Back to Build/check report for BioC 3.20 annotations |
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This page was generated on 2024-08-21 08:30 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
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 12/46 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
BioMartGOGeneSets 0.99.11 (landing page) Zuguang Gu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the BioMartGOGeneSets package: - 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: BioMartGOGeneSets |
Version: 0.99.11 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BioMartGOGeneSets.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BioMartGOGeneSets_0.99.11.tar.gz |
StartedAt: 2024-08-21 06:33:21 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 06:35:25 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 124.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BioMartGOGeneSets.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BioMartGOGeneSets.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BioMartGOGeneSets_0.99.11.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-annotation/meat/BioMartGOGeneSets.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘BioMartGOGeneSets/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioMartGOGeneSets’ version ‘0.99.11’ * 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 ‘BioMartGOGeneSets’ 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 ... OK * 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 whether startup messages can be suppressed ... 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getBioMartGOGeneSets 5.48 0.156 6.407 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.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: OK
BioMartGOGeneSets.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BioMartGOGeneSets ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BioMartGOGeneSets’ ... ** using staged installation ** R ** 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 (BioMartGOGeneSets)
BioMartGOGeneSets.Rcheck/tests/test-all.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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) > suppressWarnings(suppressPackageStartupMessages(library(BioMartGOGeneSets))) > > test_check("BioMartGOGeneSets") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 2.952 0.289 3.232
BioMartGOGeneSets.Rcheck/BioMartGOGeneSets-Ex.timings
name | user | system | elapsed | |
BioMartGOGeneSets | 0 | 0 | 0 | |
changeSeqnameStyle | 0 | 0 | 0 | |
getBioMartGOGeneSets | 5.480 | 0.156 | 6.407 | |
getBioMartGenes | 0.174 | 0.011 | 0.186 | |
getBioMartGenomeInfo | 0.089 | 0.008 | 0.404 | |
print.BioMartGOGeneSets_info | 0.001 | 0.000 | 0.001 | |
supportedOrganisms | 0.001 | 0.000 | 0.000 | |