Beth Signal
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: master |
| Last Commit: b717a48 |
| Last Changed Date: 2019-10-29 13:42:49 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:50:33 -0500 (Thu, 16 Jan 2020).
| Package 665/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.7.0 Beth Signal
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GeneStructureTools |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneStructureTools_1.7.0.tar.gz |
| StartedAt: 2020-01-16 04:47:16 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 04:57:36 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 619.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneStructureTools_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneStructureTools.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.7.0’
* 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 50.184 1.070 51.323
whippetTranscriptChangeSummary 24.493 0.235 24.772
alternativeIntronUsage 8.616 0.216 9.044
replaceJunction 8.492 0.154 8.684
UTR2UTR53 5.919 0.601 6.528
findDEXexonType 5.700 0.035 5.737
overlapTypes 5.297 0.026 5.328
summariseExonTypes 5.095 0.022 5.118
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 | 0.009 | 0.002 | 0.011 | |
| UTR2UTR53 | 5.919 | 0.601 | 6.528 | |
| addBroadTypes | 0.315 | 0.011 | 0.326 | |
| addIntronInTranscript | 4.008 | 0.145 | 4.356 | |
| alternativeIntronUsage | 8.616 | 0.216 | 9.044 | |
| annotateGeneModel | 1.651 | 0.022 | 1.681 | |
| attrChangeAltSpliced | 2.489 | 0.124 | 2.627 | |
| coordinates-methods | 0.145 | 0.100 | 0.366 | |
| diffSplicingResults-methods | 0.147 | 0.106 | 0.257 | |
| exonsToTranscripts | 0.414 | 0.019 | 0.433 | |
| filterGtfOverlap | 0.440 | 0.015 | 0.455 | |
| filterWhippetEvents | 0.150 | 0.096 | 0.251 | |
| findDEXexonType | 5.700 | 0.035 | 5.737 | |
| findExonContainingTranscripts | 0.857 | 0.122 | 0.988 | |
| findIntronContainingTranscripts | 1.159 | 0.121 | 1.287 | |
| findJunctionPairs | 2.742 | 0.122 | 2.870 | |
| formatWhippetEvents | 0.032 | 0.012 | 0.046 | |
| getOrfs | 1.489 | 0.079 | 1.568 | |
| getUOrfs | 1.041 | 0.022 | 1.063 | |
| junctions-methods | 0.148 | 0.105 | 0.261 | |
| leafcutterTranscriptChangeSummary | 50.184 | 1.070 | 51.323 | |
| makeGeneModel | 0.259 | 0.009 | 0.269 | |
| maxLocation | 0.007 | 0.001 | 0.007 | |
| orfDiff | 3.275 | 0.147 | 3.432 | |
| orfSimilarity | 0.002 | 0.001 | 0.002 | |
| overlapTypes | 5.297 | 0.026 | 5.328 | |
| readCounts-methods | 0.140 | 0.111 | 0.278 | |
| readWhippetDIFFfiles | 0.013 | 0.011 | 0.025 | |
| readWhippetDataSet | 0.15 | 0.11 | 0.27 | |
| readWhippetJNCfiles | 0.074 | 0.048 | 0.128 | |
| readWhippetPSIfiles | 0.043 | 0.049 | 0.095 | |
| removeDuplicateTranscripts | 0.466 | 0.019 | 0.485 | |
| removeSameExon | 0.390 | 0.012 | 0.402 | |
| removeVersion | 0.001 | 0.000 | 0.001 | |
| reorderExonNumbers | 0.341 | 0.019 | 0.360 | |
| replaceJunction | 8.492 | 0.154 | 8.684 | |
| skipExonInTranscript | 3.179 | 0.123 | 3.307 | |
| summariseExonTypes | 5.095 | 0.022 | 5.118 | |
| transcriptChangeSummary | 2.656 | 0.137 | 2.834 | |
| whippetTranscriptChangeSummary | 24.493 | 0.235 | 24.772 | |