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This page was generated on 2025-09-30 12:03 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 945/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWENA 1.19.0  (landing page)
Gwenaëlle Lemoine
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 Sep 2025)
git_url: https://git.bioconductor.org/packages/GWENA
git_branch: devel
git_last_commit: 66b3af1
git_last_commit_date: 2025-04-15 12:04:17 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for GWENA on nebbiolo2

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.

raw results


Summary

Package: GWENA
Version: 1.19.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GWENA_1.19.0.tar.gz
StartedAt: 2025-09-30 00:48:20 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 00:58:40 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 619.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GWENA.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GWENA_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.19.0’
* 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-3.22-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 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          14.839  0.063  16.656
compare_conditions  9.856  0.253  11.085
plot_enrichment     1.441  0.039   7.006
bio_enrich          0.984  0.006  11.849
* 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-3.22-bioc/meat/GWENA.Rcheck/00check.log’
for details.


Installation output

GWENA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GWENA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GWENA’ ...
** this is package ‘GWENA’ version ‘1.19.0’
** 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)

Tests output

GWENA.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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.

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 
420.098   8.412 260.203 

Example timings

GWENA.Rcheck/GWENA-Ex.timings

nameusersystemelapsed
associate_phenotype0.0190.0020.022
bio_enrich 0.984 0.00611.849
build_graph_from_sq_mat0.1080.0000.109
build_net2.5080.0742.584
compare_conditions 9.856 0.25311.085
detect_modules1.9600.0061.967
filter_RNA_seq0.0010.0000.001
filter_low_var0.0090.0000.009
get_fit.cor0.8760.0020.878
get_fit.expr0.8150.0420.857
get_hub_degree0.0660.0000.066
get_hub_genes0.0010.0000.000
get_hub_high_co0.0010.0000.000
get_hub_kleinberg0.1280.0040.131
get_sub_clusters1.6630.0051.667
is_data_expr000
is_gost0.0280.0032.827
is_module000
is_network0.0010.0000.000
join_gost0.0300.0001.728
plot_comparison_stats0.5050.0360.541
plot_enrichment1.4410.0397.006
plot_expression_profiles2.7770.0232.800
plot_module0.1390.0000.140
plot_modules_merge2.0360.0232.059
plot_modules_phenotype0.5570.0000.558
z_summary14.839 0.06316.656