Beth Signal
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: RELEASE_3_10 |
| Last Commit: 94b91cf |
| Last Changed Date: 2019-10-29 13:11:00 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:46:56 -0400 (Wed, 15 Apr 2020).
| Package 666/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.6.0 Beth Signal
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GeneStructureTools |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2020-04-15 02:34:32 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:41:25 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 413.4 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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 31.099 0.370 31.953
whippetTranscriptChangeSummary 18.427 0.200 18.804
alternativeIntronUsage 5.709 0.021 5.898
UTR2UTR53 4.922 0.248 5.248
replaceJunction 5.060 0.065 5.170
* 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 | 0.008 | 0.001 | 0.008 | |
| UTR2UTR53 | 4.922 | 0.248 | 5.248 | |
| addBroadTypes | 0.296 | 0.010 | 0.306 | |
| addIntronInTranscript | 3.314 | 0.081 | 3.442 | |
| alternativeIntronUsage | 5.709 | 0.021 | 5.898 | |
| annotateGeneModel | 1.233 | 0.013 | 1.273 | |
| attrChangeAltSpliced | 1.925 | 0.062 | 2.049 | |
| coordinates-methods | 0.084 | 0.045 | 0.131 | |
| diffSplicingResults-methods | 0.074 | 0.043 | 0.119 | |
| exonsToTranscripts | 0.313 | 0.012 | 0.326 | |
| filterGtfOverlap | 0.319 | 0.008 | 0.329 | |
| filterWhippetEvents | 0.100 | 0.048 | 0.152 | |
| findDEXexonType | 3.652 | 0.053 | 3.743 | |
| findExonContainingTranscripts | 0.578 | 0.067 | 0.652 | |
| findIntronContainingTranscripts | 0.932 | 0.089 | 1.044 | |
| findJunctionPairs | 1.954 | 0.060 | 2.046 | |
| formatWhippetEvents | 0.023 | 0.006 | 0.029 | |
| getOrfs | 0.964 | 0.012 | 0.992 | |
| getUOrfs | 0.826 | 0.007 | 0.845 | |
| junctions-methods | 0.088 | 0.047 | 0.138 | |
| leafcutterTranscriptChangeSummary | 31.099 | 0.370 | 31.953 | |
| makeGeneModel | 0.218 | 0.007 | 0.227 | |
| maxLocation | 0.005 | 0.000 | 0.005 | |
| orfDiff | 2.163 | 0.115 | 2.294 | |
| orfSimilarity | 0.001 | 0.000 | 0.001 | |
| overlapTypes | 3.841 | 0.018 | 3.877 | |
| readCounts-methods | 0.085 | 0.047 | 0.133 | |
| readWhippetDIFFfiles | 0.008 | 0.006 | 0.014 | |
| readWhippetDataSet | 0.085 | 0.051 | 0.140 | |
| readWhippetJNCfiles | 0.050 | 0.022 | 0.075 | |
| readWhippetPSIfiles | 0.027 | 0.023 | 0.060 | |
| removeDuplicateTranscripts | 0.383 | 0.008 | 0.397 | |
| removeSameExon | 0.318 | 0.007 | 0.332 | |
| removeVersion | 0 | 0 | 0 | |
| reorderExonNumbers | 0.248 | 0.005 | 0.255 | |
| replaceJunction | 5.060 | 0.065 | 5.170 | |
| skipExonInTranscript | 1.922 | 0.048 | 1.999 | |
| summariseExonTypes | 3.464 | 0.012 | 3.516 | |
| transcriptChangeSummary | 2.106 | 0.083 | 2.210 | |
| whippetTranscriptChangeSummary | 18.427 | 0.200 | 18.804 | |