Andrew Chen
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/hypeR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 157ce44 |
| git_last_commit_date: 2025-12-01 14:36:37 -0500 (Mon, 01 Dec 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-22 12:04 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1015/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hypeR 2.8.2 (landing page) Andrew Chen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | 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: 2.8.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hypeR_2.8.2.tar.gz |
| StartedAt: 2025-12-19 05:38:59 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 05:56:53 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 1073.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hypeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hypeR_2.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/hypeR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hypeR/DESCRIPTION’ ... OK
* this is package ‘hypeR’ version ‘2.8.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 dependencies in R code ... NOTE
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_collection’
msigdb_available: no visible binding for global variable
‘gs_subcollection’
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_collection gs_name gs_subcollection
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 ... 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
hyp_hmap 99.755 1.432 159.819
clean_genesets 91.872 0.955 95.991
hyp_to_graph 88.226 0.318 113.279
msigdb_download 34.262 0.411 41.105
msigdb_available 24.530 2.360 28.003
hyp_dots 15.881 0.418 16.880
hyp_emap 13.796 0.319 19.655
hypeR 12.329 0.635 14.183
hyp_to_excel 12.728 0.208 15.988
hyp_show 11.847 0.190 17.707
hyp_to_table 11.388 0.136 11.884
enrichr_download 0.131 0.010 6.814
* 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 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/hypeR.Rcheck/00check.log’
for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘hypeR’ ... ** this is package ‘hypeR’ version ‘2.8.2’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
2025-12-19 05:51:47.556 R[99521:142865783] XType: com.apple.fonts is not accessible.
2025-12-19 05:51:47.556 R[99521:142865783] XType: XTFontStaticRegistry is enabled.
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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 424 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 424 ]
>
> proc.time()
user system elapsed
333.473 5.526 402.341
hypeR.Rcheck/hypeR-Ex.timings
| name | user | system | elapsed | |
| clean_genesets | 91.872 | 0.955 | 95.991 | |
| dot-format_str | 0.000 | 0.000 | 0.001 | |
| dot-string_args | 0.000 | 0.001 | 0.001 | |
| enrichr_available | 0.456 | 0.091 | 0.660 | |
| enrichr_download | 0.131 | 0.010 | 6.814 | |
| enrichr_gsets | 0.127 | 0.009 | 0.339 | |
| gsets | 0.002 | 0.001 | 0.002 | |
| hyp | 0.009 | 0.002 | 0.011 | |
| hyp_dots | 15.881 | 0.418 | 16.880 | |
| hyp_emap | 13.796 | 0.319 | 19.655 | |
| hyp_hmap | 99.755 | 1.432 | 159.819 | |
| hyp_show | 11.847 | 0.190 | 17.707 | |
| hyp_to_excel | 12.728 | 0.208 | 15.988 | |
| hyp_to_graph | 88.226 | 0.318 | 113.279 | |
| hyp_to_table | 11.388 | 0.136 | 11.884 | |
| hypeR | 12.329 | 0.635 | 14.183 | |
| hyperdb_available | 0.037 | 0.004 | 0.386 | |
| hyperdb_gsets | 0.055 | 0.007 | 0.463 | |
| hyperdb_rgsets | 0.064 | 0.005 | 0.277 | |
| msigdb_available | 24.530 | 2.360 | 28.003 | |
| msigdb_check_species | 0.000 | 0.001 | 0.002 | |
| msigdb_download | 34.262 | 0.411 | 41.105 | |
| msigdb_gsets | 0.778 | 0.070 | 1.684 | |
| msigdb_info | 0.002 | 0.001 | 0.013 | |
| msigdb_species | 0.038 | 0.006 | 0.082 | |
| msigdb_version | 0.001 | 0.000 | 0.003 | |
| multihyp | 0.002 | 0.001 | 0.006 | |
| rctbl_build | 1.773 | 0.184 | 2.151 | |
| rctbl_hyp | 2.566 | 0.994 | 3.650 | |
| rctbl_mhyp | 1.686 | 0.080 | 1.799 | |