Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-22 11:35:41 -0400 (Wed, 22 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" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
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 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 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: 1.24.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GeneStructureTools_1.24.0.tar.gz |
StartedAt: 2024-05-22 02:13:14 -0400 (Wed, 22 May 2024) |
EndedAt: 2024-05-22 02:20:48 -0400 (Wed, 22 May 2024) |
EllapsedTime: 454.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GeneStructureTools_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GeneStructureTools.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GeneStructureTools/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GeneStructureTools' version '1.24.0' * 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 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 24.80 1.78 26.70 whippetTranscriptChangeSummary 15.61 0.44 17.31 UTR2UTR53 3.56 0.11 8.14 * 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: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 | 0 | 0 | |
UTR2UTR53 | 3.56 | 0.11 | 8.14 | |
addBroadTypes | 0.27 | 0.00 | 0.26 | |
addIntronInTranscript | 1.80 | 0.08 | 2.97 | |
alternativeIntronUsage | 3.76 | 0.03 | 3.80 | |
annotateGeneModel | 0.91 | 0.00 | 0.95 | |
attrChangeAltSpliced | 1.23 | 0.06 | 2.42 | |
coordinates-methods | 0.07 | 0.04 | 1.16 | |
diffSplicingResults-methods | 0.06 | 0.08 | 1.14 | |
exonsToTranscripts | 0.37 | 0.02 | 0.39 | |
filterGtfOverlap | 0.35 | 0.00 | 0.34 | |
filterWhippetEvents | 0.04 | 0.03 | 1.23 | |
findDEXexonType | 2.83 | 0.04 | 2.93 | |
findExonContainingTranscripts | 0.50 | 0.02 | 1.68 | |
findIntronContainingTranscripts | 0.85 | 0.01 | 2.05 | |
findJunctionPairs | 1.47 | 0.05 | 2.72 | |
formatWhippetEvents | 0.02 | 0.00 | 0.14 | |
getOrfs | 0.90 | 0.03 | 0.93 | |
getUOrfs | 0.71 | 0.00 | 0.71 | |
junctions-methods | 0.04 | 0.03 | 1.24 | |
leafcutterTranscriptChangeSummary | 24.80 | 1.78 | 26.70 | |
makeGeneModel | 0.26 | 0.00 | 0.27 | |
maxLocation | 0 | 0 | 0 | |
orfDiff | 1.75 | 0.09 | 3.19 | |
orfSimilarity | 0 | 0 | 0 | |
overlapTypes | 2.31 | 0.00 | 2.31 | |
readCounts-methods | 0.05 | 0.05 | 1.30 | |
readWhippetDIFFfiles | 0.00 | 0.00 | 0.12 | |
readWhippetDataSet | 0.08 | 0.02 | 1.07 | |
readWhippetJNCfiles | 0.03 | 0.03 | 0.57 | |
readWhippetPSIfiles | 0.0 | 0.0 | 0.5 | |
removeDuplicateTranscripts | 0.36 | 0.02 | 0.37 | |
removeSameExon | 0.31 | 0.02 | 0.33 | |
removeVersion | 0 | 0 | 0 | |
reorderExonNumbers | 0.28 | 0.00 | 0.28 | |
replaceJunction | 3.64 | 0.08 | 4.87 | |
skipExonInTranscript | 1.48 | 0.01 | 2.69 | |
summariseExonTypes | 2.74 | 0.00 | 2.73 | |
transcriptChangeSummary | 1.97 | 0.13 | 3.38 | |
whippetTranscriptChangeSummary | 15.61 | 0.44 | 17.31 | |