Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-01-04 11:45 -0500 (Sat, 04 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 982/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hypeR 2.5.0 (landing page) Anthony Federico
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the hypeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hypeR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: hypeR |
Version: 2.5.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hypeR_2.5.0.tar.gz |
StartedAt: 2025-01-03 19:47:19 -0500 (Fri, 03 Jan 2025) |
EndedAt: 2025-01-03 19:48:28 -0500 (Fri, 03 Jan 2025) |
EllapsedTime: 68.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: hypeR.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hypeR_2.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/hypeR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hypeR/DESCRIPTION’ ... OK * this is package ‘hypeR’ version ‘2.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 21 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 for sufficient/correct file permissions ... OK * checking whether package ‘hypeR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘tibble’ Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .dots_multi_plot : <anonymous>: no visible binding for global variable ‘pval’ .dots_multi_plot : <anonymous>: no visible binding for global variable ‘fdr’ .dots_multi_plot : <anonymous>: no visible binding for global variable ‘label’ .dots_multi_plot: no visible global function definition for ‘head’ .dots_multi_plot: no visible binding for global variable ‘.’ .dots_multi_plot: no visible binding for global variable ‘label’ .dots_multi_plot: no visible binding for global variable ‘geneset’ .dots_multi_plot: no visible binding for global variable ‘size’ .dots_multi_plot: no visible binding for global variable ‘overlap’ .dots_multi_plot: no visible binding for global variable ‘significance’ .dots_multi_plot: no visible binding for global variable ‘signature’ .dots_plot: no visible binding for global variable ‘pval’ .dots_plot: no visible binding for global variable ‘fdr’ .dots_plot: no visible binding for global variable ‘significance’ .dots_plot: no visible binding for global variable ‘size’ .enrichment_map: no visible binding for global variable ‘pval’ .enrichment_map: no visible binding for global variable ‘fdr’ .find_members: no visible binding for global variable ‘from’ .find_members: no visible binding for global variable ‘to’ .hiearchy_map: no visible binding for global variable ‘pval’ .hiearchy_map: no visible binding for global variable ‘fdr’ .hiearchy_map : <anonymous>: no visible binding for global variable ‘label’ .hyper_enrichment: no visible global function definition for ‘is’ .ks_enrichment: no visible global function definition for ‘is’ .ks_enrichment: no visible binding for global variable ‘fdr’ .ks_enrichment: no visible binding for global variable ‘pval’ .ks_enrichment: no visible binding for global variable ‘geneset’ .ks_enrichment: no visible binding for global variable ‘label’ enrichr_available: no visible binding for global variable ‘.’ ggvenn: no visible binding for global variable ‘x’ ggvenn: no visible binding for global variable ‘y’ hyp_dots: no visible global function definition for ‘is’ hyp_emap: no visible global function definition for ‘is’ hyp_hmap: no visible global function definition for ‘is’ hyp_show: no visible global function definition for ‘is’ hyp_to_excel: no visible global function definition for ‘is’ hyp_to_graph: no visible global function definition for ‘is’ hyp_to_rmd: no visible global function definition for ‘is’ hyp_to_rmd : <anonymous>: no visible global function definition for ‘is’ hyp_to_table: no visible global function definition for ‘is’ hyp_to_table: no visible global function definition for ‘write.table’ hypeR: no visible global function definition for ‘is’ hypeR: no visible global function definition for ‘packageVersion’ hypeR: no visible global function definition for ‘head’ msigdb_available: no visible binding for global variable ‘gs_cat’ msigdb_available: no visible binding for global variable ‘gs_subcat’ msigdb_download: no visible binding for global variable ‘gs_name’ msigdb_download: no visible binding for global variable ‘gene_symbol’ msigdb_version: no visible global function definition for ‘packageVersion’ rctbl_build: no visible global function definition for ‘is’ Undefined global functions or variables: . fdr from gene_symbol geneset gs_cat gs_name gs_subcat head is label overlap packageVersion pval signature significance size to write.table x y Consider adding importFrom("methods", "is", "signature") importFrom("utils", "head", "packageVersion", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'dot-dots_multi_plot.Rd': .dots_multi_plot Code: function(multihyp_data, top = 20, abrv = 50, size_by = c("genesets", "significance", "overlap", "none"), pval_cutoff = 1, fdr_cutoff = 1, val = c("fdr", "pval"), title = "") Docs: function(multihyp_data, top = 20, abrv = 50, size_by = c("genesets", "significance", "none"), pval_cutoff = 1, fdr_cutoff = 1, val = c("fdr", "pval"), title = "") Mismatches in argument default values: Name: 'size_by' Code: c("genesets", "significance", "overlap", "none") Docs: c("genesets", "significance", "none") * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed msigdb_available 6.270 0.305 6.817 enrichr_download 0.033 0.002 13.932 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/hypeR.Rcheck/00check.log’ for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘hypeR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hypeR)
hypeR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(magrittr) Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not > library(hypeR) > > test_check("hypeR") 2025-01-03 19:48:09.138 R[11549:252659318] XType: Using static font registry. /opt/homebrew/bin/pandoc +RTS -K512m -RTS hyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.1.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d5d3701c4.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS multihyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.1.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d71de141f.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS lmultihyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.1.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d2e2fcd7c.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS hyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.2.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d31506951.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS multihyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.2.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d14c8bd15.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS lmultihyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.2.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d210054d3.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS lmultihyp.3.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.3.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d35b81149.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS hyp.4.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.4.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d6d21a7fe.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS multihyp.4.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.4.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d1a2cf44b.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS combo.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.1.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d76202ae5.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS combo.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.2.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d26a75274.html --variable code_folding=hide --variable code_menu=1 /opt/homebrew/bin/pandoc +RTS -K512m -RTS combo.3.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.3.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpd90kO9/rmarkdown-str2d1d117579b0.html --variable code_folding=hide --variable code_menu=1 [ FAIL 0 | WARN 2 | SKIP 0 | PASS 424 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 424 ] > > proc.time() user system elapsed 18.187 0.862 19.380
hypeR.Rcheck/hypeR-Ex.timings
name | user | system | elapsed | |
clean_genesets | 1.002 | 0.029 | 1.032 | |
dot-format_str | 0 | 0 | 0 | |
dot-string_args | 0 | 0 | 0 | |
enrichr_available | 0.068 | 0.012 | 0.306 | |
enrichr_download | 0.033 | 0.002 | 13.932 | |
enrichr_gsets | 0.028 | 0.001 | 0.237 | |
gsets | 0.001 | 0.000 | 0.000 | |
hyp | 0.002 | 0.000 | 0.002 | |
hyp_dots | 0.378 | 0.015 | 0.392 | |
hyp_emap | 0.278 | 0.018 | 0.297 | |
hyp_hmap | 1.525 | 0.019 | 1.908 | |
hyp_show | 0.240 | 0.018 | 0.264 | |
hyp_to_excel | 0.455 | 0.016 | 0.476 | |
hyp_to_graph | 0.787 | 0.004 | 0.836 | |
hyp_to_table | 0.278 | 0.031 | 0.310 | |
hypeR | 0.224 | 0.011 | 0.237 | |
hyperdb_available | 0.008 | 0.001 | 0.215 | |
hyperdb_gsets | 0.011 | 0.001 | 0.242 | |
hyperdb_rgsets | 0.015 | 0.000 | 0.053 | |
msigdb_available | 6.270 | 0.305 | 6.817 | |
msigdb_check_species | 0 | 0 | 0 | |
msigdb_download | 0.099 | 0.011 | 0.109 | |
msigdb_gsets | 0.098 | 0.017 | 0.115 | |
msigdb_info | 0.001 | 0.000 | 0.000 | |
msigdb_species | 0.004 | 0.000 | 0.005 | |
msigdb_version | 0.001 | 0.000 | 0.000 | |
multihyp | 0 | 0 | 0 | |
rctbl_build | 0.165 | 0.027 | 0.195 | |
rctbl_hyp | 0.117 | 0.015 | 0.132 | |
rctbl_mhyp | 0.155 | 0.020 | 0.175 | |