Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-14 11:47 -0400 (Thu, 14 Aug 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" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: GeneStructureTools |
Version: 1.28.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneStructureTools_1.28.0.tar.gz |
StartedAt: 2025-08-12 09:07:38 -0000 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 09:16:22 -0000 (Tue, 12 Aug 2025) |
EllapsedTime: 523.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneStructureTools_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeneStructureTools.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * 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 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 31.914 0.231 32.233 whippetTranscriptChangeSummary 16.556 0.436 17.260 replaceJunction 6.807 0.092 6.913 alternativeIntronUsage 5.717 0.016 5.748 * 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 | 0.003 | 0.000 | 0.003 | |
UTR2UTR53 | 3.059 | 0.195 | 3.267 | |
addBroadTypes | 0.225 | 0.008 | 0.233 | |
addIntronInTranscript | 3.635 | 0.091 | 3.738 | |
alternativeIntronUsage | 5.717 | 0.016 | 5.748 | |
annotateGeneModel | 1.166 | 0.008 | 1.179 | |
attrChangeAltSpliced | 1.611 | 0.038 | 1.658 | |
coordinates-methods | 0.071 | 0.030 | 0.101 | |
diffSplicingResults-methods | 0.079 | 0.022 | 0.099 | |
exonsToTranscripts | 0.350 | 0.020 | 0.371 | |
filterGtfOverlap | 0.325 | 0.004 | 0.331 | |
filterWhippetEvents | 0.080 | 0.029 | 0.109 | |
findDEXexonType | 3.390 | 0.044 | 3.447 | |
findExonContainingTranscripts | 0.553 | 0.042 | 0.595 | |
findIntronContainingTranscripts | 0.920 | 0.041 | 0.966 | |
findJunctionPairs | 1.835 | 0.029 | 1.871 | |
formatWhippetEvents | 0.018 | 0.003 | 0.021 | |
getOrfs | 0.948 | 0.040 | 0.990 | |
getUOrfs | 0.760 | 0.032 | 0.792 | |
junctions-methods | 0.064 | 0.033 | 0.097 | |
leafcutterTranscriptChangeSummary | 31.914 | 0.231 | 32.233 | |
makeGeneModel | 0.200 | 0.000 | 0.201 | |
maxLocation | 0.003 | 0.000 | 0.004 | |
orfDiff | 2.070 | 0.047 | 2.124 | |
orfSimilarity | 0.001 | 0.000 | 0.001 | |
overlapTypes | 3.162 | 0.064 | 3.233 | |
readCounts-methods | 0.081 | 0.023 | 0.104 | |
readWhippetDIFFfiles | 0.007 | 0.004 | 0.011 | |
readWhippetDataSet | 0.079 | 0.027 | 0.106 | |
readWhippetJNCfiles | 0.033 | 0.016 | 0.048 | |
readWhippetPSIfiles | 0.025 | 0.001 | 0.027 | |
removeDuplicateTranscripts | 0.338 | 0.008 | 0.348 | |
removeSameExon | 0.285 | 0.000 | 0.286 | |
removeVersion | 0 | 0 | 0 | |
reorderExonNumbers | 0.215 | 0.004 | 0.221 | |
replaceJunction | 6.807 | 0.092 | 6.913 | |
skipExonInTranscript | 1.923 | 0.041 | 1.998 | |
summariseExonTypes | 3.405 | 0.109 | 3.591 | |
transcriptChangeSummary | 2.010 | 0.077 | 2.113 | |
whippetTranscriptChangeSummary | 16.556 | 0.436 | 17.260 | |