Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 791/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.25.0 (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 12.7.4 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: 1.25.0 |
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_1.25.0.tar.gz |
StartedAt: 2024-06-10 20:25:09 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 20:33:02 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 472.3 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_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneStructureTools.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.25.0’ * 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 24.787 0.750 25.882 whippetTranscriptChangeSummary 13.050 0.293 13.660 * 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 | 0.005 | 0.001 | 0.005 | |
UTR2UTR53 | 2.573 | 0.084 | 2.771 | |
addBroadTypes | 0.266 | 0.008 | 0.290 | |
addIntronInTranscript | 2.102 | 0.130 | 2.270 | |
alternativeIntronUsage | 4.540 | 0.029 | 4.697 | |
annotateGeneModel | 0.951 | 0.015 | 0.970 | |
attrChangeAltSpliced | 1.366 | 0.132 | 1.537 | |
coordinates-methods | 0.080 | 0.078 | 0.179 | |
diffSplicingResults-methods | 0.081 | 0.080 | 0.182 | |
exonsToTranscripts | 0.383 | 0.009 | 0.393 | |
filterGtfOverlap | 0.151 | 0.006 | 0.160 | |
filterWhippetEvents | 0.053 | 0.056 | 0.128 | |
findDEXexonType | 2.263 | 0.020 | 2.301 | |
findExonContainingTranscripts | 0.515 | 0.107 | 0.654 | |
findIntronContainingTranscripts | 0.754 | 0.103 | 0.891 | |
findJunctionPairs | 1.473 | 0.111 | 1.614 | |
formatWhippetEvents | 0.017 | 0.013 | 0.033 | |
getOrfs | 0.753 | 0.017 | 0.772 | |
getUOrfs | 0.637 | 0.015 | 0.653 | |
junctions-methods | 0.085 | 0.099 | 0.212 | |
leafcutterTranscriptChangeSummary | 24.787 | 0.750 | 25.882 | |
makeGeneModel | 0.173 | 0.006 | 0.183 | |
maxLocation | 0.001 | 0.000 | 0.002 | |
orfDiff | 1.463 | 0.081 | 1.609 | |
orfSimilarity | 0.001 | 0.001 | 0.001 | |
overlapTypes | 2.406 | 0.018 | 2.458 | |
readCounts-methods | 0.088 | 0.106 | 0.244 | |
readWhippetDIFFfiles | 0.008 | 0.012 | 0.025 | |
readWhippetDataSet | 0.083 | 0.106 | 0.236 | |
readWhippetJNCfiles | 0.042 | 0.045 | 0.102 | |
readWhippetPSIfiles | 0.024 | 0.042 | 0.087 | |
removeDuplicateTranscripts | 0.333 | 0.007 | 0.345 | |
removeSameExon | 0.277 | 0.006 | 0.287 | |
removeVersion | 0.001 | 0.000 | 0.001 | |
reorderExonNumbers | 0.228 | 0.007 | 0.239 | |
replaceJunction | 4.119 | 0.128 | 4.322 | |
skipExonInTranscript | 0.999 | 0.070 | 1.114 | |
summariseExonTypes | 2.556 | 0.018 | 2.611 | |
transcriptChangeSummary | 1.712 | 0.133 | 1.922 | |
whippetTranscriptChangeSummary | 13.050 | 0.293 | 13.660 | |