R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] BiocManager_1.30.4 loaded via a namespace (and not attached): [1] compiler_3.6.1 tools_3.6.1 Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.1 (2019-07-05) batchtools_0.9.11.tar.gz ./batchtools.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/batchtools.Rcheck’ ./batchtools.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./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: Tags ./batchtools.Rcheck/00check.log:> ### Title: Add or Remove Job Tags ./batchtools.Rcheck/00check.log:> ### Aliases: Tags addJobTags removeJobTags getUsedJobTags ./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) ./batchtools.Rcheck/00check.log:No readable configuration file found ./batchtools.Rcheck/00check.log:Created registry in '/tmp/Rtmp2DZyiR/registry352c73ba439a' using cluster functions 'Interactive' ./batchtools.Rcheck/00check.log:> ids = batchMap(sqrt, x = -3:3, reg = tmp) ./batchtools.Rcheck/00check.log:Adding 7 jobs ... ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> # Add new tag to all ids ./batchtools.Rcheck/00check.log:> addJobTags(ids, "needs.computation", reg = tmp) ./batchtools.Rcheck/00check.log:> getJobTags(reg = tmp) ./batchtools.Rcheck/00check.log: job.id tags ./batchtools.Rcheck/00check.log:1: 1 needs.computation ./batchtools.Rcheck/00check.log:2: 2 needs.computation ./batchtools.Rcheck/00check.log:3: 3 needs.computation ./batchtools.Rcheck/00check.log:4: 4 needs.computation ./batchtools.Rcheck/00check.log:5: 5 needs.computation ./batchtools.Rcheck/00check.log:6: 6 needs.computation ./batchtools.Rcheck/00check.log:7: 7 needs.computation ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> # Add more tags ./batchtools.Rcheck/00check.log:> addJobTags(findJobs(x < 0, reg = tmp), "x.neg", reg = tmp) ./batchtools.Rcheck/00check.log:> addJobTags(findJobs(x > 0, reg = tmp), "x.pos", reg = tmp) ./batchtools.Rcheck/00check.log:> getJobTags(reg = tmp) ./batchtools.Rcheck/00check.log: job.id tags ./batchtools.Rcheck/00check.log:1: 1 needs.computation,x.neg ./batchtools.Rcheck/00check.log:2: 2 needs.computation,x.neg ./batchtools.Rcheck/00check.log:3: 3 needs.computation,x.neg ./batchtools.Rcheck/00check.log:4: 4 needs.computation ./batchtools.Rcheck/00check.log:5: 5 needs.computation,x.pos ./batchtools.Rcheck/00check.log:6: 6 needs.computation,x.pos ./batchtools.Rcheck/00check.log:7: 7 needs.computation,x.pos ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> # Submit first 5 jobs and remove tag if successful ./batchtools.Rcheck/00check.log:> ids = submitJobs(1:5, reg = tmp) ./batchtools.Rcheck/00check.log:Submitting 5 jobs in 5 chunks using cluster functions 'Interactive' ... ./batchtools.Rcheck/00check.log:> if (waitForJobs(reg = tmp)) ./batchtools.Rcheck/00check.log:+ removeJobTags(ids, "needs.computation", reg = tmp) ./batchtools.Rcheck/00check.log:> getJobTags(reg = tmp) ./batchtools.Rcheck/00check.log: job.id tags ./batchtools.Rcheck/00check.log:1: 1 x.neg ./batchtools.Rcheck/00check.log:2: 2 x.neg ./batchtools.Rcheck/00check.log:3: 3 x.neg ./batchtools.Rcheck/00check.log:4: 4 ./batchtools.Rcheck/00check.log:5: 5 x.pos ./batchtools.Rcheck/00check.log:6: 6 needs.computation,x.pos ./batchtools.Rcheck/00check.log:7: 7 needs.computation,x.pos ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> # Grep for warning message and add a tag ./batchtools.Rcheck/00check.log:> addJobTags(grepLogs(pattern = "NaNs produced", reg = tmp), "div.zero", reg = tmp) ./batchtools.Rcheck/00check.log:> getJobTags(reg = tmp) ./batchtools.Rcheck/00check.log: job.id tags ./batchtools.Rcheck/00check.log:1: 1 div.zero,x.neg ./batchtools.Rcheck/00check.log:2: 2 div.zero,x.neg ./batchtools.Rcheck/00check.log:3: 3 div.zero,x.neg ./batchtools.Rcheck/00check.log:4: 4 ./batchtools.Rcheck/00check.log:5: 5 x.pos ./batchtools.Rcheck/00check.log:6: 6 needs.computation,x.pos ./batchtools.Rcheck/00check.log:7: 7 needs.computation,x.pos ./batchtools.Rcheck/00check.log:> ./batchtools.Rcheck/00check.log:> # All tags where tag x.neg is set: ./batchtools.Rcheck/00check.log:> ids = findTagged("x.neg", reg = tmp) ./batchtools.Rcheck/00check.log:> getUsedJobTags(ids, reg = tmp) ./batchtools.Rcheck/00check.log:Error in `[.data.table`(filter(reg$tags, ids), , unique(tag), on = "job.id", : ./batchtools.Rcheck/00check.log: When on= is provided but not i=, on= must be a named list or data.table|frame, and a natural join (i.e. join on common names) is invoked ./batchtools.Rcheck/00check.log:Calls: getUsedJobTags -> [ -> [.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: 1310 | SKIPPED: 6 | WARNINGS: 5 | FAILED: 32 ] ./batchtools.Rcheck/00check.log: 1. Failure: Special chars in directory names (@test_ClusterFunctions.R#87) ./batchtools.Rcheck/00check.log: 2. Error: Special chars in directory names (@test_ClusterFunctions.R#88) ./batchtools.Rcheck/00check.log: 3. Failure: read only mode (@test_Registry.R#165) ./batchtools.Rcheck/00check.log: 4. Failure: read only mode (@test_Registry.R#166) ./batchtools.Rcheck/00check.log: 5. Error: read only mode (@test_Registry.R#170) ./batchtools.Rcheck/00check.log: 6. Failure: batchMap (@test_batchMap.R#22) ./batchtools.Rcheck/00check.log: 7. Failure: batchMap (@test_batchMap.R#28) ./batchtools.Rcheck/00check.log: 8. Failure: batchReduce (@test_batchReduce.R#11) ./batchtools.Rcheck/00check.log: 9. Failure: batchReduce w/ more.args (@test_batchReduce.R#24) ./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: ‘batchtools.Rmd’using ‘UTF-8’... OK ./batchtools.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./batchtools.Rcheck/00check.log:Error(s) in re-building vignettes: ./batchtools.Rcheck/00check.log: ... ./batchtools.Rcheck/00check.log:--- re-building ‘batchtools.Rmd’ using rmarkdown ./batchtools.Rcheck/00check.log:No readable configuration file found ./batchtools.Rcheck/00check.log:Created registry in '/tmp/Rtmp1CXpbm/registry374a868be8' using cluster functions 'Interactive' ./batchtools.Rcheck/00check.log:No readable configuration file found ./batchtools.Rcheck/00check.log:Created registry in '/tmp/Rtmp1CXpbm/registry374a7191f559' using cluster functions 'Interactive' ./batchtools.Rcheck/00check.log:Quitting from lines 247-249 (batchtools.Rmd) ./batchtools.Rcheck/00check.log:Error: processing vignette 'batchtools.Rmd' failed with diagnostics: ./batchtools.Rcheck/00check.log:All jobs must be have been successfully computed ./batchtools.Rcheck/00check.log:--- failed re-building ‘batchtools.Rmd’ ./batchtools.Rcheck/00check.log:SUMMARY: processing the following file failed: ./batchtools.Rcheck/00check.log: ‘batchtools.Rmd’ ./batchtools.Rcheck/00check.log:Error: Vignette re-building failed. ./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 genderizeR_2.1.1.tar.gz ./genderizeR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/genderizeR.Rcheck’ ./genderizeR.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./genderizeR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./genderizeR.Rcheck/00check.log:* using session charset: UTF-8 ./genderizeR.Rcheck/00check.log:* checking for file ‘genderizeR/DESCRIPTION’ ... OK ./genderizeR.Rcheck/00check.log:* checking extension type ... Package ./genderizeR.Rcheck/00check.log:* this is package ‘genderizeR’ version ‘2.1.1’ ./genderizeR.Rcheck/00check.log:* package encoding: UTF-8 ./genderizeR.Rcheck/00check.log:* checking package namespace information ... OK ./genderizeR.Rcheck/00check.log:* checking package dependencies ... OK ./genderizeR.Rcheck/00check.log:* checking if this is a source package ... OK ./genderizeR.Rcheck/00check.log:* checking if there is a namespace ... OK ./genderizeR.Rcheck/00check.log:* checking for executable files ... OK ./genderizeR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./genderizeR.Rcheck/00check.log:* checking for portable file names ... OK ./genderizeR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./genderizeR.Rcheck/00check.log:* checking whether package ‘genderizeR’ can be installed ... OK ./genderizeR.Rcheck/00check.log:* checking installed package size ... OK ./genderizeR.Rcheck/00check.log:* checking package directory ... OK ./genderizeR.Rcheck/00check.log:* checking ‘build’ directory ... OK ./genderizeR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./genderizeR.Rcheck/00check.log:* checking top-level files ... OK ./genderizeR.Rcheck/00check.log:* checking for left-over files ... OK ./genderizeR.Rcheck/00check.log:* checking index information ... OK ./genderizeR.Rcheck/00check.log:* checking package subdirectories ... OK ./genderizeR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./genderizeR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./genderizeR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./genderizeR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./genderizeR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./genderizeR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./genderizeR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./genderizeR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./genderizeR.Rcheck/00check.log:* checking dependencies in R code ... OK ./genderizeR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./genderizeR.Rcheck/00check.log:* checking replacement functions ... OK ./genderizeR.Rcheck/00check.log:* checking foreign function calls ... OK ./genderizeR.Rcheck/00check.log:* checking R code for possible problems ... OK ./genderizeR.Rcheck/00check.log:* checking Rd files ... OK ./genderizeR.Rcheck/00check.log:* checking Rd metadata ... OK ./genderizeR.Rcheck/00check.log:* checking Rd cross-references ... OK ./genderizeR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./genderizeR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./genderizeR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./genderizeR.Rcheck/00check.log:* checking Rd contents ... OK ./genderizeR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./genderizeR.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./genderizeR.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./genderizeR.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./genderizeR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./genderizeR.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./genderizeR.Rcheck/00check.log:* checking examples ... OK ./genderizeR.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./genderizeR.Rcheck/00check.log:* checking tests ... ERROR ./genderizeR.Rcheck/00check.log: Running ‘testthat.R’ ./genderizeR.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./genderizeR.Rcheck/00check.log:Last 13 lines of output: ./genderizeR.Rcheck/00check.log: Lengths differ: 2 is not 1 ./genderizeR.Rcheck/00check.log: ./genderizeR.Rcheck/00check.log: ./genderizeR.Rcheck/00check.log: ./genderizeR.Rcheck/00check.log: ── 2. Failure: language_id works (@test-api_functions.R#94) ─────────────────── ./genderizeR.Rcheck/00check.log: it_result$gender not equal to "male". ./genderizeR.Rcheck/00check.log: Lengths differ: 2 is not 1 ./genderizeR.Rcheck/00check.log: ./genderizeR.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./genderizeR.Rcheck/00check.log: [ OK: 30 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ] ./genderizeR.Rcheck/00check.log: 1. Failure: language_id works (@test-api_functions.R#91) ./genderizeR.Rcheck/00check.log: 2. Failure: language_id works (@test-api_functions.R#94) ./genderizeR.Rcheck/00check.log: ./genderizeR.Rcheck/00check.log: Error: testthat unit tests failed ./genderizeR.Rcheck/00check.log: Execution halted ./genderizeR.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./genderizeR.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./genderizeR.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./genderizeR.Rcheck/00check.log: ‘tutorial.Rmd’using ‘UTF-8’... OK ./genderizeR.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./genderizeR.Rcheck/00check.log:* checking PDF version of manual ... OK ./genderizeR.Rcheck/00check.log:* DONE ./genderizeR.Rcheck/00check.log:Status: 1 ERROR genomic.autocorr_1.0-1.tar.gz ./genomic.autocorr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/genomic.autocorr.Rcheck’ ./genomic.autocorr.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./genomic.autocorr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./genomic.autocorr.Rcheck/00check.log:* using session charset: UTF-8 ./genomic.autocorr.Rcheck/00check.log:* checking for file ‘genomic.autocorr/DESCRIPTION’ ... OK ./genomic.autocorr.Rcheck/00check.log:* this is package ‘genomic.autocorr’ version ‘1.0-1’ ./genomic.autocorr.Rcheck/00check.log:* checking package namespace information ... OK ./genomic.autocorr.Rcheck/00check.log:* checking package dependencies ... OK ./genomic.autocorr.Rcheck/00check.log:* checking if this is a source package ... OK ./genomic.autocorr.Rcheck/00check.log:* checking if there is a namespace ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for executable files ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for portable file names ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./genomic.autocorr.Rcheck/00check.log:* checking whether package ‘genomic.autocorr’ can be installed ... OK ./genomic.autocorr.Rcheck/00check.log:* checking installed package size ... OK ./genomic.autocorr.Rcheck/00check.log:* checking package directory ... OK ./genomic.autocorr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./genomic.autocorr.Rcheck/00check.log:* checking top-level files ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for left-over files ... OK ./genomic.autocorr.Rcheck/00check.log:* checking index information ... OK ./genomic.autocorr.Rcheck/00check.log:* checking package subdirectories ... OK ./genomic.autocorr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./genomic.autocorr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./genomic.autocorr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./genomic.autocorr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./genomic.autocorr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./genomic.autocorr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./genomic.autocorr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./genomic.autocorr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./genomic.autocorr.Rcheck/00check.log:* checking dependencies in R code ... OK ./genomic.autocorr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./genomic.autocorr.Rcheck/00check.log:* checking replacement functions ... OK ./genomic.autocorr.Rcheck/00check.log:* checking foreign function calls ... OK ./genomic.autocorr.Rcheck/00check.log:* checking R code for possible problems ... OK ./genomic.autocorr.Rcheck/00check.log:* checking Rd files ... OK ./genomic.autocorr.Rcheck/00check.log:* checking Rd metadata ... OK ./genomic.autocorr.Rcheck/00check.log:* checking Rd cross-references ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./genomic.autocorr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./genomic.autocorr.Rcheck/00check.log:* checking Rd contents ... OK ./genomic.autocorr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./genomic.autocorr.Rcheck/00check.log:* checking examples ... ERROR ./genomic.autocorr.Rcheck/00check.log:Running examples in ‘genomic.autocorr-Ex.R’ failed ./genomic.autocorr.Rcheck/00check.log:The error most likely occurred in: ./genomic.autocorr.Rcheck/00check.log:> ### Name: acf.summary ./genomic.autocorr.Rcheck/00check.log:> ### Title: acf.summary ./genomic.autocorr.Rcheck/00check.log:> ### Aliases: acf.summary ./genomic.autocorr.Rcheck/00check.log:> ./genomic.autocorr.Rcheck/00check.log:> ### ** Examples ./genomic.autocorr.Rcheck/00check.log:> ./genomic.autocorr.Rcheck/00check.log:> ## simulate data with 10 repeated observations in a row - ie there ./genomic.autocorr.Rcheck/00check.log:> ## should be autocorrelation only within windows <= 10 ./genomic.autocorr.Rcheck/00check.log:> library(data.table) ./genomic.autocorr.Rcheck/00check.log:> data <- genomic.autocorr:::.sim.data() ./genomic.autocorr.Rcheck/00check.log:simulating 500 independent observations repeated in blocks of 10 ./genomic.autocorr.Rcheck/00check.log:> summ <- acf.summary(data,c("x","y0","y1"),lag.max=20) ./genomic.autocorr.Rcheck/00check.log:Warning in mclapply(variables, function(x) { : ./genomic.autocorr.Rcheck/00check.log: all scheduled cores encountered errors in user code ./genomic.autocorr.Rcheck/00check.log:> ./genomic.autocorr.Rcheck/00check.log:> ## plot it ./genomic.autocorr.Rcheck/00check.log:> df <- melt(summ,c("lag","variable"),variable.name="acf") ./genomic.autocorr.Rcheck/00check.log:Warning in melt(summ, c("lag", "variable"), variable.name = "acf") : ./genomic.autocorr.Rcheck/00check.log: The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(summ). In the next version, this warning will become an error. ./genomic.autocorr.Rcheck/00check.log:> par(mfrow=c(2,1)) ./genomic.autocorr.Rcheck/00check.log:> matplot(matrix(df[acf=="full",]$value,ncol=3), ./genomic.autocorr.Rcheck/00check.log:+ main="full", ./genomic.autocorr.Rcheck/00check.log:+ pch=c("x","o","+"), ./genomic.autocorr.Rcheck/00check.log:+ type="b") ./genomic.autocorr.Rcheck/00check.log:Error in acf == "full" : ./genomic.autocorr.Rcheck/00check.log: comparison (1) is possible only for atomic and list types ./genomic.autocorr.Rcheck/00check.log:Calls: matplot -> matrix -> [ -> [.data.frame ./genomic.autocorr.Rcheck/00check.log:Execution halted ./genomic.autocorr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./genomic.autocorr.Rcheck/00check.log:* checking tests ... ERROR ./genomic.autocorr.Rcheck/00check.log: Running ‘testthat.R’ ./genomic.autocorr.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./genomic.autocorr.Rcheck/00check.log:Last 13 lines of output: ./genomic.autocorr.Rcheck/00check.log: > test_check("genomic.autocorr") ./genomic.autocorr.Rcheck/00check.log: ── 1. Error: /home/mdowle/build/revdeplib/genomic.autocorr.Rcheck/00_pkg_src/gen ./genomic.autocorr.Rcheck/00check.log: comparison (1) is possible only for atomic and list types ./genomic.autocorr.Rcheck/00check.log: 1: matplot(matrix(df[acf == "full", ]$value, ncol = 3), main = "full", pch = c("x", ./genomic.autocorr.Rcheck/00check.log: "o", "+"), type = "b") ./genomic.autocorr.Rcheck/00check.log: 2: matrix(df[acf == "full", ]$value, ncol = 3) ./genomic.autocorr.Rcheck/00check.log: 3: df[acf == "full", ] ./genomic.autocorr.Rcheck/00check.log: 4: `[.data.frame`(df, acf == "full", ) ./genomic.autocorr.Rcheck/00check.log: ./genomic.autocorr.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./genomic.autocorr.Rcheck/00check.log: [ OK: 1 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ] ./genomic.autocorr.Rcheck/00check.log: 1. Error: /home/mdowle/build/revdeplib/genomic.autocorr.Rcheck/00_pkg_src/genomic.autocorr/man/acf.summary.Rd ./genomic.autocorr.Rcheck/00check.log: ./genomic.autocorr.Rcheck/00check.log: Error: testthat unit tests failed ./genomic.autocorr.Rcheck/00check.log: Execution halted ./genomic.autocorr.Rcheck/00check.log:* checking PDF version of manual ... OK ./genomic.autocorr.Rcheck/00check.log:* DONE ./genomic.autocorr.Rcheck/00check.log:Status: 2 ERRORs miceFast_0.5.1.tar.gz ./miceFast.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/miceFast.Rcheck’ ./miceFast.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./miceFast.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./miceFast.Rcheck/00check.log:* using session charset: UTF-8 ./miceFast.Rcheck/00check.log:* checking for file ‘miceFast/DESCRIPTION’ ... OK ./miceFast.Rcheck/00check.log:* this is package ‘miceFast’ version ‘0.5.1’ ./miceFast.Rcheck/00check.log:* package encoding: UTF-8 ./miceFast.Rcheck/00check.log:* checking package namespace information ... OK ./miceFast.Rcheck/00check.log:* checking package dependencies ... OK ./miceFast.Rcheck/00check.log:* checking if this is a source package ... OK ./miceFast.Rcheck/00check.log:* checking if there is a namespace ... OK ./miceFast.Rcheck/00check.log:* checking for executable files ... OK ./miceFast.Rcheck/00check.log:* checking for hidden files and directories ... OK ./miceFast.Rcheck/00check.log:* checking for portable file names ... OK ./miceFast.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./miceFast.Rcheck/00check.log:* checking whether package ‘miceFast’ can be installed ... OK ./miceFast.Rcheck/00check.log:* checking installed package size ... NOTE ./miceFast.Rcheck/00check.log: installed size is 11.0Mb ./miceFast.Rcheck/00check.log: sub-directories of 1Mb or more: ./miceFast.Rcheck/00check.log: libs 9.7Mb ./miceFast.Rcheck/00check.log:* checking package directory ... OK ./miceFast.Rcheck/00check.log:* checking ‘build’ directory ... OK ./miceFast.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./miceFast.Rcheck/00check.log:* checking top-level files ... OK ./miceFast.Rcheck/00check.log:* checking for left-over files ... OK ./miceFast.Rcheck/00check.log:* checking index information ... OK ./miceFast.Rcheck/00check.log:* checking package subdirectories ... OK ./miceFast.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./miceFast.Rcheck/00check.log:* checking R files for syntax errors ... OK ./miceFast.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./miceFast.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./miceFast.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./miceFast.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./miceFast.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./miceFast.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./miceFast.Rcheck/00check.log:* checking dependencies in R code ... OK ./miceFast.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./miceFast.Rcheck/00check.log:* checking replacement functions ... OK ./miceFast.Rcheck/00check.log:* checking foreign function calls ... OK ./miceFast.Rcheck/00check.log:* checking R code for possible problems ... OK ./miceFast.Rcheck/00check.log:* checking Rd files ... OK ./miceFast.Rcheck/00check.log:* checking Rd metadata ... OK ./miceFast.Rcheck/00check.log:* checking Rd cross-references ... OK ./miceFast.Rcheck/00check.log:* checking for missing documentation entries ... OK ./miceFast.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./miceFast.Rcheck/00check.log:* checking Rd \usage sections ... OK ./miceFast.Rcheck/00check.log:* checking Rd contents ... OK ./miceFast.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./miceFast.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./miceFast.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./miceFast.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./miceFast.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./miceFast.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./miceFast.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./miceFast.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./miceFast.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./miceFast.Rcheck/00check.log:* checking compiled code ... OK ./miceFast.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./miceFast.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./miceFast.Rcheck/00check.log:* checking examples ... OK ./miceFast.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./miceFast.Rcheck/00check.log:* checking tests ... ERROR ./miceFast.Rcheck/00check.log: Running ‘testthat.R’ ./miceFast.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./miceFast.Rcheck/00check.log:Last 13 lines of output: ./miceFast.Rcheck/00check.log: Some columns are a multi-column type (such as a matrix column): [1]. These cannot be converted to data.table by reference. Please use as.data.table() instead which will create a new column for each embedded column. ./miceFast.Rcheck/00check.log: 1: data_DT[, .(VIF(x = .SD, posit_y = "y", posit_x = c("x2", "x3", "x4", "x22", "x23"), ./miceFast.Rcheck/00check.log: correct = FALSE))] at testthat/test-imputes_funcs.R:249 ./miceFast.Rcheck/00check.log: 2: `[.data.table`(data_DT, , .(VIF(x = .SD, posit_y = "y", posit_x = c("x2", "x3", "x4", ./miceFast.Rcheck/00check.log: "x22", "x23"), correct = FALSE))) at testthat/test-imputes_funcs.R:249 ./miceFast.Rcheck/00check.log: 3: setDT(jval) ./miceFast.Rcheck/00check.log: 4: stop("Some columns are a multi-column type (such as a matrix column): ", brackify(which(idx)), ./miceFast.Rcheck/00check.log: ". These cannot be converted to data.table by reference. Please use as.data.table() instead which will create a new column for each embedded column.") ./miceFast.Rcheck/00check.log: ./miceFast.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./miceFast.Rcheck/00check.log: [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ] ./miceFast.Rcheck/00check.log: 1. Error: imputes (@test-imputes_funcs.R#249) ./miceFast.Rcheck/00check.log: ./miceFast.Rcheck/00check.log: Error: testthat unit tests failed ./miceFast.Rcheck/00check.log: Execution halted ./miceFast.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./miceFast.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./miceFast.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./miceFast.Rcheck/00check.log: ‘miceFast-intro.Rmd’using ‘UTF-8’... OK ./miceFast.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./miceFast.Rcheck/00check.log:Error(s) in re-building vignettes: ./miceFast.Rcheck/00check.log:--- re-building ‘miceFast-intro.Rmd’ using rmarkdown ./miceFast.Rcheck/00check.log:Loading required package: lattice ./miceFast.Rcheck/00check.log:Attaching package: 'mice' ./miceFast.Rcheck/00check.log:The following objects are masked from 'package:base': ./miceFast.Rcheck/00check.log: cbind, rbind ./miceFast.Rcheck/00check.log:Loading required package: carData ./miceFast.Rcheck/00check.log:Attaching package: 'dplyr' ./miceFast.Rcheck/00check.log:The following object is masked from 'package:car': ./miceFast.Rcheck/00check.log: recode ./miceFast.Rcheck/00check.log:The following objects are masked from 'package:data.table': ./miceFast.Rcheck/00check.log: between, first, last ./miceFast.Rcheck/00check.log:The following objects are masked from 'package:stats': ./miceFast.Rcheck/00check.log: filter, lag ./miceFast.Rcheck/00check.log:The following objects are masked from 'package:base': ./miceFast.Rcheck/00check.log: intersect, setdiff, setequal, union ./miceFast.Rcheck/00check.log:Quitting from lines 90-166 (miceFast-intro.Rmd) ./miceFast.Rcheck/00check.log:Error: processing vignette 'miceFast-intro.Rmd' failed with diagnostics: ./miceFast.Rcheck/00check.log:Some columns are a multi-column type (such as a matrix column): [1]. These cannot be converted to data.table by reference. Please use as.data.table() instead which will create a new column for each embedded column. ./miceFast.Rcheck/00check.log:--- failed re-building ‘miceFast-intro.Rmd’ ./miceFast.Rcheck/00check.log:SUMMARY: processing the following file failed: ./miceFast.Rcheck/00check.log: ‘miceFast-intro.Rmd’ ./miceFast.Rcheck/00check.log:Error: Vignette re-building failed. ./miceFast.Rcheck/00check.log:Execution halted ./miceFast.Rcheck/00check.log:* checking PDF version of manual ... OK ./miceFast.Rcheck/00check.log:* DONE ./miceFast.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 1 NOTE musica_0.1.3.tar.gz ./musica.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/musica.Rcheck’ ./musica.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./musica.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./musica.Rcheck/00check.log:* using session charset: UTF-8 ./musica.Rcheck/00check.log:* checking for file ‘musica/DESCRIPTION’ ... OK ./musica.Rcheck/00check.log:* checking extension type ... Package ./musica.Rcheck/00check.log:* this is package ‘musica’ version ‘0.1.3’ ./musica.Rcheck/00check.log:* checking package namespace information ... OK ./musica.Rcheck/00check.log:* checking package dependencies ... OK ./musica.Rcheck/00check.log:* checking if this is a source package ... OK ./musica.Rcheck/00check.log:* checking if there is a namespace ... OK ./musica.Rcheck/00check.log:* checking for executable files ... OK ./musica.Rcheck/00check.log:* checking for hidden files and directories ... OK ./musica.Rcheck/00check.log:* checking for portable file names ... OK ./musica.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./musica.Rcheck/00check.log:* checking whether package ‘musica’ can be installed ... OK ./musica.Rcheck/00check.log:* checking installed package size ... OK ./musica.Rcheck/00check.log:* checking package directory ... OK ./musica.Rcheck/00check.log:* checking ‘build’ directory ... OK ./musica.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./musica.Rcheck/00check.log:* checking top-level files ... OK ./musica.Rcheck/00check.log:* checking for left-over files ... OK ./musica.Rcheck/00check.log:* checking index information ... OK ./musica.Rcheck/00check.log:* checking package subdirectories ... OK ./musica.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./musica.Rcheck/00check.log:* checking R files for syntax errors ... OK ./musica.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./musica.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./musica.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./musica.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./musica.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./musica.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./musica.Rcheck/00check.log:* checking dependencies in R code ... OK ./musica.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./musica.Rcheck/00check.log:* checking replacement functions ... OK ./musica.Rcheck/00check.log:* checking foreign function calls ... OK ./musica.Rcheck/00check.log:* checking R code for possible problems ... OK ./musica.Rcheck/00check.log:* checking Rd files ... OK ./musica.Rcheck/00check.log:* checking Rd metadata ... OK ./musica.Rcheck/00check.log:* checking Rd cross-references ... OK ./musica.Rcheck/00check.log:* checking for missing documentation entries ... OK ./musica.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./musica.Rcheck/00check.log:* checking Rd \usage sections ... OK ./musica.Rcheck/00check.log:* checking Rd contents ... OK ./musica.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./musica.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./musica.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./musica.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./musica.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./musica.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./musica.Rcheck/00check.log:* checking examples ... ERROR ./musica.Rcheck/00check.log:Running examples in ‘musica-Ex.R’ failed ./musica.Rcheck/00check.log:The error most likely occurred in: ./musica.Rcheck/00check.log:> ### Name: decomp ./musica.Rcheck/00check.log:> ### Title: Decomposition of time-series ./musica.Rcheck/00check.log:> ### Aliases: decomp ./musica.Rcheck/00check.log:> ./musica.Rcheck/00check.log:> ### ** Examples ./musica.Rcheck/00check.log:> ./musica.Rcheck/00check.log:> data(basin_PT) ./musica.Rcheck/00check.log:> str(basin_PT) ./musica.Rcheck/00check.log:List of 3 ./musica.Rcheck/00check.log: $ obs_ctrl:Classes ‘data.table’ and 'data.frame': 10957 obs. of 3 variables: ./musica.Rcheck/00check.log: ..$ DTM: Date[1:10957], format: "1970-01-01" "1970-01-02" ... ./musica.Rcheck/00check.log: ..$ PR : num [1:10957] 0.07 0.08 0.13 0 0.04 0 0.18 0 0 0.04 ... ./musica.Rcheck/00check.log: ..$ TAS: num [1:10957] -2.81 -5.81 -2.91 -5.15 0.96 -5.54 -7.01 -6.89 -7.05 -5.92 ... ./musica.Rcheck/00check.log: ..- attr(*, ".internal.selfref")= ./musica.Rcheck/00check.log: ..- attr(*, "sorted")= chr "DTM" ./musica.Rcheck/00check.log: $ sim_ctrl:Classes ‘data.table’ and 'data.frame': 10957 obs. of 3 variables: ./musica.Rcheck/00check.log: ..$ DTM: Date[1:10957], format: "1970-01-01" "1970-01-02" ... ./musica.Rcheck/00check.log: ..$ PR : num [1:10957] 0.55516 2.2645 0.00679 5.35181 12.11149 ... ./musica.Rcheck/00check.log: ..$ TAS: num [1:10957] 0.398 -0.519 -7.481 -5.068 -0.714 ... ./musica.Rcheck/00check.log: ..- attr(*, "sorted")= chr "DTM" ./musica.Rcheck/00check.log: ..- attr(*, ".internal.selfref")= ./musica.Rcheck/00check.log: $ sim_scen:Classes ‘data.table’ and 'data.frame': 10957 obs. of 3 variables: ./musica.Rcheck/00check.log: ..$ DTM: Date[1:10957], format: "2070-01-01" "2070-01-02" ... ./musica.Rcheck/00check.log: ..$ PR : num [1:10957] 5.34e-01 4.01e-01 8.49e-04 2.94e-05 8.15e-01 ... ./musica.Rcheck/00check.log: ..$ TAS: num [1:10957] -5.25 -5.53 -6.53 -7.51 -6.01 ... ./musica.Rcheck/00check.log: ..- attr(*, "sorted")= chr "DTM" ./musica.Rcheck/00check.log: ..- attr(*, ".internal.selfref")= ./musica.Rcheck/00check.log:> basin_PT[['obs_ctrl']] ./musica.Rcheck/00check.log: DTM PR TAS ./musica.Rcheck/00check.log: 1: 1970-01-01 0.07 -2.81 ./musica.Rcheck/00check.log: 2: 1970-01-02 0.08 -5.81 ./musica.Rcheck/00check.log: 3: 1970-01-03 0.13 -2.91 ./musica.Rcheck/00check.log: 4: 1970-01-04 0.00 -5.15 ./musica.Rcheck/00check.log: 5: 1970-01-05 0.04 0.96 ./musica.Rcheck/00check.log: --- ./musica.Rcheck/00check.log:10953: 1999-12-27 3.07 0.77 ./musica.Rcheck/00check.log:10954: 1999-12-28 7.62 -1.08 ./musica.Rcheck/00check.log:10955: 1999-12-29 1.30 -0.74 ./musica.Rcheck/00check.log:10956: 1999-12-30 1.22 -1.45 ./musica.Rcheck/00check.log:10957: 1999-12-31 0.33 -4.03 ./musica.Rcheck/00check.log:> dobs = decomp(basin_PT[['obs_ctrl']], period = c('1 year', '1 month', '1 day')) ./musica.Rcheck/00check.log:Error in as.POSIXlt.character(as.character(x), ...) : ./musica.Rcheck/00check.log: character string is not in a standard unambiguous format ./musica.Rcheck/00check.log:Calls: decomp ... as.POSIXlt.factor -> as.POSIXlt -> as.POSIXlt.character ./musica.Rcheck/00check.log:Execution halted ./musica.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./musica.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./musica.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./musica.Rcheck/00check.log: ‘using_musica.Rmd’using ‘UTF-8’... OK ./musica.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./musica.Rcheck/00check.log:* checking PDF version of manual ... OK ./musica.Rcheck/00check.log:* DONE ./musica.Rcheck/00check.log:Status: 1 ERROR parallelMap_1.4.tar.gz ./parallelMap.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/parallelMap.Rcheck’ ./parallelMap.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./parallelMap.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./parallelMap.Rcheck/00check.log:* using session charset: UTF-8 ./parallelMap.Rcheck/00check.log:* checking for file ‘parallelMap/DESCRIPTION’ ... OK ./parallelMap.Rcheck/00check.log:* this is package ‘parallelMap’ version ‘1.4’ ./parallelMap.Rcheck/00check.log:* package encoding: UTF-8 ./parallelMap.Rcheck/00check.log:* checking package namespace information ... OK ./parallelMap.Rcheck/00check.log:* checking package dependencies ... OK ./parallelMap.Rcheck/00check.log:* checking if this is a source package ... OK ./parallelMap.Rcheck/00check.log:* checking if there is a namespace ... OK ./parallelMap.Rcheck/00check.log:* checking for executable files ... OK ./parallelMap.Rcheck/00check.log:* checking for hidden files and directories ... OK ./parallelMap.Rcheck/00check.log:* checking for portable file names ... OK ./parallelMap.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./parallelMap.Rcheck/00check.log:* checking whether package ‘parallelMap’ can be installed ... OK ./parallelMap.Rcheck/00check.log:* checking installed package size ... OK ./parallelMap.Rcheck/00check.log:* checking package directory ... OK ./parallelMap.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./parallelMap.Rcheck/00check.log:* checking top-level files ... OK ./parallelMap.Rcheck/00check.log:* checking for left-over files ... OK ./parallelMap.Rcheck/00check.log:* checking index information ... OK ./parallelMap.Rcheck/00check.log:* checking package subdirectories ... OK ./parallelMap.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./parallelMap.Rcheck/00check.log:* checking R files for syntax errors ... OK ./parallelMap.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./parallelMap.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./parallelMap.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./parallelMap.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./parallelMap.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./parallelMap.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./parallelMap.Rcheck/00check.log:* checking dependencies in R code ... OK ./parallelMap.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./parallelMap.Rcheck/00check.log:* checking replacement functions ... OK ./parallelMap.Rcheck/00check.log:* checking foreign function calls ... OK ./parallelMap.Rcheck/00check.log:* checking R code for possible problems ... OK ./parallelMap.Rcheck/00check.log:* checking Rd files ... OK ./parallelMap.Rcheck/00check.log:* checking Rd metadata ... OK ./parallelMap.Rcheck/00check.log:* checking Rd cross-references ... OK ./parallelMap.Rcheck/00check.log:* checking for missing documentation entries ... OK ./parallelMap.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./parallelMap.Rcheck/00check.log:* checking Rd \usage sections ... OK ./parallelMap.Rcheck/00check.log:* checking Rd contents ... OK ./parallelMap.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./parallelMap.Rcheck/00check.log:* checking examples ... OK ./parallelMap.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./parallelMap.Rcheck/00check.log:* checking tests ... ERROR ./parallelMap.Rcheck/00check.log: Running ‘run-all.R’ ./parallelMap.Rcheck/00check.log:Running the tests in ‘tests/run-all.R’ failed. ./parallelMap.Rcheck/00check.log:Last 13 lines of output: ./parallelMap.Rcheck/00check.log: 2: expect_equal(parallelMap(identity, 1), list(1)) at /home/mdowle/build/revdeplib/parallelMap.Rcheck/tests/testthat/helpers.R:8 ./parallelMap.Rcheck/00check.log: 3: quasi_label(enquo(object), label, arg = "object") ./parallelMap.Rcheck/00check.log: 4: eval_bare(get_expr(quo), get_env(quo)) ./parallelMap.Rcheck/00check.log: 5: parallelMap(identity, 1) ./parallelMap.Rcheck/00check.log: 6: checkResultsAndStopWithErrorsMessages(res) ./parallelMap.Rcheck/00check.log: 7: stopWithJobErrorMessages(inds, vcapply(result.list[inds], as.character)) ./parallelMap.Rcheck/00check.log: 8: stopf("Errors occurred in %i slave jobs, displaying at most 10 of them:\n\n%s\n%s", ./parallelMap.Rcheck/00check.log: n, collapse(msgs, sep = "\n"), extra.msg) ./parallelMap.Rcheck/00check.log: ./parallelMap.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./parallelMap.Rcheck/00check.log: [ OK: 63 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ] ./parallelMap.Rcheck/00check.log: 1. Error: batchtools mode (@test_batchtools.R#11) ./parallelMap.Rcheck/00check.log: ./parallelMap.Rcheck/00check.log: Error: testthat unit tests failed ./parallelMap.Rcheck/00check.log: Execution halted ./parallelMap.Rcheck/00check.log:* checking PDF version of manual ... OK ./parallelMap.Rcheck/00check.log:* DONE ./parallelMap.Rcheck/00check.log:Status: 1 ERROR tsbox_0.2.0.tar.gz ./tsbox.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/tsbox.Rcheck’ ./tsbox.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./tsbox.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./tsbox.Rcheck/00check.log:* using session charset: UTF-8 ./tsbox.Rcheck/00check.log:* checking for file ‘tsbox/DESCRIPTION’ ... OK ./tsbox.Rcheck/00check.log:* checking extension type ... Package ./tsbox.Rcheck/00check.log:* this is package ‘tsbox’ version ‘0.2.0’ ./tsbox.Rcheck/00check.log:* package encoding: UTF-8 ./tsbox.Rcheck/00check.log:* checking package namespace information ... OK ./tsbox.Rcheck/00check.log:* checking package dependencies ... OK ./tsbox.Rcheck/00check.log:* checking if this is a source package ... OK ./tsbox.Rcheck/00check.log:* checking if there is a namespace ... OK ./tsbox.Rcheck/00check.log:* checking for executable files ... OK ./tsbox.Rcheck/00check.log:* checking for hidden files and directories ... OK ./tsbox.Rcheck/00check.log:* checking for portable file names ... OK ./tsbox.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./tsbox.Rcheck/00check.log:* checking whether package ‘tsbox’ can be installed ... OK ./tsbox.Rcheck/00check.log:* checking installed package size ... OK ./tsbox.Rcheck/00check.log:* checking package directory ... OK ./tsbox.Rcheck/00check.log:* checking ‘build’ directory ... OK ./tsbox.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./tsbox.Rcheck/00check.log:* checking top-level files ... OK ./tsbox.Rcheck/00check.log:* checking for left-over files ... OK ./tsbox.Rcheck/00check.log:* checking index information ... OK ./tsbox.Rcheck/00check.log:* checking package subdirectories ... OK ./tsbox.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./tsbox.Rcheck/00check.log:* checking R files for syntax errors ... OK ./tsbox.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./tsbox.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./tsbox.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./tsbox.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./tsbox.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./tsbox.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./tsbox.Rcheck/00check.log:* checking dependencies in R code ... OK ./tsbox.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./tsbox.Rcheck/00check.log:* checking replacement functions ... OK ./tsbox.Rcheck/00check.log:* checking foreign function calls ... OK ./tsbox.Rcheck/00check.log:* checking R code for possible problems ... OK ./tsbox.Rcheck/00check.log:* checking Rd files ... OK ./tsbox.Rcheck/00check.log:* checking Rd metadata ... OK ./tsbox.Rcheck/00check.log:* checking Rd cross-references ... OK ./tsbox.Rcheck/00check.log:* checking for missing documentation entries ... OK ./tsbox.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./tsbox.Rcheck/00check.log:* checking Rd \usage sections ... OK ./tsbox.Rcheck/00check.log:* checking Rd contents ... OK ./tsbox.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./tsbox.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./tsbox.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./tsbox.Rcheck/00check.log:* checking examples ... OK ./tsbox.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./tsbox.Rcheck/00check.log:* checking tests ... ERROR ./tsbox.Rcheck/00check.log: Running ‘testthat.R’ ./tsbox.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./tsbox.Rcheck/00check.log:Last 13 lines of output: ./tsbox.Rcheck/00check.log: 5: ts_dts(x) ./tsbox.Rcheck/00check.log: 6: ts_dts.data.frame(x) ./tsbox.Rcheck/00check.log: 7: ts_dts(as.data.table(x)) ./tsbox.Rcheck/00check.log: 8: ts_dts.data.table(as.data.table(x)) ./tsbox.Rcheck/00check.log: 9: dts_init(x) ./tsbox.Rcheck/00check.log: 10: setnames(x, cname$time, "time") ./tsbox.Rcheck/00check.log: 11: stop("Some items of 'old' are duplicated (ambiguous) in column names: ", brackify(old[!tt])) ./tsbox.Rcheck/00check.log: ./tsbox.Rcheck/00check.log: "blabla" ./tsbox.Rcheck/00check.log: ══ testthat results ═══════════════════════════════════════════════════════════ ./tsbox.Rcheck/00check.log: [ OK: 451 | SKIPPED: 12 | WARNINGS: 0 | FAILED: 1 ] ./tsbox.Rcheck/00check.log: 1. Error: invalid colnames are handled correctly (@test_nonstandard_cnames.R#56) ./tsbox.Rcheck/00check.log: ./tsbox.Rcheck/00check.log: Error: testthat unit tests failed ./tsbox.Rcheck/00check.log: Execution halted ./tsbox.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./tsbox.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./tsbox.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./tsbox.Rcheck/00check.log: ‘convert.Rmd’using ‘UTF-8’... OK ./tsbox.Rcheck/00check.log: ‘ts-functions.Rmd’using ‘UTF-8’... OK ./tsbox.Rcheck/00check.log: ‘tsbox.Rmd’using ‘UTF-8’... OK ./tsbox.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./tsbox.Rcheck/00check.log:* checking PDF version of manual ... OK ./tsbox.Rcheck/00check.log:* DONE ./tsbox.Rcheck/00check.log:Status: 1 ERROR MultiFit_1.0.0.tar.gz ./MultiFit.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/MultiFit.Rcheck’ ./MultiFit.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./MultiFit.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./MultiFit.Rcheck/00check.log:* using session charset: UTF-8 ./MultiFit.Rcheck/00check.log:* checking for file ‘MultiFit/DESCRIPTION’ ... OK ./MultiFit.Rcheck/00check.log:* checking extension type ... Package ./MultiFit.Rcheck/00check.log:* this is package ‘MultiFit’ version ‘1.0.0’ ./MultiFit.Rcheck/00check.log:* checking package namespace information ... OK ./MultiFit.Rcheck/00check.log:* checking package dependencies ... OK ./MultiFit.Rcheck/00check.log:* checking if this is a source package ... OK ./MultiFit.Rcheck/00check.log:* checking if there is a namespace ... OK ./MultiFit.Rcheck/00check.log:* checking for executable files ... OK ./MultiFit.Rcheck/00check.log:* checking for hidden files and directories ... OK ./MultiFit.Rcheck/00check.log:* checking for portable file names ... OK ./MultiFit.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./MultiFit.Rcheck/00check.log:* checking whether package ‘MultiFit’ can be installed ... OK ./MultiFit.Rcheck/00check.log:* checking installed package size ... OK ./MultiFit.Rcheck/00check.log:* checking package directory ... OK ./MultiFit.Rcheck/00check.log:* checking ‘build’ directory ... OK ./MultiFit.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./MultiFit.Rcheck/00check.log:* checking top-level files ... OK ./MultiFit.Rcheck/00check.log:* checking for left-over files ... OK ./MultiFit.Rcheck/00check.log:* checking index information ... OK ./MultiFit.Rcheck/00check.log:* checking package subdirectories ... OK ./MultiFit.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./MultiFit.Rcheck/00check.log:* checking R files for syntax errors ... OK ./MultiFit.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./MultiFit.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./MultiFit.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./MultiFit.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./MultiFit.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./MultiFit.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./MultiFit.Rcheck/00check.log:* checking dependencies in R code ... OK ./MultiFit.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./MultiFit.Rcheck/00check.log:* checking replacement functions ... OK ./MultiFit.Rcheck/00check.log:* checking foreign function calls ... OK ./MultiFit.Rcheck/00check.log:* checking R code for possible problems ... OK ./MultiFit.Rcheck/00check.log:* checking Rd files ... OK ./MultiFit.Rcheck/00check.log:* checking Rd metadata ... OK ./MultiFit.Rcheck/00check.log:* checking Rd cross-references ... OK ./MultiFit.Rcheck/00check.log:* checking for missing documentation entries ... OK ./MultiFit.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./MultiFit.Rcheck/00check.log:* checking Rd \usage sections ... OK ./MultiFit.Rcheck/00check.log:* checking Rd contents ... OK ./MultiFit.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./MultiFit.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./MultiFit.Rcheck/00check.log:* checking compiled code ... OK ./MultiFit.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./MultiFit.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./MultiFit.Rcheck/00check.log:* checking examples ... OK ./MultiFit.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./MultiFit.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./MultiFit.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./MultiFit.Rcheck/00check.log: ‘multiFit.Rmd’using ‘UTF-8’... OK ./MultiFit.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./MultiFit.Rcheck/00check.log:Error(s) in re-building vignettes: ./MultiFit.Rcheck/00check.log: ... ./MultiFit.Rcheck/00check.log:--- re-building ‘multiFit.Rmd’ using rmarkdown ./MultiFit.Rcheck/00check.log:Quitting from lines 265-268 (multiFit.Rmd) ./MultiFit.Rcheck/00check.log:Error: processing vignette 'multiFit.Rmd' failed with diagnostics: ./MultiFit.Rcheck/00check.log:Some columns are a multi-column type (such as a matrix column): [4, 7, 16]. These cannot be converted to data.table by reference. Please use as.data.table() instead which will create a new column for each embedded column. ./MultiFit.Rcheck/00check.log:--- failed re-building ‘multiFit.Rmd’ ./MultiFit.Rcheck/00check.log:SUMMARY: processing the following file failed: ./MultiFit.Rcheck/00check.log: ‘multiFit.Rmd’ ./MultiFit.Rcheck/00check.log:Error: Vignette re-building failed. ./MultiFit.Rcheck/00check.log:Execution halted ./MultiFit.Rcheck/00check.log:* checking PDF version of manual ... OK ./MultiFit.Rcheck/00check.log:* DONE ./MultiFit.Rcheck/00check.log:Status: 1 WARNING optiSel_2.0.2.tar.gz ./optiSel.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/optiSel.Rcheck’ ./optiSel.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./optiSel.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./optiSel.Rcheck/00check.log:* using session charset: UTF-8 ./optiSel.Rcheck/00check.log:* checking for file ‘optiSel/DESCRIPTION’ ... OK ./optiSel.Rcheck/00check.log:* checking extension type ... Package ./optiSel.Rcheck/00check.log:* this is package ‘optiSel’ version ‘2.0.2’ ./optiSel.Rcheck/00check.log:* package encoding: UTF-8 ./optiSel.Rcheck/00check.log:* checking package namespace information ... OK ./optiSel.Rcheck/00check.log:* checking package dependencies ... OK ./optiSel.Rcheck/00check.log:* checking if this is a source package ... OK ./optiSel.Rcheck/00check.log:* checking if there is a namespace ... OK ./optiSel.Rcheck/00check.log:* checking for executable files ... OK ./optiSel.Rcheck/00check.log:* checking for hidden files and directories ... OK ./optiSel.Rcheck/00check.log:* checking for portable file names ... OK ./optiSel.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./optiSel.Rcheck/00check.log:* checking whether package ‘optiSel’ can be installed ... WARNING ./optiSel.Rcheck/00check.log:Found the following significant warnings: ./optiSel.Rcheck/00check.log: rcpp_nativecont.cpp:30:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] ./optiSel.Rcheck/00check.log: rcpp_nativecont.cpp:34:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] ./optiSel.Rcheck/00check.log: rcpp_segBreedComp.cpp:42:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] ./optiSel.Rcheck/00check.log: rcpp_segBreedComp.cpp:45:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] ./optiSel.Rcheck/00check.log: rcpp_segN.cpp:48:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] ./optiSel.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/optiSel.Rcheck/00install.out’ for details. ./optiSel.Rcheck/00check.log:* checking installed package size ... NOTE ./optiSel.Rcheck/00check.log: installed size is 8.8Mb ./optiSel.Rcheck/00check.log: sub-directories of 1Mb or more: ./optiSel.Rcheck/00check.log: extdata 1.8Mb ./optiSel.Rcheck/00check.log: libs 5.9Mb ./optiSel.Rcheck/00check.log:* checking package directory ... OK ./optiSel.Rcheck/00check.log:* checking ‘build’ directory ... OK ./optiSel.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./optiSel.Rcheck/00check.log:* checking top-level files ... OK ./optiSel.Rcheck/00check.log:* checking for left-over files ... OK ./optiSel.Rcheck/00check.log:* checking index information ... OK ./optiSel.Rcheck/00check.log:* checking package subdirectories ... OK ./optiSel.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./optiSel.Rcheck/00check.log:* checking R files for syntax errors ... OK ./optiSel.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./optiSel.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./optiSel.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./optiSel.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./optiSel.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./optiSel.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./optiSel.Rcheck/00check.log:* checking dependencies in R code ... OK ./optiSel.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./optiSel.Rcheck/00check.log:* checking replacement functions ... OK ./optiSel.Rcheck/00check.log:* checking foreign function calls ... OK ./optiSel.Rcheck/00check.log:* checking R code for possible problems ... OK ./optiSel.Rcheck/00check.log:* checking Rd files ... OK ./optiSel.Rcheck/00check.log:* checking Rd metadata ... OK ./optiSel.Rcheck/00check.log:* checking Rd cross-references ... OK ./optiSel.Rcheck/00check.log:* checking for missing documentation entries ... OK ./optiSel.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./optiSel.Rcheck/00check.log:* checking Rd \usage sections ... OK ./optiSel.Rcheck/00check.log:* checking Rd contents ... OK ./optiSel.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./optiSel.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./optiSel.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./optiSel.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./optiSel.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./optiSel.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./optiSel.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./optiSel.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./optiSel.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./optiSel.Rcheck/00check.log:* checking compiled code ... OK ./optiSel.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./optiSel.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./optiSel.Rcheck/00check.log:* checking examples ... OK ./optiSel.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./optiSel.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./optiSel.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./optiSel.Rcheck/00check.log: ‘ocs-vignette.Rmd’using ‘UTF-8’... OK ./optiSel.Rcheck/00check.log: ‘ped-vignette.Rmd’using ‘UTF-8’... OK ./optiSel.Rcheck/00check.log: ‘seg-vignette.Rmd’using ‘UTF-8’... OK ./optiSel.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./optiSel.Rcheck/00check.log:* checking PDF version of manual ... OK ./optiSel.Rcheck/00check.log:* DONE ./optiSel.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE riskRegression_2019.01.29.tar.gz ./riskRegression.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/riskRegression.Rcheck’ ./riskRegression.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./riskRegression.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./riskRegression.Rcheck/00check.log:* using session charset: UTF-8 ./riskRegression.Rcheck/00check.log:* checking for file ‘riskRegression/DESCRIPTION’ ... OK ./riskRegression.Rcheck/00check.log:* checking extension type ... Package ./riskRegression.Rcheck/00check.log:* this is package ‘riskRegression’ version ‘2019.01.29’ ./riskRegression.Rcheck/00check.log:* checking package namespace information ... OK ./riskRegression.Rcheck/00check.log:* checking package dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking if this is a source package ... OK ./riskRegression.Rcheck/00check.log:* checking if there is a namespace ... OK ./riskRegression.Rcheck/00check.log:* checking for executable files ... OK ./riskRegression.Rcheck/00check.log:* checking for hidden files and directories ... OK ./riskRegression.Rcheck/00check.log:* checking for portable file names ... OK ./riskRegression.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./riskRegression.Rcheck/00check.log:* checking whether package ‘riskRegression’ can be installed ... OK ./riskRegression.Rcheck/00check.log:* checking installed package size ... OK ./riskRegression.Rcheck/00check.log:* checking package directory ... OK ./riskRegression.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./riskRegression.Rcheck/00check.log:* checking top-level files ... OK ./riskRegression.Rcheck/00check.log:* checking for left-over files ... OK ./riskRegression.Rcheck/00check.log:* checking index information ... OK ./riskRegression.Rcheck/00check.log:* checking package subdirectories ... OK ./riskRegression.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./riskRegression.Rcheck/00check.log:* checking R files for syntax errors ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./riskRegression.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./riskRegression.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./riskRegression.Rcheck/00check.log:* checking dependencies in R code ... OK ./riskRegression.Rcheck/00check.log:* checking S3 generic/method consistency ... WARNING ./riskRegression.Rcheck/00check.log:as.data.table: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, key, ...) ./riskRegression.Rcheck/00check.log:as.data.table.ate: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, se, ...) ./riskRegression.Rcheck/00check.log:as.data.table: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, key, ...) ./riskRegression.Rcheck/00check.log:as.data.table.influenceTest: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, se, ...) ./riskRegression.Rcheck/00check.log:as.data.table: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, key, ...) ./riskRegression.Rcheck/00check.log:as.data.table.predictCSC: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, se, ...) ./riskRegression.Rcheck/00check.log:as.data.table: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, key, ...) ./riskRegression.Rcheck/00check.log:as.data.table.predictCox: ./riskRegression.Rcheck/00check.log: function(x, keep.rownames, se, ...) ./riskRegression.Rcheck/00check.log:See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ./riskRegression.Rcheck/00check.log:* checking replacement functions ... OK ./riskRegression.Rcheck/00check.log:* checking foreign function calls ... OK ./riskRegression.Rcheck/00check.log:* checking R code for possible problems ... OK ./riskRegression.Rcheck/00check.log:* checking Rd files ... OK ./riskRegression.Rcheck/00check.log:* checking Rd metadata ... OK ./riskRegression.Rcheck/00check.log:* checking Rd cross-references ... OK ./riskRegression.Rcheck/00check.log:* checking for missing documentation entries ... OK ./riskRegression.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./riskRegression.Rcheck/00check.log:* checking Rd \usage sections ... OK ./riskRegression.Rcheck/00check.log:* checking Rd contents ... OK ./riskRegression.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./riskRegression.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./riskRegression.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./riskRegression.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./riskRegression.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./riskRegression.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./riskRegression.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./riskRegression.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./riskRegression.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./riskRegression.Rcheck/00check.log:* checking compiled code ... OK ./riskRegression.Rcheck/00check.log:* checking examples ... OK ./riskRegression.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./riskRegression.Rcheck/00check.log:* checking tests ... OK ./riskRegression.Rcheck/00check.log: Running ‘test-AUC.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-BinomialRegression.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-BrierScore.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-CauseSpecificCoxRegression.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-FineGrayRegression.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-ate.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-ateRobust.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-boxplotScore.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-confidenceBand_vs_timereg.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-iidCox.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-phreg.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictCSC_vs_mstate.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictCox-CSC.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictCox-SEconfint.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictCoxPL.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictCox_vs_basehaz.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictRisk-TD.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictRisk.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-predictSurv.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-score-bootstrap.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-score.R’ ./riskRegression.Rcheck/00check.log:* checking PDF version of manual ... OK ./riskRegression.Rcheck/00check.log:* DONE ./riskRegression.Rcheck/00check.log:Status: 1 WARNING sensobol_0.2.0.tar.gz ./sensobol.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/sensobol.Rcheck’ ./sensobol.Rcheck/00check.log:* using R version 3.6.1 (2019-07-05) ./sensobol.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./sensobol.Rcheck/00check.log:* using session charset: UTF-8 ./sensobol.Rcheck/00check.log:* checking for file ‘sensobol/DESCRIPTION’ ... OK ./sensobol.Rcheck/00check.log:* this is package ‘sensobol’ version ‘0.2.0’ ./sensobol.Rcheck/00check.log:* package encoding: UTF-8 ./sensobol.Rcheck/00check.log:* checking package namespace information ... OK ./sensobol.Rcheck/00check.log:* checking package dependencies ... OK ./sensobol.Rcheck/00check.log:* checking if this is a source package ... OK ./sensobol.Rcheck/00check.log:* checking if there is a namespace ... OK ./sensobol.Rcheck/00check.log:* checking for executable files ... OK ./sensobol.Rcheck/00check.log:* checking for hidden files and directories ... OK ./sensobol.Rcheck/00check.log:* checking for portable file names ... OK ./sensobol.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./sensobol.Rcheck/00check.log:* checking whether package ‘sensobol’ can be installed ... OK ./sensobol.Rcheck/00check.log:* checking installed package size ... OK ./sensobol.Rcheck/00check.log:* checking package directory ... OK ./sensobol.Rcheck/00check.log:* checking ‘build’ directory ... OK ./sensobol.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./sensobol.Rcheck/00check.log:* checking top-level files ... OK ./sensobol.Rcheck/00check.log:* checking for left-over files ... OK ./sensobol.Rcheck/00check.log:* checking index information ... OK ./sensobol.Rcheck/00check.log:* checking package subdirectories ... OK ./sensobol.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./sensobol.Rcheck/00check.log:* checking R files for syntax errors ... OK ./sensobol.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./sensobol.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./sensobol.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./sensobol.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./sensobol.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./sensobol.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./sensobol.Rcheck/00check.log:* checking dependencies in R code ... OK ./sensobol.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./sensobol.Rcheck/00check.log:* checking replacement functions ... OK ./sensobol.Rcheck/00check.log:* checking foreign function calls ... OK ./sensobol.Rcheck/00check.log:* checking R code for possible problems ... OK ./sensobol.Rcheck/00check.log:* checking Rd files ... OK ./sensobol.Rcheck/00check.log:* checking Rd metadata ... OK ./sensobol.Rcheck/00check.log:* checking Rd cross-references ... OK ./sensobol.Rcheck/00check.log:* checking for missing documentation entries ... OK ./sensobol.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./sensobol.Rcheck/00check.log:* checking Rd \usage sections ... OK ./sensobol.Rcheck/00check.log:* checking Rd contents ... OK ./sensobol.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./sensobol.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./sensobol.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./sensobol.Rcheck/00check.log:* checking examples ... OK ./sensobol.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./sensobol.Rcheck/00check.log:* checking tests ... OK ./sensobol.Rcheck/00check.log: Running ‘testthat.R’ ./sensobol.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./sensobol.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./sensobol.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./sensobol.Rcheck/00check.log: ‘sensobol.Rmd’using ‘UTF-8’... OK ./sensobol.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./sensobol.Rcheck/00check.log:Error(s) in re-building vignettes: ./sensobol.Rcheck/00check.log: ... ./sensobol.Rcheck/00check.log:--- re-building ‘sensobol.Rmd’ using rmarkdown ./sensobol.Rcheck/00check.log:Quitting from lines 100-121 (sensobol.Rmd) ./sensobol.Rcheck/00check.log:Error: processing vignette 'sensobol.Rmd' failed with diagnostics: ./sensobol.Rcheck/00check.log:Some columns are a multi-column type (such as a matrix column): [1, 2, 3, 4, 5, 6, 7, 8]. These cannot be converted to data.table by reference. Please use as.data.table() instead which will create a new column for each embedded column. ./sensobol.Rcheck/00check.log:--- failed re-building ‘sensobol.Rmd’ ./sensobol.Rcheck/00check.log:SUMMARY: processing the following file failed: ./sensobol.Rcheck/00check.log: ‘sensobol.Rmd’ ./sensobol.Rcheck/00check.log:Error: Vignette re-building failed. ./sensobol.Rcheck/00check.log:Execution halted ./sensobol.Rcheck/00check.log:* checking PDF version of manual ... OK ./sensobol.Rcheck/00check.log:* DONE ./sensobol.Rcheck/00check.log:Status: 1 WARNING