* using log directory 'd:/RCompile/CRANincoming/R-devel/gimap.Rcheck' * using R Under development (unstable) (2025-01-22 r87618 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'gimap/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'gimap' version '1.0.1' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Candace Savonen ' New submission Non-FOSS package license (file LICENSE) Possibly misspelled words in DESCRIPTION: CRISPR (3:50, 17:95) The Description field contains . Please refer to arXiv e-prints via their arXiv DOI . * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'gimap' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [538s] ERROR Running 'testthat.R' [538s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(gimap) > > test_check("gimap") Downloading: 1.4 kB Downloading: 1.4 kB Downloading: 1.4 kB Downloading: 1.4 kB Downloading: pgPEN_annotations.txt | | | 0% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |=== | 4% | |=== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS gimap_QC_Report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output gimap_QC_Report.html --lua-filter "D:\RCompile\CRANpkg\lib\4.5\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.5\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\RCompile\CRANpkg\lib\4.5\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=spacelab --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2025_01_24_04_10_16_25709\RtmpEZF1vN\rmarkdown-stra27c4c1f254c.html" --variable code_folding=show --variable code_menu=1 Output created: gimap_QC_Report.html Results in: ./gimap_QC_Report.html processing file: gimap_QC_Report.Rmd output file: gimap_QC_Report.knit.md "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS gimap_QC_Report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output gimap_QC_Report.html --lua-filter "D:\RCompile\CRANpkg\lib\4.5\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.5\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\RCompile\CRANpkg\lib\4.5\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=spacelab --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2025_01_24_04_10_16_25709\RtmpEZF1vN\rmarkdown-stra27c2426547e.html" --variable code_folding=show --variable code_menu=1 Output created: gimap_QC_Report.html Results in: ./gimap_QC_Report.html Downloading: 1.4 kB Downloading: 1.4 kB Downloading: 1.4 kB Downloading: 1.4 kB Downloading: PP_pgPEN_HeLa_counts.txt | | | 0% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 6% | |===== | 7% | |====== | 9% | |======= | 10% | |======== | 12% | |========= | 13% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============== | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |=================== | 27% | |==================== | 28% | |==================== 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OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [50s] OK * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE