germc starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_reprod starts...finished! ./PROSPER.Rcheck/00check.log:gen_diploid starts...Warning in gen_diploid(start = c("survherb1", "survherb2"), start_comb = "weedatharvest", : ./PROSPER.Rcheck/00check.log: gen_diploid: if length(start)>1 'start_comb' should be defined ./PROSPER.Rcheck/00check.log: step 1... step 2... finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:struc_saveSimData starts... step 1... step 2... step 3... step 4...finished! ./PROSPER.Rcheck/00check.log:The simulation cycle ended. ./PROSPER.Rcheck/00check.log:time step 3 starts ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_germc starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_reprod starts...finished! ./PROSPER.Rcheck/00check.log:gen_diploid starts...Warning in gen_diploid(start = c("survherb1", "survherb2"), start_comb = "weedatharvest", : ./PROSPER.Rcheck/00check.log: gen_diploid: if length(start)>1 'start_comb' should be defined ./PROSPER.Rcheck/00check.log: step 1... step 2... finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:pop_step starts...finished! ./PROSPER.Rcheck/00check.log:struc_saveSimData starts... step 1... step 2... step 3... step 4...finished! ./PROSPER.Rcheck/00check.log:The simulation cycle ended. ./PROSPER.Rcheck/00check.log:> plot(mod_lolri) ./PROSPER.Rcheck/00check.log:Error in `[.data.table`(simdata, , list(Variable = names(.SD), flevels = lapply(.SD, : ./PROSPER.Rcheck/00check.log: Empty .SDcols is not yet supported. ./PROSPER.Rcheck/00check.log:Calls: plot ... .local -> summary -> summary -> .local -> [ -> [.data.table ./PROSPER.Rcheck/00check.log:Execution halted ./PROSPER.Rcheck/00check.log:* checking PDF version of manual ... OK ./PROSPER.Rcheck/00check.log:* DONE ./PROSPER.Rcheck/00check.log:Status: 1 ERROR ./rENA.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/rENA.Rcheck’ ./rENA.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./rENA.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./rENA.Rcheck/00check.log:* using session charset: UTF-8 ./rENA.Rcheck/00check.log:* checking for file ‘rENA/DESCRIPTION’ ... OK ./rENA.Rcheck/00check.log:* checking extension type ... Package ./rENA.Rcheck/00check.log:* this is package ‘rENA’ version ‘0.1.5’ ./rENA.Rcheck/00check.log:* checking package namespace information ... OK ./rENA.Rcheck/00check.log:* checking package dependencies ... OK ./rENA.Rcheck/00check.log:* checking if this is a source package ... OK ./rENA.Rcheck/00check.log:* checking if there is a namespace ... OK ./rENA.Rcheck/00check.log:* checking for executable files ... OK ./rENA.Rcheck/00check.log:* checking for hidden files and directories ... OK ./rENA.Rcheck/00check.log:* checking for portable file names ... OK ./rENA.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./rENA.Rcheck/00check.log:* checking whether package ‘rENA’ can be installed ... OK ./rENA.Rcheck/00check.log:* checking installed package size ... NOTE ./rENA.Rcheck/00check.log: installed size is 5.7Mb ./rENA.Rcheck/00check.log: sub-directories of 1Mb or more: ./rENA.Rcheck/00check.log: libs 5.1Mb ./rENA.Rcheck/00check.log:* checking package directory ... OK ./rENA.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./rENA.Rcheck/00check.log:* checking top-level files ... OK ./rENA.Rcheck/00check.log:* checking for left-over files ... OK ./rENA.Rcheck/00check.log:* checking index information ... OK ./rENA.Rcheck/00check.log:* checking package subdirectories ... OK ./rENA.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./rENA.Rcheck/00check.log:* checking R files for syntax errors ... OK ./rENA.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./rENA.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./rENA.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./rENA.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./rENA.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./rENA.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./rENA.Rcheck/00check.log:* checking dependencies in R code ... OK ./rENA.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./rENA.Rcheck/00check.log:* checking replacement functions ... OK ./rENA.Rcheck/00check.log:* checking foreign function calls ... OK ./rENA.Rcheck/00check.log:* checking R code for possible problems ... OK ./rENA.Rcheck/00check.log:* checking Rd files ... OK ./rENA.Rcheck/00check.log:* checking Rd metadata ... OK ./rENA.Rcheck/00check.log:* checking Rd cross-references ... OK ./rENA.Rcheck/00check.log:* checking for missing documentation entries ... OK ./rENA.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./rENA.Rcheck/00check.log:* checking Rd \usage sections ... OK ./rENA.Rcheck/00check.log:* checking Rd contents ... OK ./rENA.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./rENA.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./rENA.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./rENA.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./rENA.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./rENA.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./rENA.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./rENA.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./rENA.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./rENA.Rcheck/00check.log:* checking compiled code ... OK ./rENA.Rcheck/00check.log:* checking examples ... ERROR ./rENA.Rcheck/00check.log:Running examples in ‘rENA-Ex.R’ failed ./rENA.Rcheck/00check.log:The error most likely occurred in: ./rENA.Rcheck/00check.log:> ### Name: ena.accumulate.data ./rENA.Rcheck/00check.log:> ### Title: Accumulate data from a data frame into a set of adjacency ./rENA.Rcheck/00check.log:> ### (co-occurrence) vectors ./rENA.Rcheck/00check.log:> ### Aliases: ena.accumulate.data ./rENA.Rcheck/00check.log:> ### Keywords: accumulate data, ./rENA.Rcheck/00check.log:> ./rENA.Rcheck/00check.log:> ### ** Examples ./rENA.Rcheck/00check.log:> ./rENA.Rcheck/00check.log:> data(RS.data) ./rENA.Rcheck/00check.log:> ./rENA.Rcheck/00check.log:> codeNames = c('Data','Technical.Constraints','Performance.Parameters', ./rENA.Rcheck/00check.log:+ 'Client.and.Consultant.Requests','Design.Reasoning','Collaboration'); ./rENA.Rcheck/00check.log:> ./rENA.Rcheck/00check.log:> accum = ena.accumulate.data( ./rENA.Rcheck/00check.log:+ units = RS.data[,c("UserName","Condition")], ./rENA.Rcheck/00check.log:+ conversation = RS.data[,c("Condition","GroupName")], ./rENA.Rcheck/00check.log:+ metadata = RS.data[,c("CONFIDENCE.Change","CONFIDENCE.Pre","CONFIDENCE.Post")], ./rENA.Rcheck/00check.log:+ codes = RS.data[,codeNames], ./rENA.Rcheck/00check.log:+ window.size.back = 4 ./rENA.Rcheck/00check.log:+ ) ./rENA.Rcheck/00check.log:Error in `[.data.table`(self$raw[, { : ./rENA.Rcheck/00check.log: When i and j are both missing, no other argument should be used. Empty [] is useful after := to have the result displayed; e.g. DT[,col:=val][] ./rENA.Rcheck/00check.log:Calls: ena.accumulate.data ... -> -> -> [ -> [.data.table ./rENA.Rcheck/00check.log:Execution halted ./rENA.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./rENA.Rcheck/00check.log:* checking tests ... ERROR ./rENA.Rcheck/00check.log: Running ‘testthat.R’ ./rENA.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./rENA.Rcheck/00check.log:Last 13 lines of output: ./rENA.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./rENA.Rcheck/00check.log: OK: 0 SKIPPED: 3 FAILED: 15 ./rENA.Rcheck/00check.log: 1. Error: Simple data.frame to accumulate (@test.ena.accumulate.data.file.R#20) ./rENA.Rcheck/00check.log: 2. Error: Accumulate using conversation model (@test.ena.accumulate.data.file.R#45) ./rENA.Rcheck/00check.log: 3. Error: Accumulate weighted data. (@test.ena.accumulate.data.file.R#72) ./rENA.Rcheck/00check.log: 4. Error: Corrected adjacency.vectors equals manually corrected raw data (correction = log) (@test.ena.accumulate.data.file.R#90) ./rENA.Rcheck/00check.log: 5. Error: Simple forwarded metadata (@test.ena.accumulate.data.file.R#123) ./rENA.Rcheck/00check.log: 6. Error: Test trajectories (@test.ena.accumulate.data.file.R#142) ./rENA.Rcheck/00check.log: 7. Error: Simple Accumulation from separate data.frames VS from single data frame (@test.ena.accumulations.R#34) ./rENA.Rcheck/00check.log: 8. Error: Simple forwarded metadata (@test.ena.accumulations.R#91) ./rENA.Rcheck/00check.log: 9. Error: Test trajectories (@test.ena.accumulations.R#126) ./rENA.Rcheck/00check.log: 1. ... ./rENA.Rcheck/00check.log: ./rENA.Rcheck/00check.log: Error: testthat unit tests failed ./rENA.Rcheck/00check.log: Execution halted ./rENA.Rcheck/00check.log:* checking PDF version of manual ... OK ./rENA.Rcheck/00check.log:* DONE ./rENA.Rcheck/00check.log:Status: 2 ERRORs, 1 NOTE ./rtsdata.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/rtsdata.Rcheck’ ./rtsdata.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./rtsdata.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./rtsdata.Rcheck/00check.log:* using session charset: UTF-8 ./rtsdata.Rcheck/00check.log:* checking for file ‘rtsdata/DESCRIPTION’ ... OK ./rtsdata.Rcheck/00check.log:* checking extension type ... Package ./rtsdata.Rcheck/00check.log:* this is package ‘rtsdata’ version ‘0.1.1’ ./rtsdata.Rcheck/00check.log:* checking package namespace information ... OK ./rtsdata.Rcheck/00check.log:* checking package dependencies ... ERROR ./rtsdata.Rcheck/00check.log:Package required but not available: ‘mongolite’ ./rtsdata.Rcheck/00check.log:Package suggested but not available for checking: ‘RQuantLib’ ./rtsdata.Rcheck/00check.log:See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ./rtsdata.Rcheck/00check.log:* DONE ./rtsdata.Rcheck/00check.log:Status: 1 ERROR ./scopr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/scopr.Rcheck’ ./scopr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./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 ... ERROR ./scopr.Rcheck/00check.log:Running examples in ‘scopr-Ex.R’ failed ./scopr.Rcheck/00check.log:The error most likely occurred in: ./scopr.Rcheck/00check.log:> ### Name: load_ethoscope ./scopr.Rcheck/00check.log:> ### Title: Load data from ethoscope result files ./scopr.Rcheck/00check.log:> ### Aliases: load_ethoscope ./scopr.Rcheck/00check.log:> ./scopr.Rcheck/00check.log:> ### ** Examples ./scopr.Rcheck/00check.log:> ./scopr.Rcheck/00check.log:> dir <- paste0(scopr_example_dir(), "/ethoscope_results/") ./scopr.Rcheck/00check.log:> data(region_id_metadata) ./scopr.Rcheck/00check.log:> metadata <- link_ethoscope_metadata(region_id_metadata, dir) ./scopr.Rcheck/00check.log:> print(metadata) ./scopr.Rcheck/00check.log:> ./scopr.Rcheck/00check.log:> # Default data loading ./scopr.Rcheck/00check.log:> dt <- load_ethoscope(metadata) ./scopr.Rcheck/00check.log:Loading ROI number 1 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-01-25_21-46-14/2016-01-25_21-46-14_014.db ./scopr.Rcheck/00check.log:Loading ROI number 2 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-01-25_21-46-14/2016-01-25_21-46-14_014.db ./scopr.Rcheck/00check.log:Loading ROI number 3 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-01-25_21-46-14/2016-01-25_21-46-14_014.db ./scopr.Rcheck/00check.log:Loading ROI number 4 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-01-25_21-46-14/2016-01-25_21-46-14_014.db ./scopr.Rcheck/00check.log:Loading ROI number 5 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-01-25_21-46-14/2016-01-25_21-46-14_014.db ./scopr.Rcheck/00check.log:Loading ROI number 1 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-02-17_15-42-46/2016-02-17_15-42-46_014.db ./scopr.Rcheck/00check.log:Loading ROI number 2 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-02-17_15-42-46/2016-02-17_15-42-46_014.db ./scopr.Rcheck/00check.log:Loading ROI number 3 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-02-17_15-42-46/2016-02-17_15-42-46_014.db ./scopr.Rcheck/00check.log:Loading ROI number 4 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-02-17_15-42-46/2016-02-17_15-42-46_014.db ./scopr.Rcheck/00check.log:Loading ROI number 5 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//014/E_014/2016-02-17_15-42-46/2016-02-17_15-42-46_014.db ./scopr.Rcheck/00check.log:Loading ROI number 1 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//029/E_029/2016-01-25_21-14-55/2016-01-25_21-14-55_029.db ./scopr.Rcheck/00check.log:Loading ROI number 2 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//029/E_029/2016-01-25_21-14-55/2016-01-25_21-14-55_029.db ./scopr.Rcheck/00check.log:Loading ROI number 3 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//029/E_029/2016-01-25_21-14-55/2016-01-25_21-14-55_029.db ./scopr.Rcheck/00check.log:Loading ROI number 4 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//029/E_029/2016-01-25_21-14-55/2016-01-25_21-14-55_029.db ./scopr.Rcheck/00check.log:Loading ROI number 5 from: ./scopr.Rcheck/00check.log: /home/mdowle/build/revdeplib/scopr.Rcheck/scopr/extdata/ethoscope_results//029/E_029/2016-01-25_21-14-55/2016-01-25_21-14-55_029.db ./scopr.Rcheck/00check.log:> dt ./scopr.Rcheck/00check.log: ==== METADATA ==== ./scopr.Rcheck/00check.log: id file_info machine_name machine_id ./scopr.Rcheck/00check.log: ./scopr.Rcheck/00check.log: 1: 2016-01-25_21-14-55_029.db|01 E_029 029 ./scopr.Rcheck/00check.log: 2: 2016-01-25_21-14-55_029.db|02 E_029 029 ./scopr.Rcheck/00check.log: 3: 2016-01-25_21-14-55_029.db|03 E_029 029 ./scopr.Rcheck/00check.log: 4: 2016-01-25_21-14-55_029.db|04 E_029 029 ./scopr.Rcheck/00check.log: 5: 2016-01-25_21-14-55_029.db|05 E_029 029 ./scopr.Rcheck/00check.log: 6: 2016-01-25_21-46-14_014.db|01 E_014 014 ./scopr.Rcheck/00check.log: 7: 2016-01-25_21-46-14_014.db|02 E_014 014 ./scopr.Rcheck/00check.log: 8: 2016-01-25_21-46-14_014.db|03 E_014 014 ./scopr.Rcheck/00check.log: 9: 2016-01-25_21-46-14_014.db|04 E_014 014 ./scopr.Rcheck/00check.log:10: 2016-01-25_21-46-14_014.db|05 E_014 014 ./scopr.Rcheck/00check.log:11: 2016-02-17_15-42-46_014.db|01 E_014 014 ./scopr.Rcheck/00check.log:12: 2016-02-17_15-42-46_014.db|02 E_014 014 ./scopr.Rcheck/00check.log:13: 2016-02-17_15-42-46_014.db|03 E_014 014 ./scopr.Rcheck/00check.log:14: 2016-02-17_15-42-46_014.db|04 E_014 014 ./scopr.Rcheck/00check.log:15: 2016-02-17_15-42-46_014.db|05 E_014 014 ./scopr.Rcheck/00check.log: datetime test region_id treatment ./scopr.Rcheck/00check.log: ./scopr.Rcheck/00check.log: 1: 2016-01-25 21:14:55 3 1 2 ./scopr.Rcheck/00check.log: 2: 2016-01-25 21:14:55 3 2 3 ./scopr.Rcheck/00check.log: 3: 2016-01-25 21:14:55 3 3 1 ./scopr.Rcheck/00check.log: 4: 2016-01-25 21:14:55 3 4 2 ./scopr.Rcheck/00check.log: 5: 2016-01-25 21:14:55 3 5 3 ./scopr.Rcheck/00check.log: 6: 2016-01-25 21:46:14 1 1 1 ./scopr.Rcheck/00check.log: 7: 2016-01-25 21:46:14 1 2 2 ./scopr.Rcheck/00check.log: 8: 2016-01-25 21:46:14 1 3 3 ./scopr.Rcheck/00check.log: 9: 2016-01-25 21:46:14 1 4 1 ./scopr.Rcheck/00check.log:10: 2016-01-25 21:46:14 1 5 2 ./scopr.Rcheck/00check.log:11: 2016-02-17 15:42:46 2 1 3 ./scopr.Rcheck/00check.log:12: 2016-02-17 15:42:46 2 2 1 ./scopr.Rcheck/00check.log:13: 2016-02-17 15:42:46 2 3 2 ./scopr.Rcheck/00check.log:14: 2016-02-17 15:42:46 2 4 3 ./scopr.Rcheck/00check.log:15: 2016-02-17 15:42:46 2 5 1 ./scopr.Rcheck/00check.log: ====== DATA ====== ./scopr.Rcheck/00check.log:Error: C stack usage 7969700 is too close to the limit ./scopr.Rcheck/00check.log:Execution halted ./scopr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./scopr.Rcheck/00check.log:* checking tests ... OK ./scopr.Rcheck/00check.log: Running ‘testthat.R’ ./scopr.Rcheck/00check.log:* checking PDF version of manual ... OK ./scopr.Rcheck/00check.log:* DONE ./scopr.Rcheck/00check.log:Status: 1 ERROR ./sdcMicro.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/sdcMicro.Rcheck’ ./sdcMicro.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./sdcMicro.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./sdcMicro.Rcheck/00check.log:* using session charset: UTF-8 ./sdcMicro.Rcheck/00check.log:* checking for file ‘sdcMicro/DESCRIPTION’ ... OK ./sdcMicro.Rcheck/00check.log:* checking extension type ... Package ./sdcMicro.Rcheck/00check.log:* this is package ‘sdcMicro’ version ‘5.3.0’ ./sdcMicro.Rcheck/00check.log:* checking package namespace information ... OK ./sdcMicro.Rcheck/00check.log:* checking package dependencies ... OK ./sdcMicro.Rcheck/00check.log:* checking if this is a source package ... OK ./sdcMicro.Rcheck/00check.log:* checking if there is a namespace ... OK ./sdcMicro.Rcheck/00check.log:* checking for executable files ... OK ./sdcMicro.Rcheck/00check.log:* checking for hidden files and directories ... OK ./sdcMicro.Rcheck/00check.log:* checking for portable file names ... OK ./sdcMicro.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./sdcMicro.Rcheck/00check.log:* checking whether package ‘sdcMicro’ can be installed ... OK ./sdcMicro.Rcheck/00check.log:* checking installed package size ... OK ./sdcMicro.Rcheck/00check.log:* checking package directory ... OK ./sdcMicro.Rcheck/00check.log:* checking ‘build’ directory ... OK ./sdcMicro.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./sdcMicro.Rcheck/00check.log:* checking top-level files ... OK ./sdcMicro.Rcheck/00check.log:* checking for left-over files ... OK ./sdcMicro.Rcheck/00check.log:* checking index information ... OK ./sdcMicro.Rcheck/00check.log:* checking package subdirectories ... OK ./sdcMicro.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./sdcMicro.Rcheck/00check.log:* checking R files for syntax errors ... OK ./sdcMicro.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./sdcMicro.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./sdcMicro.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./sdcMicro.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./sdcMicro.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./sdcMicro.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./sdcMicro.Rcheck/00check.log:* checking dependencies in R code ... OK ./sdcMicro.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./sdcMicro.Rcheck/00check.log:* checking replacement functions ... OK ./sdcMicro.Rcheck/00check.log:* checking foreign function calls ... OK ./sdcMicro.Rcheck/00check.log:* checking R code for possible problems ... OK ./sdcMicro.Rcheck/00check.log:* checking Rd files ... OK ./sdcMicro.Rcheck/00check.log:* checking Rd metadata ... OK ./sdcMicro.Rcheck/00check.log:* checking Rd cross-references ... OK ./sdcMicro.Rcheck/00check.log:* checking for missing documentation entries ... OK ./sdcMicro.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./sdcMicro.Rcheck/00check.log:* checking Rd \usage sections ... OK ./sdcMicro.Rcheck/00check.log:* checking Rd contents ... OK ./sdcMicro.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./sdcMicro.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./sdcMicro.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./sdcMicro.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./sdcMicro.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./sdcMicro.Rcheck/00check.log:* checking compiled code ... OK ./sdcMicro.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./sdcMicro.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./sdcMicro.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./sdcMicro.Rcheck/00check.log:* checking examples ... ERROR ./sdcMicro.Rcheck/00check.log:Running examples in ‘sdcMicro-Ex.R’ failed ./sdcMicro.Rcheck/00check.log:The error most likely occurred in: ./sdcMicro.Rcheck/00check.log:> ### Name: mafast ./sdcMicro.Rcheck/00check.log:> ### Title: Fast and Simple Microaggregation ./sdcMicro.Rcheck/00check.log:> ### Aliases: mafast ./sdcMicro.Rcheck/00check.log:> ### Keywords: manip ./sdcMicro.Rcheck/00check.log:> ./sdcMicro.Rcheck/00check.log:> ### ** Examples ./sdcMicro.Rcheck/00check.log:> ./sdcMicro.Rcheck/00check.log:> data(Tarragona) ./sdcMicro.Rcheck/00check.log:> m1 <- mafast(Tarragona, variables=c("GROSS.PROFIT","OPERATING.PROFIT","SALES"),aggr=3) ./sdcMicro.Rcheck/00check.log:Error in `[.data.table`(erg, , by = idvariableforresorting) : ./sdcMicro.Rcheck/00check.log: When i and j are both missing, no other argument should be used. Empty [] is useful after := to have the result displayed; e.g. DT[,col:=val][] ./sdcMicro.Rcheck/00check.log:Calls: mafast ... mafastX -> mafastWORK -> data.frame -> [ -> [.data.table ./sdcMicro.Rcheck/00check.log:Execution halted ./sdcMicro.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./sdcMicro.Rcheck/00check.log:* checking tests ... ERROR ./sdcMicro.Rcheck/00check.log: Running ‘globalRecoding_test.R’ ./sdcMicro.Rcheck/00check.log: Running ‘microaggregation_test.R’ ./sdcMicro.Rcheck/00check.log:Running the tests in ‘tests/microaggregation_test.R’ failed. ./sdcMicro.Rcheck/00check.log:Last 13 lines of output: ./sdcMicro.Rcheck/00check.log: > require(sdcMicro) ./sdcMicro.Rcheck/00check.log: Loading required package: sdcMicro ./sdcMicro.Rcheck/00check.log: -------- ./sdcMicro.Rcheck/00check.log: This is sdcMicro v5.3.0. ./sdcMicro.Rcheck/00check.log: For references, please have a look at citation('sdcMicro') ./sdcMicro.Rcheck/00check.log: Note: since version 5.0.0, the graphical user-interface is a shiny-app that can be started with sdcApp(). ./sdcMicro.Rcheck/00check.log: Please submit suggestions and bugs at: https://github.com/sdcTools/sdcMicro/issues ./sdcMicro.Rcheck/00check.log: -------- ./sdcMicro.Rcheck/00check.log: > ### for a data.frame ./sdcMicro.Rcheck/00check.log: > dat <- data.frame(x = rnorm(100)) ./sdcMicro.Rcheck/00check.log: > microaggregation(obj = dat, variables = "x", method = "mdav", aggr = 3, measure = "mean") ./sdcMicro.Rcheck/00check.log: Error in `[.data.table`(erg, , by = idvariableforresorting) : ./sdcMicro.Rcheck/00check.log: When i and j are both missing, no other argument should be used. Empty [] is useful after := to have the result displayed; e.g. DT[,col:=val][] ./sdcMicro.Rcheck/00check.log: Calls: microaggregation ... mafastX -> mafastWORK -> data.frame -> [ -> [.data.table ./sdcMicro.Rcheck/00check.log: Execution halted ./sdcMicro.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./sdcMicro.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./sdcMicro.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./sdcMicro.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./sdcMicro.Rcheck/00check.log:* checking PDF version of manual ... OK ./sdcMicro.Rcheck/00check.log:* DONE ./sdcMicro.Rcheck/00check.log:Status: 2 ERRORs ./sleepr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/sleepr.Rcheck’ ./sleepr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./sleepr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./sleepr.Rcheck/00check.log:* using session charset: UTF-8 ./sleepr.Rcheck/00check.log:* checking for file ‘sleepr/DESCRIPTION’ ... OK ./sleepr.Rcheck/00check.log:* this is package ‘sleepr’ version ‘0.3.0’ ./sleepr.Rcheck/00check.log:* package encoding: UTF-8 ./sleepr.Rcheck/00check.log:* checking package namespace information ... OK ./sleepr.Rcheck/00check.log:* checking package dependencies ... OK ./sleepr.Rcheck/00check.log:* checking if this is a source package ... OK ./sleepr.Rcheck/00check.log:* checking if there is a namespace ... OK ./sleepr.Rcheck/00check.log:* checking for executable files ... OK ./sleepr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./sleepr.Rcheck/00check.log:* checking for portable file names ... OK ./sleepr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./sleepr.Rcheck/00check.log:* checking whether package ‘sleepr’ can be installed ... OK ./sleepr.Rcheck/00check.log:* checking installed package size ... OK ./sleepr.Rcheck/00check.log:* checking package directory ... OK ./sleepr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./sleepr.Rcheck/00check.log:* checking top-level files ... OK ./sleepr.Rcheck/00check.log:* checking for left-over files ... OK ./sleepr.Rcheck/00check.log:* checking index information ... OK ./sleepr.Rcheck/00check.log:* checking package subdirectories ... OK ./sleepr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./sleepr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./sleepr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./sleepr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./sleepr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./sleepr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./sleepr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./sleepr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./sleepr.Rcheck/00check.log:* checking dependencies in R code ... OK ./sleepr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./sleepr.Rcheck/00check.log:* checking replacement functions ... OK ./sleepr.Rcheck/00check.log:* checking foreign function calls ... OK ./sleepr.Rcheck/00check.log:* checking R code for possible problems ... OK ./sleepr.Rcheck/00check.log:* checking Rd files ... OK ./sleepr.Rcheck/00check.log:* checking Rd metadata ... OK ./sleepr.Rcheck/00check.log:* checking Rd cross-references ... OK ./sleepr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./sleepr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./sleepr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./sleepr.Rcheck/00check.log:* checking Rd contents ... OK ./sleepr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./sleepr.Rcheck/00check.log:* checking examples ... ERROR ./sleepr.Rcheck/00check.log:Running examples in ‘sleepr-Ex.R’ failed ./sleepr.Rcheck/00check.log:The error most likely occurred in: ./sleepr.Rcheck/00check.log:> ### Name: bout_analysis ./sleepr.Rcheck/00check.log:> ### Title: Find "bouts" in categorical time series ./sleepr.Rcheck/00check.log:> ### Aliases: bout_analysis ./sleepr.Rcheck/00check.log:> ./sleepr.Rcheck/00check.log:> ### ** Examples ./sleepr.Rcheck/00check.log:> ./sleepr.Rcheck/00check.log:> # Bout analysis on binary variable: ./sleepr.Rcheck/00check.log:> dt <- toy_dam_data() ./sleepr.Rcheck/00check.log:> dt[, moving := activity > 0] ./sleepr.Rcheck/00check.log: ==== METADATA ==== ./sleepr.Rcheck/00check.log: id ./sleepr.Rcheck/00check.log: ./sleepr.Rcheck/00check.log:1: toy_data ./sleepr.Rcheck/00check.log: ====== DATA ====== ./sleepr.Rcheck/00check.log:Error: C stack usage 7972596 is too close to the limit ./sleepr.Rcheck/00check.log:Execution halted ./sleepr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./sleepr.Rcheck/00check.log:* checking tests ... ERROR ./sleepr.Rcheck/00check.log: Running ‘testthat.R’ ./sleepr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./sleepr.Rcheck/00check.log:Complete output: ./sleepr.Rcheck/00check.log: > library(testthat) ./sleepr.Rcheck/00check.log: > library(sleepr) ./sleepr.Rcheck/00check.log: Loading required package: behavr ./sleepr.Rcheck/00check.log: Loading required package: data.table ./sleepr.Rcheck/00check.log: > ./sleepr.Rcheck/00check.log: > test_check("sleepr") ./sleepr.Rcheck/00check.log: Error: C stack usage 7969252 is too close to the limit ./sleepr.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./sleepr.Rcheck/00check.log: OK: 6 SKIPPED: 1 FAILED: 0 ./sleepr.Rcheck/00check.log: Execution halted ./sleepr.Rcheck/00check.log:* checking PDF version of manual ... OK ./sleepr.Rcheck/00check.log:* DONE ./sleepr.Rcheck/00check.log:Status: 2 ERRORs ./timeseriesdb.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/timeseriesdb.Rcheck’ ./timeseriesdb.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./timeseriesdb.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./timeseriesdb.Rcheck/00check.log:* using session charset: UTF-8 ./timeseriesdb.Rcheck/00check.log:* checking for file ‘timeseriesdb/DESCRIPTION’ ... OK ./timeseriesdb.Rcheck/00check.log:* checking extension type ... Package ./timeseriesdb.Rcheck/00check.log:* this is package ‘timeseriesdb’ version ‘0.4.1’ ./timeseriesdb.Rcheck/00check.log:* package encoding: UTF-8 ./timeseriesdb.Rcheck/00check.log:* checking package namespace information ... OK ./timeseriesdb.Rcheck/00check.log:* checking package dependencies ... OK ./timeseriesdb.Rcheck/00check.log:* checking if this is a source package ... OK ./timeseriesdb.Rcheck/00check.log:* checking if there is a namespace ... OK ./timeseriesdb.Rcheck/00check.log:* checking for executable files ... OK ./timeseriesdb.Rcheck/00check.log:* checking for hidden files and directories ... OK ./timeseriesdb.Rcheck/00check.log:* checking for portable file names ... OK ./timeseriesdb.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./timeseriesdb.Rcheck/00check.log:* checking whether package ‘timeseriesdb’ can be installed ... OK ./timeseriesdb.Rcheck/00check.log:* checking installed package size ... OK ./timeseriesdb.Rcheck/00check.log:* checking package directory ... OK ./timeseriesdb.Rcheck/00check.log:* checking ‘build’ directory ... OK ./timeseriesdb.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./timeseriesdb.Rcheck/00check.log:* checking top-level files ... OK ./timeseriesdb.Rcheck/00check.log:* checking for left-over files ... OK ./timeseriesdb.Rcheck/00check.log:* checking index information ... OK ./timeseriesdb.Rcheck/00check.log:* checking package subdirectories ... OK ./timeseriesdb.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./timeseriesdb.Rcheck/00check.log:* checking R files for syntax errors ... OK ./timeseriesdb.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./timeseriesdb.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./timeseriesdb.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./timeseriesdb.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./timeseriesdb.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./timeseriesdb.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./timeseriesdb.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./timeseriesdb.Rcheck/00check.log:Namespace in Imports field not imported from: ‘shiny’ ./timeseriesdb.Rcheck/00check.log: All declared Imports should be used. ./timeseriesdb.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./timeseriesdb.Rcheck/00check.log:* checking replacement functions ... OK ./timeseriesdb.Rcheck/00check.log:* checking foreign function calls ... OK ./timeseriesdb.Rcheck/00check.log:* checking R code for possible problems ... OK ./timeseriesdb.Rcheck/00check.log:* checking Rd files ... OK ./timeseriesdb.Rcheck/00check.log:* checking Rd metadata ... OK ./timeseriesdb.Rcheck/00check.log:* checking Rd cross-references ... OK ./timeseriesdb.Rcheck/00check.log:* checking for missing documentation entries ... OK ./timeseriesdb.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./timeseriesdb.Rcheck/00check.log:* checking Rd \usage sections ... OK ./timeseriesdb.Rcheck/00check.log:* checking Rd contents ... OK ./timeseriesdb.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./timeseriesdb.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./timeseriesdb.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./timeseriesdb.Rcheck/00check.log:* checking examples ... OK ./timeseriesdb.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./timeseriesdb.Rcheck/00check.log:* checking tests ... OK ./timeseriesdb.Rcheck/00check.log: Running ‘testthat.R’ ./timeseriesdb.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./timeseriesdb.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./timeseriesdb.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./timeseriesdb.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./timeseriesdb.Rcheck/00check.log:Error in re-building vignettes: ./timeseriesdb.Rcheck/00check.log: ... ./timeseriesdb.Rcheck/00check.log:Error: processing vignette 'timeseriesdb.Rmd' failed with diagnostics: ./timeseriesdb.Rcheck/00check.log:cannot popen '/usr/bin/which 'pandoc-citeproc' 2>/dev/null', probable reason 'Cannot allocate memory' ./timeseriesdb.Rcheck/00check.log:Execution halted ./timeseriesdb.Rcheck/00check.log:Warning: system call failed: Cannot allocate memory ./timeseriesdb.Rcheck/00check.log:* checking PDF version of manual ... WARNING ./timeseriesdb.Rcheck/00check.log:LaTeX errors when creating PDF version. ./timeseriesdb.Rcheck/00check.log:This typically indicates Rd problems. ./timeseriesdb.Rcheck/00check.log:* checking PDF version of manual without hyperrefs or index ... ERROR ./timeseriesdb.Rcheck/00check.log:Re-running with no redirection of stdout/stderr. ./timeseriesdb.Rcheck/00check.log:* DONE ./timeseriesdb.Rcheck/00check.log:Status: 1 ERROR, 2 WARNINGs, 1 NOTE ./toxboot.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/toxboot.Rcheck’ ./toxboot.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./toxboot.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./toxboot.Rcheck/00check.log:* using session charset: UTF-8 ./toxboot.Rcheck/00check.log:* checking for file ‘toxboot/DESCRIPTION’ ... OK ./toxboot.Rcheck/00check.log:* checking extension type ... Package ./toxboot.Rcheck/00check.log:* this is package ‘toxboot’ version ‘0.2.0’ ./toxboot.Rcheck/00check.log:* package encoding: UTF-8 ./toxboot.Rcheck/00check.log:* checking package namespace information ... OK ./toxboot.Rcheck/00check.log:* checking package dependencies ... NOTE ./toxboot.Rcheck/00check.log:Package suggested but not available for checking: ‘mongolite’ ./toxboot.Rcheck/00check.log:* checking if this is a source package ... OK ./toxboot.Rcheck/00check.log:* checking if there is a namespace ... OK ./toxboot.Rcheck/00check.log:* checking for executable files ... OK ./toxboot.Rcheck/00check.log:* checking for hidden files and directories ... OK ./toxboot.Rcheck/00check.log:* checking for portable file names ... OK ./toxboot.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./toxboot.Rcheck/00check.log:* checking whether package ‘toxboot’ can be installed ... OK ./toxboot.Rcheck/00check.log:* checking installed package size ... OK ./toxboot.Rcheck/00check.log:* checking package directory ... OK ./toxboot.Rcheck/00check.log:* checking ‘build’ directory ... OK ./toxboot.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./toxboot.Rcheck/00check.log:* checking top-level files ... OK ./toxboot.Rcheck/00check.log:* checking for left-over files ... OK ./toxboot.Rcheck/00check.log:* checking index information ... OK ./toxboot.Rcheck/00check.log:* checking package subdirectories ... OK ./toxboot.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./toxboot.Rcheck/00check.log:* checking R files for syntax errors ... OK ./toxboot.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./toxboot.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./toxboot.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./toxboot.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./toxboot.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./toxboot.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./toxboot.Rcheck/00check.log:* checking dependencies in R code ... OK ./toxboot.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./toxboot.Rcheck/00check.log:* checking replacement functions ... OK ./toxboot.Rcheck/00check.log:* checking foreign function calls ... OK ./toxboot.Rcheck/00check.log:* checking R code for possible problems ... OK ./toxboot.Rcheck/00check.log:* checking Rd files ... OK ./toxboot.Rcheck/00check.log:* checking Rd metadata ... OK ./toxboot.Rcheck/00check.log:* checking Rd cross-references ... OK ./toxboot.Rcheck/00check.log:* checking for missing documentation entries ... OK ./toxboot.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./toxboot.Rcheck/00check.log:* checking Rd \usage sections ... OK ./toxboot.Rcheck/00check.log:* checking Rd contents ... OK ./toxboot.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./toxboot.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./toxboot.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./toxboot.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./toxboot.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./toxboot.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./toxboot.Rcheck/00check.log:* checking examples ... OK ./toxboot.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./toxboot.Rcheck/00check.log:* checking tests ... ERROR ./toxboot.Rcheck/00check.log: Running ‘testthat.R’ ./toxboot.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./toxboot.Rcheck/00check.log:Last 13 lines of output: ./toxboot.Rcheck/00check.log: Database: Not Configured ./toxboot.Rcheck/00check.log: User: Not Configured ./toxboot.Rcheck/00check.log: > ./toxboot.Rcheck/00check.log: > test_check("toxboot") ./toxboot.Rcheck/00check.log: ── 1. Error: (unknown) (@test_toxboot.R#3) ──────────────────────────────────── ./toxboot.Rcheck/00check.log: there is no package called 'mongolite' ./toxboot.Rcheck/00check.log: 1: library(mongolite) at testthat/test_toxboot.R:3 ./toxboot.Rcheck/00check.log: 2: stop(txt, domain = NA) ./toxboot.Rcheck/00check.log: ./toxboot.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./toxboot.Rcheck/00check.log: OK: 38 SKIPPED: 0 FAILED: 1 ./toxboot.Rcheck/00check.log: 1. Error: (unknown) (@test_toxboot.R#3) ./toxboot.Rcheck/00check.log: ./toxboot.Rcheck/00check.log: Error: testthat unit tests failed ./toxboot.Rcheck/00check.log: Execution halted ./toxboot.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./toxboot.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./toxboot.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./toxboot.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./toxboot.Rcheck/00check.log:* checking PDF version of manual ... OK ./toxboot.Rcheck/00check.log:* DONE ./toxboot.Rcheck/00check.log:Status: 1 ERROR, 1 NOTE ./zeitgebr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/zeitgebr.Rcheck’ ./zeitgebr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./zeitgebr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./zeitgebr.Rcheck/00check.log:* using session charset: UTF-8 ./zeitgebr.Rcheck/00check.log:* checking for file ‘zeitgebr/DESCRIPTION’ ... OK ./zeitgebr.Rcheck/00check.log:* this is package ‘zeitgebr’ version ‘0.3.3’ ./zeitgebr.Rcheck/00check.log:* package encoding: UTF-8 ./zeitgebr.Rcheck/00check.log:* checking package namespace information ... OK ./zeitgebr.Rcheck/00check.log:* checking package dependencies ... OK ./zeitgebr.Rcheck/00check.log:* checking if this is a source package ... OK ./zeitgebr.Rcheck/00check.log:* checking if there is a namespace ... OK ./zeitgebr.Rcheck/00check.log:* checking for executable files ... OK ./zeitgebr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./zeitgebr.Rcheck/00check.log:* checking for portable file names ... OK ./zeitgebr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./zeitgebr.Rcheck/00check.log:* checking whether package ‘zeitgebr’ can be installed ... OK ./zeitgebr.Rcheck/00check.log:* checking installed package size ... OK ./zeitgebr.Rcheck/00check.log:* checking package directory ... OK ./zeitgebr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./zeitgebr.Rcheck/00check.log:* checking top-level files ... OK ./zeitgebr.Rcheck/00check.log:* checking for left-over files ... OK ./zeitgebr.Rcheck/00check.log:* checking index information ... OK ./zeitgebr.Rcheck/00check.log:* checking package subdirectories ... OK ./zeitgebr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./zeitgebr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./zeitgebr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./zeitgebr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./zeitgebr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./zeitgebr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./zeitgebr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./zeitgebr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./zeitgebr.Rcheck/00check.log:* checking dependencies in R code ... OK ./zeitgebr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./zeitgebr.Rcheck/00check.log:* checking replacement functions ... OK ./zeitgebr.Rcheck/00check.log:* checking foreign function calls ... OK ./zeitgebr.Rcheck/00check.log:* checking R code for possible problems ... OK ./zeitgebr.Rcheck/00check.log:* checking Rd files ... OK ./zeitgebr.Rcheck/00check.log:* checking Rd metadata ... OK ./zeitgebr.Rcheck/00check.log:* checking Rd cross-references ... NOTE ./zeitgebr.Rcheck/00check.log:Package unavailable to check Rd xrefs: ‘xsp’ ./zeitgebr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./zeitgebr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./zeitgebr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./zeitgebr.Rcheck/00check.log:* checking Rd contents ... OK ./zeitgebr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./zeitgebr.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./zeitgebr.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./zeitgebr.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./zeitgebr.Rcheck/00check.log:* checking examples ... ERROR ./zeitgebr.Rcheck/00check.log:Running examples in ‘zeitgebr-Ex.R’ failed ./zeitgebr.Rcheck/00check.log:The error most likely occurred in: ./zeitgebr.Rcheck/00check.log:> ### Name: find_peaks ./zeitgebr.Rcheck/00check.log:> ### Title: Find peaks in a periodogram ./zeitgebr.Rcheck/00check.log:> ### Aliases: find_peaks ./zeitgebr.Rcheck/00check.log:> ./zeitgebr.Rcheck/00check.log:> ### ** Examples ./zeitgebr.Rcheck/00check.log:> ./zeitgebr.Rcheck/00check.log:> data(dams_sample) ./zeitgebr.Rcheck/00check.log:> # only a half of the individuals for the sake of the example ./zeitgebr.Rcheck/00check.log:> dt <- dams_sample[xmv(region_id) %in% (1:16 * 2)] ./zeitgebr.Rcheck/00check.log:Error: C stack usage 7971412 is too close to the limit ./zeitgebr.Rcheck/00check.log:Execution halted ./zeitgebr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./zeitgebr.Rcheck/00check.log:* checking tests ... ERROR ./zeitgebr.Rcheck/00check.log: Running ‘testthat.R’ ./zeitgebr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./zeitgebr.Rcheck/00check.log:Complete output: ./zeitgebr.Rcheck/00check.log: > library(testthat) ./zeitgebr.Rcheck/00check.log: > library(zeitgebr) ./zeitgebr.Rcheck/00check.log: Loading required package: behavr ./zeitgebr.Rcheck/00check.log: Loading required package: data.table ./zeitgebr.Rcheck/00check.log: > ./zeitgebr.Rcheck/00check.log: > test_check("zeitgebr") ./zeitgebr.Rcheck/00check.log: Error: C stack usage 7970884 is too close to the limit ./zeitgebr.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./zeitgebr.Rcheck/00check.log: OK: 0 SKIPPED: 1 FAILED: 0 ./zeitgebr.Rcheck/00check.log: Execution halted ./zeitgebr.Rcheck/00check.log:* checking PDF version of manual ... OK ./zeitgebr.Rcheck/00check.log:* DONE ./zeitgebr.Rcheck/00check.log:Status: 2 ERRORs, 1 NOTE ./assertable.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/assertable.Rcheck’ ./assertable.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./assertable.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./assertable.Rcheck/00check.log:* using session charset: UTF-8 ./assertable.Rcheck/00check.log:* checking for file ‘assertable/DESCRIPTION’ ... OK ./assertable.Rcheck/00check.log:* checking extension type ... Package ./assertable.Rcheck/00check.log:* this is package ‘assertable’ version ‘0.2.4’ ./assertable.Rcheck/00check.log:* package encoding: UTF-8 ./assertable.Rcheck/00check.log:* checking package namespace information ... OK ./assertable.Rcheck/00check.log:* checking package dependencies ... OK ./assertable.Rcheck/00check.log:* checking if this is a source package ... OK ./assertable.Rcheck/00check.log:* checking if there is a namespace ... OK ./assertable.Rcheck/00check.log:* checking for executable files ... OK ./assertable.Rcheck/00check.log:* checking for hidden files and directories ... OK ./assertable.Rcheck/00check.log:* checking for portable file names ... OK ./assertable.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./assertable.Rcheck/00check.log:* checking whether package ‘assertable’ can be installed ... OK ./assertable.Rcheck/00check.log:* checking installed package size ... OK ./assertable.Rcheck/00check.log:* checking package directory ... OK ./assertable.Rcheck/00check.log:* checking ‘build’ directory ... OK ./assertable.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./assertable.Rcheck/00check.log:* checking top-level files ... OK ./assertable.Rcheck/00check.log:* checking for left-over files ... OK ./assertable.Rcheck/00check.log:* checking index information ... OK ./assertable.Rcheck/00check.log:* checking package subdirectories ... OK ./assertable.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./assertable.Rcheck/00check.log:* checking R files for syntax errors ... OK ./assertable.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./assertable.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./assertable.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./assertable.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./assertable.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./assertable.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./assertable.Rcheck/00check.log:* checking dependencies in R code ... OK ./assertable.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./assertable.Rcheck/00check.log:* checking replacement functions ... OK ./assertable.Rcheck/00check.log:* checking foreign function calls ... OK ./assertable.Rcheck/00check.log:* checking R code for possible problems ... OK ./assertable.Rcheck/00check.log:* checking Rd files ... OK ./assertable.Rcheck/00check.log:* checking Rd metadata ... OK ./assertable.Rcheck/00check.log:* checking Rd cross-references ... OK ./assertable.Rcheck/00check.log:* checking for missing documentation entries ... OK ./assertable.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./assertable.Rcheck/00check.log:* checking Rd \usage sections ... OK ./assertable.Rcheck/00check.log:* checking Rd contents ... OK ./assertable.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./assertable.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./assertable.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./assertable.Rcheck/00check.log:* checking examples ... OK ./assertable.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./assertable.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./assertable.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./assertable.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./assertable.Rcheck/00check.log:Error in re-building vignettes: ./assertable.Rcheck/00check.log: ... ./assertable.Rcheck/00check.log:Quitting from lines 67-73 (assertion_template.Rmd) ./assertable.Rcheck/00check.log:Error: processing vignette 'assertion_template.Rmd' failed with diagnostics: ./assertable.Rcheck/00check.log:When i and j are both missing, no other argument should be used. Empty [] is useful after := to have the result displayed; e.g. DT[,col:=val][] ./assertable.Rcheck/00check.log:Execution halted ./assertable.Rcheck/00check.log:* checking PDF version of manual ... OK ./assertable.Rcheck/00check.log:* DONE ./assertable.Rcheck/00check.log:Status: 1 WARNING ./ctsem.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ctsem.Rcheck’ ./ctsem.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./ctsem.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ctsem.Rcheck/00check.log:* using session charset: UTF-8 ./ctsem.Rcheck/00check.log:* checking for file ‘ctsem/DESCRIPTION’ ... OK ./ctsem.Rcheck/00check.log:* checking extension type ... Package ./ctsem.Rcheck/00check.log:* this is package ‘ctsem’ version ‘2.7.6’ ./ctsem.Rcheck/00check.log:* package encoding: UTF-8 ./ctsem.Rcheck/00check.log:* checking package namespace information ... OK ./ctsem.Rcheck/00check.log:* checking package dependencies ... OK ./ctsem.Rcheck/00check.log:* checking if this is a source package ... OK ./ctsem.Rcheck/00check.log:* checking if there is a namespace ... OK ./ctsem.Rcheck/00check.log:* checking for executable files ... OK ./ctsem.Rcheck/00check.log:* checking for hidden files and directories ... OK ./ctsem.Rcheck/00check.log:* checking for portable file names ... OK ./ctsem.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ctsem.Rcheck/00check.log:* checking whether package ‘ctsem’ can be installed ... OK ./ctsem.Rcheck/00check.log:* checking installed package size ... NOTE ./ctsem.Rcheck/00check.log: installed size is 98.5Mb ./ctsem.Rcheck/00check.log: sub-directories of 1Mb or more: ./ctsem.Rcheck/00check.log: data 1.8Mb ./ctsem.Rcheck/00check.log: doc 4.0Mb ./ctsem.Rcheck/00check.log: libs 91.5Mb ./ctsem.Rcheck/00check.log:* checking package directory ... OK ./ctsem.Rcheck/00check.log:* checking ‘build’ directory ... OK ./ctsem.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ctsem.Rcheck/00check.log:* checking top-level files ... OK ./ctsem.Rcheck/00check.log:* checking for left-over files ... OK ./ctsem.Rcheck/00check.log:* checking index information ... OK ./ctsem.Rcheck/00check.log:* checking package subdirectories ... OK ./ctsem.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ctsem.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ctsem.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ctsem.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ctsem.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ctsem.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ctsem.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ctsem.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ctsem.Rcheck/00check.log:* checking dependencies in R code ... OK ./ctsem.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ctsem.Rcheck/00check.log:* checking replacement functions ... OK ./ctsem.Rcheck/00check.log:* checking foreign function calls ... OK ./ctsem.Rcheck/00check.log:* checking R code for possible problems ... OK ./ctsem.Rcheck/00check.log:* checking Rd files ... OK ./ctsem.Rcheck/00check.log:* checking Rd metadata ... OK ./ctsem.Rcheck/00check.log:* checking Rd cross-references ... OK ./ctsem.Rcheck/00check.log:* checking for missing documentation entries ... OK ./ctsem.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ctsem.Rcheck/00check.log:* checking Rd \usage sections ... OK ./ctsem.Rcheck/00check.log:* checking Rd contents ... OK ./ctsem.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ctsem.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./ctsem.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./ctsem.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./ctsem.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./ctsem.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./ctsem.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./ctsem.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... NOTE ./ctsem.Rcheck/00check.log:GNU make is a SystemRequirements. ./ctsem.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./ctsem.Rcheck/00check.log:* checking compiled code ... OK ./ctsem.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./ctsem.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./ctsem.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./ctsem.Rcheck/00check.log:* checking examples ... OK ./ctsem.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./ctsem.Rcheck/00check.log:* checking tests ... OK ./ctsem.Rcheck/00check.log: Running ‘testthat.R’ ./ctsem.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./ctsem.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./ctsem.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./ctsem.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./ctsem.Rcheck/00check.log:Error in re-building vignettes: ./ctsem.Rcheck/00check.log: ... ./ctsem.Rcheck/00check.log:Solution found! Final fit=4203.313 (started at 4349.5532) (2 attempt(s): 2 valid, 0 errors) ./ctsem.Rcheck/00check.log:NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R') ./ctsem.Rcheck/00check.log:Running ctsem with 19 parameters ./ctsem.Rcheck/00check.log:Using linear Kalman filter for measurement update ./ctsem.Rcheck/00check.log:Linear model specified -- setting nldynamics = FALSE ./ctsem.Rcheck/00check.log:Using linear Kalman filter for dynamics ./ctsem.Rcheck/00check.log:Missingness in TDpreds! Replaced by zeroes... ./ctsem.Rcheck/00check.log:Missingness in TIpreds - sampling 1 values ./ctsem.Rcheck/00check.log:Sampling... ./ctsem.Rcheck/00check.log:Computing discreteDRIFT for 300 samples, may take a moment... ./ctsem.Rcheck/00check.log:Calculating time independent predictor effects... ./ctsem.Rcheck/00check.log:Uncentered data noted -- default priors *may* not be appropriate ./ctsem.Rcheck/00check.log:Unscaled data noted -- default priors may not be appropriate ./ctsem.Rcheck/00check.log:Using linear Kalman filter for measurement update ./ctsem.Rcheck/00check.log:Linear model specified -- setting nldynamics = FALSE ./ctsem.Rcheck/00check.log:Using linear Kalman filter for dynamics ./ctsem.Rcheck/00check.log:Sampling... ./ctsem.Rcheck/00check.log:Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : ./ctsem.Rcheck/00check.log: Running 'texi2dvi' on 'hierarchical.tex' failed. ./ctsem.Rcheck/00check.log:Messages: ./ctsem.Rcheck/00check.log:/usr/bin/texi2dvi: biber failed ./ctsem.Rcheck/00check.log:Calls: buildVignettes -> texi2pdf -> texi2dvi ./ctsem.Rcheck/00check.log:Execution halted ./ctsem.Rcheck/00check.log:* checking PDF version of manual ... OK ./ctsem.Rcheck/00check.log:* DONE ./ctsem.Rcheck/00check.log:Status: 1 WARNING, 2 NOTEs ./SpaDES.core.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/SpaDES.core.Rcheck’ ./SpaDES.core.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./SpaDES.core.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./SpaDES.core.Rcheck/00check.log:* using session charset: UTF-8 ./SpaDES.core.Rcheck/00check.log:* checking for file ‘SpaDES.core/DESCRIPTION’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking extension type ... Package ./SpaDES.core.Rcheck/00check.log:* this is package ‘SpaDES.core’ version ‘0.2.3’ ./SpaDES.core.Rcheck/00check.log:* package encoding: UTF-8 ./SpaDES.core.Rcheck/00check.log:* checking package namespace information ... OK ./SpaDES.core.Rcheck/00check.log:* checking package dependencies ... OK ./SpaDES.core.Rcheck/00check.log:* checking if this is a source package ... OK ./SpaDES.core.Rcheck/00check.log:* checking if there is a namespace ... OK ./SpaDES.core.Rcheck/00check.log:* checking for executable files ... OK ./SpaDES.core.Rcheck/00check.log:* checking for hidden files and directories ... OK ./SpaDES.core.Rcheck/00check.log:* checking for portable file names ... OK ./SpaDES.core.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether package ‘SpaDES.core’ can be installed ... OK ./SpaDES.core.Rcheck/00check.log:* checking installed package size ... OK ./SpaDES.core.Rcheck/00check.log:* checking package directory ... OK ./SpaDES.core.Rcheck/00check.log:* checking ‘build’ directory ... OK ./SpaDES.core.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./SpaDES.core.Rcheck/00check.log:* checking top-level files ... OK ./SpaDES.core.Rcheck/00check.log:* checking for left-over files ... OK ./SpaDES.core.Rcheck/00check.log:* checking index information ... OK ./SpaDES.core.Rcheck/00check.log:* checking package subdirectories ... OK ./SpaDES.core.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./SpaDES.core.Rcheck/00check.log:* checking R files for syntax errors ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./SpaDES.core.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./SpaDES.core.Rcheck/00check.log:* checking dependencies in R code ... OK ./SpaDES.core.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./SpaDES.core.Rcheck/00check.log:* checking replacement functions ... OK ./SpaDES.core.Rcheck/00check.log:* checking foreign function calls ... OK ./SpaDES.core.Rcheck/00check.log:* checking R code for possible problems ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd files ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd metadata ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd cross-references ... OK ./SpaDES.core.Rcheck/00check.log:* checking for missing documentation entries ... OK ./SpaDES.core.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd \usage sections ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd contents ... OK ./SpaDES.core.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./SpaDES.core.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking examples ... OK ./SpaDES.core.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking tests ... OK ./SpaDES.core.Rcheck/00check.log: Running ‘test-all.R’ ./SpaDES.core.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./SpaDES.core.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./SpaDES.core.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./SpaDES.core.Rcheck/00check.log:Error in re-building vignettes: ./SpaDES.core.Rcheck/00check.log: ... ./SpaDES.core.Rcheck/00check.log:Loading required package: RandomFieldsUtils ./SpaDES.core.Rcheck/00check.log:Attaching package: 'RandomFields' ./SpaDES.core.Rcheck/00check.log:The following object is masked from 'package:RandomFieldsUtils': ./SpaDES.core.Rcheck/00check.log: RFoptions ./SpaDES.core.Rcheck/00check.log:The following objects are masked from 'package:base': ./SpaDES.core.Rcheck/00check.log: abs, acosh, asin, asinh, atan, atan2, atanh, cos, cosh, exp, ./SpaDES.core.Rcheck/00check.log: expm1, floor, gamma, lgamma, log, log1p, log2, logb, max, min, ./SpaDES.core.Rcheck/00check.log: round, sin, sinh, sqrt, tan, tanh, trunc ./SpaDES.core.Rcheck/00check.log:Attaching package: 'data.table' ./SpaDES.core.Rcheck/00check.log:The following object is masked from 'package:raster': ./SpaDES.core.Rcheck/00check.log: shift ./SpaDES.core.Rcheck/00check.log:Quitting from lines 637-677 (ii-modules.Rmd) ./SpaDES.core.Rcheck/00check.log:Error: processing vignette 'ii-modules.Rmd' failed with diagnostics: ./SpaDES.core.Rcheck/00check.log:Column 6 of by= (5) is type 'list', not yet supported ./SpaDES.core.Rcheck/00check.log:Execution halted ./SpaDES.core.Rcheck/00check.log:* checking PDF version of manual ... OK ./SpaDES.core.Rcheck/00check.log:* DONE ./SpaDES.core.Rcheck/00check.log:Status: 1 WARNING ./tidytext.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/tidytext.Rcheck’ ./tidytext.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./tidytext.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./tidytext.Rcheck/00check.log:* using session charset: UTF-8 ./tidytext.Rcheck/00check.log:* checking for file ‘tidytext/DESCRIPTION’ ... OK ./tidytext.Rcheck/00check.log:* checking extension type ... Package ./tidytext.Rcheck/00check.log:* this is package ‘tidytext’ version ‘0.2.0’ ./tidytext.Rcheck/00check.log:* package encoding: UTF-8 ./tidytext.Rcheck/00check.log:* checking package namespace information ... OK ./tidytext.Rcheck/00check.log:* checking package dependencies ... OK ./tidytext.Rcheck/00check.log:* checking if this is a source package ... OK ./tidytext.Rcheck/00check.log:* checking if there is a namespace ... OK ./tidytext.Rcheck/00check.log:* checking for executable files ... OK ./tidytext.Rcheck/00check.log:* checking for hidden files and directories ... OK ./tidytext.Rcheck/00check.log:* checking for portable file names ... OK ./tidytext.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./tidytext.Rcheck/00check.log:* checking whether package ‘tidytext’ can be installed ... OK ./tidytext.Rcheck/00check.log:* checking installed package size ... OK ./tidytext.Rcheck/00check.log:* checking package directory ... OK ./tidytext.Rcheck/00check.log:* checking ‘build’ directory ... OK ./tidytext.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./tidytext.Rcheck/00check.log:* checking top-level files ... OK ./tidytext.Rcheck/00check.log:* checking for left-over files ... OK ./tidytext.Rcheck/00check.log:* checking index information ... OK ./tidytext.Rcheck/00check.log:* checking package subdirectories ... OK ./tidytext.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./tidytext.Rcheck/00check.log:* checking R files for syntax errors ... OK ./tidytext.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./tidytext.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./tidytext.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./tidytext.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./tidytext.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./tidytext.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./tidytext.Rcheck/00check.log:* checking dependencies in R code ... OK ./tidytext.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./tidytext.Rcheck/00check.log:* checking replacement functions ... OK ./tidytext.Rcheck/00check.log:* checking foreign function calls ... OK ./tidytext.Rcheck/00check.log:* checking R code for possible problems ... OK ./tidytext.Rcheck/00check.log:* checking Rd files ... OK ./tidytext.Rcheck/00check.log:* checking Rd metadata ... OK ./tidytext.Rcheck/00check.log:* checking Rd cross-references ... OK ./tidytext.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./tidytext.Rcheck/00check.log:Warning: system call failed: Cannot allocate memory ./tidytext.Rcheck/00check.log:All user-level objects in a package should have documentation entries. ./tidytext.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./tidytext.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./tidytext.Rcheck/00check.log:* checking Rd \usage sections ... OK ./tidytext.Rcheck/00check.log:* checking Rd contents ... OK ./tidytext.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./tidytext.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./tidytext.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./tidytext.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./tidytext.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./tidytext.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./tidytext.Rcheck/00check.log:* checking examples ... OK ./tidytext.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./tidytext.Rcheck/00check.log:* checking tests ... OK ./tidytext.Rcheck/00check.log: Running ‘testthat.R’ ./tidytext.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./tidytext.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./tidytext.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./tidytext.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./tidytext.Rcheck/00check.log:* checking PDF version of manual ... OK ./tidytext.Rcheck/00check.log:* DONE ./tidytext.Rcheck/00check.log:Status: 1 WARNING ./CAGEr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CAGEr.Rcheck’ ./CAGEr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./CAGEr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CAGEr.Rcheck/00check.log:* using session charset: UTF-8 ./CAGEr.Rcheck/00check.log:* checking for file ‘CAGEr/DESCRIPTION’ ... OK ./CAGEr.Rcheck/00check.log:* this is package ‘CAGEr’ version ‘1.22.3’ ./CAGEr.Rcheck/00check.log:* package encoding: UTF-8 ./CAGEr.Rcheck/00check.log:* checking package namespace information ... OK ./CAGEr.Rcheck/00check.log:* checking package dependencies ... OK ./CAGEr.Rcheck/00check.log:* checking if this is a source package ... OK ./CAGEr.Rcheck/00check.log:* checking if there is a namespace ... OK ./CAGEr.Rcheck/00check.log:* checking for executable files ... OK ./CAGEr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./CAGEr.Rcheck/00check.log:* checking for portable file names ... OK ./CAGEr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CAGEr.Rcheck/00check.log:* checking whether package ‘CAGEr’ can be installed ... OK ./CAGEr.Rcheck/00check.log:* checking installed package size ... NOTE ./CAGEr.Rcheck/00check.log: installed size is 6.4Mb ./CAGEr.Rcheck/00check.log: sub-directories of 1Mb or more: ./CAGEr.Rcheck/00check.log: R 1.5Mb ./CAGEr.Rcheck/00check.log: doc 3.2Mb ./CAGEr.Rcheck/00check.log:* checking package directory ... OK ./CAGEr.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CAGEr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./CAGEr.Rcheck/00check.log:* checking top-level files ... OK ./CAGEr.Rcheck/00check.log:* checking for left-over files ... OK ./CAGEr.Rcheck/00check.log:* checking index information ... OK ./CAGEr.Rcheck/00check.log:* checking package subdirectories ... OK ./CAGEr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CAGEr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CAGEr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CAGEr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CAGEr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CAGEr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CAGEr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CAGEr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CAGEr.Rcheck/00check.log:* checking dependencies in R code ... OK ./CAGEr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CAGEr.Rcheck/00check.log:* checking replacement functions ... OK ./CAGEr.Rcheck/00check.log:* checking foreign function calls ... OK ./CAGEr.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./CAGEr.Rcheck/00check.log:clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for '<<-' ./CAGEr.Rcheck/00check.log: assignment to ‘idx’ ./CAGEr.Rcheck/00check.log:clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for global ./CAGEr.Rcheck/00check.log: variable ‘idx’ ./CAGEr.Rcheck/00check.log:clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for '<<-' ./CAGEr.Rcheck/00check.log: assignment to ‘idx’ ./CAGEr.Rcheck/00check.log:clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for global ./CAGEr.Rcheck/00check.log: variable ‘idx’ ./CAGEr.Rcheck/00check.log:clusterCTSS,CAGEset: no visible binding for global variable ‘idx’ ./CAGEr.Rcheck/00check.log:Undefined global functions or variables: ./CAGEr.Rcheck/00check.log: idx ./CAGEr.Rcheck/00check.log:* checking Rd files ... OK ./CAGEr.Rcheck/00check.log:* checking Rd metadata ... OK ./CAGEr.Rcheck/00check.log:* checking Rd cross-references ... OK ./CAGEr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./CAGEr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CAGEr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./CAGEr.Rcheck/00check.log:* checking Rd contents ... OK ./CAGEr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CAGEr.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./CAGEr.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./CAGEr.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./CAGEr.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./CAGEr.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CAGEr.Rcheck/00check.log:* checking examples ... ERROR ./CAGEr.Rcheck/00check.log:Running examples in ‘CAGEr-Ex.R’ failed ./CAGEr.Rcheck/00check.log:The error most likely occurred in: ./CAGEr.Rcheck/00check.log:> ### Name: importPublicData ./CAGEr.Rcheck/00check.log:> ### Title: Importing publicly available CAGE data from various resources ./CAGEr.Rcheck/00check.log:> ### Aliases: importPublicData ./CAGEr.Rcheck/00check.log:> ### importPublicData,character,character,ANY,character-method ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> ### ** Examples ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> ### importing FANTOM5 data ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> # list of FANTOM5 human tissue samples ./CAGEr.Rcheck/00check.log:> data(FANTOM5humanSamples) ./CAGEr.Rcheck/00check.log:> head(subset(FANTOM5humanSamples, type == "tissue")) ./CAGEr.Rcheck/00check.log: sample type description library_id ./CAGEr.Rcheck/00check.log:959 achilles_tendon__donor2 tissue achilles tendon, donor2 CNhs13435 ./CAGEr.Rcheck/00check.log:840 adipose_tissue__adult__pool1 tissue adipose tissue, adult, pool1 CNhs10615 ./CAGEr.Rcheck/00check.log:913 adrenal_gland__adult__pool1 tissue adrenal gland, adult, pool1 CNhs11793 ./CAGEr.Rcheck/00check.log:973 amygdala_-_adult__donor10196 tissue amygdala - adult, donor10196 CNhs13793 ./CAGEr.Rcheck/00check.log:923 amygdala__adult__donor10252 tissue amygdala, adult, donor10252 CNhs12311 ./CAGEr.Rcheck/00check.log:885 aorta__adult__pool1 tissue aorta, adult, pool1 CNhs11760 ./CAGEr.Rcheck/00check.log: data_url ./CAGEr.Rcheck/00check.log:959 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/achilles%2520tendon%252c%2520donor2.CNhs13435.10292-104G4.hg19.ctss.bed.gz ./CAGEr.Rcheck/00check.log:840 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adipose%2520tissue%252c%2520adult%252c%2520pool1.CNhs10615.10010-101C1.hg19.ctss.bed.gz ./CAGEr.Rcheck/00check.log:913 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adrenal%2520gland%252c%2520adult%252c%2520pool1.CNhs11793.10081-102A9.hg19.ctss.bed.gz ./CAGEr.Rcheck/00check.log:973 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/amygdala%2520-%2520adult%252c%2520donor10196.CNhs13793.10167-103B5.hg19.ctss.bed.gz ./CAGEr.Rcheck/00check.log:923 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/amygdala%252c%2520adult%252c%2520donor10252.CNhs12311.10151-102I7.hg19.ctss.bed.gz ./CAGEr.Rcheck/00check.log:885 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/aorta%252c%2520adult%252c%2520pool1.CNhs11760.10052-101G7.hg19.ctss.bed.gz ./CAGEr.Rcheck/00check.log:> ./CAGEr.Rcheck/00check.log:> # import selected samples ./CAGEr.Rcheck/00check.log:> exampleCAGEset <- importPublicData(source="FANTOM5", dataset = "human", ./CAGEr.Rcheck/00check.log:+ sample = c("adipose_tissue__adult__pool1", "adrenal_gland__adult__pool1", ./CAGEr.Rcheck/00check.log:+ "aorta__adult__pool1")) ./CAGEr.Rcheck/00check.log:Fetching sample: adipose_tissue__adult__pool1... ./CAGEr.Rcheck/00check.log:Warning in scan(con, what = list(character(), NULL, integer(), NULL, integer(), : ./CAGEr.Rcheck/00check.log: cannot open URL 'http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adipose%2520tissue%252c%2520adult%252c%2520pool1.CNhs10615.10010-101C1.hg19.ctss.bed.gz': HTTP status was '503 Service Unavailable' ./CAGEr.Rcheck/00check.log:Error in scan(con, what = list(character(), NULL, integer(), NULL, integer(), : ./CAGEr.Rcheck/00check.log: cannot open the connection to 'http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/adipose%2520tissue%252c%2520adult%252c%2520pool1.CNhs10615.10010-101C1.hg19.ctss.bed.gz' ./CAGEr.Rcheck/00check.log:Calls: importPublicData -> importPublicData -> scan ./CAGEr.Rcheck/00check.log:Execution halted ./CAGEr.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CAGEr.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CAGEr.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./CAGEr.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./CAGEr.Rcheck/00check.log:Error in re-building vignettes: ./CAGEr.Rcheck/00check.log: ... ./CAGEr.Rcheck/00check.log: -> zf_prim6 ./CAGEr.Rcheck/00check.log:Getting positions of quantiles within clusters... ./CAGEr.Rcheck/00check.log: -> zf_30p_dome ./CAGEr.Rcheck/00check.log: -> zf_high ./CAGEr.Rcheck/00check.log: -> zf_unfertilized_egg ./CAGEr.Rcheck/00check.log: -> zf_prim6 ./CAGEr.Rcheck/00check.log:bedGraph file(s) for CTSS normalized counts have been created in your working directory (/home/mdowle/build/revdeplib/CAGEr.Rcheck/vign_test/CAGEr/vignettes) ./CAGEr.Rcheck/00check.log:BigWig file(s) for CTSS normalized counts have been created in your working directory (/home/mdowle/build/revdeplib/CAGEr.Rcheck/vign_test/CAGEr/vignettes) ./CAGEr.Rcheck/00check.log:File 'All.samples.tagClusters.qLow0.1_qUp0.9.bed' has been created in your working directory (/home/mdowle/build/revdeplib/CAGEr.Rcheck/vign_test/CAGEr/vignettes) ./CAGEr.Rcheck/00check.log:Loading required namespace: DESeq2 ./CAGEr.Rcheck/00check.log:Calculating cumulative sum of CAGE signal along clusters... ./CAGEr.Rcheck/00check.log: -> zf_unfertilized_egg ./CAGEr.Rcheck/00check.log: -> zf_high ./CAGEr.Rcheck/00check.log: -> zf_30p_dome ./CAGEr.Rcheck/00check.log: -> zf_prim6 ./CAGEr.Rcheck/00check.log:Fetching sample: Astrocyte_-_cerebellum__donor1... ./CAGEr.Rcheck/00check.log:Quitting from lines 1115-1118 (CAGEexp.Rmd) ./CAGEr.Rcheck/00check.log:Error: processing vignette 'CAGEexp.Rmd' failed with diagnostics: ./CAGEr.Rcheck/00check.log:cannot open the connection to 'http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor1.CNhs11321.11500-119F6.hg19.ctss.bed.gz' ./CAGEr.Rcheck/00check.log:Execution halted ./CAGEr.Rcheck/00check.log:* checking PDF version of manual ... OK ./CAGEr.Rcheck/00check.log:* DONE ./CAGEr.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 2 NOTEs ./facopy.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/facopy.Rcheck’ ./facopy.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./facopy.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./facopy.Rcheck/00check.log:* using session charset: UTF-8 ./facopy.Rcheck/00check.log:* checking for file ‘facopy/DESCRIPTION’ ... OK ./facopy.Rcheck/00check.log:* checking extension type ... Package ./facopy.Rcheck/00check.log:* this is package ‘facopy’ version ‘1.13.0’ ./facopy.Rcheck/00check.log:* checking package namespace information ... OK ./facopy.Rcheck/00check.log:* checking package dependencies ... NOTE ./facopy.Rcheck/00check.log:Depends: includes the non-default packages: ./facopy.Rcheck/00check.log: ‘cgdsr’ ‘coin’ ‘ggplot2’ ‘gridExtra’ ‘facopy.annot’ ‘grid’ ./facopy.Rcheck/00check.log:Adding so many packages to the search path is excessive and importing selectively is preferable. ./facopy.Rcheck/00check.log:* checking if this is a source package ... OK ./facopy.Rcheck/00check.log:* checking if there is a namespace ... OK ./facopy.Rcheck/00check.log:* checking for executable files ... OK ./facopy.Rcheck/00check.log:* checking for hidden files and directories ... OK ./facopy.Rcheck/00check.log:* checking for portable file names ... OK ./facopy.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./facopy.Rcheck/00check.log:* checking whether package ‘facopy’ can be installed ... ERROR ./facopy.Rcheck/00check.log:Installation failed. ./facopy.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/facopy.Rcheck/00install.out’ for details. ./facopy.Rcheck/00check.log:* DONE ./facopy.Rcheck/00check.log:Status: 1 ERROR, 1 NOTE ./GenVisR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/GenVisR.Rcheck’ ./GenVisR.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./GenVisR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./GenVisR.Rcheck/00check.log:* using session charset: UTF-8 ./GenVisR.Rcheck/00check.log:* checking for file ‘GenVisR/DESCRIPTION’ ... OK ./GenVisR.Rcheck/00check.log:* this is package ‘GenVisR’ version ‘1.12.1’ ./GenVisR.Rcheck/00check.log:* checking package namespace information ... OK ./GenVisR.Rcheck/00check.log:* checking package dependencies ... OK ./GenVisR.Rcheck/00check.log:* checking if this is a source package ... OK ./GenVisR.Rcheck/00check.log:* checking if there is a namespace ... OK ./GenVisR.Rcheck/00check.log:* checking for executable files ... OK ./GenVisR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./GenVisR.Rcheck/00check.log:* checking for portable file names ... OK ./GenVisR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./GenVisR.Rcheck/00check.log:* checking whether package ‘GenVisR’ can be installed ... OK ./GenVisR.Rcheck/00check.log:* checking installed package size ... NOTE ./GenVisR.Rcheck/00check.log: installed size is 14.0Mb ./GenVisR.Rcheck/00check.log: sub-directories of 1Mb or more: ./GenVisR.Rcheck/00check.log: doc 11.5Mb ./GenVisR.Rcheck/00check.log: extdata 1.0Mb ./GenVisR.Rcheck/00check.log:* checking package directory ... OK ./GenVisR.Rcheck/00check.log:* checking ‘build’ directory ... OK ./GenVisR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./GenVisR.Rcheck/00check.log:* checking top-level files ... OK ./GenVisR.Rcheck/00check.log:* checking for left-over files ... OK ./GenVisR.Rcheck/00check.log:* checking index information ... OK ./GenVisR.Rcheck/00check.log:* checking package subdirectories ... OK ./GenVisR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./GenVisR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./GenVisR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./GenVisR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./GenVisR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./GenVisR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./GenVisR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./GenVisR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./GenVisR.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./GenVisR.Rcheck/00check.log:Namespace in Imports field not imported from: ‘reshape2’ ./GenVisR.Rcheck/00check.log: All declared Imports should be used. ./GenVisR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./GenVisR.Rcheck/00check.log:* checking replacement functions ... OK ./GenVisR.Rcheck/00check.log:* checking foreign function calls ... OK ./GenVisR.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./GenVisR.Rcheck/00check.log:setTierTwo,data.table : a: no visible binding for global variable ‘tmp’ ./GenVisR.Rcheck/00check.log:toLolliplot,GMS: no visible binding for global variable ‘missingINdex’ ./GenVisR.Rcheck/00check.log:toLolliplot,VEP: no visible binding for global variable ‘missingINdex’ ./GenVisR.Rcheck/00check.log:Undefined global functions or variables: ./GenVisR.Rcheck/00check.log: missingINdex tmp ./GenVisR.Rcheck/00check.log:* checking Rd files ... OK ./GenVisR.Rcheck/00check.log:* checking Rd metadata ... OK ./GenVisR.Rcheck/00check.log:* checking Rd cross-references ... OK ./GenVisR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./GenVisR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./GenVisR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./GenVisR.Rcheck/00check.log:* checking Rd contents ... OK ./GenVisR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./GenVisR.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./GenVisR.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./GenVisR.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./GenVisR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./GenVisR.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./GenVisR.Rcheck/00check.log:* checking examples ... OK ./GenVisR.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./GenVisR.Rcheck/00check.log:* checking tests ... ERROR ./GenVisR.Rcheck/00check.log: Running ‘testthat.R’ ./GenVisR.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./GenVisR.Rcheck/00check.log:Last 13 lines of output: ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: NULL ./GenVisR.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./GenVisR.Rcheck/00check.log: OK: 553 SKIPPED: 45 FAILED: 1 ./GenVisR.Rcheck/00check.log: 1. Failure: setDomainHeights domains are nested correctly (@test-Lolliplot-class.R#525) ./GenVisR.Rcheck/00check.log: ./GenVisR.Rcheck/00check.log: Error: testthat unit tests failed ./GenVisR.Rcheck/00check.log: Execution halted ./GenVisR.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./GenVisR.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./GenVisR.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./GenVisR.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./GenVisR.Rcheck/00check.log:* checking PDF version of manual ... OK ./GenVisR.Rcheck/00check.log:* DONE ./GenVisR.Rcheck/00check.log:Status: 1 ERROR, 3 NOTEs ./ImmuneSpaceR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ImmuneSpaceR.Rcheck’ ./ImmuneSpaceR.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./ImmuneSpaceR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ImmuneSpaceR.Rcheck/00check.log:* using session charset: UTF-8 ./ImmuneSpaceR.Rcheck/00check.log:* checking for file ‘ImmuneSpaceR/DESCRIPTION’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking extension type ... Package ./ImmuneSpaceR.Rcheck/00check.log:* this is package ‘ImmuneSpaceR’ version ‘1.8.2’ ./ImmuneSpaceR.Rcheck/00check.log:* checking package namespace information ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking package dependencies ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking if this is a source package ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking if there is a namespace ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for executable files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for portable file names ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether package ‘ImmuneSpaceR’ can be installed ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking installed package size ... NOTE ./ImmuneSpaceR.Rcheck/00check.log: installed size is 7.4Mb ./ImmuneSpaceR.Rcheck/00check.log: sub-directories of 1Mb or more: ./ImmuneSpaceR.Rcheck/00check.log: doc 6.8Mb ./ImmuneSpaceR.Rcheck/00check.log:* checking package directory ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking ‘build’ directory ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking top-level files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for left-over files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking index information ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking package subdirectories ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./ImmuneSpaceR.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./ImmuneSpaceR.Rcheck/00check.log: ‘Rlabkey:::.lkdefaults’ ‘Rlabkey:::labkey.getRequestOptions’ ./ImmuneSpaceR.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./ImmuneSpaceR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking replacement functions ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking foreign function calls ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./ImmuneSpaceR.Rcheck/00check.log:.getDataToPlot: no visible binding for global variable ‘value_reported’ ./ImmuneSpaceR.Rcheck/00check.log:Undefined global functions or variables: ./ImmuneSpaceR.Rcheck/00check.log: value_reported ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd files ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd metadata ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd cross-references ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking Rd contents ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking examples ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking tests ... ERROR ./ImmuneSpaceR.Rcheck/00check.log: Running ‘testthat.R’ ./ImmuneSpaceR.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./ImmuneSpaceR.Rcheck/00check.log:Last 13 lines of output: ./ImmuneSpaceR.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./ImmuneSpaceR.Rcheck/00check.log: OK: 140 SKIPPED: 0 FAILED: 24 ./ImmuneSpaceR.Rcheck/00check.log: 1. Failure: returns df of GE analysis using cohort filter (@test-getGEAnalysis.R#35) ./ImmuneSpaceR.Rcheck/00check.log: 2. Error: gets TIV_2008 eSet non-summary (@test-getGEMatrix.R#26) ./ImmuneSpaceR.Rcheck/00check.log: 3. Error: gets TIV_2008 eSet raw (@test-getGEMatrix.R#32) ./ImmuneSpaceR.Rcheck/00check.log: 4. Error: gets TIV_young eSet raw (@test-getGEMatrix.R#38) ./ImmuneSpaceR.Rcheck/00check.log: 5. Error: gets TIV_2008 eSet summary (@test-getGEMatrix.R#43) ./ImmuneSpaceR.Rcheck/00check.log: 6. Error: get_multiple matrices non-summary (@test-getGEMatrix.R#48) ./ImmuneSpaceR.Rcheck/00check.log: 7. Error: get_multiple matrices summary (@test-getGEMatrix.R#53) ./ImmuneSpaceR.Rcheck/00check.log: 8. Error: get_multiple matrices summary without cache error (@test-getGEMatrix.R#58) ./ImmuneSpaceR.Rcheck/00check.log: 9. Error: get_multiple matrices summary with reload (@test-getGEMatrix.R#63) ./ImmuneSpaceR.Rcheck/00check.log: 1. ... ./ImmuneSpaceR.Rcheck/00check.log: ./ImmuneSpaceR.Rcheck/00check.log: Error: testthat unit tests failed ./ImmuneSpaceR.Rcheck/00check.log: Execution halted ./ImmuneSpaceR.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./ImmuneSpaceR.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./ImmuneSpaceR.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./ImmuneSpaceR.Rcheck/00check.log:Error in re-building vignettes: ./ImmuneSpaceR.Rcheck/00check.log: ... ./ImmuneSpaceR.Rcheck/00check.log:Loading required package: httr ./ImmuneSpaceR.Rcheck/00check.log:Loading required package: jsonlite ./ImmuneSpaceR.Rcheck/00check.log:Quitting from lines 105-106 (Intro_to_ImmuneSpaceR.Rmd) ./ImmuneSpaceR.Rcheck/00check.log:Error: processing vignette 'Intro_to_ImmuneSpaceR.Rmd' failed with diagnostics: ./ImmuneSpaceR.Rcheck/00check.log:No matrix LAIV_2008 in study ./ImmuneSpaceR.Rcheck/00check.log:Execution halted ./ImmuneSpaceR.Rcheck/00check.log:* checking PDF version of manual ... OK ./ImmuneSpaceR.Rcheck/00check.log:* DONE ./ImmuneSpaceR.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 3 NOTEs ./LowMACA.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/LowMACA.Rcheck’ ./LowMACA.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./LowMACA.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./LowMACA.Rcheck/00check.log:* using session charset: UTF-8 ./LowMACA.Rcheck/00check.log:* checking for file ‘LowMACA/DESCRIPTION’ ... OK ./LowMACA.Rcheck/00check.log:* checking extension type ... Package ./LowMACA.Rcheck/00check.log:* this is package ‘LowMACA’ version ‘1.12.0’ ./LowMACA.Rcheck/00check.log:* checking package namespace information ... OK ./LowMACA.Rcheck/00check.log:* checking package dependencies ... OK ./LowMACA.Rcheck/00check.log:* checking if this is a source package ... OK ./LowMACA.Rcheck/00check.log:* checking if there is a namespace ... OK ./LowMACA.Rcheck/00check.log:* checking for executable files ... OK ./LowMACA.Rcheck/00check.log:* checking for hidden files and directories ... OK ./LowMACA.Rcheck/00check.log:* checking for portable file names ... OK ./LowMACA.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./LowMACA.Rcheck/00check.log:* checking whether package ‘LowMACA’ can be installed ... OK ./LowMACA.Rcheck/00check.log:* checking installed package size ... OK ./LowMACA.Rcheck/00check.log:* checking package directory ... OK ./LowMACA.Rcheck/00check.log:* checking ‘build’ directory ... OK ./LowMACA.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./LowMACA.Rcheck/00check.log:* checking top-level files ... OK ./LowMACA.Rcheck/00check.log:* checking for left-over files ... OK ./LowMACA.Rcheck/00check.log:* checking index information ... OK ./LowMACA.Rcheck/00check.log:* checking package subdirectories ... OK ./LowMACA.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./LowMACA.Rcheck/00check.log:* checking R files for syntax errors ... OK ./LowMACA.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./LowMACA.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./LowMACA.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./LowMACA.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./LowMACA.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./LowMACA.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./LowMACA.Rcheck/00check.log:* checking dependencies in R code ... OK ./LowMACA.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./LowMACA.Rcheck/00check.log:* checking replacement functions ... OK ./LowMACA.Rcheck/00check.log:* checking foreign function calls ... OK ./LowMACA.Rcheck/00check.log:* checking R code for possible problems ... OK ./LowMACA.Rcheck/00check.log:* checking Rd files ... OK ./LowMACA.Rcheck/00check.log:* checking Rd metadata ... OK ./LowMACA.Rcheck/00check.log:* checking Rd cross-references ... OK ./LowMACA.Rcheck/00check.log:* checking for missing documentation entries ... OK ./LowMACA.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./LowMACA.Rcheck/00check.log:* checking Rd \usage sections ... OK ./LowMACA.Rcheck/00check.log:* checking Rd contents ... OK ./LowMACA.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./LowMACA.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./LowMACA.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./LowMACA.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./LowMACA.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./LowMACA.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./LowMACA.Rcheck/00check.log:* checking examples ... ERROR ./LowMACA.Rcheck/00check.log:Running examples in ‘LowMACA-Ex.R’ failed ./LowMACA.Rcheck/00check.log:The error most likely occurred in: ./LowMACA.Rcheck/00check.log:> ### Name: getMutations ./LowMACA.Rcheck/00check.log:> ### Title: Retrieve mutation data for a LowMACA object ./LowMACA.Rcheck/00check.log:> ### Aliases: getMutations ./LowMACA.Rcheck/00check.log:> ./LowMACA.Rcheck/00check.log:> ### ** Examples ./LowMACA.Rcheck/00check.log:> ./LowMACA.Rcheck/00check.log:> #Create an object of class LowMACA ./LowMACA.Rcheck/00check.log:> lm <- newLowMACA(pfam="PF12906") ./LowMACA.Rcheck/00check.log:> #Change some paramters ./LowMACA.Rcheck/00check.log:> #By default, LowMACA retrieve only missense mutations. ./LowMACA.Rcheck/00check.log:> #We want all mutations ./LowMACA.Rcheck/00check.log:> lmParams(lm)[['mutation_type']] <- 'all' ./LowMACA.Rcheck/00check.log:> #By default, LowMACA takes mutations from all the kinds of tumor ./LowMACA.Rcheck/00check.log:> #We want just prostate cancer samples ./LowMACA.Rcheck/00check.log:> lmParams(lm)[['tumor_type']] <- 'prad' ./LowMACA.Rcheck/00check.log:> lm <- getMutations(lm) ./LowMACA.Rcheck/00check.log:Getting mutations from cancers studies... ./LowMACA.Rcheck/00check.log:Warning in file(file, "rt") : ./LowMACA.Rcheck/00check.log: cannot open URL 'http://www.cbioportal.org/webservice.do?cmd=getGeneticProfiles&cancer_study_id=prad_fhcrc': HTTP status was '503 Service Unavailable' ./LowMACA.Rcheck/00check.log:Error in value[[3L]](cond) : ./LowMACA.Rcheck/00check.log: Problems with cBioPortal Connection at http://www.cbioportal.org/public-portal/webservice.do?cmd=getGeneticProfiles&&cancer_study_id=prad_fhcrc ./LowMACA.Rcheck/00check.log:Calls: getMutations ... tryCatch -> tryCatchList -> tryCatchOne -> ./LowMACA.Rcheck/00check.log:Execution halted ./LowMACA.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./LowMACA.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./LowMACA.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./LowMACA.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./LowMACA.Rcheck/00check.log:* checking PDF version of manual ... OK ./LowMACA.Rcheck/00check.log:* DONE ./LowMACA.Rcheck/00check.log:Status: 1 ERROR ./LymphoSeq.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/LymphoSeq.Rcheck’ ./LymphoSeq.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./LymphoSeq.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./LymphoSeq.Rcheck/00check.log:* using session charset: UTF-8 ./LymphoSeq.Rcheck/00check.log:* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK ./LymphoSeq.Rcheck/00check.log:* this is package ‘LymphoSeq’ version ‘1.8.0’ ./LymphoSeq.Rcheck/00check.log:* checking package namespace information ... OK ./LymphoSeq.Rcheck/00check.log:* checking package dependencies ... OK ./LymphoSeq.Rcheck/00check.log:* checking if this is a source package ... OK ./LymphoSeq.Rcheck/00check.log:* checking if there is a namespace ... OK ./LymphoSeq.Rcheck/00check.log:* checking for executable files ... OK ./LymphoSeq.Rcheck/00check.log:* checking for hidden files and directories ... OK ./LymphoSeq.Rcheck/00check.log:* checking for portable file names ... OK ./LymphoSeq.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./LymphoSeq.Rcheck/00check.log:* checking whether package ‘LymphoSeq’ can be installed ... ERROR ./LymphoSeq.Rcheck/00check.log:Installation failed. ./LymphoSeq.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/LymphoSeq.Rcheck/00install.out’ for details. ./LymphoSeq.Rcheck/00check.log:* DONE ./LymphoSeq.Rcheck/00check.log:Status: 1 ERROR ./MAST.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/MAST.Rcheck’ ./MAST.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./MAST.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./MAST.Rcheck/00check.log:* using session charset: UTF-8 ./MAST.Rcheck/00check.log:* checking for file ‘MAST/DESCRIPTION’ ... OK ./MAST.Rcheck/00check.log:* checking extension type ... Package ./MAST.Rcheck/00check.log:* this is package ‘MAST’ version ‘1.6.1’ ./MAST.Rcheck/00check.log:* checking package namespace information ... OK ./MAST.Rcheck/00check.log:* checking package dependencies ... OK ./MAST.Rcheck/00check.log:* checking if this is a source package ... OK ./MAST.Rcheck/00check.log:* checking if there is a namespace ... OK ./MAST.Rcheck/00check.log:* checking for executable files ... OK ./MAST.Rcheck/00check.log:* checking for hidden files and directories ... NOTE ./MAST.Rcheck/00check.log:Found the following hidden files and directories: ./MAST.Rcheck/00check.log: .travis.yml ./MAST.Rcheck/00check.log:These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ./MAST.Rcheck/00check.log:* checking for portable file names ... OK ./MAST.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./MAST.Rcheck/00check.log:* checking whether package ‘MAST’ can be installed ... OK ./MAST.Rcheck/00check.log:* checking installed package size ... NOTE ./MAST.Rcheck/00check.log: installed size is 8.7Mb ./MAST.Rcheck/00check.log: sub-directories of 1Mb or more: ./MAST.Rcheck/00check.log: R 1.0Mb ./MAST.Rcheck/00check.log: data 3.7Mb ./MAST.Rcheck/00check.log: doc 3.7Mb ./MAST.Rcheck/00check.log:* checking package directory ... OK ./MAST.Rcheck/00check.log:* checking ‘build’ directory ... OK ./MAST.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./MAST.Rcheck/00check.log:* checking top-level files ... OK ./MAST.Rcheck/00check.log:* checking for left-over files ... OK ./MAST.Rcheck/00check.log:* checking index information ... OK ./MAST.Rcheck/00check.log:* checking package subdirectories ... OK ./MAST.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./MAST.Rcheck/00check.log:* checking R files for syntax errors ... OK ./MAST.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./MAST.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./MAST.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./MAST.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./MAST.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./MAST.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./MAST.Rcheck/00check.log:* checking dependencies in R code ... OK ./MAST.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./MAST.Rcheck/00check.log:* checking replacement functions ... OK ./MAST.Rcheck/00check.log:* checking foreign function calls ... OK ./MAST.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./MAST.Rcheck/00check.log:assay_idx: no visible global function definition for ‘assayNames’ ./MAST.Rcheck/00check.log:collectResiduals: no visible global function definition for ./MAST.Rcheck/00check.log: ‘assayNames’ ./MAST.Rcheck/00check.log:collectResiduals: no visible global function definition for ‘assay<-’ ./MAST.Rcheck/00check.log:collectResiduals: no visible global function definition for ./MAST.Rcheck/00check.log: ‘assayNames<-’ ./MAST.Rcheck/00check.log:primerAverage: no visible global function definition for ‘assay<-’ ./MAST.Rcheck/00check.log:primerAverage: no visible global function definition for ‘rowData<-’ ./MAST.Rcheck/00check.log:assay<-,SingleCellAssay-missing: no visible global function definition ./MAST.Rcheck/00check.log: for ‘assay<-’ ./MAST.Rcheck/00check.log:assayNames<-,SingleCellAssay-character: no visible global function ./MAST.Rcheck/00check.log: definition for ‘assayNames’ ./MAST.Rcheck/00check.log:assayNames<-,SingleCellAssay-character: no visible global function ./MAST.Rcheck/00check.log: definition for ‘assays<-’ ./MAST.Rcheck/00check.log:exprs<-,SingleCellAssay-ANY: no visible global function definition for ./MAST.Rcheck/00check.log: ‘assay<-’ ./MAST.Rcheck/00check.log:Undefined global functions or variables: ./MAST.Rcheck/00check.log: assay<- assayNames assayNames<- assays<- rowData<- ./MAST.Rcheck/00check.log:* checking Rd files ... OK ./MAST.Rcheck/00check.log:* checking Rd metadata ... OK ./MAST.Rcheck/00check.log:* checking Rd cross-references ... OK ./MAST.Rcheck/00check.log:* checking for missing documentation entries ... OK ./MAST.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./MAST.Rcheck/00check.log:* checking Rd \usage sections ... OK ./MAST.Rcheck/00check.log:* checking Rd contents ... OK ./MAST.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./MAST.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./MAST.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./MAST.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./MAST.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./MAST.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./MAST.Rcheck/00check.log:* checking examples ... OK ./MAST.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./MAST.Rcheck/00check.log:* checking tests ... ERROR ./MAST.Rcheck/00check.log: Running ‘testthat.R’ ./MAST.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./MAST.Rcheck/00check.log:Last 13 lines of output: ./MAST.Rcheck/00check.log: NAs in V(mu) ./MAST.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./MAST.Rcheck/00check.log: OK: 269 SKIPPED: 5 FAILED: 9 ./MAST.Rcheck/00check.log: 1. Failure: Can fit ./MAST.Rcheck/00check.log: 2. Failure: Can fit ./MAST.Rcheck/00check.log: 3. Failure: Handle Singular Designs ./MAST.Rcheck/00check.log: 4. Failure: Handle 100% expression ./MAST.Rcheck/00check.log: 5. Failure: log likelihood agrees with individual model objects ./MAST.Rcheck/00check.log: 6. Failure: log likelihood agrees with individual model objects ./MAST.Rcheck/00check.log: 7. Failure: Can get variance/cov ./MAST.Rcheck/00check.log: 8. Failure: Can get variance/cov ./MAST.Rcheck/00check.log: 9. Failure: Contrast Hypothesis Work ./MAST.Rcheck/00check.log: ./MAST.Rcheck/00check.log: Error: testthat unit tests failed ./MAST.Rcheck/00check.log: Execution halted ./MAST.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./MAST.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./MAST.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./MAST.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./MAST.Rcheck/00check.log:* checking PDF version of manual ... OK ./MAST.Rcheck/00check.log:* DONE ./MAST.Rcheck/00check.log:Status: 1 ERROR, 3 NOTEs ./phantasus.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/phantasus.Rcheck’ ./phantasus.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./phantasus.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./phantasus.Rcheck/00check.log:* using session charset: UTF-8 ./phantasus.Rcheck/00check.log:* checking for file ‘phantasus/DESCRIPTION’ ... OK ./phantasus.Rcheck/00check.log:* this is package ‘phantasus’ version ‘1.0.2’ ./phantasus.Rcheck/00check.log:* package encoding: UTF-8 ./phantasus.Rcheck/00check.log:* checking package namespace information ... OK ./phantasus.Rcheck/00check.log:* checking package dependencies ... OK ./phantasus.Rcheck/00check.log:* checking if this is a source package ... OK ./phantasus.Rcheck/00check.log:* checking if there is a namespace ... OK ./phantasus.Rcheck/00check.log:* checking for executable files ... OK ./phantasus.Rcheck/00check.log:* checking for hidden files and directories ... OK ./phantasus.Rcheck/00check.log:* checking for portable file names ... OK ./phantasus.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./phantasus.Rcheck/00check.log:* checking whether package ‘phantasus’ can be installed ... OK ./phantasus.Rcheck/00check.log:* checking installed package size ... NOTE ./phantasus.Rcheck/00check.log: installed size is 18.1Mb ./phantasus.Rcheck/00check.log: sub-directories of 1Mb or more: ./phantasus.Rcheck/00check.log: doc 4.6Mb ./phantasus.Rcheck/00check.log: www 12.8Mb ./phantasus.Rcheck/00check.log:* checking package directory ... OK ./phantasus.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./phantasus.Rcheck/00check.log:Package listed in more than one of Depends, Imports, Suggests, Enhances: ./phantasus.Rcheck/00check.log: ‘svglite’ ./phantasus.Rcheck/00check.log:A package should be listed in only one of these fields. ./phantasus.Rcheck/00check.log:* checking top-level files ... OK ./phantasus.Rcheck/00check.log:* checking for left-over files ... OK ./phantasus.Rcheck/00check.log:* checking index information ... OK ./phantasus.Rcheck/00check.log:* checking package subdirectories ... OK ./phantasus.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./phantasus.Rcheck/00check.log:* checking R files for syntax errors ... OK ./phantasus.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./phantasus.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./phantasus.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./phantasus.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./phantasus.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./phantasus.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./phantasus.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./phantasus.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./phantasus.Rcheck/00check.log: 'GEOquery:::getDirListing' 'opencpu:::rookhandler' ./phantasus.Rcheck/00check.log: 'opencpu:::tmp_root' 'opencpu:::win_or_mac' ./phantasus.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./phantasus.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./phantasus.Rcheck/00check.log:* checking replacement functions ... OK ./phantasus.Rcheck/00check.log:* checking foreign function calls ... OK ./phantasus.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./phantasus.Rcheck/00check.log:gseaPlot: no visible global function definition for 'setNames' ./phantasus.Rcheck/00check.log:read.gct: no visible global function definition for 'head' ./phantasus.Rcheck/00check.log:Undefined global functions or variables: ./phantasus.Rcheck/00check.log: head setNames ./phantasus.Rcheck/00check.log:Consider adding ./phantasus.Rcheck/00check.log: importFrom("stats", "setNames") ./phantasus.Rcheck/00check.log: importFrom("utils", "head") ./phantasus.Rcheck/00check.log:to your NAMESPACE file. ./phantasus.Rcheck/00check.log:* checking Rd files ... OK ./phantasus.Rcheck/00check.log:* checking Rd metadata ... OK ./phantasus.Rcheck/00check.log:* checking Rd cross-references ... OK ./phantasus.Rcheck/00check.log:* checking for missing documentation entries ... OK ./phantasus.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./phantasus.Rcheck/00check.log:* checking Rd \usage sections ... OK ./phantasus.Rcheck/00check.log:* checking Rd contents ... OK ./phantasus.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./phantasus.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./phantasus.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./phantasus.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./phantasus.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./phantasus.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./phantasus.Rcheck/00check.log:* checking examples ... OK ./phantasus.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./phantasus.Rcheck/00check.log:* checking tests ... ERROR ./phantasus.Rcheck/00check.log: Running ‘testthat.R’ ./phantasus.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./phantasus.Rcheck/00check.log:Last 13 lines of output: ./phantasus.Rcheck/00check.log: 8: datamat[[1]] ./phantasus.Rcheck/00check.log: 9: `[[.tbl_df`(datamat, 1) ./phantasus.Rcheck/00check.log: ./phantasus.Rcheck/00check.log: trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz' ./phantasus.Rcheck/00check.log: Content type 'application/x-gzip' length 3389 bytes ./phantasus.Rcheck/00check.log: ================================================== ./phantasus.Rcheck/00check.log: downloaded 3389 bytes ./phantasus.Rcheck/00check.log: ./phantasus.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./phantasus.Rcheck/00check.log: OK: 56 SKIPPED: 0 FAILED: 2 ./phantasus.Rcheck/00check.log: 1. Error: loadGEO finishes with result (@testloadGEO.R#23) ./phantasus.Rcheck/00check.log: 2. Error: reparseCachedGSEs works (@testloadGEO.R#33) ./phantasus.Rcheck/00check.log: ./phantasus.Rcheck/00check.log: Error: testthat unit tests failed ./phantasus.Rcheck/00check.log: Execution halted ./phantasus.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./phantasus.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./phantasus.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./phantasus.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./phantasus.Rcheck/00check.log:Error in re-building vignettes: ./phantasus.Rcheck/00check.log: ... ./phantasus.Rcheck/00check.log: 'browseVignettes()'. To cite Bioconductor, see ./phantasus.Rcheck/00check.log: 'citation("Biobase")', and for packages 'citation("pkgname")'. ./phantasus.Rcheck/00check.log:Setting options('download.file.method.GEOquery'='auto') ./phantasus.Rcheck/00check.log:Setting options('GEOquery.inmemory.gpl'=FALSE) ./phantasus.Rcheck/00check.log:Attaching package: 'limma' ./phantasus.Rcheck/00check.log:The following object is masked from 'package:BiocGenerics': ./phantasus.Rcheck/00check.log: plotMA ./phantasus.Rcheck/00check.log:Found 1 file(s) ./phantasus.Rcheck/00check.log:GSE14308_series_matrix.txt.gz ./phantasus.Rcheck/00check.log:trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz' ./phantasus.Rcheck/00check.log:Content type 'application/x-gzip' length 1807565 bytes (1.7 MB) ./phantasus.Rcheck/00check.log:================================================== ./phantasus.Rcheck/00check.log:downloaded 1.7 MB ./phantasus.Rcheck/00check.log:Parsed with column specification: ./phantasus.Rcheck/00check.log:cols() ./phantasus.Rcheck/00check.log:Quitting from lines 360-375 (phantasus-tutorial.Rmd) ./phantasus.Rcheck/00check.log:Error: processing vignette 'phantasus-tutorial.Rmd' failed with diagnostics: ./phantasus.Rcheck/00check.log:subscript out of bounds ./phantasus.Rcheck/00check.log:Execution halted ./phantasus.Rcheck/00check.log:* checking PDF version of manual ... OK ./phantasus.Rcheck/00check.log:* DONE ./phantasus.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 4 NOTEs ./RGMQL.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/RGMQL.Rcheck’ ./RGMQL.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./RGMQL.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./RGMQL.Rcheck/00check.log:* using session charset: UTF-8 ./RGMQL.Rcheck/00check.log:* checking for file ‘RGMQL/DESCRIPTION’ ... OK ./RGMQL.Rcheck/00check.log:* checking extension type ... Package ./RGMQL.Rcheck/00check.log:* this is package ‘RGMQL’ version ‘1.0.2’ ./RGMQL.Rcheck/00check.log:* package encoding: UTF-8 ./RGMQL.Rcheck/00check.log:* checking package namespace information ... OK ./RGMQL.Rcheck/00check.log:* checking package dependencies ... OK ./RGMQL.Rcheck/00check.log:* checking if this is a source package ... OK ./RGMQL.Rcheck/00check.log:* checking if there is a namespace ... OK ./RGMQL.Rcheck/00check.log:* checking for executable files ... OK ./RGMQL.Rcheck/00check.log:* checking for hidden files and directories ... OK ./RGMQL.Rcheck/00check.log:* checking for portable file names ... OK ./RGMQL.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./RGMQL.Rcheck/00check.log:* checking whether package ‘RGMQL’ can be installed ... OK ./RGMQL.Rcheck/00check.log:* checking installed package size ... NOTE ./RGMQL.Rcheck/00check.log: installed size is 20.4Mb ./RGMQL.Rcheck/00check.log: sub-directories of 1Mb or more: ./RGMQL.Rcheck/00check.log: example 19.5Mb ./RGMQL.Rcheck/00check.log:* checking package directory ... OK ./RGMQL.Rcheck/00check.log:* checking ‘build’ directory ... OK ./RGMQL.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./RGMQL.Rcheck/00check.log:* checking top-level files ... OK ./RGMQL.Rcheck/00check.log:* checking for left-over files ... OK ./RGMQL.Rcheck/00check.log:* checking index information ... OK ./RGMQL.Rcheck/00check.log:* checking package subdirectories ... OK ./RGMQL.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./RGMQL.Rcheck/00check.log:* checking R files for syntax errors ... OK ./RGMQL.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./RGMQL.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./RGMQL.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./RGMQL.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./RGMQL.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./RGMQL.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./RGMQL.Rcheck/00check.log:* checking dependencies in R code ... OK ./RGMQL.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./RGMQL.Rcheck/00check.log:* checking replacement functions ... OK ./RGMQL.Rcheck/00check.log:* checking foreign function calls ... OK ./RGMQL.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./RGMQL.Rcheck/00check.log:File ‘RGMQL/R/onLoad.R’: ./RGMQL.Rcheck/00check.log: .onLoad calls: ./RGMQL.Rcheck/00check.log: packageStartupMessage("Check if GMQL credentials are expired... \n") ./RGMQL.Rcheck/00check.log:See section ‘Good practice’ in '?.onAttach'. ./RGMQL.Rcheck/00check.log:* checking Rd files ... OK ./RGMQL.Rcheck/00check.log:* checking Rd metadata ... OK ./RGMQL.Rcheck/00check.log:* checking Rd cross-references ... OK ./RGMQL.Rcheck/00check.log:* checking for missing documentation entries ... OK ./RGMQL.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./RGMQL.Rcheck/00check.log:* checking Rd \usage sections ... OK ./RGMQL.Rcheck/00check.log:* checking Rd contents ... OK ./RGMQL.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./RGMQL.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./RGMQL.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./RGMQL.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./RGMQL.Rcheck/00check.log:* checking examples ... ERROR ./RGMQL.Rcheck/00check.log:Running examples in ‘RGMQL-Ex.R’ failed ./RGMQL.Rcheck/00check.log:The error most likely occurred in: ./RGMQL.Rcheck/00check.log:> ### Name: compile_query ./RGMQL.Rcheck/00check.log:> ### Title: Compile GMQL query ./RGMQL.Rcheck/00check.log:> ### Aliases: compile_query compile_query compile_query_fromfile ./RGMQL.Rcheck/00check.log:> ./RGMQL.Rcheck/00check.log:> ### ** Examples ./RGMQL.Rcheck/00check.log:> ./RGMQL.Rcheck/00check.log:> ./RGMQL.Rcheck/00check.log:> ## Login to GMQL REST services suite as guest ./RGMQL.Rcheck/00check.log:> ./RGMQL.Rcheck/00check.log:> remote_url = "http://www.gmql.eu/gmql-rest/" ./RGMQL.Rcheck/00check.log:> login_gmql(remote_url) ./RGMQL.Rcheck/00check.log:[1] "your Token is 0eaa460b-32c3-4cf3-8127-aa24e63803ea" ./RGMQL.Rcheck/00check.log:> ./RGMQL.Rcheck/00check.log:> ## This statement gets the query as text string and runs the compile ./RGMQL.Rcheck/00check.log:> ## web service ./RGMQL.Rcheck/00check.log:> ./RGMQL.Rcheck/00check.log:> compile_query(remote_url, "DATASET = SELECT() Example_Dataset_1; ./RGMQL.Rcheck/00check.log:+ MATERIALIZE DATASET INTO RESULT_DS;") ./RGMQL.Rcheck/00check.log:No encoding supplied: defaulting to UTF-8. ./RGMQL.Rcheck/00check.log:Error in compile_query(remote_url, "DATASET = SELECT() Example_Dataset_1;\n MATERIALIZE DATASET INTO RESULT_DS;") : ./RGMQL.Rcheck/00check.log: ./RGMQL.Rcheck/00check.log:Execution halted ./RGMQL.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./RGMQL.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./RGMQL.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./RGMQL.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./RGMQL.Rcheck/00check.log:Error in re-building vignettes: ./RGMQL.Rcheck/00check.log: ... ./RGMQL.Rcheck/00check.log:18/12/18 17:42:20 INFO SparkEnv: Registering MapOutputTracker ./RGMQL.Rcheck/00check.log:18/12/18 17:42:20 INFO SparkEnv: Registering BlockManagerMaster ./RGMQL.Rcheck/00check.log:18/12/18 17:42:20 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information ./RGMQL.Rcheck/00check.log:18/12/18 17:42:20 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up ./RGMQL.Rcheck/00check.log:18/12/18 17:42:20 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-1004e613-96e3-42aa-9551-05e6d4b3914d ./RGMQL.Rcheck/00check.log:18/12/18 17:42:20 INFO MemoryStore: MemoryStore started with capacity 127.2 MB ./RGMQL.Rcheck/00check.log:18/12/18 17:42:20 INFO SparkEnv: Registering OutputCommitCoordinator ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO Utils: Successfully started service 'SparkUI' on port 4040. ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.0.59:4040 ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO Executor: Starting executor ID driver on host localhost ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 43759. ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO NettyBlockTransferService: Server created on 192.168.0.59:43759 ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.0.59, 43759, None) ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.0.59:43759 with 127.2 MB RAM, BlockManagerId(driver, 192.168.0.59, 43759, None) ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.0.59, 43759, None) ./RGMQL.Rcheck/00check.log:18/12/18 17:42:21 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.0.59, 43759, None) ./RGMQL.Rcheck/00check.log:GMQL Server is up ./RGMQL.Rcheck/00check.log:18/12/18 17:42:25 WARN SparkContext: Using an existing SparkContext; some configuration may not take effect. ./RGMQL.Rcheck/00check.log:GMQL Server is up ./RGMQL.Rcheck/00check.log:18/12/18 17:42:25 WARN SparkContext: Using an existing SparkContext; some configuration may not take effect. ./RGMQL.Rcheck/00check.log:GMQL Server is up ./RGMQL.Rcheck/00check.log:Quitting from lines 528-563 (RGMQL-vignette.Rmd) ./RGMQL.Rcheck/00check.log:Error: processing vignette 'RGMQL-vignette.Rmd' failed with diagnostics: ./RGMQL.Rcheck/00check.log:Execution halted ./RGMQL.Rcheck/00check.log:* checking PDF version of manual ... OK ./RGMQL.Rcheck/00check.log:* DONE ./RGMQL.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 2 NOTEs ./scater.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/scater.Rcheck’ ./scater.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./scater.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./scater.Rcheck/00check.log:* using session charset: UTF-8 ./scater.Rcheck/00check.log:* checking for file ‘scater/DESCRIPTION’ ... OK ./scater.Rcheck/00check.log:* checking extension type ... Package ./scater.Rcheck/00check.log:* this is package ‘scater’ version ‘1.8.4’ ./scater.Rcheck/00check.log:* checking package namespace information ... OK ./scater.Rcheck/00check.log:* checking package dependencies ... OK ./scater.Rcheck/00check.log:* checking if this is a source package ... OK ./scater.Rcheck/00check.log:* checking if there is a namespace ... OK ./scater.Rcheck/00check.log:* checking for executable files ... OK ./scater.Rcheck/00check.log:* checking for hidden files and directories ... OK ./scater.Rcheck/00check.log:* checking for portable file names ... OK ./scater.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./scater.Rcheck/00check.log:* checking whether package ‘scater’ can be installed ... OK ./scater.Rcheck/00check.log:* checking installed package size ... NOTE ./scater.Rcheck/00check.log: installed size is 12.2Mb ./scater.Rcheck/00check.log: sub-directories of 1Mb or more: ./scater.Rcheck/00check.log: doc 5.4Mb ./scater.Rcheck/00check.log: extdata 2.9Mb ./scater.Rcheck/00check.log: libs 2.2Mb ./scater.Rcheck/00check.log:* checking package directory ... OK ./scater.Rcheck/00check.log:* checking ‘build’ directory ... OK ./scater.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./scater.Rcheck/00check.log:* checking top-level files ... OK ./scater.Rcheck/00check.log:* checking for left-over files ... OK ./scater.Rcheck/00check.log:* checking index information ... OK ./scater.Rcheck/00check.log:* checking package subdirectories ... OK ./scater.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./scater.Rcheck/00check.log:* checking R files for syntax errors ... OK ./scater.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./scater.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./scater.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./scater.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./scater.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./scater.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./scater.Rcheck/00check.log:* checking dependencies in R code ... OK ./scater.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./scater.Rcheck/00check.log:* checking replacement functions ... OK ./scater.Rcheck/00check.log:* checking foreign function calls ... OK ./scater.Rcheck/00check.log:* checking R code for possible problems ... OK ./scater.Rcheck/00check.log:* checking Rd files ... OK ./scater.Rcheck/00check.log:* checking Rd metadata ... OK ./scater.Rcheck/00check.log:* checking Rd cross-references ... OK ./scater.Rcheck/00check.log:* checking for missing documentation entries ... OK ./scater.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./scater.Rcheck/00check.log:* checking Rd \usage sections ... OK ./scater.Rcheck/00check.log:* checking Rd contents ... OK ./scater.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./scater.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./scater.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./scater.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./scater.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./scater.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./scater.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./scater.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./scater.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./scater.Rcheck/00check.log:* checking compiled code ... OK ./scater.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./scater.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./scater.Rcheck/00check.log:* checking examples ... WARNING ./scater.Rcheck/00check.log:Found the following significant warnings: ./scater.Rcheck/00check.log: Warning: 'read10xResults' is deprecated. ./scater.Rcheck/00check.log: Warning: 'downsampleCounts' is deprecated. ./scater.Rcheck/00check.log: Warning: 'normalizeExprs' is deprecated. ./scater.Rcheck/00check.log: Warning: 'normalizeExprs' is deprecated. ./scater.Rcheck/00check.log: Warning: 'normalizeExprs' is deprecated. ./scater.Rcheck/00check.log: Warning: 'normalizeExprs' is deprecated. ./scater.Rcheck/00check.log: Warning: 'normalizeExprs' is deprecated. ./scater.Rcheck/00check.log: Warning: 'normalizeExprs' is deprecated. ./scater.Rcheck/00check.log: Warning: 'read10xResults' is deprecated. ./scater.Rcheck/00check.log:Deprecated functions may be defunct as soon as of the next release of R. ./scater.Rcheck/00check.log:See ?Deprecated. ./scater.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./scater.Rcheck/00check.log:* checking tests ... ERROR ./scater.Rcheck/00check.log: Running ‘testthat.R’ ./scater.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./scater.Rcheck/00check.log:Last 13 lines of output: ./scater.Rcheck/00check.log: dims = ncomponents, check_duplicates = FALSE, ...) ./scater.Rcheck/00check.log: 9: Rtsne.default(vals, initial_dims = initial_dims, pca = pca, perplexity = perplexity, ./scater.Rcheck/00check.log: dims = ncomponents, check_duplicates = FALSE, ...) ./scater.Rcheck/00check.log: 10: .check_tsne_params(nrow(X), dims = dims, perplexity = perplexity, theta = theta, ./scater.Rcheck/00check.log: max_iter = max_iter, verbose = verbose, Y_init = Y_init, stop_lying_iter = stop_lying_iter, ./scater.Rcheck/00check.log: mom_switch_iter = mom_switch_iter, momentum = momentum, final_momentum = final_momentum, ./scater.Rcheck/00check.log: eta = eta, exaggeration_factor = exaggeration_factor) ./scater.Rcheck/00check.log: 11: stop("dims should be either 1, 2 or 3") ./scater.Rcheck/00check.log: ./scater.Rcheck/00check.log: Collapsing expression to 500 features.Kallisto log not provided - assuming all runs successful══ testthat results ═══════════════════════════════════════════════════════════ ./scater.Rcheck/00check.log: OK: 1012 SKIPPED: 0 FAILED: 1 ./scater.Rcheck/00check.log: 1. Error: we can produce TSNE plots (@test-plotting.R#330) ./scater.Rcheck/00check.log: ./scater.Rcheck/00check.log: Error: testthat unit tests failed ./scater.Rcheck/00check.log: Execution halted ./scater.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./scater.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./scater.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./scater.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./scater.Rcheck/00check.log:* checking PDF version of manual ... OK ./scater.Rcheck/00check.log:* DONE ./scater.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 1 NOTE ./TIN.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/TIN.Rcheck’ ./TIN.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./TIN.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./TIN.Rcheck/00check.log:* using session charset: UTF-8 ./TIN.Rcheck/00check.log:* checking for file ‘TIN/DESCRIPTION’ ... OK ./TIN.Rcheck/00check.log:* checking extension type ... Package ./TIN.Rcheck/00check.log:* this is package ‘TIN’ version ‘1.12.0’ ./TIN.Rcheck/00check.log:* checking package namespace information ... OK ./TIN.Rcheck/00check.log:* checking package dependencies ... OK ./TIN.Rcheck/00check.log:* checking if this is a source package ... OK ./TIN.Rcheck/00check.log:* checking if there is a namespace ... OK ./TIN.Rcheck/00check.log:* checking for executable files ... OK ./TIN.Rcheck/00check.log:* checking for hidden files and directories ... OK ./TIN.Rcheck/00check.log:* checking for portable file names ... OK ./TIN.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./TIN.Rcheck/00check.log:* checking whether package ‘TIN’ can be installed ... ERROR ./TIN.Rcheck/00check.log:Installation failed. ./TIN.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/TIN.Rcheck/00install.out’ for details. ./TIN.Rcheck/00check.log:* DONE ./TIN.Rcheck/00check.log:Status: 1 ERROR ./TitanCNA.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/TitanCNA.Rcheck’ ./TitanCNA.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./TitanCNA.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./TitanCNA.Rcheck/00check.log:* using session charset: UTF-8 ./TitanCNA.Rcheck/00check.log:* checking for file ‘TitanCNA/DESCRIPTION’ ... OK ./TitanCNA.Rcheck/00check.log:* checking extension type ... Package ./TitanCNA.Rcheck/00check.log:* this is package ‘TitanCNA’ version ‘1.18.0’ ./TitanCNA.Rcheck/00check.log:* checking package namespace information ... OK ./TitanCNA.Rcheck/00check.log:* checking package dependencies ... OK ./TitanCNA.Rcheck/00check.log:* checking if this is a source package ... OK ./TitanCNA.Rcheck/00check.log:* checking if there is a namespace ... OK ./TitanCNA.Rcheck/00check.log:* checking for executable files ... OK ./TitanCNA.Rcheck/00check.log:* checking for hidden files and directories ... OK ./TitanCNA.Rcheck/00check.log:* checking for portable file names ... OK ./TitanCNA.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./TitanCNA.Rcheck/00check.log:* checking whether package ‘TitanCNA’ can be installed ... ERROR ./TitanCNA.Rcheck/00check.log:Installation failed. ./TitanCNA.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/TitanCNA.Rcheck/00install.out’ for details. ./TitanCNA.Rcheck/00check.log:* DONE ./TitanCNA.Rcheck/00check.log:Status: 1 ERROR ./bsseq.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/bsseq.Rcheck’ ./bsseq.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./bsseq.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./bsseq.Rcheck/00check.log:* using session charset: UTF-8 ./bsseq.Rcheck/00check.log:* checking for file ‘bsseq/DESCRIPTION’ ... OK ./bsseq.Rcheck/00check.log:* this is package ‘bsseq’ version ‘1.16.1’ ./bsseq.Rcheck/00check.log:* package encoding: UTF-8 ./bsseq.Rcheck/00check.log:* checking package namespace information ... OK ./bsseq.Rcheck/00check.log:* checking package dependencies ... OK ./bsseq.Rcheck/00check.log:* checking if this is a source package ... OK ./bsseq.Rcheck/00check.log:* checking if there is a namespace ... OK ./bsseq.Rcheck/00check.log:* checking for executable files ... OK ./bsseq.Rcheck/00check.log:* checking for hidden files and directories ... OK ./bsseq.Rcheck/00check.log:* checking for portable file names ... OK ./bsseq.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./bsseq.Rcheck/00check.log:* checking whether package ‘bsseq’ can be installed ... OK ./bsseq.Rcheck/00check.log:* checking installed package size ... NOTE ./bsseq.Rcheck/00check.log: installed size is 10.6Mb ./bsseq.Rcheck/00check.log: sub-directories of 1Mb or more: ./bsseq.Rcheck/00check.log: data 7.7Mb ./bsseq.Rcheck/00check.log: doc 1.9Mb ./bsseq.Rcheck/00check.log:* checking package directory ... OK ./bsseq.Rcheck/00check.log:* checking ‘build’ directory ... OK ./bsseq.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./bsseq.Rcheck/00check.log:* checking top-level files ... OK ./bsseq.Rcheck/00check.log:* checking for left-over files ... OK ./bsseq.Rcheck/00check.log:* checking index information ... OK ./bsseq.Rcheck/00check.log:* checking package subdirectories ... OK ./bsseq.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./bsseq.Rcheck/00check.log:* checking R files for syntax errors ... OK ./bsseq.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./bsseq.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./bsseq.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./bsseq.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./bsseq.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./bsseq.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./bsseq.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./bsseq.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./bsseq.Rcheck/00check.log: ‘DelayedArray:::RealizationSink’ ./bsseq.Rcheck/00check.log: ‘DelayedArray:::get_max_block_length’ ./bsseq.Rcheck/00check.log: ‘DelayedArray:::get_spacings_for_linear_capped_length_blocks’ ./bsseq.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./bsseq.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./bsseq.Rcheck/00check.log:* checking replacement functions ... OK ./bsseq.Rcheck/00check.log:* checking foreign function calls ... OK ./bsseq.Rcheck/00check.log:* checking R code for possible problems ... OK ./bsseq.Rcheck/00check.log:* checking Rd files ... OK ./bsseq.Rcheck/00check.log:* checking Rd metadata ... OK ./bsseq.Rcheck/00check.log:* checking Rd cross-references ... OK ./bsseq.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./bsseq.Rcheck/00check.log:Undocumented S4 methods: ./bsseq.Rcheck/00check.log: generic 'dimnames' and siglist 'arrayRealizationSink' ./bsseq.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./bsseq.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./bsseq.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./bsseq.Rcheck/00check.log:* checking Rd \usage sections ... OK ./bsseq.Rcheck/00check.log:* checking Rd contents ... OK ./bsseq.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./bsseq.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./bsseq.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./bsseq.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./bsseq.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./bsseq.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./bsseq.Rcheck/00check.log:* checking examples ... OK ./bsseq.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./bsseq.Rcheck/00check.log:* checking tests ... OK ./bsseq.Rcheck/00check.log: Running ‘runTests.R’ ./bsseq.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./bsseq.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./bsseq.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./bsseq.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./bsseq.Rcheck/00check.log:* checking PDF version of manual ... OK ./bsseq.Rcheck/00check.log:* DONE ./bsseq.Rcheck/00check.log:Status: 1 WARNING, 2 NOTEs ./CONFESS.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CONFESS.Rcheck’ ./CONFESS.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./CONFESS.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CONFESS.Rcheck/00check.log:* using session charset: UTF-8 ./CONFESS.Rcheck/00check.log:* checking for file ‘CONFESS/DESCRIPTION’ ... OK ./CONFESS.Rcheck/00check.log:* checking extension type ... Package ./CONFESS.Rcheck/00check.log:* this is package ‘CONFESS’ version ‘1.8.0’ ./CONFESS.Rcheck/00check.log:* checking package namespace information ... OK ./CONFESS.Rcheck/00check.log:* checking package dependencies ... OK ./CONFESS.Rcheck/00check.log:* checking if this is a source package ... OK ./CONFESS.Rcheck/00check.log:* checking if there is a namespace ... OK ./CONFESS.Rcheck/00check.log:* checking for executable files ... OK ./CONFESS.Rcheck/00check.log:* checking for hidden files and directories ... NOTE ./CONFESS.Rcheck/00check.log:Found the following hidden files and directories: ./CONFESS.Rcheck/00check.log: .BBSoptions ./CONFESS.Rcheck/00check.log:These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ./CONFESS.Rcheck/00check.log:* checking for portable file names ... OK ./CONFESS.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CONFESS.Rcheck/00check.log:* checking whether package ‘CONFESS’ can be installed ... WARNING ./CONFESS.Rcheck/00check.log:Found the following significant warnings: ./CONFESS.Rcheck/00check.log: Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’ ./CONFESS.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/CONFESS.Rcheck/00install.out’ for details. ./CONFESS.Rcheck/00check.log:* checking installed package size ... OK ./CONFESS.Rcheck/00check.log:* checking package directory ... OK ./CONFESS.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CONFESS.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./CONFESS.Rcheck/00check.log:* checking top-level files ... OK ./CONFESS.Rcheck/00check.log:* checking for left-over files ... OK ./CONFESS.Rcheck/00check.log:* checking index information ... OK ./CONFESS.Rcheck/00check.log:* checking package subdirectories ... OK ./CONFESS.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CONFESS.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CONFESS.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CONFESS.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CONFESS.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CONFESS.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CONFESS.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CONFESS.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CONFESS.Rcheck/00check.log:* checking dependencies in R code ... OK ./CONFESS.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CONFESS.Rcheck/00check.log:* checking replacement functions ... OK ./CONFESS.Rcheck/00check.log:* checking foreign function calls ... OK ./CONFESS.Rcheck/00check.log:* checking R code for possible problems ... OK ./CONFESS.Rcheck/00check.log:* checking Rd files ... OK ./CONFESS.Rcheck/00check.log:* checking Rd metadata ... OK ./CONFESS.Rcheck/00check.log:* checking Rd cross-references ... OK ./CONFESS.Rcheck/00check.log:* checking for missing documentation entries ... OK ./CONFESS.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CONFESS.Rcheck/00check.log:* checking Rd \usage sections ... OK ./CONFESS.Rcheck/00check.log:* checking Rd contents ... OK ./CONFESS.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CONFESS.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./CONFESS.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./CONFESS.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./CONFESS.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./CONFESS.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./CONFESS.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CONFESS.Rcheck/00check.log:* checking examples ... OK ./CONFESS.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CONFESS.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CONFESS.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./CONFESS.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./CONFESS.Rcheck/00check.log:* checking PDF version of manual ... OK ./CONFESS.Rcheck/00check.log:* DONE ./CONFESS.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE ./CRISPRseek.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CRISPRseek.Rcheck’ ./CRISPRseek.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./CRISPRseek.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CRISPRseek.Rcheck/00check.log:* using session charset: UTF-8 ./CRISPRseek.Rcheck/00check.log:* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK ./CRISPRseek.Rcheck/00check.log:* checking extension type ... Package ./CRISPRseek.Rcheck/00check.log:* this is package ‘CRISPRseek’ version ‘1.20.0’ ./CRISPRseek.Rcheck/00check.log:* package encoding: UTF-8 ./CRISPRseek.Rcheck/00check.log:* checking package namespace information ... OK ./CRISPRseek.Rcheck/00check.log:* checking package dependencies ... OK ./CRISPRseek.Rcheck/00check.log:* checking if this is a source package ... OK ./CRISPRseek.Rcheck/00check.log:* checking if there is a namespace ... OK ./CRISPRseek.Rcheck/00check.log:* checking for executable files ... OK ./CRISPRseek.Rcheck/00check.log:* checking for hidden files and directories ... OK ./CRISPRseek.Rcheck/00check.log:* checking for portable file names ... OK ./CRISPRseek.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CRISPRseek.Rcheck/00check.log:* checking whether package ‘CRISPRseek’ can be installed ... WARNING ./CRISPRseek.Rcheck/00check.log:Found the following significant warnings: ./CRISPRseek.Rcheck/00check.log: Note: possible error in 'fold(s = gRNA.backbone, ': unused arguments (s = gRNA.backbone, t = temperature) ./CRISPRseek.Rcheck/00check.log: Note: possible error in 'fold(paste(gRNAs[i], ': unused argument (t = temperature) ./CRISPRseek.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/CRISPRseek.Rcheck/00install.out’ for details. ./CRISPRseek.Rcheck/00check.log:Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. ./CRISPRseek.Rcheck/00check.log:* checking installed package size ... OK ./CRISPRseek.Rcheck/00check.log:* checking package directory ... OK ./CRISPRseek.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CRISPRseek.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./CRISPRseek.Rcheck/00check.log:* checking top-level files ... OK ./CRISPRseek.Rcheck/00check.log:* checking for left-over files ... OK ./CRISPRseek.Rcheck/00check.log:* checking index information ... OK ./CRISPRseek.Rcheck/00check.log:* checking package subdirectories ... OK ./CRISPRseek.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CRISPRseek.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CRISPRseek.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CRISPRseek.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CRISPRseek.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CRISPRseek.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CRISPRseek.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CRISPRseek.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CRISPRseek.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./CRISPRseek.Rcheck/00check.log:':::' call which should be '::': ‘S4Vectors:::orderIntegerPairs’ ./CRISPRseek.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./CRISPRseek.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CRISPRseek.Rcheck/00check.log:* checking replacement functions ... OK ./CRISPRseek.Rcheck/00check.log:* checking foreign function calls ... OK ./CRISPRseek.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./CRISPRseek.Rcheck/00check.log:annotateOffTargets: no visible global function definition for ‘GRanges’ ./CRISPRseek.Rcheck/00check.log:annotateOffTargets: no visible global function definition for ‘as’ ./CRISPRseek.Rcheck/00check.log:annotateOffTargets: no visible global function definition for ‘exons’ ./CRISPRseek.Rcheck/00check.log:annotateOffTargets: no visible global function definition for ./CRISPRseek.Rcheck/00check.log: ‘seqlevels<-’ ./CRISPRseek.Rcheck/00check.log:annotateOffTargets: no visible global function definition for ./CRISPRseek.Rcheck/00check.log: ‘seqlevels’ ./CRISPRseek.Rcheck/00check.log:annotateOffTargets: no visible global function definition for ‘genes’ ./CRISPRseek.Rcheck/00check.log:annotateOffTargets: no visible global function definition for ‘toTable’ ./CRISPRseek.Rcheck/00check.log:buildFeatureVectorForScoring: no visible global function definition for ./CRISPRseek.Rcheck/00check.log: ‘as’ ./CRISPRseek.Rcheck/00check.log:buildFeatureVectorForScoring2: no visible global function definition ./CRISPRseek.Rcheck/00check.log: for ‘as’ ./CRISPRseek.Rcheck/00check.log:filterOffTarget: no visible global function definition for ‘seqlengths’ ./CRISPRseek.Rcheck/00check.log:foldgRNAs: no visible global function definition for ‘fold’ ./CRISPRseek.Rcheck/00check.log:getSeqFromBed: no visible global function definition for ‘seqlengths’ ./CRISPRseek.Rcheck/00check.log:uniqueREs: no visible global function definition for ‘seqlengths’ ./CRISPRseek.Rcheck/00check.log:writeHits: no visible global function definition for ‘as’ ./CRISPRseek.Rcheck/00check.log:writeHits2: no visible global function definition for ‘as’ ./CRISPRseek.Rcheck/00check.log:Undefined global functions or variables: ./CRISPRseek.Rcheck/00check.log: GRanges as exons fold genes seqlengths seqlevels seqlevels<- toTable ./CRISPRseek.Rcheck/00check.log:Consider adding ./CRISPRseek.Rcheck/00check.log: importFrom("methods", "as") ./CRISPRseek.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./CRISPRseek.Rcheck/00check.log:* checking Rd files ... NOTE ./CRISPRseek.Rcheck/00check.log:prepare_Rd: annotateOffTargets.Rd:47-49: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: annotateOffTargets.Rd:59-61: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: buildFeatureVectorForScoring.Rd:48-50: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: buildFeatureVectorForScoring.Rd:77-79: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: buildFeatureVectorForScoring.Rd:71-73: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: calculategRNAEfficiency.Rd:49-51: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: compare2Sequences.Rd:217-219: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: compare2Sequences.Rd:259-261: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: filterOffTarget.Rd:98-100: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: filterOffTarget.Rd:112-114: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: filtergRNA.Rd:48-50: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: filtergRNA.Rd:62-64: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: filtergRNA.Rd:56-58: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: findgRNAs.Rd:110-112: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: foldgRNAs.Rd:28-30: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: foldgRNAs.Rd:44-46: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: foldgRNAs.Rd:38-40: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: getOfftargetScore.Rd:73-75: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: isPatternUnique.Rd:22-24: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: isPatternUnique.Rd:34-36: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: isPatternUnique.Rd:28-30: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: isPatternUnique.Rd:40-41: Dropping empty section \seealso ./CRISPRseek.Rcheck/00check.log:prepare_Rd: offTargetAnalysis.Rd:284-286: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: offTargetAnalysis.Rd:307-309: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: searchHits.Rd:58-60: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: searchHits.Rd:80-82: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: searchHits.Rd:74-76: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: searchHits2.Rd:66-68: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: searchHits2.Rd:88-90: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: searchHits2.Rd:82-84: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: translatePattern.Rd:34-36: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: translatePattern.Rd:28-30: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: translatePattern.Rd:40-42: Dropping empty section \seealso ./CRISPRseek.Rcheck/00check.log:prepare_Rd: uniqueREs.Rd:40-42: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: uniqueREs.Rd:53-55: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: uniqueREs.Rd:47-49: Dropping empty section \references ./CRISPRseek.Rcheck/00check.log:prepare_Rd: uniqueREs.Rd:59-60: Dropping empty section \seealso ./CRISPRseek.Rcheck/00check.log:prepare_Rd: writeHits.Rd:73-75: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: writeHits.Rd:85-87: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:prepare_Rd: writeHits2.Rd:76-78: Dropping empty section \details ./CRISPRseek.Rcheck/00check.log:prepare_Rd: writeHits2.Rd:88-90: Dropping empty section \note ./CRISPRseek.Rcheck/00check.log:* checking Rd metadata ... OK ./CRISPRseek.Rcheck/00check.log:* checking Rd cross-references ... OK ./CRISPRseek.Rcheck/00check.log:* checking for missing documentation entries ... OK ./CRISPRseek.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CRISPRseek.Rcheck/00check.log:* checking Rd \usage sections ... OK ./CRISPRseek.Rcheck/00check.log:* checking Rd contents ... OK ./CRISPRseek.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CRISPRseek.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./CRISPRseek.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./CRISPRseek.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CRISPRseek.Rcheck/00check.log:* checking examples ... OK ./CRISPRseek.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./CRISPRseek.Rcheck/00check.log:* checking tests ... OK ./CRISPRseek.Rcheck/00check.log: Running ‘runTests.R’ ./CRISPRseek.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CRISPRseek.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CRISPRseek.Rcheck/00check.log:* checking running R code from vignettes ... OK ./CRISPRseek.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./CRISPRseek.Rcheck/00check.log:* checking PDF version of manual ... OK ./CRISPRseek.Rcheck/00check.log:* DONE ./CRISPRseek.Rcheck/00check.log:Status: 1 WARNING, 3 NOTEs ./crossmeta.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/crossmeta.Rcheck’ ./crossmeta.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./crossmeta.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./crossmeta.Rcheck/00check.log:* using session charset: UTF-8 ./crossmeta.Rcheck/00check.log:* checking for file ‘crossmeta/DESCRIPTION’ ... OK ./crossmeta.Rcheck/00check.log:* this is package ‘crossmeta’ version ‘1.6.0’ ./crossmeta.Rcheck/00check.log:* package encoding: UTF-8 ./crossmeta.Rcheck/00check.log:* checking package namespace information ... OK ./crossmeta.Rcheck/00check.log:* checking package dependencies ... OK ./crossmeta.Rcheck/00check.log:* checking if this is a source package ... OK ./crossmeta.Rcheck/00check.log:* checking if there is a namespace ... OK ./crossmeta.Rcheck/00check.log:* checking for executable files ... OK ./crossmeta.Rcheck/00check.log:* checking for hidden files and directories ... OK ./crossmeta.Rcheck/00check.log:* checking for portable file names ... OK ./crossmeta.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./crossmeta.Rcheck/00check.log:* checking whether package ‘crossmeta’ can be installed ... OK ./crossmeta.Rcheck/00check.log:* checking installed package size ... OK ./crossmeta.Rcheck/00check.log:* checking package directory ... OK ./crossmeta.Rcheck/00check.log:* checking ‘build’ directory ... OK ./crossmeta.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./crossmeta.Rcheck/00check.log:* checking top-level files ... OK ./crossmeta.Rcheck/00check.log:* checking for left-over files ... OK ./crossmeta.Rcheck/00check.log:* checking index information ... OK ./crossmeta.Rcheck/00check.log:* checking package subdirectories ... OK ./crossmeta.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./crossmeta.Rcheck/00check.log:* checking R files for syntax errors ... OK ./crossmeta.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./crossmeta.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./crossmeta.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./crossmeta.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./crossmeta.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./crossmeta.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./crossmeta.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./crossmeta.Rcheck/00check.log:Missing or unexported objects: ./crossmeta.Rcheck/00check.log: ‘crossmeta::gs.names’ ‘crossmeta::gslist’ ./crossmeta.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./crossmeta.Rcheck/00check.log:* checking replacement functions ... OK ./crossmeta.Rcheck/00check.log:* checking foreign function calls ... OK ./crossmeta.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./crossmeta.Rcheck/00check.log:explore_paths : server: no visible binding for global variable ‘gslist’ ./crossmeta.Rcheck/00check.log:explore_paths : server: no visible binding for global variable ./crossmeta.Rcheck/00check.log: ‘gs.names’ ./crossmeta.Rcheck/00check.log:Undefined global functions or variables: ./crossmeta.Rcheck/00check.log: gs.names gslist ./crossmeta.Rcheck/00check.log:* checking Rd files ... OK ./crossmeta.Rcheck/00check.log:* checking Rd metadata ... OK ./crossmeta.Rcheck/00check.log:* checking Rd cross-references ... NOTE ./crossmeta.Rcheck/00check.log:Packages unavailable to check Rd xrefs: ‘PADOG’, ‘GeneMeta’ ./crossmeta.Rcheck/00check.log:* checking for missing documentation entries ... OK ./crossmeta.Rcheck/00check.log:* checking for code/documentation mismatches ... WARNING ./crossmeta.Rcheck/00check.log:Data with usage in documentation object 'gs.names' but not in code: ./crossmeta.Rcheck/00check.log: gs.names ./crossmeta.Rcheck/00check.log:Data with usage in documentation object 'gslist' but not in code: ./crossmeta.Rcheck/00check.log: gslist ./crossmeta.Rcheck/00check.log:* checking Rd \usage sections ... OK ./crossmeta.Rcheck/00check.log:* checking Rd contents ... OK ./crossmeta.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./crossmeta.Rcheck/00check.log:* checking R/sysdata.rda ... OK ./crossmeta.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./crossmeta.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./crossmeta.Rcheck/00check.log:* checking examples ... OK ./crossmeta.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./crossmeta.Rcheck/00check.log:* checking tests ... OK ./crossmeta.Rcheck/00check.log: Running ‘testthat.R’ ./crossmeta.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./crossmeta.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./crossmeta.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./crossmeta.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./crossmeta.Rcheck/00check.log:* checking PDF version of manual ... OK ./crossmeta.Rcheck/00check.log:* DONE ./crossmeta.Rcheck/00check.log:Status: 1 WARNING, 3 NOTEs ./eQTL.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/eQTL.Rcheck’ ./eQTL.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./eQTL.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./eQTL.Rcheck/00check.log:* using session charset: UTF-8 ./eQTL.Rcheck/00check.log:* checking for file ‘eQTL/DESCRIPTION’ ... OK ./eQTL.Rcheck/00check.log:* this is package ‘eQTL’ version ‘1.2.0’ ./eQTL.Rcheck/00check.log:* package encoding: UTF-8 ./eQTL.Rcheck/00check.log:* checking package namespace information ... OK ./eQTL.Rcheck/00check.log:* checking package dependencies ... NOTE ./eQTL.Rcheck/00check.log:Depends: includes the non-default packages: ./eQTL.Rcheck/00check.log: ‘GGdata’ ‘GGtools’ ‘GenomeInfoDb’ ‘S4Vectors’ ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’ ‘bibtex’ ‘biglm’ ‘data.table’ ‘doParallel’ ‘foreach’ ‘knitcitations’ ‘lumi’ ‘lumiHumanAll.db’ ./eQTL.Rcheck/00check.log: ‘parallel’ ‘rmeta’ ‘scatterplot3d’ ‘snpStats’ ‘grid’ ‘yri1kgv’ ./eQTL.Rcheck/00check.log:Adding so many packages to the search path is excessive and importing selectively is preferable. ./eQTL.Rcheck/00check.log:* checking if this is a source package ... OK ./eQTL.Rcheck/00check.log:* checking if there is a namespace ... OK ./eQTL.Rcheck/00check.log:* checking for executable files ... OK ./eQTL.Rcheck/00check.log:* checking for hidden files and directories ... OK ./eQTL.Rcheck/00check.log:* checking for portable file names ... OK ./eQTL.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./eQTL.Rcheck/00check.log:* checking whether package ‘eQTL’ can be installed ... OK ./eQTL.Rcheck/00check.log:* checking installed package size ... NOTE ./eQTL.Rcheck/00check.log: installed size is 58.9Mb ./eQTL.Rcheck/00check.log: sub-directories of 1Mb or more: ./eQTL.Rcheck/00check.log: data 57.9Mb ./eQTL.Rcheck/00check.log:* checking package directory ... OK ./eQTL.Rcheck/00check.log:* checking ‘build’ directory ... OK ./eQTL.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./eQTL.Rcheck/00check.log:* checking top-level files ... OK ./eQTL.Rcheck/00check.log:* checking for left-over files ... OK ./eQTL.Rcheck/00check.log:* checking index information ... OK ./eQTL.Rcheck/00check.log:* checking package subdirectories ... OK ./eQTL.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./eQTL.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./eQTL.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./eQTL.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./eQTL.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./eQTL.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./eQTL.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./eQTL.Rcheck/00check.log:Undocumented code objects: ./eQTL.Rcheck/00check.log: 'partceu100k_dt' 'sensSave' ./eQTL.Rcheck/00check.log:Undocumented data sets: ./eQTL.Rcheck/00check.log: 'partceu100k_dt' 'sensSave' ./eQTL.Rcheck/00check.log:All user-level objects in a package should have documentation entries. ./eQTL.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./eQTL.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./eQTL.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./eQTL.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... WARNING ./eQTL.Rcheck/00check.log: ./eQTL.Rcheck/00check.log: Note: significantly better compression could be obtained ./eQTL.Rcheck/00check.log: by using R CMD build --resave-data ./eQTL.Rcheck/00check.log: old_size new_size compress ./eQTL.Rcheck/00check.log: partceu100k_dt.rda 58.4Mb 35.1Mb xz ./eQTL.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./eQTL.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./eQTL.Rcheck/00check.log:* checking examples ... NONE ./eQTL.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... NOTE ./eQTL.Rcheck/00check.log:'library' or 'require' calls not declared from: ./eQTL.Rcheck/00check.log: ‘ggplot2’ ‘reshape2’ ./eQTL.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./eQTL.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./eQTL.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./eQTL.Rcheck/00check.log:* checking PDF version of manual ... OK ./eQTL.Rcheck/00check.log:* DONE ./eQTL.Rcheck/00check.log:Status: 2 WARNINGs, 3 NOTEs ./GenoGAM.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/GenoGAM.Rcheck’ ./GenoGAM.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./GenoGAM.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./GenoGAM.Rcheck/00check.log:* using session charset: UTF-8 ./GenoGAM.Rcheck/00check.log:* checking for file ‘GenoGAM/DESCRIPTION’ ... OK ./GenoGAM.Rcheck/00check.log:* checking extension type ... Package ./GenoGAM.Rcheck/00check.log:* this is package ‘GenoGAM’ version ‘1.8.0’ ./GenoGAM.Rcheck/00check.log:* checking package namespace information ... OK ./GenoGAM.Rcheck/00check.log:* checking package dependencies ... OK ./GenoGAM.Rcheck/00check.log:* checking if this is a source package ... OK ./GenoGAM.Rcheck/00check.log:* checking if there is a namespace ... OK ./GenoGAM.Rcheck/00check.log:* checking for executable files ... OK ./GenoGAM.Rcheck/00check.log:* checking for hidden files and directories ... OK ./GenoGAM.Rcheck/00check.log:* checking for portable file names ... OK ./GenoGAM.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./GenoGAM.Rcheck/00check.log:* checking whether package ‘GenoGAM’ can be installed ... WARNING ./GenoGAM.Rcheck/00check.log:Found the following significant warnings: ./GenoGAM.Rcheck/00check.log: Note: break used in wrong context: no loop is visible ./GenoGAM.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/GenoGAM.Rcheck/00install.out’ for details. ./GenoGAM.Rcheck/00check.log:Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. ./GenoGAM.Rcheck/00check.log:* checking installed package size ... OK ./GenoGAM.Rcheck/00check.log:* checking package directory ... OK ./GenoGAM.Rcheck/00check.log:* checking ‘build’ directory ... OK ./GenoGAM.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./GenoGAM.Rcheck/00check.log:* checking top-level files ... OK ./GenoGAM.Rcheck/00check.log:* checking for left-over files ... OK ./GenoGAM.Rcheck/00check.log:* checking index information ... OK ./GenoGAM.Rcheck/00check.log:* checking package subdirectories ... OK ./GenoGAM.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./GenoGAM.Rcheck/00check.log:* checking R files for syntax errors ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./GenoGAM.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./GenoGAM.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./GenoGAM.Rcheck/00check.log:* checking dependencies in R code ... OK ./GenoGAM.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./GenoGAM.Rcheck/00check.log:* checking replacement functions ... OK ./GenoGAM.Rcheck/00check.log:* checking foreign function calls ... OK ./GenoGAM.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./GenoGAM.Rcheck/00check.log:.doCrossValidation: no visible global function definition for ‘optim’ ./GenoGAM.Rcheck/00check.log:.loglik : : no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘dnbinom’ ./GenoGAM.Rcheck/00check.log:.pvals: no visible global function definition for ‘pnorm’ ./GenoGAM.Rcheck/00check.log:.updateFormula: no visible global function definition for ‘as.formula’ ./GenoGAM.Rcheck/00check.log:callBroadPeaks: no visible binding for global variable ‘pval’ ./GenoGAM.Rcheck/00check.log:callPeaks: no visible binding for global variable ‘fdr’ ./GenoGAM.Rcheck/00check.log:computeBroadPeakSignificance: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘p.adjust’ ./GenoGAM.Rcheck/00check.log:computeBroadPeakSignificance: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘pval’ ./GenoGAM.Rcheck/00check.log:computeBroadPeakSignificance: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘region’ ./GenoGAM.Rcheck/00check.log:computeBroadPeakSignificance: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘estimate’ ./GenoGAM.Rcheck/00check.log:computePeakSignificance: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘zscore’ ./GenoGAM.Rcheck/00check.log:computePeakSignificance: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘pnorm’ ./GenoGAM.Rcheck/00check.log:computeRegionSignificance: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘p.adjust’ ./GenoGAM.Rcheck/00check.log:computeRegionSignificance: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘pvalue’ ./GenoGAM.Rcheck/00check.log:computeRegionSignificance: no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘gene’ ./GenoGAM.Rcheck/00check.log:computeTileExtremes: no visible binding for global variable ‘id’ ./GenoGAM.Rcheck/00check.log:computeZscore: no visible global function definition for ‘pnorm’ ./GenoGAM.Rcheck/00check.log:extractSplines: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘coefficients’ ./GenoGAM.Rcheck/00check.log:genogam: no visible global function definition for ‘as.formula’ ./GenoGAM.Rcheck/00check.log:getExtremes: no visible binding for global variable ‘position’ ./GenoGAM.Rcheck/00check.log:getFunctions: no visible global function definition for ‘coefficients’ ./GenoGAM.Rcheck/00check.log:makeTestGenoGAM: no visible global function definition for ‘runif’ ./GenoGAM.Rcheck/00check.log:parsePeaks : : no visible binding for global variable ./GenoGAM.Rcheck/00check.log: ‘position’ ./GenoGAM.Rcheck/00check.log:parsePeaks: no visible binding for global variable ‘zscore’ ./GenoGAM.Rcheck/00check.log:plot.GenoGAM: no visible binding for global variable ‘fit’ ./GenoGAM.Rcheck/00check.log:plotQC_GenoGAMDataSet: no visible global function definition for ‘png’ ./GenoGAM.Rcheck/00check.log:plotQC_GenoGAMDataSet: no visible global function definition for ‘par’ ./GenoGAM.Rcheck/00check.log:plotQC_GenoGAMDataSet: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘abline’ ./GenoGAM.Rcheck/00check.log:plotQC_GenoGAMDataSet: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘dev.off’ ./GenoGAM.Rcheck/00check.log:plotQC_hist: no visible global function definition for ‘png’ ./GenoGAM.Rcheck/00check.log:plotQC_hist: no visible global function definition for ‘par’ ./GenoGAM.Rcheck/00check.log:plotQC_hist: no visible global function definition for ‘hist’ ./GenoGAM.Rcheck/00check.log:plotQC_hist: no visible global function definition for ‘abline’ ./GenoGAM.Rcheck/00check.log:plotQC_hist: no visible global function definition for ‘axis’ ./GenoGAM.Rcheck/00check.log:plotQC_hist: no visible global function definition for ‘dev.off’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘par’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘plot’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘lines’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘abline’ ./GenoGAM.Rcheck/00check.log:plot_base: no visible global function definition for ‘mtext’ ./GenoGAM.Rcheck/00check.log:writeToBroadPeaks: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘write.table’ ./GenoGAM.Rcheck/00check.log:writeToNarrowPeaks: no visible global function definition for ./GenoGAM.Rcheck/00check.log: ‘write.table’ ./GenoGAM.Rcheck/00check.log:xsd : : no visible binding for global variable ‘position’ ./GenoGAM.Rcheck/00check.log:xsd: no visible binding for global variable ‘position’ ./GenoGAM.Rcheck/00check.log:Undefined global functions or variables: ./GenoGAM.Rcheck/00check.log: abline as.formula axis coefficients dev.off dnbinom estimate fdr fit ./GenoGAM.Rcheck/00check.log: gene hist id lines mtext optim p.adjust par plot png pnorm position ./GenoGAM.Rcheck/00check.log: pval pvalue region runif write.table zscore ./GenoGAM.Rcheck/00check.log:Consider adding ./GenoGAM.Rcheck/00check.log: importFrom("grDevices", "dev.off", "png") ./GenoGAM.Rcheck/00check.log: importFrom("graphics", "abline", "axis", "hist", "lines", "mtext", ./GenoGAM.Rcheck/00check.log: "par", "plot") ./GenoGAM.Rcheck/00check.log: importFrom("stats", "as.formula", "coefficients", "dnbinom", "optim", ./GenoGAM.Rcheck/00check.log: "p.adjust", "pnorm", "runif") ./GenoGAM.Rcheck/00check.log: importFrom("utils", "write.table") ./GenoGAM.Rcheck/00check.log:to your NAMESPACE file. ./GenoGAM.Rcheck/00check.log:* checking Rd files ... OK ./GenoGAM.Rcheck/00check.log:* checking Rd metadata ... OK ./GenoGAM.Rcheck/00check.log:* checking Rd cross-references ... OK ./GenoGAM.Rcheck/00check.log:* checking for missing documentation entries ... OK ./GenoGAM.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./GenoGAM.Rcheck/00check.log:* checking Rd \usage sections ... NOTE ./GenoGAM.Rcheck/00check.log:S3 methods shown with full name in documentation object 'plot.GenoGAM': ./GenoGAM.Rcheck/00check.log: ‘plot.GenoGAM’ ./GenoGAM.Rcheck/00check.log:The \usage entries for S3 methods should use the \method markup and not their full name. ./GenoGAM.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./GenoGAM.Rcheck/00check.log:* checking Rd contents ... OK ./GenoGAM.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./GenoGAM.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./GenoGAM.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./GenoGAM.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./GenoGAM.Rcheck/00check.log:* checking examples ... OK ./GenoGAM.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./GenoGAM.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./GenoGAM.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./GenoGAM.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./GenoGAM.Rcheck/00check.log:* checking PDF version of manual ... OK ./GenoGAM.Rcheck/00check.log:* DONE ./GenoGAM.Rcheck/00check.log:Status: 1 WARNING, 2 NOTEs ./iCNV.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/iCNV.Rcheck’ ./iCNV.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./iCNV.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./iCNV.Rcheck/00check.log:* using session charset: UTF-8 ./iCNV.Rcheck/00check.log:* checking for file ‘iCNV/DESCRIPTION’ ... OK ./iCNV.Rcheck/00check.log:* this is package ‘iCNV’ version ‘1.0.0’ ./iCNV.Rcheck/00check.log:* package encoding: UTF-8 ./iCNV.Rcheck/00check.log:* checking package namespace information ... OK ./iCNV.Rcheck/00check.log:* checking package dependencies ... OK ./iCNV.Rcheck/00check.log:* checking if this is a source package ... OK ./iCNV.Rcheck/00check.log:* checking if there is a namespace ... OK ./iCNV.Rcheck/00check.log:* checking for executable files ... OK ./iCNV.Rcheck/00check.log:* checking for hidden files and directories ... OK ./iCNV.Rcheck/00check.log:* checking for portable file names ... OK ./iCNV.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./iCNV.Rcheck/00check.log:* checking whether package ‘iCNV’ can be installed ... WARNING ./iCNV.Rcheck/00check.log:Found the following significant warnings: ./iCNV.Rcheck/00check.log: Note: break used in wrong context: no loop is visible ./iCNV.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/iCNV.Rcheck/00install.out’ for details. ./iCNV.Rcheck/00check.log:Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. ./iCNV.Rcheck/00check.log:* checking installed package size ... OK ./iCNV.Rcheck/00check.log:* checking package directory ... OK ./iCNV.Rcheck/00check.log:* checking ‘build’ directory ... OK ./iCNV.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./iCNV.Rcheck/00check.log:* checking top-level files ... OK ./iCNV.Rcheck/00check.log:* checking for left-over files ... OK ./iCNV.Rcheck/00check.log:* checking index information ... OK ./iCNV.Rcheck/00check.log:* checking package subdirectories ... OK ./iCNV.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./iCNV.Rcheck/00check.log:* checking R files for syntax errors ... OK ./iCNV.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./iCNV.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./iCNV.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./iCNV.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./iCNV.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./iCNV.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./iCNV.Rcheck/00check.log:* checking dependencies in R code ... OK ./iCNV.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./iCNV.Rcheck/00check.log:* checking replacement functions ... OK ./iCNV.Rcheck/00check.log:* checking foreign function calls ... OK ./iCNV.Rcheck/00check.log:* checking R code for possible problems ... OK ./iCNV.Rcheck/00check.log:* checking Rd files ... OK ./iCNV.Rcheck/00check.log:* checking Rd metadata ... OK ./iCNV.Rcheck/00check.log:* checking Rd cross-references ... OK ./iCNV.Rcheck/00check.log:* checking for missing documentation entries ... OK ./iCNV.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./iCNV.Rcheck/00check.log:* checking Rd \usage sections ... OK ./iCNV.Rcheck/00check.log:* checking Rd contents ... OK ./iCNV.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./iCNV.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./iCNV.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./iCNV.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./iCNV.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./iCNV.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./iCNV.Rcheck/00check.log:* checking examples ... OK ./iCNV.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./iCNV.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./iCNV.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./iCNV.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./iCNV.Rcheck/00check.log:* checking PDF version of manual ... OK ./iCNV.Rcheck/00check.log:* DONE ./iCNV.Rcheck/00check.log:Status: 1 WARNING ./IrisSpatialFeatures.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/IrisSpatialFeatures.Rcheck’ ./IrisSpatialFeatures.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./IrisSpatialFeatures.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./IrisSpatialFeatures.Rcheck/00check.log:* using session charset: UTF-8 ./IrisSpatialFeatures.Rcheck/00check.log:* checking for file ‘IrisSpatialFeatures/DESCRIPTION’ ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking extension type ... Package ./IrisSpatialFeatures.Rcheck/00check.log:* this is package ‘IrisSpatialFeatures’ version ‘1.3.0’ ./IrisSpatialFeatures.Rcheck/00check.log:* checking package namespace information ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking package dependencies ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking if this is a source package ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking if there is a namespace ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for executable files ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for hidden files and directories ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for portable file names ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking whether package ‘IrisSpatialFeatures’ can be installed ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking installed package size ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking package directory ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking ‘build’ directory ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking top-level files ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for left-over files ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking index information ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking package subdirectories ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking R files for syntax errors ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking dependencies in R code ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking replacement functions ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking foreign function calls ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking R code for possible problems ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking Rd files ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking Rd metadata ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking Rd cross-references ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for missing documentation entries ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking Rd \usage sections ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking Rd contents ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking compiled code ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking examples ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking tests ... OK ./IrisSpatialFeatures.Rcheck/00check.log: Running ‘testthat.R’ ./IrisSpatialFeatures.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./IrisSpatialFeatures.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./IrisSpatialFeatures.Rcheck/00check.log:Error in re-building vignettes: ./IrisSpatialFeatures.Rcheck/00check.log: ... ./IrisSpatialFeatures.Rcheck/00check.log:! LaTeX Error: Unknown graphics extension: .png?raw=true. ./IrisSpatialFeatures.Rcheck/00check.log:Error: processing vignette 'IrisSpatialFeatures.Rmd' failed with diagnostics: ./IrisSpatialFeatures.Rcheck/00check.log:Failed to compile IrisSpatialFeatures.tex. See IrisSpatialFeatures.log for more info. ./IrisSpatialFeatures.Rcheck/00check.log:Execution halted ./IrisSpatialFeatures.Rcheck/00check.log:* checking PDF version of manual ... OK ./IrisSpatialFeatures.Rcheck/00check.log:* DONE ./IrisSpatialFeatures.Rcheck/00check.log:Status: 1 WARNING ./methylPipe.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/methylPipe.Rcheck’ ./methylPipe.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./methylPipe.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./methylPipe.Rcheck/00check.log:* using session charset: UTF-8 ./methylPipe.Rcheck/00check.log:* checking for file ‘methylPipe/DESCRIPTION’ ... OK ./methylPipe.Rcheck/00check.log:* checking extension type ... Package ./methylPipe.Rcheck/00check.log:* this is package ‘methylPipe’ version ‘1.14.0’ ./methylPipe.Rcheck/00check.log:* checking package namespace information ... OK ./methylPipe.Rcheck/00check.log:* checking package dependencies ... OK ./methylPipe.Rcheck/00check.log:* checking if this is a source package ... OK ./methylPipe.Rcheck/00check.log:* checking if there is a namespace ... OK ./methylPipe.Rcheck/00check.log:* checking for executable files ... OK ./methylPipe.Rcheck/00check.log:* checking for hidden files and directories ... OK ./methylPipe.Rcheck/00check.log:* checking for portable file names ... OK ./methylPipe.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./methylPipe.Rcheck/00check.log:* checking whether package ‘methylPipe’ can be installed ... OK ./methylPipe.Rcheck/00check.log:* checking installed package size ... OK ./methylPipe.Rcheck/00check.log:* checking package directory ... OK ./methylPipe.Rcheck/00check.log:* checking ‘build’ directory ... OK ./methylPipe.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./methylPipe.Rcheck/00check.log:* checking top-level files ... OK ./methylPipe.Rcheck/00check.log:* checking for left-over files ... OK ./methylPipe.Rcheck/00check.log:* checking index information ... OK ./methylPipe.Rcheck/00check.log:* checking package subdirectories ... OK ./methylPipe.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./methylPipe.Rcheck/00check.log:* checking R files for syntax errors ... OK ./methylPipe.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./methylPipe.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./methylPipe.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./methylPipe.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./methylPipe.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./methylPipe.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./methylPipe.Rcheck/00check.log:* checking dependencies in R code ... OK ./methylPipe.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./methylPipe.Rcheck/00check.log:* checking replacement functions ... OK ./methylPipe.Rcheck/00check.log:* checking foreign function calls ... OK ./methylPipe.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./methylPipe.Rcheck/00check.log:BSprepare : binomTestMulti: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'binom.test' ./methylPipe.Rcheck/00check.log:BSprepare : binomTestMulti : pVfun: no visible global function ./methylPipe.Rcheck/00check.log: definition for 'binom.test' ./methylPipe.Rcheck/00check.log:BSprepare : binomTestMulti: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'p.adjust' ./methylPipe.Rcheck/00check.log:chiCombP: no visible global function definition for 'pchisq' ./methylPipe.Rcheck/00check.log:consolidateDMRs: no visible global function definition for 'p.adjust' ./methylPipe.Rcheck/00check.log:plotMeth: no visible global function definition for 'rainbow' ./methylPipe.Rcheck/00check.log:process.hmc: no visible global function definition for 'write.table' ./methylPipe.Rcheck/00check.log:findDMR,BSdataSet : DMRchr: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'kruskal.test' ./methylPipe.Rcheck/00check.log:findDMR,BSdataSet : DMRchr: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'wilcox.test' ./methylPipe.Rcheck/00check.log:findDMR,BSdataSet: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'stopCluster' ./methylPipe.Rcheck/00check.log:findPMDs,BSdata : PMDchr: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'segmentPMDs' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'smooth.spline' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for 'box' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for 'axis' ./methylPipe.Rcheck/00check.log:mCsmoothing,BSdata: no visible global function definition for 'mtext' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'stopCluster' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.cor: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'par' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.cor: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'cor.test' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.cor: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'text' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.smooth: no visible global function ./methylPipe.Rcheck/00check.log: definition for 'points' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.smooth: no visible global function ./methylPipe.Rcheck/00check.log: definition for 'lines' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.hist: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'par' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.hist: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'hist' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet : panel.hist: no visible global function definition ./methylPipe.Rcheck/00check.log: for 'rect' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'pairs' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'dist' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'hclust' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for ./methylPipe.Rcheck/00check.log: 'dev.new' ./methylPipe.Rcheck/00check.log:methstats,BSdataSet: no visible global function definition for 'plot' ./methylPipe.Rcheck/00check.log:show,BSdata: no visible global function definition for 'organism' ./methylPipe.Rcheck/00check.log:show,BSdataSet: no visible global function definition for 'organism' ./methylPipe.Rcheck/00check.log:Undefined global functions or variables: ./methylPipe.Rcheck/00check.log: axis binom.test box cor.test dev.new dist hclust hist kruskal.test ./methylPipe.Rcheck/00check.log: lines mtext organism p.adjust pairs par pchisq plot points rainbow ./methylPipe.Rcheck/00check.log: rect segmentPMDs smooth.spline stopCluster text wilcox.test ./methylPipe.Rcheck/00check.log: write.table ./methylPipe.Rcheck/00check.log:Consider adding ./methylPipe.Rcheck/00check.log: importFrom("grDevices", "dev.new", "rainbow") ./methylPipe.Rcheck/00check.log: importFrom("graphics", "axis", "box", "hist", "lines", "mtext", ./methylPipe.Rcheck/00check.log: "pairs", "par", "plot", "points", "rect", "text") ./methylPipe.Rcheck/00check.log: importFrom("stats", "binom.test", "cor.test", "dist", "hclust", ./methylPipe.Rcheck/00check.log: "kruskal.test", "p.adjust", "pchisq", "smooth.spline", ./methylPipe.Rcheck/00check.log: "wilcox.test") ./methylPipe.Rcheck/00check.log: importFrom("utils", "write.table") ./methylPipe.Rcheck/00check.log:to your NAMESPACE file. ./methylPipe.Rcheck/00check.log:* checking Rd files ... OK ./methylPipe.Rcheck/00check.log:* checking Rd metadata ... OK ./methylPipe.Rcheck/00check.log:* checking Rd cross-references ... OK ./methylPipe.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./methylPipe.Rcheck/00check.log:Undocumented S4 methods: ./methylPipe.Rcheck/00check.log: generic '[' and siglist 'BSdataSet,ANY,ANY,ANY' ./methylPipe.Rcheck/00check.log: generic '[' and siglist 'GElist,ANY,ANY,ANY' ./methylPipe.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./methylPipe.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./methylPipe.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./methylPipe.Rcheck/00check.log:* checking Rd \usage sections ... OK ./methylPipe.Rcheck/00check.log:* checking Rd contents ... OK ./methylPipe.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./methylPipe.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./methylPipe.Rcheck/00check.log:* checking compiled code ... OK ./methylPipe.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./methylPipe.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./methylPipe.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./methylPipe.Rcheck/00check.log:* checking examples ... WARNING ./methylPipe.Rcheck/00check.log:Found the following significant warnings: ./methylPipe.Rcheck/00check.log: Warning: working directory was changed to '/tmp/RtmpiIspXu', resetting ./methylPipe.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./methylPipe.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./methylPipe.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./methylPipe.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./methylPipe.Rcheck/00check.log:* checking PDF version of manual ... OK ./methylPipe.Rcheck/00check.log:* DONE ./methylPipe.Rcheck/00check.log:Status: 2 WARNINGs, 1 NOTE ./minfi.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/minfi.Rcheck’ ./minfi.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./minfi.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./minfi.Rcheck/00check.log:* using session charset: UTF-8 ./minfi.Rcheck/00check.log:* checking for file ‘minfi/DESCRIPTION’ ... OK ./minfi.Rcheck/00check.log:* this is package ‘minfi’ version ‘1.26.2’ ./minfi.Rcheck/00check.log:* checking package namespace information ... OK ./minfi.Rcheck/00check.log:* checking package dependencies ... OK ./minfi.Rcheck/00check.log:* checking if this is a source package ... OK ./minfi.Rcheck/00check.log:* checking if there is a namespace ... OK ./minfi.Rcheck/00check.log:* checking for executable files ... OK ./minfi.Rcheck/00check.log:* checking for hidden files and directories ... OK ./minfi.Rcheck/00check.log:* checking for portable file names ... OK ./minfi.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./minfi.Rcheck/00check.log:* checking whether package ‘minfi’ can be installed ... OK ./minfi.Rcheck/00check.log:* checking installed package size ... OK ./minfi.Rcheck/00check.log:* checking package directory ... OK ./minfi.Rcheck/00check.log:* checking ‘build’ directory ... OK ./minfi.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./minfi.Rcheck/00check.log:* checking top-level files ... OK ./minfi.Rcheck/00check.log:* checking for left-over files ... OK ./minfi.Rcheck/00check.log:* checking index information ... OK ./minfi.Rcheck/00check.log:* checking package subdirectories ... WARNING ./minfi.Rcheck/00check.log:Problems with news in ‘inst/NEWS.Rd’: ./minfi.Rcheck/00check.log: inst/NEWS.Rd:6: unknown macro '\item' ./minfi.Rcheck/00check.log: inst/NEWS.Rd:9: unknown macro '\item' ./minfi.Rcheck/00check.log: inst/NEWS.Rd:13: unknown macro '\item' ./minfi.Rcheck/00check.log: inst/NEWS.Rd:17: unexpected '}' ./minfi.Rcheck/00check.log: Malformed NEWS.Rd file: ./minfi.Rcheck/00check.log: Chunk starting ./minfi.Rcheck/00check.log: \item Fix bug in \code{preprocessQuantile()} that arose when ./minfi.Rcheck/00check.log: contains no \itemize. ./minfi.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./minfi.Rcheck/00check.log:* checking R files for syntax errors ... OK ./minfi.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./minfi.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./minfi.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./minfi.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./minfi.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./minfi.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./minfi.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./minfi.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./minfi.Rcheck/00check.log: ‘DelayedArray:::.as_array_or_matrix’ ‘DelayedArray:::.normarg_grid’ ./minfi.Rcheck/00check.log: ‘DelayedArray:::extract_block’ ‘DelayedArray:::get_max_block_length’ ./minfi.Rcheck/00check.log: ‘DelayedArray:::get_spacings_for_hypercube_capped_length_blocks’ ./minfi.Rcheck/00check.log: ‘DelayedArray:::get_spacings_for_linear_capped_length_blocks’ ./minfi.Rcheck/00check.log: ‘DelayedArray:::get_verbose_block_processing’ ./minfi.Rcheck/00check.log: ‘bumphunter:::.getEstimate’ ./minfi.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./minfi.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./minfi.Rcheck/00check.log:* checking replacement functions ... OK ./minfi.Rcheck/00check.log:* checking foreign function calls ... OK ./minfi.Rcheck/00check.log:* checking R code for possible problems ... OK ./minfi.Rcheck/00check.log:* checking Rd files ... OK ./minfi.Rcheck/00check.log:* checking Rd metadata ... OK ./minfi.Rcheck/00check.log:* checking Rd cross-references ... OK ./minfi.Rcheck/00check.log:* checking for missing documentation entries ... OK ./minfi.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./minfi.Rcheck/00check.log:* checking Rd \usage sections ... OK ./minfi.Rcheck/00check.log:* checking Rd contents ... OK ./minfi.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./minfi.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./minfi.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./minfi.Rcheck/00check.log:* checking examples ... OK ./minfi.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./minfi.Rcheck/00check.log:* checking tests ... OK ./minfi.Rcheck/00check.log: Running ‘runTests.R’ ./minfi.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./minfi.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./minfi.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./minfi.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./minfi.Rcheck/00check.log:* checking PDF version of manual ... OK ./minfi.Rcheck/00check.log:* DONE ./minfi.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE ./MinimumDistance.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/MinimumDistance.Rcheck’ ./MinimumDistance.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./MinimumDistance.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./MinimumDistance.Rcheck/00check.log:* using session charset: UTF-8 ./MinimumDistance.Rcheck/00check.log:* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK ./MinimumDistance.Rcheck/00check.log:* this is package ‘MinimumDistance’ version ‘1.24.1’ ./MinimumDistance.Rcheck/00check.log:* checking package namespace information ... OK ./MinimumDistance.Rcheck/00check.log:* checking package dependencies ... OK ./MinimumDistance.Rcheck/00check.log:* checking if this is a source package ... OK ./MinimumDistance.Rcheck/00check.log:* checking if there is a namespace ... OK ./MinimumDistance.Rcheck/00check.log:* checking for executable files ... OK ./MinimumDistance.Rcheck/00check.log:* checking for hidden files and directories ... OK ./MinimumDistance.Rcheck/00check.log:* checking for portable file names ... OK ./MinimumDistance.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether package ‘MinimumDistance’ can be installed ... OK ./MinimumDistance.Rcheck/00check.log:* checking installed package size ... OK ./MinimumDistance.Rcheck/00check.log:* checking package directory ... OK ./MinimumDistance.Rcheck/00check.log:* checking ‘build’ directory ... OK ./MinimumDistance.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./MinimumDistance.Rcheck/00check.log:* checking top-level files ... OK ./MinimumDistance.Rcheck/00check.log:* checking for left-over files ... OK ./MinimumDistance.Rcheck/00check.log:* checking index information ... OK ./MinimumDistance.Rcheck/00check.log:* checking package subdirectories ... OK ./MinimumDistance.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./MinimumDistance.Rcheck/00check.log:* checking R files for syntax errors ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./MinimumDistance.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./MinimumDistance.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./MinimumDistance.Rcheck/00check.log:* checking dependencies in R code ... OK ./MinimumDistance.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./MinimumDistance.Rcheck/00check.log:* checking replacement functions ... OK ./MinimumDistance.Rcheck/00check.log:* checking foreign function calls ... OK ./MinimumDistance.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./MinimumDistance.Rcheck/00check.log:callDenovoSegments: no visible global function definition for ./MinimumDistance.Rcheck/00check.log: ‘read.bsfiles’ ./MinimumDistance.Rcheck/00check.log:pruneTrioSet: no visible global function definition for ./MinimumDistance.Rcheck/00check.log: ‘RangedDataList’ ./MinimumDistance.Rcheck/00check.log:read.bsfiles2: no visible binding for global variable ‘read.bsfiles’ ./MinimumDistance.Rcheck/00check.log:GenomeAnnotatedDataFrameFrom,character: no visible global function ./MinimumDistance.Rcheck/00check.log: definition for ‘read.bsfiles’ ./MinimumDistance.Rcheck/00check.log:calculateMindist,list: no visible binding for global variable ‘elt’ ./MinimumDistance.Rcheck/00check.log:Undefined global functions or variables: ./MinimumDistance.Rcheck/00check.log: RangedDataList elt read.bsfiles ./MinimumDistance.Rcheck/00check.log:* checking Rd files ... OK ./MinimumDistance.Rcheck/00check.log:* checking Rd metadata ... OK ./MinimumDistance.Rcheck/00check.log:* checking Rd cross-references ... OK ./MinimumDistance.Rcheck/00check.log:* checking for missing documentation entries ... OK ./MinimumDistance.Rcheck/00check.log:* checking for code/documentation mismatches ... WARNING ./MinimumDistance.Rcheck/00check.log:Functions or methods with usage in documentation object 'coerce' but not in code: ./MinimumDistance.Rcheck/00check.log: as ./MinimumDistance.Rcheck/00check.log:* checking Rd \usage sections ... OK ./MinimumDistance.Rcheck/00check.log:* checking Rd contents ... OK ./MinimumDistance.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./MinimumDistance.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./MinimumDistance.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./MinimumDistance.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./MinimumDistance.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./MinimumDistance.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./MinimumDistance.Rcheck/00check.log:* checking include directives in Makefiles ... OK ./MinimumDistance.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking examples ... OK ./MinimumDistance.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking tests ... OK ./MinimumDistance.Rcheck/00check.log: Running ‘doRUnit.R’ ./MinimumDistance.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./MinimumDistance.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./MinimumDistance.Rcheck/00check.log:* checking running R code from vignettes ... OK ./MinimumDistance.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./MinimumDistance.Rcheck/00check.log:* checking PDF version of manual ... OK ./MinimumDistance.Rcheck/00check.log:* DONE ./MinimumDistance.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE ./paxtoolsr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/paxtoolsr.Rcheck’ ./paxtoolsr.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./paxtoolsr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./paxtoolsr.Rcheck/00check.log:* using session charset: UTF-8 ./paxtoolsr.Rcheck/00check.log:* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK ./paxtoolsr.Rcheck/00check.log:* checking extension type ... Package ./paxtoolsr.Rcheck/00check.log:* this is package ‘paxtoolsr’ version ‘1.14.0’ ./paxtoolsr.Rcheck/00check.log:* checking package namespace information ... OK ./paxtoolsr.Rcheck/00check.log:* checking package dependencies ... OK ./paxtoolsr.Rcheck/00check.log:* checking if this is a source package ... OK ./paxtoolsr.Rcheck/00check.log:* checking if there is a namespace ... OK ./paxtoolsr.Rcheck/00check.log:* checking for executable files ... OK ./paxtoolsr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./paxtoolsr.Rcheck/00check.log:* checking for portable file names ... OK ./paxtoolsr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./paxtoolsr.Rcheck/00check.log:* checking whether package ‘paxtoolsr’ can be installed ... OK ./paxtoolsr.Rcheck/00check.log:* checking installed package size ... NOTE ./paxtoolsr.Rcheck/00check.log: installed size is 32.0Mb ./paxtoolsr.Rcheck/00check.log: sub-directories of 1Mb or more: ./paxtoolsr.Rcheck/00check.log: doc 1.6Mb ./paxtoolsr.Rcheck/00check.log: extdata 5.6Mb ./paxtoolsr.Rcheck/00check.log: java 24.5Mb ./paxtoolsr.Rcheck/00check.log:* checking package directory ... OK ./paxtoolsr.Rcheck/00check.log:* checking ‘build’ directory ... OK ./paxtoolsr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./paxtoolsr.Rcheck/00check.log:* checking top-level files ... OK ./paxtoolsr.Rcheck/00check.log:* checking for left-over files ... OK ./paxtoolsr.Rcheck/00check.log:* checking index information ... OK ./paxtoolsr.Rcheck/00check.log:* checking package subdirectories ... OK ./paxtoolsr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./paxtoolsr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./paxtoolsr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./paxtoolsr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./paxtoolsr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./paxtoolsr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./paxtoolsr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./paxtoolsr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./paxtoolsr.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./paxtoolsr.Rcheck/00check.log:Namespace in Imports field not imported from: ‘jsonlite’ ./paxtoolsr.Rcheck/00check.log: All declared Imports should be used. ./paxtoolsr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./paxtoolsr.Rcheck/00check.log:* checking replacement functions ... OK ./paxtoolsr.Rcheck/00check.log:* checking foreign function calls ... OK ./paxtoolsr.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./paxtoolsr.Rcheck/00check.log:.onLoad: no visible global function definition for ‘write.table’ ./paxtoolsr.Rcheck/00check.log:downloadFile: no visible global function definition for ‘URLencode’ ./paxtoolsr.Rcheck/00check.log:downloadFile: no visible global function definition for ‘read.table’ ./paxtoolsr.Rcheck/00check.log:downloadFile: no visible global function definition for ‘write.table’ ./paxtoolsr.Rcheck/00check.log:downloadPc2: no visible global function definition for ‘select.list’ ./paxtoolsr.Rcheck/00check.log:downloadSignedPC: no visible global function definition for ./paxtoolsr.Rcheck/00check.log: ‘read.table’ ./paxtoolsr.Rcheck/00check.log:getPcRequest: no visible global function definition for ‘URLencode’ ./paxtoolsr.Rcheck/00check.log:readSifnx: no visible global function definition for ‘read.table’ ./paxtoolsr.Rcheck/00check.log:splitSifnxByPathway: no visible global function definition for ./paxtoolsr.Rcheck/00check.log: ‘txtProgressBar’ ./paxtoolsr.Rcheck/00check.log:splitSifnxByPathway: no visible global function definition for ./paxtoolsr.Rcheck/00check.log: ‘%dopar%’ ./paxtoolsr.Rcheck/00check.log:splitSifnxByPathway: no visible global function definition for ./paxtoolsr.Rcheck/00check.log: ‘setTxtProgressBar’ ./paxtoolsr.Rcheck/00check.log:Undefined global functions or variables: ./paxtoolsr.Rcheck/00check.log: %dopar% URLencode read.table select.list setTxtProgressBar ./paxtoolsr.Rcheck/00check.log: txtProgressBar write.table ./paxtoolsr.Rcheck/00check.log:Consider adding ./paxtoolsr.Rcheck/00check.log: importFrom("utils", "URLencode", "read.table", "select.list", ./paxtoolsr.Rcheck/00check.log: "setTxtProgressBar", "txtProgressBar", "write.table") ./paxtoolsr.Rcheck/00check.log:to your NAMESPACE file. ./paxtoolsr.Rcheck/00check.log:* checking Rd files ... OK ./paxtoolsr.Rcheck/00check.log:* checking Rd metadata ... OK ./paxtoolsr.Rcheck/00check.log:* checking Rd cross-references ... OK ./paxtoolsr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./paxtoolsr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./paxtoolsr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./paxtoolsr.Rcheck/00check.log:* checking Rd contents ... OK ./paxtoolsr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./paxtoolsr.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./paxtoolsr.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./paxtoolsr.Rcheck/00check.log:* checking examples ... OK ./paxtoolsr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./paxtoolsr.Rcheck/00check.log:* checking tests ... OK ./paxtoolsr.Rcheck/00check.log: Running ‘testthat.R’ ./paxtoolsr.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./paxtoolsr.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./paxtoolsr.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./paxtoolsr.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./paxtoolsr.Rcheck/00check.log:Error in re-building vignettes: ./paxtoolsr.Rcheck/00check.log: ... ./paxtoolsr.Rcheck/00check.log:Loading required package: rJava ./paxtoolsr.Rcheck/00check.log:Loading required package: XML ./paxtoolsr.Rcheck/00check.log:Attaching package: 'XML' ./paxtoolsr.Rcheck/00check.log:The following object is masked from 'package:tools': ./paxtoolsr.Rcheck/00check.log: toHTML ./paxtoolsr.Rcheck/00check.log:2018-12-18 15:54:06,867 2101 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found) ./paxtoolsr.Rcheck/00check.log:2018-12-18 15:54:07,136 2370 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found) ./paxtoolsr.Rcheck/00check.log:Attaching package: 'plyr' ./paxtoolsr.Rcheck/00check.log:The following object is masked from 'package:paxtoolsr': ./paxtoolsr.Rcheck/00check.log: summarize ./paxtoolsr.Rcheck/00check.log:Quitting from lines 218-233 (using_paxtoolsr.Rmd) ./paxtoolsr.Rcheck/00check.log:Error: processing vignette 'using_paxtoolsr.Rmd' failed with diagnostics: ./paxtoolsr.Rcheck/00check.log:XML content does not seem to be XML: '{"propertyPath":"ProteinReference/entityFeature:ModificationFeature","version":"10","traverseEntry":[{"uri":"http://identifiers.org/uniprot/P31749","value":["http://pathwaycommons.org/pc2/ModificationFeature_01696e37142d7d4e695ca728f4a23304","http://pathwaycommons.org/pc2/ModificationFeature_cbd93b4c45efae1d3e95c377f5a75851","http://pathwaycommons.org/pc2/ModificationFeature_95cbd7039bd2a68180c0bb57bce9b995","http://pathwaycommons.org/pc2/ModificationFeature_1d9a0475e0ec0a464ae1b4c312862807","http://pathwaycommons.org/pc2/ModificationFeature_3822bddb1a9319e273f180903f6440e1","http://pathwaycommons.org/pc2/ModificationFeature_dd35f02813e403d9809fdd09738ed8c7","http://pathwaycommons.org/pc2/ModificationFeature_fa22523ffc0ad03502e7dd9a04b9d79d","http://pathwaycommons.org/pc2/ModificationFeature_c331ff0905dc3993147b47ac0a42bf54","http://pathwaycommons.org/pc2/ModificationFeature ./paxtoolsr.Rcheck/00check.log:Execution halted ./paxtoolsr.Rcheck/00check.log:* checking PDF version of manual ... OK ./paxtoolsr.Rcheck/00check.log:* DONE ./paxtoolsr.Rcheck/00check.log:Status: 1 WARNING, 3 NOTEs ./RiboProfiling.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/RiboProfiling.Rcheck’ ./RiboProfiling.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./RiboProfiling.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./RiboProfiling.Rcheck/00check.log:* using session charset: UTF-8 ./RiboProfiling.Rcheck/00check.log:* checking for file ‘RiboProfiling/DESCRIPTION’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking extension type ... Package ./RiboProfiling.Rcheck/00check.log:* this is package ‘RiboProfiling’ version ‘1.10.0’ ./RiboProfiling.Rcheck/00check.log:* checking package namespace information ... OK ./RiboProfiling.Rcheck/00check.log:* checking package dependencies ... OK ./RiboProfiling.Rcheck/00check.log:* checking if this is a source package ... OK ./RiboProfiling.Rcheck/00check.log:* checking if there is a namespace ... OK ./RiboProfiling.Rcheck/00check.log:* checking for executable files ... OK ./RiboProfiling.Rcheck/00check.log:* checking for hidden files and directories ... OK ./RiboProfiling.Rcheck/00check.log:* checking for portable file names ... OK ./RiboProfiling.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether package ‘RiboProfiling’ can be installed ... WARNING ./RiboProfiling.Rcheck/00check.log:Found the following significant warnings: ./RiboProfiling.Rcheck/00check.log: Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’ ./RiboProfiling.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/RiboProfiling.Rcheck/00install.out’ for details. ./RiboProfiling.Rcheck/00check.log:* checking installed package size ... OK ./RiboProfiling.Rcheck/00check.log:* checking package directory ... OK ./RiboProfiling.Rcheck/00check.log:* checking ‘build’ directory ... OK ./RiboProfiling.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./RiboProfiling.Rcheck/00check.log:* checking top-level files ... OK ./RiboProfiling.Rcheck/00check.log:* checking for left-over files ... OK ./RiboProfiling.Rcheck/00check.log:* checking index information ... OK ./RiboProfiling.Rcheck/00check.log:* checking package subdirectories ... OK ./RiboProfiling.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./RiboProfiling.Rcheck/00check.log:* checking R files for syntax errors ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./RiboProfiling.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./RiboProfiling.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./RiboProfiling.Rcheck/00check.log:* checking dependencies in R code ... OK ./RiboProfiling.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./RiboProfiling.Rcheck/00check.log:* checking replacement functions ... OK ./RiboProfiling.Rcheck/00check.log:* checking foreign function calls ... OK ./RiboProfiling.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./RiboProfiling.Rcheck/00check.log:applyShiftFeature: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:aroundPromoter: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:codonInfo: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:countShiftReads: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:histMatchLength: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:orfRelativePos: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:plotSummarizedCov: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:readStartCov: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:readsToStartOrEnd: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:riboSeqFromBAM: no visible global function definition for 'is' ./RiboProfiling.Rcheck/00check.log:Undefined global functions or variables: ./RiboProfiling.Rcheck/00check.log: is ./RiboProfiling.Rcheck/00check.log:Consider adding ./RiboProfiling.Rcheck/00check.log: importFrom("methods", "is") ./RiboProfiling.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./RiboProfiling.Rcheck/00check.log:* checking Rd files ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd metadata ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd cross-references ... OK ./RiboProfiling.Rcheck/00check.log:* checking for missing documentation entries ... OK ./RiboProfiling.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd \usage sections ... OK ./RiboProfiling.Rcheck/00check.log:* checking Rd contents ... OK ./RiboProfiling.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./RiboProfiling.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./RiboProfiling.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./RiboProfiling.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./RiboProfiling.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking examples ... OK ./RiboProfiling.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking tests ... OK ./RiboProfiling.Rcheck/00check.log: Running ‘testthat.R’ ./RiboProfiling.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./RiboProfiling.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./RiboProfiling.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./RiboProfiling.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./RiboProfiling.Rcheck/00check.log:* checking PDF version of manual ... OK ./RiboProfiling.Rcheck/00check.log:* DONE ./RiboProfiling.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE ./rTANDEM.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/rTANDEM.Rcheck’ ./rTANDEM.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./rTANDEM.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./rTANDEM.Rcheck/00check.log:* using session charset: UTF-8 ./rTANDEM.Rcheck/00check.log:* checking for file ‘rTANDEM/DESCRIPTION’ ... OK ./rTANDEM.Rcheck/00check.log:* checking extension type ... Package ./rTANDEM.Rcheck/00check.log:* this is package ‘rTANDEM’ version ‘1.20.0’ ./rTANDEM.Rcheck/00check.log:* checking package namespace information ... OK ./rTANDEM.Rcheck/00check.log:* checking package dependencies ... OK ./rTANDEM.Rcheck/00check.log:* checking if this is a source package ... OK ./rTANDEM.Rcheck/00check.log:* checking if there is a namespace ... OK ./rTANDEM.Rcheck/00check.log:* checking for executable files ... OK ./rTANDEM.Rcheck/00check.log:* checking for hidden files and directories ... OK ./rTANDEM.Rcheck/00check.log:* checking for portable file names ... OK ./rTANDEM.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./rTANDEM.Rcheck/00check.log:* checking whether package ‘rTANDEM’ can be installed ... WARNING ./rTANDEM.Rcheck/00check.log:Found the following significant warnings: ./rTANDEM.Rcheck/00check.log: loadmspectrum.cpp:685:18: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] ./rTANDEM.Rcheck/00check.log: loadmspectrum.cpp:875:18: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] ./rTANDEM.Rcheck/00check.log: saxhandler.cpp:315:18: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] ./rTANDEM.Rcheck/00check.log: saxhandler.cpp:327:18: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] ./rTANDEM.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/rTANDEM.Rcheck/00install.out’ for details. ./rTANDEM.Rcheck/00check.log:* checking installed package size ... NOTE ./rTANDEM.Rcheck/00check.log: installed size is 5.9Mb ./rTANDEM.Rcheck/00check.log: sub-directories of 1Mb or more: ./rTANDEM.Rcheck/00check.log: extdata 3.2Mb ./rTANDEM.Rcheck/00check.log: libs 2.3Mb ./rTANDEM.Rcheck/00check.log:* checking package directory ... OK ./rTANDEM.Rcheck/00check.log:* checking ‘build’ directory ... OK ./rTANDEM.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./rTANDEM.Rcheck/00check.log:* checking top-level files ... OK ./rTANDEM.Rcheck/00check.log:* checking for left-over files ... OK ./rTANDEM.Rcheck/00check.log:* checking index information ... OK ./rTANDEM.Rcheck/00check.log:* checking package subdirectories ... OK ./rTANDEM.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./rTANDEM.Rcheck/00check.log:* checking R files for syntax errors ... OK ./rTANDEM.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./rTANDEM.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./rTANDEM.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./rTANDEM.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./rTANDEM.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./rTANDEM.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./rTANDEM.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./rTANDEM.Rcheck/00check.log:Namespace in Imports field not imported from: ‘methods’ ./rTANDEM.Rcheck/00check.log: All declared Imports should be used. ./rTANDEM.Rcheck/00check.log:Packages in Depends field not imported from: ./rTANDEM.Rcheck/00check.log: ‘Rcpp’ ‘XML’ ‘data.table’ ./rTANDEM.Rcheck/00check.log: These packages need to be imported from (in the NAMESPACE file) ./rTANDEM.Rcheck/00check.log: for when this namespace is loaded but not attached. ./rTANDEM.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./rTANDEM.Rcheck/00check.log:* checking replacement functions ... OK ./rTANDEM.Rcheck/00check.log:* checking foreign function calls ... OK ./rTANDEM.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./rTANDEM.Rcheck/00check.log:GetParamFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlTreeParse’ ./rTANDEM.Rcheck/00check.log:GetParamFromXML: no visible global function definition for ‘xmlRoot’ ./rTANDEM.Rcheck/00check.log:GetParamFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlChildren’ ./rTANDEM.Rcheck/00check.log:GetParamFromXML: no visible global function definition for ‘xmlName’ ./rTANDEM.Rcheck/00check.log:GetParamFromXML: no visible global function definition for ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:GetParamFromXML: no visible global function definition for ‘xmlValue’ ./rTANDEM.Rcheck/00check.log:GetPeptides: no visible global function definition for ‘setnames’ ./rTANDEM.Rcheck/00check.log:GetProteins: no visible global function definition for ‘setkey’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML: no visible global function definition for ‘new’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : protein: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : protein: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : protein: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : file: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : domain: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : domain: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : domain: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : aa: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : aa: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : aa: no visible global function definition for ‘set’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlChildren’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlGetAttr’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlValue’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : note: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : note: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlValue’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML : note: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlEventParse’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML: no visible global function definition for ‘setkey’ ./rTANDEM.Rcheck/00check.log:GetResultsFromXML: no visible global function definition for ‘set’ ./rTANDEM.Rcheck/00check.log:GetTaxoFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlTreeParse’ ./rTANDEM.Rcheck/00check.log:GetTaxoFromXML: no visible global function definition for ‘getNodeSet’ ./rTANDEM.Rcheck/00check.log:GetTaxoFromXML: no visible global function definition for ‘xmlRoot’ ./rTANDEM.Rcheck/00check.log:GetTaxoFromXML: no visible global function definition for ‘xmlChildren’ ./rTANDEM.Rcheck/00check.log:GetTaxoFromXML: no visible global function definition for ‘xmlName’ ./rTANDEM.Rcheck/00check.log:GetTaxoFromXML: no visible global function definition for ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:WriteParamToXML: no visible global function definition for ‘xmlNode’ ./rTANDEM.Rcheck/00check.log:WriteParamToXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘addChildren’ ./rTANDEM.Rcheck/00check.log:WriteParamToXML: no visible global function definition for ‘saveXML’ ./rTANDEM.Rcheck/00check.log:WriteTaxoToXML: no visible global function definition for ‘xmlNode’ ./rTANDEM.Rcheck/00check.log:WriteTaxoToXML: no visible global function definition for ‘addChildren’ ./rTANDEM.Rcheck/00check.log:WriteTaxoToXML: no visible global function definition for ‘saveXML’ ./rTANDEM.Rcheck/00check.log:getParamFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlTreeParse’ ./rTANDEM.Rcheck/00check.log:getParamFromXML: no visible global function definition for ‘xmlRoot’ ./rTANDEM.Rcheck/00check.log:getParamFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlChildren’ ./rTANDEM.Rcheck/00check.log:getParamFromXML: no visible global function definition for ‘xmlName’ ./rTANDEM.Rcheck/00check.log:getParamFromXML: no visible global function definition for ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:getParamFromXML: no visible global function definition for ‘xmlValue’ ./rTANDEM.Rcheck/00check.log:getPeptides: no visible global function definition for ‘setnames’ ./rTANDEM.Rcheck/00check.log:getProteins: no visible global function definition for ‘setkey’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML: no visible global function definition for ‘new’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : protein: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : protein: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : protein: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : file: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : domain: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : domain: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : domain: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : aa: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : aa: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : aa: no visible global function definition for ‘set’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘data.table’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘rbindlist’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlChildren’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlGetAttr’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlValue’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : trace: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : note: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : note: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlValue’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML : note: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘set’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlEventParse’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML: no visible global function definition for ‘setkey’ ./rTANDEM.Rcheck/00check.log:getResultsFromXML: no visible global function definition for ‘set’ ./rTANDEM.Rcheck/00check.log:getTaxoFromXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘xmlTreeParse’ ./rTANDEM.Rcheck/00check.log:getTaxoFromXML: no visible global function definition for ‘getNodeSet’ ./rTANDEM.Rcheck/00check.log:getTaxoFromXML: no visible global function definition for ‘xmlRoot’ ./rTANDEM.Rcheck/00check.log:getTaxoFromXML: no visible global function definition for ‘xmlChildren’ ./rTANDEM.Rcheck/00check.log:getTaxoFromXML: no visible global function definition for ‘xmlName’ ./rTANDEM.Rcheck/00check.log:getTaxoFromXML: no visible global function definition for ‘xmlAttrs’ ./rTANDEM.Rcheck/00check.log:ms2.plot: no visible global function definition for ‘is’ ./rTANDEM.Rcheck/00check.log:ms2.plot: no visible global function definition for ‘plot’ ./rTANDEM.Rcheck/00check.log:writeParamToXML: no visible global function definition for ‘xmlNode’ ./rTANDEM.Rcheck/00check.log:writeParamToXML: no visible global function definition for ./rTANDEM.Rcheck/00check.log: ‘addChildren’ ./rTANDEM.Rcheck/00check.log:writeParamToXML: no visible global function definition for ‘saveXML’ ./rTANDEM.Rcheck/00check.log:writeTaxoToXML: no visible global function definition for ‘xmlNode’ ./rTANDEM.Rcheck/00check.log:writeTaxoToXML: no visible global function definition for ‘addChildren’ ./rTANDEM.Rcheck/00check.log:writeTaxoToXML: no visible global function definition for ‘saveXML’ ./rTANDEM.Rcheck/00check.log:Undefined global functions or variables: ./rTANDEM.Rcheck/00check.log: addChildren data.table getNodeSet is new plot rbindlist saveXML set ./rTANDEM.Rcheck/00check.log: setkey setnames xmlAttrs xmlChildren xmlEventParse xmlGetAttr xmlName ./rTANDEM.Rcheck/00check.log: xmlNode xmlRoot xmlTreeParse xmlValue ./rTANDEM.Rcheck/00check.log:Consider adding ./rTANDEM.Rcheck/00check.log: importFrom("graphics", "plot") ./rTANDEM.Rcheck/00check.log: importFrom("methods", "is", "new") ./rTANDEM.Rcheck/00check.log:to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). ./rTANDEM.Rcheck/00check.log:* checking Rd files ... OK ./rTANDEM.Rcheck/00check.log:* checking Rd metadata ... OK ./rTANDEM.Rcheck/00check.log:* checking Rd cross-references ... OK ./rTANDEM.Rcheck/00check.log:* checking for missing documentation entries ... OK ./rTANDEM.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./rTANDEM.Rcheck/00check.log:* checking Rd \usage sections ... OK ./rTANDEM.Rcheck/00check.log:* checking Rd contents ... OK ./rTANDEM.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./rTANDEM.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./rTANDEM.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./rTANDEM.Rcheck/00check.log:* checking compilation flags in Makevars ... NOTE ./rTANDEM.Rcheck/00check.log:Package has both ‘src/Makevars.in’ and ‘src/Makevars’. ./rTANDEM.Rcheck/00check.log:Installation with --no-configure' is unlikely to work. If you intended ./rTANDEM.Rcheck/00check.log:‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ ./rTANDEM.Rcheck/00check.log:otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ./rTANDEM.Rcheck/00check.log:‘cleanup’ script. ./rTANDEM.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./rTANDEM.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./rTANDEM.Rcheck/00check.log:* checking compiled code ... NOTE ./rTANDEM.Rcheck/00check.log:File ‘rTANDEM/libs/rTANDEM.so’: ./rTANDEM.Rcheck/00check.log: Found ‘rand’, possibly from ‘rand’ (C) ./rTANDEM.Rcheck/00check.log: Object: ‘mreport.o’ ./rTANDEM.Rcheck/00check.log: Found ‘srand’, possibly from ‘srand’ (C) ./rTANDEM.Rcheck/00check.log: Object: ‘mreport.o’ ./rTANDEM.Rcheck/00check.log:File ‘rTANDEM/libs/rTANDEM.so’: ./rTANDEM.Rcheck/00check.log: Found non-API call to R: ‘R_CStackLimit’ ./rTANDEM.Rcheck/00check.log:Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. ./rTANDEM.Rcheck/00check.log:Compiled code should not call non-API entry points in R. ./rTANDEM.Rcheck/00check.log:See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ./rTANDEM.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./rTANDEM.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./rTANDEM.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./rTANDEM.Rcheck/00check.log:* checking examples ... OK ./rTANDEM.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./rTANDEM.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./rTANDEM.Rcheck/00check.log:* checking running R code from vignettes ... OK ./rTANDEM.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./rTANDEM.Rcheck/00check.log:* checking PDF version of manual ... OK ./rTANDEM.Rcheck/00check.log:* DONE ./rTANDEM.Rcheck/00check.log:Status: 1 WARNING, 5 NOTEs ./S4Vectors.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/S4Vectors.Rcheck’ ./S4Vectors.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./S4Vectors.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./S4Vectors.Rcheck/00check.log:* using session charset: UTF-8 ./S4Vectors.Rcheck/00check.log:* checking for file ‘S4Vectors/DESCRIPTION’ ... OK ./S4Vectors.Rcheck/00check.log:* this is package ‘S4Vectors’ version ‘0.18.3’ ./S4Vectors.Rcheck/00check.log:* package encoding: UTF-8 ./S4Vectors.Rcheck/00check.log:* checking package namespace information ... OK ./S4Vectors.Rcheck/00check.log:* checking package dependencies ... OK ./S4Vectors.Rcheck/00check.log:* checking if this is a source package ... OK ./S4Vectors.Rcheck/00check.log:* checking if there is a namespace ... OK ./S4Vectors.Rcheck/00check.log:* checking for executable files ... OK ./S4Vectors.Rcheck/00check.log:* checking for hidden files and directories ... OK ./S4Vectors.Rcheck/00check.log:* checking for portable file names ... OK ./S4Vectors.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./S4Vectors.Rcheck/00check.log:* checking whether package ‘S4Vectors’ can be installed ... OK ./S4Vectors.Rcheck/00check.log:* checking installed package size ... OK ./S4Vectors.Rcheck/00check.log:* checking package directory ... OK ./S4Vectors.Rcheck/00check.log:* checking ‘build’ directory ... OK ./S4Vectors.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./S4Vectors.Rcheck/00check.log:* checking top-level files ... OK ./S4Vectors.Rcheck/00check.log:* checking for left-over files ... OK ./S4Vectors.Rcheck/00check.log:* checking index information ... OK ./S4Vectors.Rcheck/00check.log:* checking package subdirectories ... OK ./S4Vectors.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./S4Vectors.Rcheck/00check.log:* checking R files for syntax errors ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./S4Vectors.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./S4Vectors.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./S4Vectors.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./S4Vectors.Rcheck/00check.log:Unexported objects imported by ':::' calls: ./S4Vectors.Rcheck/00check.log: ‘data.table:::as.data.frame.data.table’ ./S4Vectors.Rcheck/00check.log: ‘stats:::na.exclude.data.frame’ ‘stats:::na.omit.data.frame’ ./S4Vectors.Rcheck/00check.log: See the note in ?`:::` about the use of this operator. ./S4Vectors.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./S4Vectors.Rcheck/00check.log:* checking replacement functions ... OK ./S4Vectors.Rcheck/00check.log:* checking foreign function calls ... OK ./S4Vectors.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./S4Vectors.Rcheck/00check.log:evalSeparately,FilterRules : : no visible global function ./S4Vectors.Rcheck/00check.log: definition for ‘.’ ./S4Vectors.Rcheck/00check.log:Undefined global functions or variables: ./S4Vectors.Rcheck/00check.log: . ./S4Vectors.Rcheck/00check.log:* checking Rd files ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd metadata ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd cross-references ... WARNING ./S4Vectors.Rcheck/00check.log:Missing link or links in documentation object 'Vector-comparison.Rd': ./S4Vectors.Rcheck/00check.log: ‘[IRanges]{IntegerRanges-comparison}’ ./S4Vectors.Rcheck/00check.log:See section 'Cross-references' in the 'Writing R Extensions' manual. ./S4Vectors.Rcheck/00check.log:* checking for missing documentation entries ... WARNING ./S4Vectors.Rcheck/00check.log:Undocumented code objects: ./S4Vectors.Rcheck/00check.log: ‘cbind.DataFrame’ ‘head.LLint’ ‘pcompareRecursively’ ‘phead’ ‘ptail’ ./S4Vectors.Rcheck/00check.log: ‘rbind.DataFrame’ ‘selectHits’ ‘t.Hits’ ‘t.HitsList’ ‘tail.LLint’ ./S4Vectors.Rcheck/00check.log: ‘window.LLint’ ./S4Vectors.Rcheck/00check.log:Undocumented S4 classes: ./S4Vectors.Rcheck/00check.log: ‘integer_OR_LLint’ ‘list_OR_List’ ./S4Vectors.Rcheck/00check.log:Undocumented S4 methods: ./S4Vectors.Rcheck/00check.log: generic '!' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic '<=' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic '<=' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic '<=' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic '==' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic '==' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic '==' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic 'NSBS' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic '[' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'anyDuplicated' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'anyDuplicated' and siglist 'RleNSBS' ./S4Vectors.Rcheck/00check.log: generic 'anyNA' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'anyNA' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'as.integer' and siglist 'RleNSBS' ./S4Vectors.Rcheck/00check.log: generic 'by' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'coerce' and siglist 'ANY,DataTable_OR_NULL' ./S4Vectors.Rcheck/00check.log: generic 'countMatches' and siglist 'ANY' ./S4Vectors.Rcheck/00check.log: generic 'do.call' and siglist 'ANY,List' ./S4Vectors.Rcheck/00check.log: generic 'droplevels' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'duplicated' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'eval' and siglist 'expression,Vector' ./S4Vectors.Rcheck/00check.log: generic 'eval' and siglist 'language,Vector' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'DataFrame,ANY' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'LLint,ANY' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'LLint,NSBS' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'LLint,RangeNSBS' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'Rle,NSBS' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'Rle,RleNSBS' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'SortedByQueryHits,ANY' ./S4Vectors.Rcheck/00check.log: generic 'extractROWS' and siglist 'Vector,ANY' ./S4Vectors.Rcheck/00check.log: generic 'filterRules' and siglist 'FilterResults' ./S4Vectors.Rcheck/00check.log: generic 'from' and siglist 'HitsList' ./S4Vectors.Rcheck/00check.log: generic 'getListElement' and siglist 'SimpleList' ./S4Vectors.Rcheck/00check.log: generic 'grep' and siglist 'ANY,Rle' ./S4Vectors.Rcheck/00check.log: generic 'grepl' and siglist 'ANY,Rle' ./S4Vectors.Rcheck/00check.log: generic 'head' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'is.na' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'is.unsorted' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'isStrictlySorted' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'isStrictlySorted' and siglist 'RleNSBS' ./S4Vectors.Rcheck/00check.log: generic 'length' and siglist 'RleNSBS' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'ANY,Rle' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,Vector' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'List,vector' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'Rle,Rle' ./S4Vectors.Rcheck/00check.log: generic 'match' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic 'order' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'order' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'pcompare' and siglist 'List,List' ./S4Vectors.Rcheck/00check.log: generic 'pcompare' and siglist 'List,list' ./S4Vectors.Rcheck/00check.log: generic 'pcompare' and siglist 'list,List' ./S4Vectors.Rcheck/00check.log: generic 'pcompareRecursively' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'pcompareRecursively' and siglist 'list' ./S4Vectors.Rcheck/00check.log: generic 'rank' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'rank' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'rep.int' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'rep.int' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'rep' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'replaceROWS' and siglist 'DataFrame' ./S4Vectors.Rcheck/00check.log: generic 'replaceROWS' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log: generic 'sort' and siglist 'DataTable' ./S4Vectors.Rcheck/00check.log: generic 'sort' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'sort' and siglist 'SortedByQueryHits' ./S4Vectors.Rcheck/00check.log: generic 'summary' and siglist 'FilterResults' ./S4Vectors.Rcheck/00check.log: generic 't' and siglist 'Pairs' ./S4Vectors.Rcheck/00check.log: generic 'tail' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'to' and siglist 'HitsList' ./S4Vectors.Rcheck/00check.log: generic 'transform' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'unique' and siglist 'List' ./S4Vectors.Rcheck/00check.log: generic 'unique' and siglist 'SimpleList' ./S4Vectors.Rcheck/00check.log: generic 'updateObject' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'window' and siglist 'LLint' ./S4Vectors.Rcheck/00check.log: generic 'with' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'xtabs' and siglist 'Vector' ./S4Vectors.Rcheck/00check.log: generic 'xtfrm' and siglist 'Rle' ./S4Vectors.Rcheck/00check.log:All user-level objects in a package (including S4 classes and methods) should have documentation entries. ./S4Vectors.Rcheck/00check.log:See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ./S4Vectors.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd \usage sections ... OK ./S4Vectors.Rcheck/00check.log:* checking Rd contents ... OK ./S4Vectors.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./S4Vectors.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./S4Vectors.Rcheck/00check.log:* checking compiled code ... OK ./S4Vectors.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./S4Vectors.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./S4Vectors.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./S4Vectors.Rcheck/00check.log:* checking examples ... OK ./S4Vectors.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./S4Vectors.Rcheck/00check.log:* checking tests ... OK ./S4Vectors.Rcheck/00check.log: Running ‘run_unitTests.R’ ./S4Vectors.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./S4Vectors.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./S4Vectors.Rcheck/00check.log:* checking running R code from vignettes ... OK ./S4Vectors.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./S4Vectors.Rcheck/00check.log:* checking PDF version of manual ... OK ./S4Vectors.Rcheck/00check.log:* DONE ./S4Vectors.Rcheck/00check.log:Status: 2 WARNINGs, 2 NOTEs ./SISPA.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/SISPA.Rcheck’ ./SISPA.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./SISPA.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./SISPA.Rcheck/00check.log:* using session charset: UTF-8 ./SISPA.Rcheck/00check.log:* checking for file ‘SISPA/DESCRIPTION’ ... OK ./SISPA.Rcheck/00check.log:* checking extension type ... Package ./SISPA.Rcheck/00check.log:* this is package ‘SISPA’ version ‘1.10.0’ ./SISPA.Rcheck/00check.log:* checking package namespace information ... OK ./SISPA.Rcheck/00check.log:* checking package dependencies ... OK ./SISPA.Rcheck/00check.log:* checking if this is a source package ... OK ./SISPA.Rcheck/00check.log:* checking if there is a namespace ... OK ./SISPA.Rcheck/00check.log:* checking for executable files ... OK ./SISPA.Rcheck/00check.log:* checking for hidden files and directories ... OK ./SISPA.Rcheck/00check.log:* checking for portable file names ... OK ./SISPA.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./SISPA.Rcheck/00check.log:* checking whether package ‘SISPA’ can be installed ... OK ./SISPA.Rcheck/00check.log:* checking installed package size ... OK ./SISPA.Rcheck/00check.log:* checking package directory ... OK ./SISPA.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./SISPA.Rcheck/00check.log:* checking top-level files ... OK ./SISPA.Rcheck/00check.log:* checking for left-over files ... OK ./SISPA.Rcheck/00check.log:* checking index information ... OK ./SISPA.Rcheck/00check.log:* checking package subdirectories ... OK ./SISPA.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./SISPA.Rcheck/00check.log:* checking R files for syntax errors ... OK ./SISPA.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./SISPA.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./SISPA.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./SISPA.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./SISPA.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./SISPA.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./SISPA.Rcheck/00check.log:* checking dependencies in R code ... OK ./SISPA.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./SISPA.Rcheck/00check.log:* checking replacement functions ... OK ./SISPA.Rcheck/00check.log:* checking foreign function calls ... OK ./SISPA.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./SISPA.Rcheck/00check.log:cptSamples : cptsPlot: no visible global function definition for ./SISPA.Rcheck/00check.log: ‘abline’ ./SISPA.Rcheck/00check.log:cptSamples : cptsPlot: no visible global function definition for ‘text’ ./SISPA.Rcheck/00check.log:Undefined global functions or variables: ./SISPA.Rcheck/00check.log: abline text ./SISPA.Rcheck/00check.log:Consider adding ./SISPA.Rcheck/00check.log: importFrom("graphics", "abline", "text") ./SISPA.Rcheck/00check.log:to your NAMESPACE file. ./SISPA.Rcheck/00check.log:* checking Rd files ... OK ./SISPA.Rcheck/00check.log:* checking Rd metadata ... OK ./SISPA.Rcheck/00check.log:* checking Rd cross-references ... OK ./SISPA.Rcheck/00check.log:* checking for missing documentation entries ... OK ./SISPA.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./SISPA.Rcheck/00check.log:* checking Rd \usage sections ... OK ./SISPA.Rcheck/00check.log:* checking Rd contents ... OK ./SISPA.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./SISPA.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./SISPA.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./SISPA.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./SISPA.Rcheck/00check.log:* checking files in ‘vignettes’ ... WARNING ./SISPA.Rcheck/00check.log:Files in the 'vignettes' directory but no files in 'inst/doc': ./SISPA.Rcheck/00check.log: ‘SISPA.Rmd’, ‘SISPA.md’, ‘SISPA_data.Rda’, ‘SISPA_files/figure-html/unnamed-chunk-2-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-3-1.png’, ./SISPA.Rcheck/00check.log: ‘SISPA_files/figure-html/unnamed-chunk-4-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-5-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-6-1.png’, ./SISPA.Rcheck/00check.log: ‘SISPA_files/figure-html/unnamed-chunk-7-1.png’, ‘sispa_overview.png’ ./SISPA.Rcheck/00check.log:Files named as vignettes but with no recognized vignette engine: ./SISPA.Rcheck/00check.log: ‘vignettes/SISPA.Rmd’ ./SISPA.Rcheck/00check.log:(Is a VignetteBuilder field missing?) ./SISPA.Rcheck/00check.log:* checking examples ... OK ./SISPA.Rcheck/00check.log:* checking PDF version of manual ... OK ./SISPA.Rcheck/00check.log:* DONE ./SISPA.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE ./TFutils.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/TFutils.Rcheck’ ./TFutils.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./TFutils.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./TFutils.Rcheck/00check.log:* using session charset: UTF-8 ./TFutils.Rcheck/00check.log:* checking for file ‘TFutils/DESCRIPTION’ ... OK ./TFutils.Rcheck/00check.log:* this is package ‘TFutils’ version ‘1.0.0’ ./TFutils.Rcheck/00check.log:* checking package namespace information ... OK ./TFutils.Rcheck/00check.log:* checking package dependencies ... OK ./TFutils.Rcheck/00check.log:* checking if this is a source package ... OK ./TFutils.Rcheck/00check.log:* checking if there is a namespace ... OK ./TFutils.Rcheck/00check.log:* checking for executable files ... OK ./TFutils.Rcheck/00check.log:* checking for hidden files and directories ... OK ./TFutils.Rcheck/00check.log:* checking for portable file names ... OK ./TFutils.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./TFutils.Rcheck/00check.log:* checking whether package ‘TFutils’ can be installed ... OK ./TFutils.Rcheck/00check.log:* checking installed package size ... OK ./TFutils.Rcheck/00check.log:* checking package directory ... OK ./TFutils.Rcheck/00check.log:* checking ‘build’ directory ... OK ./TFutils.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./TFutils.Rcheck/00check.log:* checking top-level files ... OK ./TFutils.Rcheck/00check.log:* checking for left-over files ... OK ./TFutils.Rcheck/00check.log:* checking index information ... OK ./TFutils.Rcheck/00check.log:* checking package subdirectories ... OK ./TFutils.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./TFutils.Rcheck/00check.log:* checking R files for syntax errors ... OK ./TFutils.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./TFutils.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./TFutils.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./TFutils.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./TFutils.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./TFutils.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./TFutils.Rcheck/00check.log:* checking dependencies in R code ... OK ./TFutils.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./TFutils.Rcheck/00check.log:* checking replacement functions ... WARNING ./TFutils.Rcheck/00check.log:Warning: system call failed: Cannot allocate memory ./TFutils.Rcheck/00check.log:The argument of a replacement function which corresponds to the right hand side must be named ‘value’. ./TFutils.Rcheck/00check.log:* checking foreign function calls ... OK ./TFutils.Rcheck/00check.log:* checking R code for possible problems ... OK ./TFutils.Rcheck/00check.log:* checking Rd files ... OK ./TFutils.Rcheck/00check.log:* checking Rd metadata ... OK ./TFutils.Rcheck/00check.log:* checking Rd cross-references ... OK ./TFutils.Rcheck/00check.log:* checking for missing documentation entries ... OK ./TFutils.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./TFutils.Rcheck/00check.log:* checking Rd \usage sections ... OK ./TFutils.Rcheck/00check.log:* checking Rd contents ... OK ./TFutils.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./TFutils.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./TFutils.Rcheck/00check.log:* checking data for non-ASCII characters ... NOTE ./TFutils.Rcheck/00check.log: Note: found 62 marked UTF-8 strings ./TFutils.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./TFutils.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./TFutils.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./TFutils.Rcheck/00check.log:* checking examples ... OK ./TFutils.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./TFutils.Rcheck/00check.log:* checking tests ... OK ./TFutils.Rcheck/00check.log: Running ‘testthat.R’ ./TFutils.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./TFutils.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./TFutils.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./TFutils.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./TFutils.Rcheck/00check.log:* checking PDF version of manual ... OK ./TFutils.Rcheck/00check.log:* DONE ./TFutils.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE ./Uniquorn.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/Uniquorn.Rcheck’ ./Uniquorn.Rcheck/00check.log:* using R version 3.5.1 (2018-07-02) ./Uniquorn.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./Uniquorn.Rcheck/00check.log:* using session charset: UTF-8 ./Uniquorn.Rcheck/00check.log:* checking for file ‘Uniquorn/DESCRIPTION’ ... OK ./Uniquorn.Rcheck/00check.log:* checking extension type ... Package ./Uniquorn.Rcheck/00check.log:* this is package ‘Uniquorn’ version ‘2.0.0’ ./Uniquorn.Rcheck/00check.log:* package encoding: UTF-8 ./Uniquorn.Rcheck/00check.log:* checking package namespace information ... OK ./Uniquorn.Rcheck/00check.log:* checking package dependencies ... OK ./Uniquorn.Rcheck/00check.log:* checking if this is a source package ... OK ./Uniquorn.Rcheck/00check.log:* checking if there is a namespace ... OK ./Uniquorn.Rcheck/00check.log:* checking for executable files ... OK ./Uniquorn.Rcheck/00check.log:* checking for hidden files and directories ... OK ./Uniquorn.Rcheck/00check.log:* checking for portable file names ... OK ./Uniquorn.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./Uniquorn.Rcheck/00check.log:* checking whether package ‘Uniquorn’ can be installed ... WARNING ./Uniquorn.Rcheck/00check.log:Found the following significant warnings: ./Uniquorn.Rcheck/00check.log: Note: possible error in 'create_bed_file(match_t, ': unused argument (manual_identifier_bed_file) ./Uniquorn.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/Uniquorn.Rcheck/00install.out’ for details. ./Uniquorn.Rcheck/00check.log:Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. ./Uniquorn.Rcheck/00check.log:* checking installed package size ... NOTE ./Uniquorn.Rcheck/00check.log: installed size is 5.2Mb ./Uniquorn.Rcheck/00check.log: sub-directories of 1Mb or more: ./Uniquorn.Rcheck/00check.log: extdata 4.1Mb ./Uniquorn.Rcheck/00check.log:* checking package directory ... OK ./Uniquorn.Rcheck/00check.log:* checking ‘build’ directory ... OK ./Uniquorn.Rcheck/00check.log:* checking DESCRIPTION meta-information ... NOTE ./Uniquorn.Rcheck/00check.log:Malformed Description field: should contain one or more complete sentences. ./Uniquorn.Rcheck/00check.log:* checking top-level files ... OK ./Uniquorn.Rcheck/00check.log:* checking for left-over files ... OK ./Uniquorn.Rcheck/00check.log:* checking index information ... OK ./Uniquorn.Rcheck/00check.log:* checking package subdirectories ... OK ./Uniquorn.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./Uniquorn.Rcheck/00check.log:* checking R files for syntax errors ... OK ./Uniquorn.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./Uniquorn.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./Uniquorn.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./Uniquorn.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./Uniquorn.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./Uniquorn.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./Uniquorn.Rcheck/00check.log:* checking dependencies in R code ... OK ./Uniquorn.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./Uniquorn.Rcheck/00check.log:* checking replacement functions ... OK ./Uniquorn.Rcheck/00check.log:* checking foreign function calls ... OK ./Uniquorn.Rcheck/00check.log:* checking R code for possible problems ... NOTE ./Uniquorn.Rcheck/00check.log:add_p_q_values_statistics: no visible binding for '<<-' assignment to ./Uniquorn.Rcheck/00check.log: ‘sig_vec’ ./Uniquorn.Rcheck/00check.log:add_p_q_values_statistics: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘sig_vec’ ./Uniquorn.Rcheck/00check.log:create_bed_file: no visible binding for global variable ‘res_table’ ./Uniquorn.Rcheck/00check.log:create_bed_file: no visible binding for global variable ‘sim_list’ ./Uniquorn.Rcheck/00check.log:identify_vcf_file: possible error in create_bed_file(match_t, ./Uniquorn.Rcheck/00check.log: vcf_fingerprint, res_table, output_file, ref_gen, ./Uniquorn.Rcheck/00check.log: manual_identifier_bed_file): unused argument ./Uniquorn.Rcheck/00check.log: (manual_identifier_bed_file) ./Uniquorn.Rcheck/00check.log:identify_vcf_file: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘vcf_fingerprint’ ./Uniquorn.Rcheck/00check.log:identify_vcf_file: no visible binding for global variable ‘res_table’ ./Uniquorn.Rcheck/00check.log:identify_vcf_file: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘output_file_xls’ ./Uniquorn.Rcheck/00check.log:init_and_load_identification: no visible global function definition for ./Uniquorn.Rcheck/00check.log: ‘tail’ ./Uniquorn.Rcheck/00check.log:parse_ccle_genotype_data: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘Tumor_Sample_Barcode’ ./Uniquorn.Rcheck/00check.log:parse_ccle_genotype_data: no visible binding for global variable ‘.SD’ ./Uniquorn.Rcheck/00check.log:parse_ccle_genotype_data: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘Index’ ./Uniquorn.Rcheck/00check.log:parse_cosmic_genotype_data: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘position’ ./Uniquorn.Rcheck/00check.log:parse_cosmic_genotype_data: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘.SD’ ./Uniquorn.Rcheck/00check.log:parse_cosmic_genotype_data: no visible binding for global variable ./Uniquorn.Rcheck/00check.log: ‘Index’ ./Uniquorn.Rcheck/00check.log:show_contained_ccls: no visible binding for '<<-' assignment to ./Uniquorn.Rcheck/00check.log: ‘ccls_all’ ./Uniquorn.Rcheck/00check.log:show_contained_ccls: no visible binding for global variable ‘ccls_all’ ./Uniquorn.Rcheck/00check.log:write_w0_and_split_w0_into_lower_weights: no visible binding for '<<-' ./Uniquorn.Rcheck/00check.log: assignment to ‘g_mat_exclude’ ./Uniquorn.Rcheck/00check.log:write_w0_and_split_w0_into_lower_weights: no visible binding for global ./Uniquorn.Rcheck/00check.log: variable ‘g_mat_exclude’ ./Uniquorn.Rcheck/00check.log:Undefined global functions or variables: ./Uniquorn.Rcheck/00check.log: .SD Index Tumor_Sample_Barcode ccls_all g_mat_exclude output_file_xls ./Uniquorn.Rcheck/00check.log: position res_table sig_vec sim_list tail vcf_fingerprint ./Uniquorn.Rcheck/00check.log:Consider adding ./Uniquorn.Rcheck/00check.log: importFrom("utils", "tail") ./Uniquorn.Rcheck/00check.log:to your NAMESPACE file. ./Uniquorn.Rcheck/00check.log:* checking Rd files ... OK ./Uniquorn.Rcheck/00check.log:* checking Rd metadata ... OK ./Uniquorn.Rcheck/00check.log:* checking Rd cross-references ... OK ./Uniquorn.Rcheck/00check.log:* checking for missing documentation entries ... OK ./Uniquorn.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./Uniquorn.Rcheck/00check.log:* checking Rd \usage sections ... OK ./Uniquorn.Rcheck/00check.log:* checking Rd contents ... OK ./Uniquorn.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./Uniquorn.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./Uniquorn.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./Uniquorn.Rcheck/00check.log:* checking examples ... OK ./Uniquorn.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./Uniquorn.Rcheck/00check.log:* checking tests ... OK ./Uniquorn.Rcheck/00check.log: Running ‘testthat.R’ ./Uniquorn.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./Uniquorn.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./Uniquorn.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./Uniquorn.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./Uniquorn.Rcheck/00check.log:* checking PDF version of manual ... OK ./Uniquorn.Rcheck/00check.log:* DONE ./Uniquorn.Rcheck/00check.log:Status: 1 WARNING, 3 NOTEs