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This page was generated on 2023-10-16 11:37:07 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 907/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWENA 1.10.0  (landing page)
Gwenaëlle Lemoine
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GWENA
git_branch: RELEASE_3_17
git_last_commit: 1d67dc7
git_last_commit_date: 2023-07-03 06:15:24 -0400 (Mon, 03 Jul 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for GWENA on merida1


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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2023-10-16 02:32:42 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 02:48:14 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 931.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GWENA.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GWENA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.10.0’
* 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-3.17-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 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          14.707  0.139  20.279
compare_conditions  9.640  0.149  13.727
plot_enrichment     2.815  0.228   9.869
bio_enrich          0.214  0.025  10.309
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/GWENA.Rcheck/00check.log’
for details.



Installation output

GWENA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GWENA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
461.183   5.814 375.946 

Example timings

GWENA.Rcheck/GWENA-Ex.timings

nameusersystemelapsed
associate_phenotype0.0460.0040.065
bio_enrich 0.214 0.02510.309
build_graph_from_sq_mat0.2690.0050.283
build_net3.4880.0544.466
compare_conditions 9.640 0.14913.727
detect_modules1.9770.0442.626
filter_RNA_seq0.0010.0000.002
filter_low_var0.0310.0010.039
get_fit.cor0.9760.0141.256
get_fit.expr0.9470.0101.205
get_hub_degree0.2240.0020.286
get_hub_genes0.0020.0010.004
get_hub_high_co0.0010.0000.001
get_hub_kleinberg0.4520.0040.586
get_sub_clusters2.0320.0242.598
is_data_expr0.0000.0000.001
is_gost0.0440.0052.270
is_module0.0010.0000.001
is_network0.0010.0010.001
join_gost0.0410.0061.475
plot_comparison_stats0.6360.0110.744
plot_enrichment2.8150.2289.869
plot_expression_profiles3.8140.0694.901
plot_module0.4200.0310.582
plot_modules_merge2.1900.0262.827
plot_modules_phenotype0.6700.0060.866
z_summary14.707 0.13920.279