Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:58 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 817/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.24.0 (landing page) Beth Signal
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.24.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeneStructureTools_1.24.0.tar.gz |
StartedAt: 2024-05-31 04:00:49 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 04:09:01 -0400 (Fri, 31 May 2024) |
EllapsedTime: 492.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeneStructureTools_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeneStructureTools.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.24.0’ * 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 21.231 0.340 21.572 whippetTranscriptChangeSummary 10.970 0.175 11.145 replaceJunction 5.282 0.047 5.330 * 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-3.19-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘GeneStructureTools’ ... ** 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 | 0.004 | |
UTR2UTR53 | 2.059 | 0.144 | 2.204 | |
addBroadTypes | 0.169 | 0.007 | 0.176 | |
addIntronInTranscript | 1.696 | 0.065 | 1.761 | |
alternativeIntronUsage | 3.783 | 0.072 | 3.856 | |
annotateGeneModel | 0.761 | 0.020 | 0.781 | |
attrChangeAltSpliced | 1.092 | 0.020 | 1.113 | |
coordinates-methods | 0.055 | 0.004 | 0.059 | |
diffSplicingResults-methods | 0.058 | 0.005 | 0.063 | |
exonsToTranscripts | 0.260 | 0.024 | 0.285 | |
filterGtfOverlap | 0.225 | 0.000 | 0.225 | |
filterWhippetEvents | 0.066 | 0.001 | 0.066 | |
findDEXexonType | 2.276 | 0.016 | 2.291 | |
findExonContainingTranscripts | 0.379 | 0.010 | 0.389 | |
findIntronContainingTranscripts | 0.577 | 0.010 | 0.586 | |
findJunctionPairs | 1.157 | 0.050 | 1.206 | |
formatWhippetEvents | 0.009 | 0.005 | 0.015 | |
getOrfs | 0.636 | 0.028 | 0.664 | |
getUOrfs | 0.507 | 0.016 | 0.523 | |
junctions-methods | 0.057 | 0.004 | 0.061 | |
leafcutterTranscriptChangeSummary | 21.231 | 0.340 | 21.572 | |
makeGeneModel | 0.134 | 0.004 | 0.138 | |
maxLocation | 0.003 | 0.000 | 0.003 | |
orfDiff | 1.324 | 0.024 | 1.348 | |
orfSimilarity | 0.000 | 0.000 | 0.001 | |
overlapTypes | 2.013 | 0.024 | 2.038 | |
readCounts-methods | 0.056 | 0.013 | 0.067 | |
readWhippetDIFFfiles | 0.005 | 0.002 | 0.007 | |
readWhippetDataSet | 0.060 | 0.006 | 0.066 | |
readWhippetJNCfiles | 0.031 | 0.003 | 0.035 | |
readWhippetPSIfiles | 0.017 | 0.003 | 0.019 | |
removeDuplicateTranscripts | 0.362 | 0.008 | 0.371 | |
removeSameExon | 0.373 | 0.012 | 0.385 | |
removeVersion | 0.001 | 0.000 | 0.000 | |
reorderExonNumbers | 0.255 | 0.003 | 0.259 | |
replaceJunction | 5.282 | 0.047 | 5.330 | |
skipExonInTranscript | 1.409 | 0.049 | 1.458 | |
summariseExonTypes | 2.883 | 0.032 | 2.914 | |
transcriptChangeSummary | 2.161 | 0.092 | 2.252 | |
whippetTranscriptChangeSummary | 10.970 | 0.175 | 11.145 | |