Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-11 20:42 -0400 (Fri, 11 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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 939/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GWENA 1.14.0 (landing page) Gwenaëlle Lemoine
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2024-10-10 23:25:22 -0400 (Thu, 10 Oct 2024) |
EndedAt: 2024-10-10 23:35:25 -0400 (Thu, 10 Oct 2024) |
EllapsedTime: 603.1 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GWENA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 ‘/Users/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 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 17.129 0.166 20.155 compare_conditions 10.720 0.104 12.289 plot_enrichment 1.327 0.084 6.225 bio_enrich 0.310 0.035 8.442 * 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 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-3.19-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/4.4-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 374.585 7.084 303.416
GWENA.Rcheck/GWENA-Ex.timings
name | user | system | elapsed | |
associate_phenotype | 0.029 | 0.004 | 0.034 | |
bio_enrich | 0.310 | 0.035 | 8.442 | |
build_graph_from_sq_mat | 0.117 | 0.003 | 0.121 | |
build_net | 4.134 | 0.052 | 4.301 | |
compare_conditions | 10.720 | 0.104 | 12.289 | |
detect_modules | 1.994 | 0.031 | 2.095 | |
filter_RNA_seq | 0.002 | 0.000 | 0.002 | |
filter_low_var | 0.015 | 0.000 | 0.015 | |
get_fit.cor | 0.896 | 0.010 | 0.976 | |
get_fit.expr | 0.909 | 0.008 | 0.947 | |
get_hub_degree | 0.083 | 0.002 | 0.090 | |
get_hub_genes | 0.000 | 0.001 | 0.001 | |
get_hub_high_co | 0.000 | 0.000 | 0.001 | |
get_hub_kleinberg | 0.161 | 0.002 | 0.169 | |
get_sub_clusters | 1.996 | 0.033 | 2.156 | |
is_data_expr | 0.000 | 0.000 | 0.001 | |
is_gost | 0.026 | 0.004 | 1.888 | |
is_module | 0 | 0 | 0 | |
is_network | 0.001 | 0.001 | 0.000 | |
join_gost | 0.029 | 0.005 | 0.810 | |
plot_comparison_stats | 0.256 | 0.008 | 0.271 | |
plot_enrichment | 1.327 | 0.084 | 6.225 | |
plot_expression_profiles | 2.881 | 0.059 | 3.128 | |
plot_module | 0.182 | 0.004 | 0.195 | |
plot_modules_merge | 2.210 | 0.024 | 2.315 | |
plot_modules_phenotype | 0.438 | 0.005 | 0.464 | |
z_summary | 17.129 | 0.166 | 20.155 | |