Package: GeneStructureTools

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneStructureTools_1.2.1.tar.gz

StartedAt: 2019-04-16 00:10:14 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:16:47 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 392.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneStructureTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneStructureTools_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 32.457  0.377  33.598
whippetTranscriptChangeSummary    17.727  0.244  18.387
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneStructureTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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	0.006	0.000	0.007
UTR2UTR53	1.687	0.090	1.809
addBroadTypes	0.239	0.008	0.253
addIntronInTranscript	3.134	0.076	3.290
alternativeIntronUsage	4.400	0.031	4.547
annotateGeneModel	0.994	0.011	1.019
attrChangeAltSpliced	1.596	0.062	1.739
coordinates-methods	0.091	0.050	0.144
diffSplicingResults-methods	0.099	0.052	0.155
exonsToTranscripts	0.258	0.007	0.265
filterGtfOverlap	0.344	0.008	0.353
filterWhippetEvents	0.098	0.048	0.150
findDEXexonType	1.883	0.014	1.927
findExonContainingTranscripts	0.470	0.062	0.545
findIntronContainingTranscripts	0.750	0.060	0.829
findJunctionPairs	1.279	0.064	1.363
formatWhippetEvents	0.022	0.006	0.029
getOrfs	1.074	0.012	1.097
getUOrfs	0.741	0.009	0.768
junctions-methods	0.088	0.047	0.138
leafcutterTranscriptChangeSummary	32.457	0.377	33.598
makeGeneModel	0.224	0.006	0.238
maxLocation	0.003	0.000	0.003
orfDiff	1.909	0.069	2.037
orfSimilarity	0.001	0.000	0.001
overlapTypes	1.652	0.009	1.703
readCounts-methods	0.092	0.047	0.146
readWhippetDIFFfiles	0.009	0.005	0.015
readWhippetDataSet	0.090	0.049	0.142
readWhippetJNCfiles	0.050	0.022	0.073
readWhippetPSIfiles	0.026	0.022	0.049
removeDuplicateTranscripts	0.289	0.006	0.302
removeSameExon	0.283	0.006	0.294
removeVersion	0.001	0.000	0.001
reorderExonNumbers	0.198	0.005	0.204
replaceJunction	4.221	0.066	4.380
skipExonInTranscript	1.524	0.063	1.602
summariseExonTypes	2.263	0.025	2.334
transcriptChangeSummary	2.037	0.106	2.209
whippetTranscriptChangeSummary	17.727	0.244	18.387