Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:07 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 817/2320 | 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: /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_1.29.0.tar.gz |
StartedAt: 2025-08-29 19:33:53 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 19:36:23 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 149.8 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_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-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 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.29.0’ * 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 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 7.031 0.258 7.316 * 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 ‘1.29.0’ ** 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 | 0.001 | 0.000 | 0.002 | |
UTR2UTR53 | 0.654 | 0.018 | 0.678 | |
addBroadTypes | 0.072 | 0.002 | 0.075 | |
addIntronInTranscript | 0.575 | 0.035 | 0.625 | |
alternativeIntronUsage | 1.209 | 0.005 | 1.215 | |
annotateGeneModel | 0.289 | 0.006 | 0.295 | |
attrChangeAltSpliced | 0.389 | 0.036 | 0.441 | |
coordinates-methods | 0.024 | 0.033 | 0.073 | |
diffSplicingResults-methods | 0.023 | 0.032 | 0.067 | |
exonsToTranscripts | 0.092 | 0.003 | 0.095 | |
filterGtfOverlap | 0.091 | 0.003 | 0.094 | |
filterWhippetEvents | 0.027 | 0.030 | 0.065 | |
findDEXexonType | 0.722 | 0.005 | 0.729 | |
findExonContainingTranscripts | 0.156 | 0.028 | 0.193 | |
findIntronContainingTranscripts | 0.204 | 0.032 | 0.251 | |
findJunctionPairs | 0.412 | 0.034 | 0.453 | |
formatWhippetEvents | 0.005 | 0.004 | 0.010 | |
getOrfs | 0.235 | 0.006 | 0.244 | |
getUOrfs | 0.184 | 0.004 | 0.188 | |
junctions-methods | 0.025 | 0.027 | 0.069 | |
leafcutterTranscriptChangeSummary | 7.031 | 0.258 | 7.316 | |
makeGeneModel | 0.065 | 0.003 | 0.068 | |
maxLocation | 0.001 | 0.000 | 0.001 | |
orfDiff | 0.488 | 0.040 | 0.540 | |
orfSimilarity | 0.001 | 0.001 | 0.000 | |
overlapTypes | 0.647 | 0.005 | 0.654 | |
readCounts-methods | 0.024 | 0.026 | 0.059 | |
readWhippetDIFFfiles | 0.003 | 0.005 | 0.008 | |
readWhippetDataSet | 0.023 | 0.027 | 0.059 | |
readWhippetJNCfiles | 0.010 | 0.011 | 0.028 | |
readWhippetPSIfiles | 0.006 | 0.013 | 0.022 | |
removeDuplicateTranscripts | 0.095 | 0.003 | 0.100 | |
removeSameExon | 0.079 | 0.002 | 0.081 | |
removeVersion | 0.001 | 0.000 | 0.000 | |
reorderExonNumbers | 0.068 | 0.002 | 0.071 | |
replaceJunction | 1.108 | 0.029 | 1.150 | |
skipExonInTranscript | 0.419 | 0.033 | 0.464 | |
summariseExonTypes | 0.694 | 0.004 | 0.702 | |
transcriptChangeSummary | 0.454 | 0.037 | 0.506 | |
whippetTranscriptChangeSummary | 3.629 | 0.084 | 3.766 | |