Beth Signal
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: master |
| Last Commit: 74bed05 |
| Last Changed Date: 2019-01-04 13:34:09 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:36:37 -0400 (Tue, 09 Apr 2019).
| Package 632/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.3.1 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: GeneStructureTools |
| Version: 1.3.1 |
| 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_1.3.1.tar.gz |
| StartedAt: 2019-04-09 01:06:11 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:12:43 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 392.4 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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneStructureTools.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.1’
* 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 28.522 0.350 29.250
whippetTranscriptChangeSummary 15.593 0.143 15.898
* 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’ ... ** 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 * DONE (GeneStructureTools)
GeneStructureTools.Rcheck/GeneStructureTools-Ex.timings
| name | user | system | elapsed | |
| DEXSeqIdsToGeneIds | 0.005 | 0.000 | 0.006 | |
| UTR2UTR53 | 3.771 | 0.279 | 4.085 | |
| addBroadTypes | 1.152 | 0.014 | 1.179 | |
| addIntronInTranscript | 2.220 | 0.077 | 2.350 | |
| alternativeIntronUsage | 4.242 | 0.013 | 4.294 | |
| annotateGeneModel | 0.931 | 0.009 | 0.952 | |
| attrChangeAltSpliced | 1.553 | 0.066 | 1.628 | |
| coordinates-methods | 0.115 | 0.061 | 0.179 | |
| diffSplicingResults-methods | 0.114 | 0.061 | 0.182 | |
| exonsToTranscripts | 0.287 | 0.009 | 0.296 | |
| filterGtfOverlap | 0.246 | 0.007 | 0.253 | |
| filterWhippetEvents | 0.090 | 0.046 | 0.182 | |
| findDEXexonType | 3.421 | 0.024 | 3.497 | |
| findExonContainingTranscripts | 0.552 | 0.072 | 0.628 | |
| findIntronContainingTranscripts | 0.679 | 0.078 | 0.768 | |
| findJunctionPairs | 1.497 | 0.067 | 1.577 | |
| formatWhippetEvents | 0.022 | 0.007 | 0.030 | |
| getOrfs | 1.053 | 0.036 | 1.099 | |
| getUOrfs | 0.744 | 0.008 | 0.764 | |
| junctions-methods | 0.099 | 0.052 | 0.154 | |
| leafcutterTranscriptChangeSummary | 28.522 | 0.350 | 29.250 | |
| makeGeneModel | 0.177 | 0.004 | 0.181 | |
| maxLocation | 0.005 | 0.000 | 0.006 | |
| orfDiff | 1.672 | 0.071 | 1.770 | |
| orfSimilarity | 0.001 | 0.000 | 0.001 | |
| overlapTypes | 3.481 | 0.016 | 3.546 | |
| readCounts-methods | 0.095 | 0.047 | 0.146 | |
| readWhippetDIFFfiles | 0.009 | 0.006 | 0.015 | |
| readWhippetDataSet | 0.094 | 0.052 | 0.150 | |
| readWhippetJNCfiles | 0.047 | 0.026 | 0.074 | |
| readWhippetPSIfiles | 0.032 | 0.023 | 0.057 | |
| removeDuplicateTranscripts | 0.328 | 0.007 | 0.339 | |
| removeSameExon | 0.260 | 0.007 | 0.268 | |
| removeVersion | 0.000 | 0.001 | 0.001 | |
| reorderExonNumbers | 0.264 | 0.006 | 0.271 | |
| replaceJunction | 3.781 | 0.130 | 3.957 | |
| skipExonInTranscript | 1.509 | 0.056 | 1.585 | |
| summariseExonTypes | 3.611 | 0.013 | 3.680 | |
| transcriptChangeSummary | 1.821 | 0.071 | 1.918 | |
| whippetTranscriptChangeSummary | 15.593 | 0.143 | 15.898 | |