Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 801/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.27.0 (landing page) Beth Signal
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.27.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeneStructureTools_1.27.0.tar.gz |
StartedAt: 2024-12-23 22:18:06 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:26:10 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 484.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeneStructureTools_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeneStructureTools.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.27.0’ * 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 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 21.019 0.328 21.348 whippetTranscriptChangeSummary 11.382 0.219 11.600 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * 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-3.21-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 | 2.127 | 0.119 | 2.247 | |
addBroadTypes | 0.160 | 0.005 | 0.165 | |
addIntronInTranscript | 1.701 | 0.054 | 1.757 | |
alternativeIntronUsage | 3.931 | 0.036 | 3.968 | |
annotateGeneModel | 0.821 | 0.036 | 0.857 | |
attrChangeAltSpliced | 1.183 | 0.049 | 1.231 | |
coordinates-methods | 0.052 | 0.026 | 0.077 | |
diffSplicingResults-methods | 0.051 | 0.020 | 0.071 | |
exonsToTranscripts | 0.327 | 0.013 | 0.340 | |
filterGtfOverlap | 0.243 | 0.016 | 0.259 | |
filterWhippetEvents | 0.055 | 0.022 | 0.076 | |
findDEXexonType | 3.506 | 0.160 | 3.667 | |
findExonContainingTranscripts | 0.371 | 0.028 | 0.400 | |
findIntronContainingTranscripts | 0.571 | 0.027 | 0.598 | |
findJunctionPairs | 1.211 | 0.021 | 1.232 | |
formatWhippetEvents | 0.011 | 0.002 | 0.014 | |
getOrfs | 0.637 | 0.014 | 0.652 | |
getUOrfs | 0.554 | 0.013 | 0.567 | |
junctions-methods | 0.043 | 0.020 | 0.062 | |
leafcutterTranscriptChangeSummary | 21.019 | 0.328 | 21.348 | |
makeGeneModel | 0.144 | 0.006 | 0.149 | |
maxLocation | 0.003 | 0.001 | 0.003 | |
orfDiff | 1.421 | 0.070 | 1.490 | |
orfSimilarity | 0 | 0 | 0 | |
overlapTypes | 2.095 | 0.005 | 2.100 | |
readCounts-methods | 0.043 | 0.025 | 0.067 | |
readWhippetDIFFfiles | 0.003 | 0.003 | 0.006 | |
readWhippetDataSet | 0.043 | 0.023 | 0.065 | |
readWhippetJNCfiles | 0.023 | 0.008 | 0.031 | |
readWhippetPSIfiles | 0.008 | 0.008 | 0.018 | |
removeDuplicateTranscripts | 0.241 | 0.002 | 0.243 | |
removeSameExon | 0.193 | 0.007 | 0.200 | |
removeVersion | 0.001 | 0.000 | 0.001 | |
reorderExonNumbers | 0.153 | 0.006 | 0.159 | |
replaceJunction | 3.622 | 0.039 | 3.661 | |
skipExonInTranscript | 1.307 | 0.048 | 1.357 | |
summariseExonTypes | 2.211 | 0.013 | 2.225 | |
transcriptChangeSummary | 1.319 | 0.083 | 1.401 | |
whippetTranscriptChangeSummary | 11.382 | 0.219 | 11.600 | |