Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-13 17:33 -0400 (Fri, 13 Sep 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" | 4760 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
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 203/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbKegg 1.10.2 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the biodbKegg package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbKegg.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: biodbKegg |
Version: 1.10.2 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbKegg_1.10.2.tar.gz |
StartedAt: 2024-09-11 20:56:40 -0400 (Wed, 11 Sep 2024) |
EndedAt: 2024-09-11 21:11:09 -0400 (Wed, 11 Sep 2024) |
EllapsedTime: 868.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbKegg.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbKegg_1.10.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbKegg.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 ‘biodbKegg/DESCRIPTION’ ... OK * this is package ‘biodbKegg’ version ‘1.10.2’ * 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 ‘biodbKegg’ can be installed ... OK * checking installed package size ... OK * checking package 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 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 KeggEnzymeConn 14.759 0.572 124.615 KeggPathwayConn 6.847 0.241 54.525 KeggCompoundConn 2.599 0.222 13.571 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
biodbKegg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbKegg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘biodbKegg’ ... ** 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 (biodbKegg)
biodbKegg.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: 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. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbKegg) > library(withr) > Sys.setenv(TESTTHAT_REPORTER = "summary") > test_check("biodbKegg") trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png?17261034081927514' downloaded 158 KB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 560 ] > > proc.time() user system elapsed 103.065 6.301 566.107
biodbKegg.Rcheck/biodbKegg-Ex.timings
name | user | system | elapsed | |
KeggCircle | 0.008 | 0.000 | 0.008 | |
KeggCompoundConn | 2.599 | 0.222 | 13.571 | |
KeggCompoundEntry | 0.309 | 0.025 | 1.820 | |
KeggConn | 0.350 | 0.002 | 2.524 | |
KeggEntry | 0.190 | 0.028 | 0.218 | |
KeggEnzymeConn | 14.759 | 0.572 | 124.615 | |
KeggEnzymeEntry | 0.317 | 0.020 | 1.832 | |
KeggGenesConn | 0.386 | 0.060 | 1.925 | |
KeggGenesEntry | 0.188 | 0.001 | 0.189 | |
KeggGlycanConn | 0.156 | 0.000 | 0.155 | |
KeggGlycanEntry | 0.344 | 0.000 | 1.805 | |
KeggModuleConn | 0.446 | 0.005 | 1.948 | |
KeggModuleEntry | 0.170 | 0.008 | 0.178 | |
KeggOrthologyConn | 0.486 | 0.009 | 2.308 | |
KeggOrthologyEntry | 0.275 | 0.028 | 0.305 | |
KeggPathwayConn | 6.847 | 0.241 | 54.525 | |
KeggPathwayEntry | 0.294 | 0.021 | 1.793 | |
KeggReactionConn | 0.310 | 0.026 | 1.815 | |
KeggReactionEntry | 0.162 | 0.000 | 0.162 | |
KeggRect | 0.004 | 0.000 | 0.004 | |
KeggShape | 0.001 | 0.000 | 0.001 | |