Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:42 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the GeneStructureTools package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 701/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneStructureTools 1.10.0 (landing page) Beth Signal
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GeneStructureTools |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneStructureTools_1.10.0.tar.gz |
StartedAt: 2021-05-06 01:51:36 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:59:34 -0400 (Thu, 06 May 2021) |
EllapsedTime: 477.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneStructureTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneStructureTools_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/GeneStructureTools.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneStructureTools’ version ‘1.10.0’ * 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 R 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 30.800 0.196 31.135 whippetTranscriptChangeSummary 18.164 0.768 19.595 replaceJunction 5.904 0.736 6.698 alternativeIntronUsage 5.920 0.004 5.957 UTR2UTR53 4.844 0.204 5.078 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-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 | 0.004 | 0.000 | 0.004 | |
UTR2UTR53 | 4.844 | 0.204 | 5.078 | |
addBroadTypes | 0.268 | 0.000 | 0.270 | |
addIntronInTranscript | 3.232 | 0.812 | 4.219 | |
alternativeIntronUsage | 5.920 | 0.004 | 5.957 | |
annotateGeneModel | 1.204 | 0.000 | 1.218 | |
attrChangeAltSpliced | 2.100 | 0.744 | 2.908 | |
coordinates-methods | 0.060 | 0.732 | 0.833 | |
diffSplicingResults-methods | 0.072 | 0.664 | 0.799 | |
exonsToTranscripts | 0.372 | 0.008 | 0.378 | |
filterGtfOverlap | 0.388 | 0.008 | 0.396 | |
filterWhippetEvents | 0.084 | 0.668 | 0.804 | |
findDEXexonType | 3.920 | 0.104 | 4.052 | |
findExonContainingTranscripts | 0.716 | 0.756 | 1.523 | |
findIntronContainingTranscripts | 1.116 | 0.760 | 1.930 | |
findJunctionPairs | 1.932 | 0.704 | 2.691 | |
formatWhippetEvents | 0.016 | 0.048 | 0.071 | |
getOrfs | 0.968 | 0.040 | 1.016 | |
getUOrfs | 0.824 | 0.048 | 0.876 | |
junctions-methods | 0.052 | 0.548 | 0.649 | |
leafcutterTranscriptChangeSummary | 30.800 | 0.196 | 31.135 | |
makeGeneModel | 0.148 | 0.004 | 0.154 | |
maxLocation | 0.000 | 0.000 | 0.003 | |
orfDiff | 3.680 | 0.868 | 4.631 | |
orfSimilarity | 0.000 | 0.000 | 0.002 | |
overlapTypes | 3.108 | 0.000 | 3.115 | |
readCounts-methods | 0.076 | 0.616 | 0.727 | |
readWhippetDIFFfiles | 0.008 | 0.072 | 0.083 | |
readWhippetDataSet | 0.060 | 0.692 | 0.795 | |
readWhippetJNCfiles | 0.032 | 0.312 | 0.371 | |
readWhippetPSIfiles | 0.004 | 0.260 | 0.286 | |
removeDuplicateTranscripts | 0.224 | 0.028 | 0.252 | |
removeSameExon | 0.208 | 0.004 | 0.211 | |
removeVersion | 0.000 | 0.000 | 0.001 | |
reorderExonNumbers | 0.176 | 0.008 | 0.183 | |
replaceJunction | 5.904 | 0.736 | 6.698 | |
skipExonInTranscript | 1.976 | 0.772 | 2.823 | |
summariseExonTypes | 3.408 | 0.012 | 3.424 | |
transcriptChangeSummary | 2.272 | 0.848 | 3.182 | |
whippetTranscriptChangeSummary | 18.164 | 0.768 | 19.595 | |