Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-06 11:40 -0400 (Mon, 06 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
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 822/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.28.0 (landing page) Beth Signal
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneStructureTools_1.28.0.tar.gz |
StartedAt: 2025-10-03 22:14:16 -0400 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 22:21:44 -0400 (Fri, 03 Oct 2025) |
EllapsedTime: 448.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneStructureTools_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeneStructureTools.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.28.0’ * 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 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 20.973 0.746 21.914 whippetTranscriptChangeSummary 11.535 0.266 11.920 * 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: OK
GeneStructureTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GeneStructureTools’ ... ** this is package ‘GeneStructureTools’ version ‘1.28.0’ ** 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 | 0.004 | 0.001 | 0.005 | |
UTR2UTR53 | 2.660 | 0.149 | 2.933 | |
addBroadTypes | 0.248 | 0.013 | 0.275 | |
addIntronInTranscript | 3.524 | 0.200 | 3.859 | |
alternativeIntronUsage | 4.267 | 0.043 | 4.376 | |
annotateGeneModel | 0.882 | 0.013 | 0.895 | |
attrChangeAltSpliced | 1.322 | 0.129 | 1.497 | |
coordinates-methods | 0.079 | 0.098 | 0.205 | |
diffSplicingResults-methods | 0.079 | 0.097 | 0.203 | |
exonsToTranscripts | 0.308 | 0.007 | 0.316 | |
filterGtfOverlap | 0.332 | 0.008 | 0.340 | |
filterWhippetEvents | 0.093 | 0.092 | 0.209 | |
findDEXexonType | 2.486 | 0.019 | 2.511 | |
findExonContainingTranscripts | 0.528 | 0.101 | 0.662 | |
findIntronContainingTranscripts | 0.730 | 0.105 | 0.870 | |
findJunctionPairs | 1.439 | 0.101 | 1.578 | |
formatWhippetEvents | 0.017 | 0.010 | 0.029 | |
getOrfs | 0.655 | 0.017 | 0.675 | |
getUOrfs | 0.278 | 0.011 | 0.293 | |
junctions-methods | 0.051 | 0.061 | 0.130 | |
leafcutterTranscriptChangeSummary | 20.973 | 0.746 | 21.914 | |
makeGeneModel | 0.133 | 0.006 | 0.140 | |
maxLocation | 0.003 | 0.001 | 0.003 | |
orfDiff | 1.407 | 0.079 | 1.538 | |
orfSimilarity | 0.001 | 0.000 | 0.001 | |
overlapTypes | 3.708 | 0.029 | 3.750 | |
readCounts-methods | 0.073 | 0.079 | 0.173 | |
readWhippetDIFFfiles | 0.008 | 0.008 | 0.019 | |
readWhippetDataSet | 0.074 | 0.083 | 0.181 | |
readWhippetJNCfiles | 0.037 | 0.035 | 0.082 | |
readWhippetPSIfiles | 0.021 | 0.035 | 0.063 | |
removeDuplicateTranscripts | 0.319 | 0.013 | 0.333 | |
removeSameExon | 0.266 | 0.009 | 0.284 | |
removeVersion | 0.001 | 0.000 | 0.001 | |
reorderExonNumbers | 0.228 | 0.009 | 0.237 | |
replaceJunction | 3.699 | 0.120 | 3.847 | |
skipExonInTranscript | 1.450 | 0.096 | 1.574 | |
summariseExonTypes | 2.461 | 0.019 | 2.484 | |
transcriptChangeSummary | 1.577 | 0.127 | 1.744 | |
whippetTranscriptChangeSummary | 11.535 | 0.266 | 11.920 | |