Beth Signal
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: RELEASE_3_7 |
| Last Commit: 291ec3a |
| Last Changed Date: 2018-04-30 10:35:49 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:59:40 -0400 (Wed, 17 Oct 2018).
| Package 579/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.0.0 Beth Signal
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GeneStructureTools |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2018-10-16 21:36:47 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:42:54 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 367.3 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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 29.958 0.338 30.554
whippetTranscriptChangeSummary 16.737 0.165 17.055
alternativeIntronUsage 5.178 0.068 5.286
* 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/3.5/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 | 0.008 | 0.001 | 0.009 | |
| UTR2UTR53 | 1.787 | 0.182 | 2.003 | |
| addBroadTypes | 0.257 | 0.009 | 0.267 | |
| addIntronInTranscript | 2.407 | 0.095 | 2.535 | |
| alternativeIntronUsage | 5.178 | 0.068 | 5.286 | |
| annotateGeneModel | 0.896 | 0.038 | 0.941 | |
| attrChangeAltSpliced | 1.741 | 0.071 | 1.820 | |
| coordinates-methods | 0.110 | 0.059 | 0.172 | |
| diffSplicingResults-methods | 0.112 | 0.055 | 0.170 | |
| exonsToTranscripts | 0.334 | 0.008 | 0.342 | |
| filterGtfOverlap | 0.358 | 0.006 | 0.366 | |
| filterWhippetEvents | 0.124 | 0.058 | 0.186 | |
| findDEXexonType | 1.881 | 0.014 | 1.914 | |
| findExonContainingTranscripts | 0.596 | 0.068 | 0.671 | |
| findIntronContainingTranscripts | 0.859 | 0.065 | 0.929 | |
| findJunctionPairs | 1.693 | 0.063 | 1.765 | |
| formatWhippetEvents | 0.023 | 0.007 | 0.030 | |
| getOrfs | 1.060 | 0.010 | 1.085 | |
| getUOrfs | 0.792 | 0.009 | 0.806 | |
| junctions-methods | 0.118 | 0.066 | 0.187 | |
| leafcutterTranscriptChangeSummary | 29.958 | 0.338 | 30.554 | |
| makeGeneModel | 0.205 | 0.004 | 0.210 | |
| maxLocation | 0.007 | 0.001 | 0.008 | |
| orfDiff | 1.984 | 0.082 | 2.093 | |
| orfSimilarity | 0.003 | 0.000 | 0.002 | |
| overlapTypes | 1.628 | 0.008 | 1.643 | |
| readCounts-methods | 0.106 | 0.060 | 0.172 | |
| readWhippetDIFFfiles | 0.013 | 0.007 | 0.020 | |
| readWhippetDataSet | 0.098 | 0.054 | 0.155 | |
| readWhippetJNCfiles | 0.051 | 0.023 | 0.076 | |
| readWhippetPSIfiles | 0.035 | 0.024 | 0.061 | |
| removeDuplicateTranscripts | 0.318 | 0.008 | 0.329 | |
| removeSameExon | 0.264 | 0.005 | 0.271 | |
| removeVersion | 0.001 | 0.000 | 0.001 | |
| reorderExonNumbers | 0.270 | 0.008 | 0.280 | |
| replaceJunction | 3.883 | 0.073 | 4.008 | |
| skipExonInTranscript | 1.744 | 0.062 | 1.824 | |
| summariseExonTypes | 1.927 | 0.013 | 1.959 | |
| transcriptChangeSummary | 1.812 | 0.066 | 1.894 | |
| whippetTranscriptChangeSummary | 16.737 | 0.165 | 17.055 | |