| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:14 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 957/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hypeR 1.16.0 (landing page) Anthony Federico
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.16.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hypeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings hypeR_1.16.0.tar.gz |
| StartedAt: 2023-10-16 03:06:52 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 03:09:38 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 166.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: hypeR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hypeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings hypeR_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/hypeR.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* 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 '1.16.0'
* 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 R 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 ... OK
* 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 'significance'
.dots_multi_plot: no visible binding for global variable 'signature'
.dots_multi_plot: no visible binding for global variable 'label'
.dots_multi_plot: no visible binding for global variable 'size'
.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'
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 gs_cat gs_name gs_subcat head is label
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 ... OK
* 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 15.02 0.45 15.47
enrichr_download 0.08 0.00 6.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
1. ├─... %>% hyp_dots_tests() at test-hyp_dots.R:23:4
2. ├─hypeR (local) hyp_dots_tests(.)
3. │ └─hypeR::hyp_dots(hyp_obj, "gg") at test-hyp_dots.R:8:4
4. │ └─hypeR:::.dots_plot(...)
5. │ └─... %>% purrr::when(!is.null(top) ~ head(., top), ~.)
6. └─purrr::when(., !is.null(top) ~ head(., top), ~.)
7. └─base::eval(dots[[i]][[action]], env, env)
8. └─base::eval(dots[[i]][[action]], env, env)
9. ├─utils::head(., top)
10. └─utils (local) head.data.frame(., top)
11. └─utils:::checkHT(n, d <- dim(x))
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 364 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc/meat/hypeR.Rcheck/00check.log'
for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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.fail
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f0b0a78a4.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f058c75982.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f0b027390.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f062185ca7.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f029713942.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f079265f2e.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f02aa0631c.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f07c311cb4.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f03c5de02.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f045681648.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f02a067a91.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-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-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-3.17-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-3.17-bioc\tmpdir\RtmpumrGZs\rmarkdown-str47f05c0f3dad.html" --variable code_folding=hide --variable code_menu=1
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 364 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-hyp_dots.R:23:5'): hyp_dots() is working ───────────────────────
Error in `head.data.frame(., top)`: invalid 'n' - must be numeric, possibly NA.
Backtrace:
▆
1. ├─... %>% hyp_dots_tests() at test-hyp_dots.R:23:4
2. ├─hypeR (local) hyp_dots_tests(.)
3. │ └─hypeR::hyp_dots(hyp_obj, "gg") at test-hyp_dots.R:8:4
4. │ └─hypeR:::.dots_plot(...)
5. │ └─... %>% purrr::when(!is.null(top) ~ head(., top), ~.)
6. └─purrr::when(., !is.null(top) ~ head(., top), ~.)
7. └─base::eval(dots[[i]][[action]], env, env)
8. └─base::eval(dots[[i]][[action]], env, env)
9. ├─utils::head(., top)
10. └─utils (local) head.data.frame(., top)
11. └─utils:::checkHT(n, d <- dim(x))
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 364 ]
Error: Test failures
Execution halted
hypeR.Rcheck/hypeR-Ex.timings
| name | user | system | elapsed | |
| clean_genesets | 2.17 | 0.08 | 2.27 | |
| dot-format_str | 0 | 0 | 0 | |
| dot-string_args | 0 | 0 | 0 | |
| enrichr_available | 0.16 | 0.09 | 0.30 | |
| enrichr_download | 0.08 | 0.00 | 6.62 | |
| enrichr_gsets | 0.11 | 0.00 | 0.31 | |
| gsets | 0 | 0 | 0 | |
| hyp | 0 | 0 | 0 | |
| hyp_dots | 0.87 | 0.03 | 0.91 | |
| hyp_emap | 0.78 | 0.06 | 0.86 | |
| hyp_hmap | 4.03 | 0.07 | 4.42 | |
| hyp_show | 0.78 | 0.05 | 1.56 | |
| hyp_to_excel | 1.46 | 0.06 | 1.73 | |
| hyp_to_graph | 2.54 | 0.00 | 2.58 | |
| hyp_to_table | 0.74 | 0.00 | 0.74 | |
| hypeR | 0.75 | 0.00 | 0.75 | |
| hyperdb_available | 0.01 | 0.00 | 0.14 | |
| hyperdb_gsets | 0.04 | 0.00 | 0.24 | |
| hyperdb_rgsets | 0.04 | 0.00 | 0.04 | |
| msigdb_available | 15.02 | 0.45 | 15.47 | |
| msigdb_check_species | 0 | 0 | 0 | |
| msigdb_download | 0.26 | 0.03 | 0.30 | |
| msigdb_gsets | 0.32 | 0.03 | 0.34 | |
| msigdb_info | 0 | 0 | 0 | |
| msigdb_species | 0.01 | 0.00 | 0.02 | |
| msigdb_version | 0 | 0 | 0 | |
| multihyp | 0 | 0 | 0 | |
| rctbl_build | 0.42 | 0.05 | 0.46 | |
| rctbl_hyp | 0.39 | 0.01 | 0.41 | |
| rctbl_mhyp | 0.35 | 0.05 | 0.39 | |