Gwenaëlle Lemoine
| Snapshot Date: 2025-11-02 13:40 -0500 (Sun, 02 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/GWENA |
| git_branch: devel |
| git_last_commit: 28d0013 |
| git_last_commit_date: 2025-10-29 11:00:28 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-03 11:33 -0500 (Mon, 03 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4775 |
| 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 941/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GWENA 1.21.0 (landing page) Gwenaëlle Lemoine
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.21.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GWENA_1.21.0.tar.gz |
| StartedAt: 2025-11-02 23:54:04 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-03 00:05:10 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 666.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GWENA.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GWENA_1.21.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GWENA.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.21.0’
* 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 ‘/home/biocbuild/bbs-3.23-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 loading without being on the library search path ... 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 12.642 0.615 14.995
compare_conditions 8.091 0.344 9.398
plot_enrichment 1.493 0.188 7.754
bio_enrich 0.301 0.038 11.411
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/GWENA.Rcheck/00check.log’
for details.
GWENA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GWENA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘GWENA’ ... ** this is package ‘GWENA’ version ‘1.21.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
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Type 'contributors()' for more information and
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> 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
469.585 7.635 311.428
GWENA.Rcheck/GWENA-Ex.timings
| name | user | system | elapsed | |
| associate_phenotype | 0.021 | 0.002 | 0.024 | |
| bio_enrich | 0.301 | 0.038 | 11.411 | |
| build_graph_from_sq_mat | 0.107 | 0.012 | 0.119 | |
| build_net | 2.918 | 0.198 | 3.115 | |
| compare_conditions | 8.091 | 0.344 | 9.398 | |
| detect_modules | 1.608 | 0.051 | 1.661 | |
| filter_RNA_seq | 0.000 | 0.001 | 0.001 | |
| filter_low_var | 0.009 | 0.000 | 0.009 | |
| get_fit.cor | 0.711 | 0.001 | 0.712 | |
| get_fit.expr | 0.757 | 0.004 | 0.761 | |
| get_hub_degree | 0.065 | 0.001 | 0.066 | |
| get_hub_genes | 0.001 | 0.000 | 0.001 | |
| get_hub_high_co | 0.001 | 0.000 | 0.000 | |
| get_hub_kleinberg | 0.131 | 0.001 | 0.131 | |
| get_sub_clusters | 1.478 | 0.005 | 1.483 | |
| is_data_expr | 0.001 | 0.000 | 0.000 | |
| is_gost | 0.045 | 0.016 | 2.855 | |
| is_module | 0.000 | 0.001 | 0.002 | |
| is_network | 0.001 | 0.000 | 0.001 | |
| join_gost | 0.029 | 0.006 | 1.830 | |
| plot_comparison_stats | 0.481 | 0.063 | 0.544 | |
| plot_enrichment | 1.493 | 0.188 | 7.754 | |
| plot_expression_profiles | 2.651 | 0.273 | 2.924 | |
| plot_module | 0.225 | 0.017 | 0.242 | |
| plot_modules_merge | 1.837 | 0.165 | 2.002 | |
| plot_modules_phenotype | 0.533 | 0.024 | 0.556 | |
| z_summary | 12.642 | 0.615 | 14.995 | |