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 12:05 -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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneStructureTools_1.26.0.tar.gz |
StartedAt: 2024-12-20 01:52:00 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:00:11 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 491.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneStructureTools_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeneStructureTools.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * 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 '1.26.0' * 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 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 33.44 2.00 35.48 whippetTranscriptChangeSummary 16.39 0.25 17.58 alternativeIntronUsage 5.91 0.11 6.01 replaceJunction 4.87 0.08 5.95 * 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-3.20-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 | 0.01 | 0.00 | 0.01 | |
UTR2UTR53 | 3.99 | 0.15 | 4.21 | |
addBroadTypes | 0.43 | 0.00 | 0.42 | |
addIntronInTranscript | 2.57 | 0.07 | 3.79 | |
alternativeIntronUsage | 5.91 | 0.11 | 6.01 | |
annotateGeneModel | 1.09 | 0.03 | 1.13 | |
attrChangeAltSpliced | 1.55 | 0.00 | 2.59 | |
coordinates-methods | 0.09 | 0.04 | 1.14 | |
diffSplicingResults-methods | 0.07 | 0.06 | 1.14 | |
exonsToTranscripts | 0.5 | 0.0 | 0.5 | |
filterGtfOverlap | 0.34 | 0.05 | 0.39 | |
filterWhippetEvents | 0.05 | 0.02 | 1.03 | |
findDEXexonType | 3.68 | 0.04 | 3.76 | |
findExonContainingTranscripts | 0.54 | 0.02 | 1.54 | |
findIntronContainingTranscripts | 0.81 | 0.08 | 1.85 | |
findJunctionPairs | 1.92 | 0.04 | 3.04 | |
formatWhippetEvents | 0.02 | 0.00 | 0.19 | |
getOrfs | 1.11 | 0.01 | 1.14 | |
getUOrfs | 0.93 | 0.05 | 0.98 | |
junctions-methods | 0.08 | 0.04 | 1.14 | |
leafcutterTranscriptChangeSummary | 33.44 | 2.00 | 35.48 | |
makeGeneModel | 0.44 | 0.00 | 0.44 | |
maxLocation | 0 | 0 | 0 | |
orfDiff | 2.37 | 0.05 | 3.46 | |
orfSimilarity | 0 | 0 | 0 | |
overlapTypes | 2.59 | 0.02 | 2.60 | |
readCounts-methods | 0.03 | 0.04 | 1.13 | |
readWhippetDIFFfiles | 0.02 | 0.00 | 0.10 | |
readWhippetDataSet | 0.03 | 0.05 | 1.07 | |
readWhippetJNCfiles | 0.03 | 0.06 | 0.53 | |
readWhippetPSIfiles | 0.02 | 0.00 | 0.40 | |
removeDuplicateTranscripts | 0.39 | 0.00 | 0.40 | |
removeSameExon | 0.51 | 0.02 | 0.53 | |
removeVersion | 0 | 0 | 0 | |
reorderExonNumbers | 0.44 | 0.03 | 0.47 | |
replaceJunction | 4.87 | 0.08 | 5.95 | |
skipExonInTranscript | 1.80 | 0.03 | 2.76 | |
summariseExonTypes | 2.92 | 0.06 | 2.99 | |
transcriptChangeSummary | 1.83 | 0.11 | 2.90 | |
whippetTranscriptChangeSummary | 16.39 | 0.25 | 17.58 | |