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 12:13:53 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneStructureTools_1.6.0.tar.gz |
| StartedAt: 2020-04-15 05:31:42 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:38:31 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 409.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneStructureTools_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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 29.644 0.324 30.067
whippetTranscriptChangeSummary 16.776 0.964 17.844
replaceJunction 5.052 0.696 5.828
* 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-3.10-bioc/R/bin/R CMD INSTALL GeneStructureTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 | 0.000 | 0.004 | 0.006 | |
| UTR2UTR53 | 4.532 | 0.120 | 4.804 | |
| addBroadTypes | 0.284 | 0.000 | 0.285 | |
| addIntronInTranscript | 3.216 | 0.812 | 4.169 | |
| alternativeIntronUsage | 4.620 | 0.016 | 4.642 | |
| annotateGeneModel | 0.732 | 0.004 | 0.737 | |
| attrChangeAltSpliced | 1.588 | 0.660 | 2.326 | |
| coordinates-methods | 0.052 | 0.696 | 0.829 | |
| diffSplicingResults-methods | 0.056 | 0.548 | 0.669 | |
| exonsToTranscripts | 0.216 | 0.024 | 0.244 | |
| filterGtfOverlap | 0.368 | 0.012 | 0.388 | |
| filterWhippetEvents | 0.068 | 0.520 | 0.651 | |
| findDEXexonType | 4.104 | 0.156 | 4.391 | |
| findExonContainingTranscripts | 0.452 | 0.604 | 1.128 | |
| findIntronContainingTranscripts | 0.888 | 0.696 | 1.639 | |
| findJunctionPairs | 1.612 | 0.684 | 2.389 | |
| formatWhippetEvents | 0.012 | 0.056 | 0.073 | |
| getOrfs | 0.800 | 0.040 | 0.839 | |
| getUOrfs | 0.784 | 0.052 | 0.837 | |
| junctions-methods | 0.052 | 0.724 | 0.833 | |
| leafcutterTranscriptChangeSummary | 29.644 | 0.324 | 30.067 | |
| makeGeneModel | 0.204 | 0.000 | 0.202 | |
| maxLocation | 0.004 | 0.000 | 0.005 | |
| orfDiff | 2.004 | 0.820 | 2.913 | |
| orfSimilarity | 0.000 | 0.000 | 0.001 | |
| overlapTypes | 3.676 | 0.108 | 3.791 | |
| readCounts-methods | 0.060 | 0.508 | 0.613 | |
| readWhippetDIFFfiles | 0.004 | 0.052 | 0.061 | |
| readWhippetDataSet | 0.064 | 0.508 | 0.663 | |
| readWhippetJNCfiles | 0.016 | 0.204 | 0.238 | |
| readWhippetPSIfiles | 0.012 | 0.192 | 0.229 | |
| removeDuplicateTranscripts | 0.312 | 0.012 | 0.326 | |
| removeSameExon | 0.184 | 0.020 | 0.203 | |
| removeVersion | 0.000 | 0.000 | 0.001 | |
| reorderExonNumbers | 0.180 | 0.012 | 0.191 | |
| replaceJunction | 5.052 | 0.696 | 5.828 | |
| skipExonInTranscript | 1.812 | 0.640 | 2.509 | |
| summariseExonTypes | 3.280 | 0.024 | 3.311 | |
| transcriptChangeSummary | 2.340 | 0.740 | 3.144 | |
| whippetTranscriptChangeSummary | 16.776 | 0.964 | 17.844 | |