| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:42 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
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To the developers/maintainers of the hypeR package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 923/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hypeR 1.15.0 (landing page) Anthony Federico
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: hypeR |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings hypeR_1.15.0.tar.gz |
| StartedAt: 2023-02-28 05:54:43 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 05:58:39 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 236.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: hypeR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings hypeR_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/hypeR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘hypeR/DESCRIPTION’ ... OK
* this is package ‘hypeR’ version ‘1.15.0’
* 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 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 31.056 1.320 32.378
hyp_hmap 10.388 0.068 11.620
enrichr_download 0.088 0.004 10.862
* 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 ...
‘hypeR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/hypeR.Rcheck/00check.log’
for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library ‘/home/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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")
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra78097582c0ed.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra780932b8f621.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra78096a143972.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra780952061ebb.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra780913e2fd7e.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra78093afc5552.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra78095d7cd976.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra780942612cce.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra78091e3d0162.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra7809333601d2.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra780964af2f6f.html --variable code_folding=hide --variable code_menu=1
/usr/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/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/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 /home/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 /tmp/RtmpcOHdFw/rmarkdown-stra7809183e7981.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'): hyp_dots() is working ─────────────────────────
Error in `checkHT(n, d <- dim(x))`: 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 | 3.018 | 0.206 | 3.225 | |
| dot-format_str | 0 | 0 | 0 | |
| dot-string_args | 0 | 0 | 0 | |
| enrichr_available | 0.249 | 0.024 | 1.992 | |
| enrichr_download | 0.088 | 0.004 | 10.862 | |
| enrichr_gsets | 0.059 | 0.000 | 1.067 | |
| gsets | 0.000 | 0.000 | 0.001 | |
| hyp | 0.006 | 0.000 | 0.006 | |
| hyp_dots | 1.458 | 0.092 | 1.551 | |
| hyp_emap | 1.395 | 0.016 | 1.413 | |
| hyp_hmap | 10.388 | 0.068 | 11.620 | |
| hyp_show | 1.283 | 0.032 | 1.348 | |
| hyp_to_excel | 1.923 | 0.048 | 1.971 | |
| hyp_to_graph | 3.786 | 0.044 | 4.440 | |
| hyp_to_table | 1.264 | 0.004 | 1.268 | |
| hypeR | 1.234 | 0.000 | 1.234 | |
| hyperdb_available | 0.063 | 0.008 | 0.659 | |
| hyperdb_gsets | 0.028 | 0.000 | 1.076 | |
| hyperdb_rgsets | 0.040 | 0.000 | 0.415 | |
| msigdb_available | 31.056 | 1.320 | 32.378 | |
| msigdb_check_species | 0 | 0 | 0 | |
| msigdb_download | 0.642 | 0.060 | 0.701 | |
| msigdb_gsets | 0.611 | 0.076 | 0.687 | |
| msigdb_info | 0.001 | 0.000 | 0.001 | |
| msigdb_species | 0.023 | 0.004 | 0.027 | |
| msigdb_version | 0.001 | 0.000 | 0.001 | |
| multihyp | 0.000 | 0.001 | 0.001 | |
| rctbl_build | 0.896 | 0.022 | 0.918 | |
| rctbl_hyp | 0.721 | 0.000 | 0.721 | |
| rctbl_mhyp | 0.854 | 0.040 | 0.894 | |