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 11:50:09 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneStructureTools_1.3.1.tar.gz |
| StartedAt: 2019-04-09 00:44:23 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:51:08 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 404.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneStructureTools_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GeneStructureTools.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 28.204 0.237 28.564
whippetTranscriptChangeSummary 15.882 0.825 16.827
* 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: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 | 0.000 | 0.006 | |
| UTR2UTR53 | 3.411 | 0.159 | 3.614 | |
| addBroadTypes | 0.239 | 0.004 | 0.242 | |
| addIntronInTranscript | 3.161 | 0.886 | 4.507 | |
| alternativeIntronUsage | 3.603 | 0.000 | 3.777 | |
| annotateGeneModel | 0.618 | 0.005 | 0.623 | |
| attrChangeAltSpliced | 0.960 | 0.566 | 1.528 | |
| coordinates-methods | 0.041 | 0.602 | 0.690 | |
| diffSplicingResults-methods | 0.063 | 0.616 | 0.693 | |
| exonsToTranscripts | 0.289 | 0.024 | 0.315 | |
| filterGtfOverlap | 0.316 | 0.012 | 0.329 | |
| filterWhippetEvents | 0.073 | 0.623 | 0.803 | |
| findDEXexonType | 3.555 | 0.129 | 3.710 | |
| findExonContainingTranscripts | 0.526 | 0.681 | 1.437 | |
| findIntronContainingTranscripts | 0.669 | 0.672 | 1.670 | |
| findJunctionPairs | 1.403 | 0.701 | 2.177 | |
| formatWhippetEvents | 0.006 | 0.081 | 0.097 | |
| getOrfs | 0.896 | 0.044 | 0.946 | |
| getUOrfs | 0.714 | 0.036 | 0.859 | |
| junctions-methods | 0.034 | 0.654 | 1.425 | |
| leafcutterTranscriptChangeSummary | 28.204 | 0.237 | 28.564 | |
| makeGeneModel | 0.209 | 0.004 | 0.213 | |
| maxLocation | 0.004 | 0.000 | 0.004 | |
| orfDiff | 1.931 | 0.736 | 2.710 | |
| orfSimilarity | 0.001 | 0.000 | 0.001 | |
| overlapTypes | 3.716 | 0.021 | 3.738 | |
| readCounts-methods | 0.057 | 0.652 | 0.712 | |
| readWhippetDIFFfiles | 0.005 | 0.069 | 0.073 | |
| readWhippetDataSet | 0.055 | 0.699 | 0.763 | |
| readWhippetJNCfiles | 0.032 | 0.327 | 0.360 | |
| readWhippetPSIfiles | 0.023 | 0.273 | 0.300 | |
| removeDuplicateTranscripts | 0.345 | 0.008 | 0.353 | |
| removeSameExon | 0.300 | 0.008 | 0.308 | |
| removeVersion | 0.001 | 0.000 | 0.000 | |
| reorderExonNumbers | 0.279 | 0.028 | 0.314 | |
| replaceJunction | 4.129 | 0.744 | 4.874 | |
| skipExonInTranscript | 1.627 | 0.767 | 2.395 | |
| summariseExonTypes | 3.802 | 0.033 | 3.843 | |
| transcriptChangeSummary | 1.989 | 0.758 | 2.773 | |
| whippetTranscriptChangeSummary | 15.882 | 0.825 | 16.827 | |