Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 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" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | 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: 2024-06-05 23:20:43 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 23:29:12 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 509.1 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 22.058 0.372 22.430 whippetTranscriptChangeSummary 16.992 0.240 17.232 * 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 | 0.004 | 0.000 | 0.003 | |
UTR2UTR53 | 2.063 | 0.124 | 2.187 | |
addBroadTypes | 0.172 | 0.000 | 0.172 | |
addIntronInTranscript | 1.728 | 0.073 | 1.802 | |
alternativeIntronUsage | 4.008 | 0.056 | 4.064 | |
annotateGeneModel | 0.784 | 0.020 | 0.805 | |
attrChangeAltSpliced | 1.133 | 0.044 | 1.177 | |
coordinates-methods | 0.053 | 0.007 | 0.060 | |
diffSplicingResults-methods | 0.051 | 0.009 | 0.059 | |
exonsToTranscripts | 0.297 | 0.004 | 0.301 | |
filterGtfOverlap | 0.234 | 0.004 | 0.238 | |
filterWhippetEvents | 0.066 | 0.007 | 0.072 | |
findDEXexonType | 2.523 | 0.020 | 2.544 | |
findExonContainingTranscripts | 0.373 | 0.020 | 0.393 | |
findIntronContainingTranscripts | 0.602 | 0.034 | 0.635 | |
findJunctionPairs | 1.295 | 0.024 | 1.320 | |
formatWhippetEvents | 0.016 | 0.001 | 0.017 | |
getOrfs | 0.698 | 0.020 | 0.719 | |
getUOrfs | 0.533 | 0.024 | 0.558 | |
junctions-methods | 0.043 | 0.023 | 0.065 | |
leafcutterTranscriptChangeSummary | 22.058 | 0.372 | 22.430 | |
makeGeneModel | 0.135 | 0.016 | 0.151 | |
maxLocation | 0.002 | 0.000 | 0.003 | |
orfDiff | 1.428 | 0.034 | 1.462 | |
orfSimilarity | 0.001 | 0.000 | 0.001 | |
overlapTypes | 2.108 | 0.003 | 2.111 | |
readCounts-methods | 0.049 | 0.014 | 0.062 | |
readWhippetDIFFfiles | 0.006 | 0.000 | 0.006 | |
readWhippetDataSet | 0.052 | 0.009 | 0.061 | |
readWhippetJNCfiles | 0.030 | 0.002 | 0.031 | |
readWhippetPSIfiles | 0.015 | 0.000 | 0.016 | |
removeDuplicateTranscripts | 0.227 | 0.020 | 0.247 | |
removeSameExon | 0.202 | 0.000 | 0.203 | |
removeVersion | 0.000 | 0.000 | 0.001 | |
reorderExonNumbers | 0.155 | 0.012 | 0.168 | |
replaceJunction | 3.536 | 0.018 | 3.553 | |
skipExonInTranscript | 1.228 | 0.024 | 1.253 | |
summariseExonTypes | 2.262 | 0.003 | 2.263 | |
transcriptChangeSummary | 2.189 | 0.086 | 2.275 | |
whippetTranscriptChangeSummary | 16.992 | 0.240 | 17.232 | |