Package: GeneStructureTools

Version: 1.0.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GeneStructureTools_1.0.0.tar.gz

StartedAt: 2018-10-16 00:41:05 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:45:39 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 274.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneStructureTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GeneStructureTools_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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 21.584  0.192  21.851
whippetTranscriptChangeSummary    10.360  0.572  11.181
* 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-3.7-bioc/R/bin/R CMD INSTALL GeneStructureTools
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* installing to library ‘/home/biocbuild/bbs-3.7-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	0.008	0.000	0.005
UTR2UTR53	1.156	0.040	1.215
addBroadTypes	0.160	0.000	0.163
addIntronInTranscript	2.540	0.456	3.052
alternativeIntronUsage	2.976	0.016	2.993
annotateGeneModel	0.564	0.004	0.580
attrChangeAltSpliced	1.104	0.476	1.635
coordinates-methods	0.052	0.352	0.448
diffSplicingResults-methods	0.060	0.436	0.531
exonsToTranscripts	0.176	0.012	0.189
filterGtfOverlap	0.228	0.008	0.238
filterWhippetEvents	0.040	0.336	0.411
findDEXexonType	1.528	0.048	1.632
findExonContainingTranscripts	0.380	0.372	0.804
findIntronContainingTranscripts	0.620	0.352	1.010
findJunctionPairs	1.016	0.376	1.430
formatWhippetEvents	0.012	0.032	0.047
getOrfs	0.672	0.056	0.730
getUOrfs	0.528	0.004	0.533
junctions-methods	0.028	0.320	0.383
leafcutterTranscriptChangeSummary	21.584	0.192	21.851
makeGeneModel	0.124	0.008	0.131
maxLocation	0.004	0.000	0.003
orfDiff	2.264	0.516	2.837
orfSimilarity	0.000	0.000	0.001
overlapTypes	1.232	0.004	1.236
readCounts-methods	0.056	0.332	0.440
readWhippetDIFFfiles	0.004	0.040	0.053
readWhippetDataSet	0.068	0.348	0.464
readWhippetJNCfiles	0.028	0.168	0.226
readWhippetPSIfiles	0.012	0.148	0.183
removeDuplicateTranscripts	0.220	0.020	0.238
removeSameExon	0.208	0.000	0.209
removeVersion	0.004	0.000	0.001
reorderExonNumbers	0.168	0.000	0.168
replaceJunction	2.664	0.424	3.144
skipExonInTranscript	1.084	0.376	1.500
summariseExonTypes	1.252	0.008	1.259
transcriptChangeSummary	1.260	0.356	1.652
whippetTranscriptChangeSummary	10.360	0.572	11.181