Beth Signal
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: RELEASE_3_9 |
| Last Commit: 0263272 |
| Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:01:57 -0400 (Wed, 16 Oct 2019).
| Package 641/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.4.0 Beth Signal
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2019-10-16 03:06:28 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:14:54 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 505.9 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 38.855 0.747 39.924
whippetTranscriptChangeSummary 17.598 0.236 17.924
UTR2UTR53 5.750 0.255 6.009
alternativeIntronUsage 5.075 0.035 5.135
replaceJunction 4.861 0.138 5.004
* 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/3.6/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 | 0.006 | 0.001 | 0.007 | |
| UTR2UTR53 | 5.750 | 0.255 | 6.009 | |
| addBroadTypes | 0.183 | 0.010 | 0.193 | |
| addIntronInTranscript | 2.726 | 0.135 | 2.881 | |
| alternativeIntronUsage | 5.075 | 0.035 | 5.135 | |
| annotateGeneModel | 1.362 | 0.021 | 1.393 | |
| attrChangeAltSpliced | 1.956 | 0.126 | 2.091 | |
| coordinates-methods | 0.128 | 0.105 | 0.240 | |
| diffSplicingResults-methods | 0.126 | 0.107 | 0.262 | |
| exonsToTranscripts | 0.274 | 0.018 | 0.293 | |
| filterGtfOverlap | 0.391 | 0.018 | 0.408 | |
| filterWhippetEvents | 0.136 | 0.111 | 0.252 | |
| findDEXexonType | 4.503 | 0.036 | 4.544 | |
| findExonContainingTranscripts | 0.576 | 0.112 | 0.695 | |
| findIntronContainingTranscripts | 0.884 | 0.113 | 1.002 | |
| findJunctionPairs | 1.476 | 0.119 | 1.627 | |
| formatWhippetEvents | 0.025 | 0.012 | 0.040 | |
| getOrfs | 1.184 | 0.016 | 1.200 | |
| getUOrfs | 0.797 | 0.014 | 0.862 | |
| junctions-methods | 0.121 | 0.094 | 0.220 | |
| leafcutterTranscriptChangeSummary | 38.855 | 0.747 | 39.924 | |
| makeGeneModel | 0.259 | 0.015 | 0.274 | |
| maxLocation | 0.005 | 0.001 | 0.006 | |
| orfDiff | 2.558 | 0.135 | 2.700 | |
| orfSimilarity | 0.002 | 0.001 | 0.002 | |
| overlapTypes | 4.226 | 0.018 | 4.244 | |
| readCounts-methods | 0.121 | 0.100 | 0.228 | |
| readWhippetDIFFfiles | 0.013 | 0.011 | 0.026 | |
| readWhippetDataSet | 0.124 | 0.104 | 0.274 | |
| readWhippetJNCfiles | 0.060 | 0.042 | 0.105 | |
| readWhippetPSIfiles | 0.039 | 0.044 | 0.086 | |
| removeDuplicateTranscripts | 0.352 | 0.013 | 0.366 | |
| removeSameExon | 0.338 | 0.016 | 0.354 | |
| removeVersion | 0.000 | 0.001 | 0.001 | |
| reorderExonNumbers | 0.321 | 0.013 | 0.334 | |
| replaceJunction | 4.861 | 0.138 | 5.004 | |
| skipExonInTranscript | 2.677 | 0.149 | 2.833 | |
| summariseExonTypes | 4.560 | 0.256 | 4.816 | |
| transcriptChangeSummary | 2.174 | 0.137 | 2.314 | |
| whippetTranscriptChangeSummary | 17.598 | 0.236 | 17.924 | |