Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:35:59 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 807/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.22.0 (landing page) Beth Signal
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.22.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GeneStructureTools_1.22.0.tar.gz |
StartedAt: 2024-03-27 22:45:10 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 22:53:17 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 487.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GeneStructureTools_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GeneStructureTools.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘1.22.0’ * 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 R 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 22.358 0.264 22.622 whippetTranscriptChangeSummary 11.492 0.062 11.555 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Vignette.Rmd’ using ‘UTF-8’... OK NONE * 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-3.18-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 | 0.003 | |
UTR2UTR53 | 3.459 | 0.184 | 3.643 | |
addBroadTypes | 0.181 | 0.000 | 0.180 | |
addIntronInTranscript | 1.763 | 0.052 | 1.816 | |
alternativeIntronUsage | 4.063 | 0.064 | 4.127 | |
annotateGeneModel | 0.852 | 0.004 | 0.855 | |
attrChangeAltSpliced | 1.280 | 0.011 | 1.290 | |
coordinates-methods | 0.058 | 0.008 | 0.067 | |
diffSplicingResults-methods | 0.058 | 0.005 | 0.063 | |
exonsToTranscripts | 0.268 | 0.000 | 0.267 | |
filterGtfOverlap | 0.255 | 0.000 | 0.255 | |
filterWhippetEvents | 0.068 | 0.003 | 0.071 | |
findDEXexonType | 2.405 | 0.052 | 2.458 | |
findExonContainingTranscripts | 0.416 | 0.009 | 0.425 | |
findIntronContainingTranscripts | 0.654 | 0.035 | 0.688 | |
findJunctionPairs | 1.295 | 0.027 | 1.322 | |
formatWhippetEvents | 0.012 | 0.007 | 0.019 | |
getOrfs | 0.679 | 0.020 | 0.697 | |
getUOrfs | 0.553 | 0.012 | 0.565 | |
junctions-methods | 0.061 | 0.005 | 0.067 | |
leafcutterTranscriptChangeSummary | 22.358 | 0.264 | 22.622 | |
makeGeneModel | 0.156 | 0.004 | 0.160 | |
maxLocation | 0.003 | 0.000 | 0.003 | |
orfDiff | 1.440 | 0.016 | 1.457 | |
orfSimilarity | 0.001 | 0.000 | 0.001 | |
overlapTypes | 2.178 | 0.024 | 2.203 | |
readCounts-methods | 0.058 | 0.006 | 0.063 | |
readWhippetDIFFfiles | 0.003 | 0.002 | 0.006 | |
readWhippetDataSet | 0.056 | 0.007 | 0.063 | |
readWhippetJNCfiles | 0.028 | 0.000 | 0.028 | |
readWhippetPSIfiles | 0.015 | 0.000 | 0.015 | |
removeDuplicateTranscripts | 0.254 | 0.004 | 0.259 | |
removeSameExon | 0.221 | 0.004 | 0.226 | |
removeVersion | 0.000 | 0.000 | 0.001 | |
reorderExonNumbers | 0.165 | 0.012 | 0.177 | |
replaceJunction | 3.793 | 0.034 | 3.828 | |
skipExonInTranscript | 1.367 | 0.006 | 1.372 | |
summariseExonTypes | 2.366 | 0.052 | 2.418 | |
transcriptChangeSummary | 1.380 | 0.009 | 1.390 | |
whippetTranscriptChangeSummary | 11.492 | 0.062 | 11.555 | |