Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-25 11:42 -0400 (Thu, 25 Sep 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" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
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. - 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: 2025-09-23 10:06:32 -0000 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 10:15:16 -0000 (Tue, 23 Sep 2025) |
EllapsedTime: 523.5 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 32.550 0.260 32.900 whippetTranscriptChangeSummary 17.430 0.124 17.600 replaceJunction 6.853 0.143 7.015 alternativeIntronUsage 5.774 0.072 5.876 * 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 | 0.004 | 0.000 | 0.004 | |
UTR2UTR53 | 3.103 | 0.160 | 3.277 | |
addBroadTypes | 0.229 | 0.012 | 0.241 | |
addIntronInTranscript | 3.600 | 0.105 | 3.731 | |
alternativeIntronUsage | 5.774 | 0.072 | 5.876 | |
annotateGeneModel | 1.140 | 0.012 | 1.155 | |
attrChangeAltSpliced | 1.577 | 0.045 | 1.624 | |
coordinates-methods | 0.077 | 0.021 | 0.096 | |
diffSplicingResults-methods | 0.077 | 0.020 | 0.097 | |
exonsToTranscripts | 0.363 | 0.004 | 0.368 | |
filterGtfOverlap | 0.314 | 0.016 | 0.330 | |
filterWhippetEvents | 0.097 | 0.008 | 0.104 | |
findDEXexonType | 3.363 | 0.028 | 3.402 | |
findExonContainingTranscripts | 0.571 | 0.018 | 0.590 | |
findIntronContainingTranscripts | 0.894 | 0.028 | 0.926 | |
findJunctionPairs | 1.897 | 0.026 | 1.928 | |
formatWhippetEvents | 0.016 | 0.007 | 0.021 | |
getOrfs | 0.962 | 0.024 | 0.988 | |
getUOrfs | 0.735 | 0.007 | 0.744 | |
junctions-methods | 0.075 | 0.023 | 0.098 | |
leafcutterTranscriptChangeSummary | 32.55 | 0.26 | 32.90 | |
makeGeneModel | 0.200 | 0.004 | 0.205 | |
maxLocation | 0.004 | 0.000 | 0.004 | |
orfDiff | 2.139 | 0.051 | 2.196 | |
orfSimilarity | 0.001 | 0.000 | 0.001 | |
overlapTypes | 3.289 | 0.024 | 3.321 | |
readCounts-methods | 0.067 | 0.033 | 0.100 | |
readWhippetDIFFfiles | 0.004 | 0.005 | 0.009 | |
readWhippetDataSet | 0.073 | 0.025 | 0.096 | |
readWhippetJNCfiles | 0.040 | 0.005 | 0.046 | |
readWhippetPSIfiles | 0.017 | 0.011 | 0.027 | |
removeDuplicateTranscripts | 0.350 | 0.000 | 0.351 | |
removeSameExon | 0.286 | 0.008 | 0.295 | |
removeVersion | 0.001 | 0.000 | 0.001 | |
reorderExonNumbers | 0.224 | 0.008 | 0.232 | |
replaceJunction | 6.853 | 0.143 | 7.015 | |
skipExonInTranscript | 1.959 | 0.062 | 2.024 | |
summariseExonTypes | 3.559 | 0.008 | 3.576 | |
transcriptChangeSummary | 2.118 | 0.073 | 2.198 | |
whippetTranscriptChangeSummary | 17.430 | 0.124 | 17.600 | |