Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 807/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.26.0 (landing page) Beth Signal
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 | |||||||||
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: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneStructureTools_1.26.0.tar.gz |
StartedAt: 2024-12-20 20:21:13 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 20:28:37 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 443.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneStructureTools_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneStructureTools.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.26.0’ * 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 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 23.385 0.772 24.233 whippetTranscriptChangeSummary 11.523 0.224 11.792 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 | 0.005 | |
UTR2UTR53 | 2.310 | 0.096 | 2.406 | |
addBroadTypes | 0.234 | 0.007 | 0.242 | |
addIntronInTranscript | 1.971 | 0.096 | 2.096 | |
alternativeIntronUsage | 4.148 | 0.022 | 4.177 | |
annotateGeneModel | 0.874 | 0.013 | 0.889 | |
attrChangeAltSpliced | 1.254 | 0.111 | 1.396 | |
coordinates-methods | 0.075 | 0.083 | 0.185 | |
diffSplicingResults-methods | 0.075 | 0.083 | 0.182 | |
exonsToTranscripts | 0.304 | 0.006 | 0.312 | |
filterGtfOverlap | 0.358 | 0.009 | 0.368 | |
filterWhippetEvents | 0.086 | 0.096 | 0.214 | |
findDEXexonType | 2.451 | 0.017 | 2.473 | |
findExonContainingTranscripts | 0.475 | 0.085 | 0.581 | |
findIntronContainingTranscripts | 0.673 | 0.093 | 0.789 | |
findJunctionPairs | 1.367 | 0.092 | 1.485 | |
formatWhippetEvents | 0.018 | 0.011 | 0.031 | |
getOrfs | 0.723 | 0.017 | 0.741 | |
getUOrfs | 0.598 | 0.014 | 0.612 | |
junctions-methods | 0.059 | 0.068 | 0.144 | |
leafcutterTranscriptChangeSummary | 23.385 | 0.772 | 24.233 | |
makeGeneModel | 0.212 | 0.006 | 0.220 | |
maxLocation | 0.002 | 0.000 | 0.003 | |
orfDiff | 1.567 | 0.115 | 1.708 | |
orfSimilarity | 0.001 | 0.001 | 0.001 | |
overlapTypes | 2.201 | 0.015 | 2.219 | |
readCounts-methods | 0.073 | 0.085 | 0.185 | |
readWhippetDIFFfiles | 0.006 | 0.011 | 0.020 | |
readWhippetDataSet | 0.070 | 0.076 | 0.167 | |
readWhippetJNCfiles | 0.036 | 0.034 | 0.081 | |
readWhippetPSIfiles | 0.024 | 0.043 | 0.078 | |
removeDuplicateTranscripts | 0.321 | 0.009 | 0.331 | |
removeSameExon | 0.264 | 0.010 | 0.275 | |
removeVersion | 0.000 | 0.000 | 0.001 | |
reorderExonNumbers | 0.189 | 0.007 | 0.197 | |
replaceJunction | 3.793 | 0.108 | 3.928 | |
skipExonInTranscript | 1.472 | 0.101 | 1.598 | |
summariseExonTypes | 2.389 | 0.014 | 2.404 | |
transcriptChangeSummary | 1.572 | 0.106 | 1.704 | |
whippetTranscriptChangeSummary | 11.523 | 0.224 | 11.792 | |