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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 939/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWENA 1.14.0  (landing page)
Gwenaëlle Lemoine
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/GWENA
git_branch: RELEASE_3_19
git_last_commit: 165ba47
git_last_commit_date: 2024-04-30 11:25:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for GWENA on nebbiolo1

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: 1.14.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GWENA_1.14.0.tar.gz
StartedAt: 2024-06-16 23:58:13 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-17 00:08:33 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 620.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GWENA.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GWENA_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GWENA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.14.0’
* 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-3.19-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 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 ... 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          14.420  0.277  16.479
compare_conditions  8.858  0.450  10.294
plot_enrichment     1.008  0.092   7.326
bio_enrich          0.345  0.020  11.600
is_gost             0.038  0.003   5.342
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GWENA.Rcheck/00check.log’
for details.


Installation output

GWENA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GWENA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 0 | SKIP 0 | PASS 278 ]
> 
> proc.time()
   user  system elapsed 
391.016  12.357 267.927 

Example timings

GWENA.Rcheck/GWENA-Ex.timings

nameusersystemelapsed
associate_phenotype0.0210.0050.025
bio_enrich 0.345 0.02011.600
build_graph_from_sq_mat0.1390.0040.142
build_net3.3950.2803.674
compare_conditions 8.858 0.45010.294
detect_modules1.7380.0531.790
filter_RNA_seq0.0010.0000.001
filter_low_var0.010.000.01
get_fit.cor0.8710.0430.915
get_fit.expr0.8980.0000.898
get_hub_degree0.0690.0030.072
get_hub_genes0.0010.0010.001
get_hub_high_co0.0000.0010.001
get_hub_kleinberg0.1350.0020.137
get_sub_clusters1.7060.0151.722
is_data_expr0.0010.0010.001
is_gost0.0380.0035.342
is_module0.0000.0000.001
is_network0.0000.0000.001
join_gost0.0270.0061.243
plot_comparison_stats0.2860.0000.287
plot_enrichment1.0080.0927.326
plot_expression_profiles2.5110.1362.647
plot_module0.1430.0080.151
plot_modules_merge1.8120.0201.833
plot_modules_phenotype0.380.000.38
z_summary14.420 0.27716.479