Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-23 12:03 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 822/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.29.0 (landing page) Beth Signal
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the GeneStructureTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneStructureTools.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: GeneStructureTools |
Version: 1.29.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GeneStructureTools_1.29.0.tar.gz |
StartedAt: 2025-09-23 00:05:30 -0400 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 00:13:47 -0400 (Tue, 23 Sep 2025) |
EllapsedTime: 496.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GeneStructureTools_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeneStructureTools.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.29.0’ * 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 ‘GeneStructureTools’ 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 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 leafcutterTranscriptChangeSummary 20.737 0.128 20.866 whippetTranscriptChangeSummary 11.644 0.089 11.734 alternativeIntronUsage 5.069 0.154 5.224 * 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
GeneStructureTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘GeneStructureTools’ ... ** this is package ‘GeneStructureTools’ version ‘1.29.0’ ** 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 (GeneStructureTools)
GeneStructureTools.Rcheck/GeneStructureTools-Ex.timings
name | user | system | elapsed | |
DEXSeqIdsToGeneIds | 0.003 | 0.000 | 0.003 | |
UTR2UTR53 | 2.12 | 0.08 | 2.20 | |
addBroadTypes | 0.162 | 0.002 | 0.164 | |
addIntronInTranscript | 1.826 | 0.051 | 1.880 | |
alternativeIntronUsage | 5.069 | 0.154 | 5.224 | |
annotateGeneModel | 0.802 | 0.067 | 0.870 | |
attrChangeAltSpliced | 1.087 | 0.048 | 1.135 | |
coordinates-methods | 0.045 | 0.018 | 0.063 | |
diffSplicingResults-methods | 0.042 | 0.018 | 0.060 | |
exonsToTranscripts | 0.233 | 0.009 | 0.241 | |
filterGtfOverlap | 0.239 | 0.001 | 0.240 | |
filterWhippetEvents | 0.064 | 0.014 | 0.079 | |
findDEXexonType | 2.252 | 0.059 | 2.312 | |
findExonContainingTranscripts | 0.363 | 0.026 | 0.389 | |
findIntronContainingTranscripts | 0.596 | 0.039 | 0.635 | |
findJunctionPairs | 1.266 | 0.066 | 1.332 | |
formatWhippetEvents | 0.014 | 0.002 | 0.017 | |
getOrfs | 0.663 | 0.007 | 0.670 | |
getUOrfs | 0.499 | 0.002 | 0.502 | |
junctions-methods | 0.043 | 0.022 | 0.064 | |
leafcutterTranscriptChangeSummary | 20.737 | 0.128 | 20.866 | |
makeGeneModel | 0.136 | 0.005 | 0.141 | |
maxLocation | 0.002 | 0.000 | 0.003 | |
orfDiff | 1.381 | 0.035 | 1.417 | |
orfSimilarity | 0.001 | 0.000 | 0.000 | |
overlapTypes | 2.140 | 0.046 | 2.186 | |
readCounts-methods | 0.046 | 0.016 | 0.062 | |
readWhippetDIFFfiles | 0.003 | 0.002 | 0.005 | |
readWhippetDataSet | 0.043 | 0.018 | 0.060 | |
readWhippetJNCfiles | 0.025 | 0.004 | 0.029 | |
readWhippetPSIfiles | 0.007 | 0.008 | 0.015 | |
removeDuplicateTranscripts | 0.232 | 0.004 | 0.236 | |
removeSameExon | 0.193 | 0.003 | 0.196 | |
removeVersion | 0 | 0 | 0 | |
reorderExonNumbers | 0.149 | 0.001 | 0.150 | |
replaceJunction | 3.720 | 0.087 | 3.807 | |
skipExonInTranscript | 1.287 | 0.021 | 1.309 | |
summariseExonTypes | 2.324 | 0.006 | 2.330 | |
transcriptChangeSummary | 1.391 | 0.045 | 1.447 | |
whippetTranscriptChangeSummary | 11.644 | 0.089 | 11.734 | |