Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:07 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 |
To the developers/maintainers of the GWENA package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 874/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GWENA 1.9.0 (landing page) Gwenaëlle Lemoine
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: GWENA |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GWENA_1.9.0.tar.gz |
StartedAt: 2023-02-07 04:08:38 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 04:29:12 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 1233.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GWENA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GWENA_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GWENA.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘GWENA/DESCRIPTION’ ... OK * this is package ‘GWENA’ version ‘1.9.0’ * 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 ... OK * 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 checkRd: (5) compare_conditions.Rd:90-91: \item in \describe must have non-empty label checkRd: (5) compare_conditions.Rd:92-96: \item in \describe must have non-empty label checkRd: (5) compare_conditions.Rd:97-98: \item in \describe must have non-empty label checkRd: (5) compare_conditions.Rd:99-100: \item in \describe must have non-empty label * 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 14.261 0.081 16.113 compare_conditions 9.598 0.102 10.853 plot_enrichment 1.598 0.132 28.565 bio_enrich 0.130 0.276 64.431 is_gost 0.032 0.000 34.983 * 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: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/GWENA.Rcheck/00check.log’ for details.
GWENA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GWENA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 *** 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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 561.862 2.711 613.731
GWENA.Rcheck/GWENA-Ex.timings
name | user | system | elapsed | |
associate_phenotype | 0.032 | 0.004 | 0.043 | |
bio_enrich | 0.130 | 0.276 | 64.431 | |
build_graph_from_sq_mat | 0.205 | 0.028 | 0.247 | |
build_net | 2.947 | 0.020 | 2.997 | |
compare_conditions | 9.598 | 0.102 | 10.853 | |
detect_modules | 2.003 | 0.004 | 2.021 | |
filter_RNA_seq | 0.001 | 0.001 | 0.001 | |
filter_low_var | 0.015 | 0.003 | 0.017 | |
get_fit.cor | 0.877 | 0.000 | 0.878 | |
get_fit.expr | 0.885 | 0.000 | 0.886 | |
get_hub_degree | 0.126 | 0.000 | 0.125 | |
get_hub_genes | 0.001 | 0.000 | 0.001 | |
get_hub_high_co | 0.001 | 0.000 | 0.000 | |
get_hub_kleinberg | 0.250 | 0.000 | 0.252 | |
get_sub_clusters | 1.996 | 0.011 | 2.010 | |
is_data_expr | 0.000 | 0.000 | 0.001 | |
is_gost | 0.032 | 0.000 | 34.983 | |
is_module | 0.001 | 0.000 | 0.001 | |
is_network | 0.001 | 0.000 | 0.001 | |
join_gost | 0.013 | 0.004 | 3.234 | |
plot_comparison_stats | 0.365 | 0.007 | 0.381 | |
plot_enrichment | 1.598 | 0.132 | 28.565 | |
plot_expression_profiles | 2.993 | 0.120 | 3.139 | |
plot_module | 0.247 | 0.016 | 0.273 | |
plot_modules_merge | 2.116 | 0.051 | 2.169 | |
plot_modules_phenotype | 0.390 | 0.028 | 0.417 | |
z_summary | 14.261 | 0.081 | 16.113 | |