Anthony Federico
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: hypeR |
| Version: 2.4.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hypeR_2.4.0.tar.gz |
| StartedAt: 2024-11-20 08:54:08 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 08:57:41 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 213.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hypeR.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hypeR_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/hypeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 loading without being on the library search path ... 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 30.321 0.727 31.101
hyp_hmap 6.450 0.068 7.456
enrichr_download 0.064 0.000 12.949
* 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
‘/home/biocbuild/bbs-3.20-bioc/meat/hypeR.Rcheck/00check.log’
for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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")
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd250113c447e8.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd250159c4a9dc.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd250118480ca5.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd25017fb7e8f5.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd250116ee5a43.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd2501a1c532b.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd250140e6ca6.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd25011e9c2fa1.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd250139223d1.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd25012c4849a.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd2501593e0e5b.html --variable code_folding=hide --variable code_menu=1
/home/biocbuild/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 /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/R/R-4.4.1/site-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 /home/biocbuild/tmp/RtmpdtQPRx/rmarkdown-strd25012aff79a8.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
78.812 1.382 80.463
hypeR.Rcheck/hypeR-Ex.timings
| name | user | system | elapsed | |
| clean_genesets | 2.735 | 0.096 | 2.884 | |
| dot-format_str | 0 | 0 | 0 | |
| dot-string_args | 0.000 | 0.000 | 0.001 | |
| enrichr_available | 0.242 | 0.032 | 2.028 | |
| enrichr_download | 0.064 | 0.000 | 12.949 | |
| enrichr_gsets | 0.062 | 0.000 | 1.419 | |
| gsets | 0.000 | 0.000 | 0.001 | |
| hyp | 0.006 | 0.000 | 0.006 | |
| hyp_dots | 1.694 | 0.039 | 1.741 | |
| hyp_emap | 1.293 | 0.027 | 1.328 | |
| hyp_hmap | 6.450 | 0.068 | 7.456 | |
| hyp_show | 1.179 | 0.008 | 1.227 | |
| hyp_to_excel | 1.576 | 0.036 | 1.617 | |
| hyp_to_graph | 4.397 | 0.016 | 4.452 | |
| hyp_to_table | 1.095 | 0.008 | 1.105 | |
| hypeR | 1.119 | 0.016 | 1.137 | |
| hyperdb_available | 0.026 | 0.000 | 0.636 | |
| hyperdb_gsets | 0.022 | 0.004 | 0.998 | |
| hyperdb_rgsets | 0.036 | 0.000 | 0.060 | |
| msigdb_available | 30.321 | 0.727 | 31.101 | |
| msigdb_check_species | 0 | 0 | 0 | |
| msigdb_download | 0.762 | 0.012 | 0.775 | |
| msigdb_gsets | 0.548 | 0.032 | 0.581 | |
| msigdb_info | 0.002 | 0.000 | 0.001 | |
| msigdb_species | 0.023 | 0.000 | 0.023 | |
| msigdb_version | 0.001 | 0.000 | 0.001 | |
| multihyp | 0.001 | 0.000 | 0.001 | |
| rctbl_build | 0.687 | 0.032 | 0.719 | |
| rctbl_hyp | 0.704 | 0.008 | 0.713 | |
| rctbl_mhyp | 0.675 | 0.000 | 0.678 | |