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

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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

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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)

name	user	system	elapsed
DEXSeqIdsToGeneIds	0.004	0.000	0.006
UTR2UTR53	1.728	0.044	1.820
addBroadTypes	0.236	0.008	0.244
addIntronInTranscript	3.388	0.584	4.080
alternativeIntronUsage	3.128	0.008	3.156
annotateGeneModel	0.580	0.000	0.582
attrChangeAltSpliced	1.476	0.412	1.936
coordinates-methods	0.060	0.428	0.609
diffSplicingResults-methods	0.048	0.352	0.447
exonsToTranscripts	0.328	0.020	0.347
filterGtfOverlap	0.352	0.024	0.376
filterWhippetEvents	0.048	0.528	0.633
findDEXexonType	1.496	0.052	1.574
findExonContainingTranscripts	0.452	0.492	1.032
findIntronContainingTranscripts	0.560	0.492	1.098
findJunctionPairs	1.212	0.484	1.736
formatWhippetEvents	0.020	0.052	0.076
getOrfs	1.008	0.040	1.050
getUOrfs	0.720	0.008	0.731
junctions-methods	0.048	0.404	0.495
leafcutterTranscriptChangeSummary	29.112	0.364	29.535
makeGeneModel	0.164	0.004	0.168
maxLocation	0.008	0.000	0.005
orfDiff	1.696	0.584	2.415
orfSimilarity	0.000	0.004	0.002
overlapTypes	1.628	0.000	1.644
readCounts-methods	0.100	0.636	0.903
readWhippetDIFFfiles	0.004	0.072	0.112
readWhippetDataSet	0.064	0.572	0.764
readWhippetJNCfiles	0.036	0.224	0.315
readWhippetPSIfiles	0.012	0.256	0.321
removeDuplicateTranscripts	0.340	0.008	0.356
removeSameExon	0.300	0.016	0.314
removeVersion	0.000	0.000	0.001
reorderExonNumbers	0.240	0.008	0.249
replaceJunction	4.160	0.744	5.335
skipExonInTranscript	1.656	0.744	2.545
summariseExonTypes	1.992	0.032	2.051
transcriptChangeSummary	1.572	0.748	2.511
whippetTranscriptChangeSummary	14.272	0.708	15.112