Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-23 11:42 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 981/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hypeR 2.5.0  (landing page)
Anthony Federico
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/hypeR
git_branch: devel
git_last_commit: 2152271
git_last_commit_date: 2024-10-29 10:35:13 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for hypeR on palomino7

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.

raw results


Summary

Package: hypeR
Version: 2.5.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hypeR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings hypeR_2.5.0.tar.gz
StartedAt: 2024-12-23 01:37:43 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 01:41:30 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 227.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: hypeR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hypeR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings hypeR_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/hypeR.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... 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 '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 19.03   1.53   20.56
hyp_hmap          5.90   0.09    6.33
hyp_show          0.93   0.08    7.78
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/hypeR.Rcheck/00check.log'
for details.


Installation output

hypeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL hypeR
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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)

Tests output

hypeR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str1824019f1f53.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182404b7e3ff1.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182401b163f69.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182407f08610f.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182404b10dde.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182406836589.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182404b2d6837.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str1824035151c14.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182405e743ed1.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str1824011154285.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str18240373d6bd3.html" --variable code_folding=hide --variable code_menu=1 
"C:/PROGRA~1/Pandoc/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 "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --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 "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpSc0LlS\rmarkdown-str182403aca726a.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 
  60.59    3.43  107.34 

Example timings

hypeR.Rcheck/hypeR-Ex.timings

nameusersystemelapsed
clean_genesets2.310.252.60
dot-format_str000
dot-string_args000
enrichr_available0.250.060.42
enrichr_download0.170.022.39
enrichr_gsets0.100.000.38
gsets000
hyp000
hyp_dots1.280.081.36
hyp_emap1.140.121.84
hyp_hmap5.900.096.33
hyp_show0.930.087.78
hyp_to_excel1.230.103.98
hyp_to_graph3.550.033.68
hyp_to_table0.810.060.89
hypeR0.840.060.90
hyperdb_available0.020.020.17
hyperdb_gsets0.010.000.25
hyperdb_rgsets0.040.000.08
msigdb_available19.03 1.5320.56
msigdb_check_species000
msigdb_download0.410.050.45
msigdb_gsets0.260.040.32
msigdb_info0.020.000.01
msigdb_species0.020.000.02
msigdb_version000
multihyp000
rctbl_build0.390.050.44
rctbl_hyp0.500.080.57
rctbl_mhyp0.470.060.53