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This page was generated on 2024-02-29 11:35:59 -0500 (Thu, 29 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 928/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWENA 1.12.0  (landing page)
Gwenaëlle Lemoine
Snapshot Date: 2024-02-28 14:05:05 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/GWENA
git_branch: RELEASE_3_18
git_last_commit: 76d08ee
git_last_commit_date: 2023-10-24 11:23:28 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.12.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GWENA_1.12.0.tar.gz
StartedAt: 2024-02-28 22:58:17 -0500 (Wed, 28 Feb 2024)
EndedAt: 2024-02-28 23:08:05 -0500 (Wed, 28 Feb 2024)
EllapsedTime: 587.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GWENA.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GWENA_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GWENA.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.12.0’
* 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-3.18-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 ... 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 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 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 ... 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 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          13.324  0.757  15.886
compare_conditions  8.219  0.380   9.585
plot_enrichment     1.153  0.148   7.715
bio_enrich          0.847  0.147  14.475
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GWENA_guide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GWENA.Rcheck/00check.log’
for details.



Installation output

GWENA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GWENA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘GWENA’ ...
** 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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(GWENA)

> 
> test_check("GWENA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
> 
> proc.time()
   user  system elapsed 
371.064  14.520 244.376 

Example timings

GWENA.Rcheck/GWENA-Ex.timings

nameusersystemelapsed
associate_phenotype0.0270.0000.027
bio_enrich 0.847 0.14714.475
build_graph_from_sq_mat0.1330.0080.141
build_net2.3760.1882.564
compare_conditions8.2190.3809.585
detect_modules1.4550.1041.559
filter_RNA_seq0.0010.0000.001
filter_low_var0.010.000.01
get_fit.cor0.7200.0760.795
get_fit.expr0.7120.0040.716
get_hub_degree0.0720.0000.072
get_hub_genes0.0010.0000.001
get_hub_high_co0.0010.0000.000
get_hub_kleinberg0.1390.0040.142
get_sub_clusters1.5610.0401.601
is_data_expr0.0000.0000.001
is_gost0.0350.0002.939
is_module000
is_network000
join_gost0.0230.0080.979
plot_comparison_stats0.2190.0080.227
plot_enrichment1.1530.1487.715
plot_expression_profiles2.5080.2322.739
plot_module0.1380.0040.142
plot_modules_merge1.8200.1641.984
plot_modules_phenotype0.4110.0000.411
z_summary13.324 0.75715.886