R Under development (unstable) (2025-01-20 r87609 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> # 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")
Annotating Data
Rows: 1884 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): gene, gene_symbol, entrez_id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
`curl` package not installed, falling back to using `url()`
trying URL 'https://figshare.com/ndownloader/files/34989919'
Content type 'text/csv' length 428612351 bytes (408.8 MB)
==================================================
downloaded 408.8 MB

trying URL 'https://figshare.com/ndownloader/files/34989937'
Content type 'text/csv' length 840532069 bytes (801.6 MB)
==================================================
downloaded 801.6 MB

Annotating Data
Rows: 1884 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): gene, gene_symbol, entrez_id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Normalizing Log Fold Change
Annotating Data
Rows: 1884 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): gene, gene_symbol, entrez_id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Normalizing Log Fold Change
Annotating Data
Rows: 1884 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): gene, gene_symbol, entrez_id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
`curl` package not installed, falling back to using `url()`
2035 :number of genes have matches in the custom_tpm data 
99% :percent of genes with matches in the custom_tpm data
Normalizing Log Fold Change
Annotating Data
Rows: 1884 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): gene, gene_symbol, entrez_id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
`curl` package not installed, falling back to using `url()`
Normalizing Log Fold Change
Calculating Genetic Interaction scores
Annotating Data
Rows: 1884 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (3): gene, gene_symbol, entrez_id

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
`curl` package not installed, falling back to using `url()`
Normalizing Log Fold Change


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_21_14_50_16_25566\RtmpaOGewL\rmarkdown-str2c810d191c14.html" --variable code_folding=show --variable code_menu=1 

Output created: gimap_QC_Report.html
Results in: ./gimap_QC_Report.html
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 20 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
 683.81  683.21  657.20