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 13:19:59 -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 02:12:42 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:21:01 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 499.4 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) (2019-03-18 r76245)
* 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 35.270 0.749 36.091
whippetTranscriptChangeSummary 18.358 0.240 18.608
UTR2UTR53 4.969 0.510 5.482
alternativeIntronUsage 5.310 0.043 5.412
* 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 | 0.002 | 0.010 | |
| UTR2UTR53 | 4.969 | 0.510 | 5.482 | |
| addBroadTypes | 0.303 | 0.014 | 0.318 | |
| addIntronInTranscript | 4.161 | 0.169 | 4.355 | |
| alternativeIntronUsage | 5.310 | 0.043 | 5.412 | |
| annotateGeneModel | 1.224 | 0.019 | 1.243 | |
| attrChangeAltSpliced | 1.912 | 0.128 | 2.045 | |
| coordinates-methods | 0.134 | 0.111 | 0.253 | |
| diffSplicingResults-methods | 0.129 | 0.106 | 0.277 | |
| exonsToTranscripts | 0.352 | 0.010 | 0.364 | |
| filterGtfOverlap | 0.329 | 0.013 | 0.342 | |
| filterWhippetEvents | 0.140 | 0.108 | 0.293 | |
| findDEXexonType | 4.651 | 0.035 | 4.690 | |
| findExonContainingTranscripts | 0.690 | 0.108 | 0.822 | |
| findIntronContainingTranscripts | 0.879 | 0.112 | 1.008 | |
| findJunctionPairs | 1.854 | 0.117 | 2.004 | |
| formatWhippetEvents | 0.026 | 0.014 | 0.040 | |
| getOrfs | 1.161 | 0.016 | 1.217 | |
| getUOrfs | 0.745 | 0.018 | 0.764 | |
| junctions-methods | 0.121 | 0.104 | 0.235 | |
| leafcutterTranscriptChangeSummary | 35.270 | 0.749 | 36.091 | |
| makeGeneModel | 0.254 | 0.013 | 0.266 | |
| maxLocation | 0.007 | 0.001 | 0.007 | |
| orfDiff | 2.376 | 0.136 | 2.571 | |
| orfSimilarity | 0.001 | 0.000 | 0.001 | |
| overlapTypes | 4.384 | 0.021 | 4.404 | |
| readCounts-methods | 0.123 | 0.109 | 0.237 | |
| readWhippetDIFFfiles | 0.012 | 0.012 | 0.028 | |
| readWhippetDataSet | 0.130 | 0.109 | 0.245 | |
| readWhippetJNCfiles | 0.063 | 0.047 | 0.113 | |
| readWhippetPSIfiles | 0.044 | 0.050 | 0.096 | |
| removeDuplicateTranscripts | 0.379 | 0.014 | 0.392 | |
| removeSameExon | 0.305 | 0.012 | 0.317 | |
| removeVersion | 0.000 | 0.000 | 0.001 | |
| reorderExonNumbers | 0.319 | 0.012 | 0.330 | |
| replaceJunction | 4.273 | 0.191 | 4.470 | |
| skipExonInTranscript | 1.987 | 0.148 | 2.140 | |
| summariseExonTypes | 4.432 | 0.023 | 4.460 | |
| transcriptChangeSummary | 2.052 | 0.118 | 2.176 | |
| whippetTranscriptChangeSummary | 18.358 | 0.240 | 18.608 | |