Anthony Federico
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/hypeR |
| git_branch: RELEASE_3_20 |
| git_last_commit: bb550b1 |
| git_last_commit_date: 2024-10-29 10:35:13 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:04 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 988/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hypeR 2.4.0 (landing page) Anthony Federico
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 2.4.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hypeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings hypeR_2.4.0.tar.gz |
| StartedAt: 2024-12-31 02:23:31 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 02:27:42 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 251.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hypeR.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hypeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings hypeR_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/hypeR.Rcheck'
* using R version 4.4.2 (2024-10-31 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
* using option '--no-vignettes'
* checking for file 'hypeR/DESCRIPTION' ... OK
* this is package 'hypeR' version '2.4.0'
* 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 20.33 1.69 22.02
hyp_hmap 5.89 0.09 6.36
hyp_show 0.81 0.08 7.23
enrichr_download 0.11 0.00 19.02
* 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
'F:/biocbuild/bbs-3.20-bioc/meat/hypeR.Rcheck/00check.log'
for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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)
hypeR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b451115081.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b436d43c58.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b43a247789.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b423444d28.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b47bcc7c72.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b465e873b6.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b4a017a05.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b427155273.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b44edd5c3c.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b42bf54fbc.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b42438781.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 "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-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 "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqEiU7a\rmarkdown-str206b47b4fba.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
62.43 3.60 110.34
hypeR.Rcheck/hypeR-Ex.timings
| name | user | system | elapsed | |
| clean_genesets | 2.28 | 0.27 | 2.60 | |
| dot-format_str | 0 | 0 | 0 | |
| dot-string_args | 0 | 0 | 0 | |
| enrichr_available | 0.24 | 0.11 | 0.42 | |
| enrichr_download | 0.11 | 0.00 | 19.02 | |
| enrichr_gsets | 0.14 | 0.00 | 0.40 | |
| gsets | 0 | 0 | 0 | |
| hyp | 0 | 0 | 0 | |
| hyp_dots | 1.56 | 0.03 | 1.59 | |
| hyp_emap | 0.96 | 0.14 | 3.19 | |
| hyp_hmap | 5.89 | 0.09 | 6.36 | |
| hyp_show | 0.81 | 0.08 | 7.23 | |
| hyp_to_excel | 1.17 | 0.11 | 3.25 | |
| hyp_to_graph | 3.78 | 0.06 | 3.93 | |
| hyp_to_table | 0.83 | 0.03 | 0.85 | |
| hypeR | 0.85 | 0.05 | 0.91 | |
| hyperdb_available | 0.01 | 0.00 | 0.19 | |
| hyperdb_gsets | 0.05 | 0.00 | 0.26 | |
| hyperdb_rgsets | 0.03 | 0.00 | 0.08 | |
| msigdb_available | 20.33 | 1.69 | 22.02 | |
| msigdb_check_species | 0 | 0 | 0 | |
| msigdb_download | 0.40 | 0.04 | 0.45 | |
| msigdb_gsets | 0.32 | 0.07 | 0.38 | |
| msigdb_info | 0.00 | 0.01 | 0.01 | |
| msigdb_species | 0.01 | 0.00 | 0.02 | |
| msigdb_version | 0 | 0 | 0 | |
| multihyp | 0 | 0 | 0 | |
| rctbl_build | 0.39 | 0.13 | 0.51 | |
| rctbl_hyp | 0.47 | 0.11 | 0.58 | |
| rctbl_mhyp | 0.47 | 0.01 | 0.49 | |