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CHECK report for GeneStructureTools on malbec1

This page was generated on 2019-04-16 11:53:20 -0400 (Tue, 16 Apr 2019).

Package 610/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.2.1
Beth Signal
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GeneStructureTools
Branch: RELEASE_3_8
Last Commit: 2a83f22
Last Changed Date: 2019-01-04 13:34:13 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneStructureTools
Version: 1.2.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GeneStructureTools_1.2.1.tar.gz
StartedAt: 2019-04-16 00:10:05 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:15:56 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 351.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GeneStructureTools_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.1’
* 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 29.112  0.364  29.535
whippetTranscriptChangeSummary    14.272  0.708  15.112
replaceJunction                    4.160  0.744   5.335
* 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


Installation output

GeneStructureTools.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GeneStructureTools
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output


Example timings

GeneStructureTools.Rcheck/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds0.0040.0000.006
UTR2UTR531.7280.0441.820
addBroadTypes0.2360.0080.244
addIntronInTranscript3.3880.5844.080
alternativeIntronUsage3.1280.0083.156
annotateGeneModel0.5800.0000.582
attrChangeAltSpliced1.4760.4121.936
coordinates-methods0.0600.4280.609
diffSplicingResults-methods0.0480.3520.447
exonsToTranscripts0.3280.0200.347
filterGtfOverlap0.3520.0240.376
filterWhippetEvents0.0480.5280.633
findDEXexonType1.4960.0521.574
findExonContainingTranscripts0.4520.4921.032
findIntronContainingTranscripts0.5600.4921.098
findJunctionPairs1.2120.4841.736
formatWhippetEvents0.0200.0520.076
getOrfs1.0080.0401.050
getUOrfs0.7200.0080.731
junctions-methods0.0480.4040.495
leafcutterTranscriptChangeSummary29.112 0.36429.535
makeGeneModel0.1640.0040.168
maxLocation0.0080.0000.005
orfDiff1.6960.5842.415
orfSimilarity0.0000.0040.002
overlapTypes1.6280.0001.644
readCounts-methods0.1000.6360.903
readWhippetDIFFfiles0.0040.0720.112
readWhippetDataSet0.0640.5720.764
readWhippetJNCfiles0.0360.2240.315
readWhippetPSIfiles0.0120.2560.321
removeDuplicateTranscripts0.3400.0080.356
removeSameExon0.3000.0160.314
removeVersion0.0000.0000.001
reorderExonNumbers0.2400.0080.249
replaceJunction4.1600.7445.335
skipExonInTranscript1.6560.7442.545
summariseExonTypes1.9920.0322.051
transcriptChangeSummary1.5720.7482.511
whippetTranscriptChangeSummary14.272 0.70815.112