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) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:07 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (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 907/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GWENA 1.10.0 (landing page) Gwenaëlle Lemoine
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.10.0 |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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)
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
GWENA.Rcheck/GWENA-Ex.timings
| name | user | system | elapsed | |
| associate_phenotype | 0.046 | 0.004 | 0.065 | |
| bio_enrich | 0.214 | 0.025 | 10.309 | |
| build_graph_from_sq_mat | 0.269 | 0.005 | 0.283 | |
| build_net | 3.488 | 0.054 | 4.466 | |
| compare_conditions | 9.640 | 0.149 | 13.727 | |
| detect_modules | 1.977 | 0.044 | 2.626 | |
| filter_RNA_seq | 0.001 | 0.000 | 0.002 | |
| filter_low_var | 0.031 | 0.001 | 0.039 | |
| get_fit.cor | 0.976 | 0.014 | 1.256 | |
| get_fit.expr | 0.947 | 0.010 | 1.205 | |
| get_hub_degree | 0.224 | 0.002 | 0.286 | |
| get_hub_genes | 0.002 | 0.001 | 0.004 | |
| get_hub_high_co | 0.001 | 0.000 | 0.001 | |
| get_hub_kleinberg | 0.452 | 0.004 | 0.586 | |
| get_sub_clusters | 2.032 | 0.024 | 2.598 | |
| is_data_expr | 0.000 | 0.000 | 0.001 | |
| is_gost | 0.044 | 0.005 | 2.270 | |
| is_module | 0.001 | 0.000 | 0.001 | |
| is_network | 0.001 | 0.001 | 0.001 | |
| join_gost | 0.041 | 0.006 | 1.475 | |
| plot_comparison_stats | 0.636 | 0.011 | 0.744 | |
| plot_enrichment | 2.815 | 0.228 | 9.869 | |
| plot_expression_profiles | 3.814 | 0.069 | 4.901 | |
| plot_module | 0.420 | 0.031 | 0.582 | |
| plot_modules_merge | 2.190 | 0.026 | 2.827 | |
| plot_modules_phenotype | 0.670 | 0.006 | 0.866 | |
| z_summary | 14.707 | 0.139 | 20.279 | |