Gwenaëlle Lemoine
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/GWENA |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9621d77 |
| git_last_commit_date: 2025-10-29 11:00:28 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:06 -0500 (Thu, 20 Nov 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" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 953/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GWENA 1.20.0 (landing page) Gwenaëlle Lemoine
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the GWENA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GWENA.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: GWENA |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWENA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWENA_1.20.0.tar.gz |
| StartedAt: 2025-11-18 07:30:36 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 07:35:24 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 287.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GWENA.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWENA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWENA_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.20.0’
* 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 ‘GWENA’ can be installed ... WARNING
Found the following significant warnings:
Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
build_net.Rd: adjacency.fromSimilarity
get_fit.cor.Rd: pickSoftThreshold.fromSimilarity
get_fit.expr.Rd: pickSoftThreshold.fromSimilarity
plot_module.Rd: igraph.plotting
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
z_summary 6.124 0.046 9.146
compare_conditions 3.778 0.029 5.273
plot_enrichment 0.662 0.045 6.895
bio_enrich 0.105 0.012 10.246
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/00check.log’
for details.
GWENA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GWENA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GWENA’ ... ** this is package ‘GWENA’ version ‘1.20.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Warning: bad markup (extra space?) at compare_conditions.Rd:91:72 Warning: bad markup (extra space?) at compare_conditions.Rd:96:77 Warning: bad markup (extra space?) at compare_conditions.Rd:98:74 Warning: bad markup (extra space?) at compare_conditions.Rd:100:69 *** 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 (GWENA)
GWENA.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(GWENA)
>
> test_check("GWENA")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 278 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 278 ]
>
> proc.time()
user system elapsed
129.475 1.883 143.138
GWENA.Rcheck/GWENA-Ex.timings
| name | user | system | elapsed | |
| associate_phenotype | 0.009 | 0.001 | 0.010 | |
| bio_enrich | 0.105 | 0.012 | 10.246 | |
| build_graph_from_sq_mat | 0.035 | 0.000 | 0.036 | |
| build_net | 1.442 | 0.011 | 1.617 | |
| compare_conditions | 3.778 | 0.029 | 5.273 | |
| detect_modules | 0.734 | 0.012 | 0.826 | |
| filter_RNA_seq | 0 | 0 | 0 | |
| filter_low_var | 0.004 | 0.001 | 0.005 | |
| get_fit.cor | 0.358 | 0.002 | 0.376 | |
| get_fit.expr | 0.360 | 0.003 | 0.380 | |
| get_hub_degree | 0.028 | 0.001 | 0.035 | |
| get_hub_genes | 0.001 | 0.000 | 0.000 | |
| get_hub_high_co | 0 | 0 | 0 | |
| get_hub_kleinberg | 0.051 | 0.000 | 0.053 | |
| get_sub_clusters | 0.756 | 0.010 | 0.965 | |
| is_data_expr | 0 | 0 | 0 | |
| is_gost | 0.015 | 0.002 | 1.879 | |
| is_module | 0.000 | 0.001 | 0.000 | |
| is_network | 0 | 0 | 0 | |
| join_gost | 0.017 | 0.003 | 1.815 | |
| plot_comparison_stats | 0.189 | 0.008 | 0.205 | |
| plot_enrichment | 0.662 | 0.045 | 6.895 | |
| plot_expression_profiles | 1.144 | 0.026 | 1.446 | |
| plot_module | 0.094 | 0.002 | 0.110 | |
| plot_modules_merge | 0.859 | 0.009 | 1.051 | |
| plot_modules_phenotype | 0.249 | 0.005 | 0.322 | |
| z_summary | 6.124 | 0.046 | 9.146 | |