Package: GeneStructureTools

Version: 1.4.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneStructureTools_1.4.0.tar.gz

StartedAt: 2019-10-16 01:52:32 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:58:58 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 386.2 seconds

RetCode: 0

Status:  OK

CheckDir: GeneStructureTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GeneStructureTools_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GeneStructureTools.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 27.709  0.241  27.950
whippetTranscriptChangeSummary    13.020  0.563  13.586
* 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-3.9-bioc/R/bin/R CMD INSTALL GeneStructureTools
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* installing to library ‘/home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
DEXSeqIdsToGeneIds	0.006	0.000	0.006
UTR2UTR53	4.310	0.165	4.788
addBroadTypes	0.241	0.008	0.249
addIntronInTranscript	1.938	0.733	2.961
alternativeIntronUsage	3.942	0.029	3.987
annotateGeneModel	0.956	0.000	0.963
attrChangeAltSpliced	1.333	0.687	2.675
coordinates-methods	0.054	0.640	0.854
diffSplicingResults-methods	0.063	0.588	0.719
exonsToTranscripts	0.302	0.012	0.318
filterGtfOverlap	0.333	0.005	0.338
filterWhippetEvents	0.064	0.679	0.860
findDEXexonType	3.519	0.069	3.687
findExonContainingTranscripts	0.452	0.629	1.331
findIntronContainingTranscripts	0.735	0.567	1.420
findJunctionPairs	1.254	0.738	2.328
formatWhippetEvents	0.010	0.071	0.103
getOrfs	0.904	0.040	0.951
getUOrfs	0.700	0.020	0.737
junctions-methods	0.056	0.606	0.750
leafcutterTranscriptChangeSummary	27.709	0.241	27.950
makeGeneModel	0.136	0.000	0.136
maxLocation	0.003	0.000	0.003
orfDiff	2.017	0.709	2.733
orfSimilarity	0.002	0.000	0.002
overlapTypes	3.734	0.036	3.773
readCounts-methods	0.080	0.547	0.629
readWhippetDIFFfiles	0.002	0.068	0.071
readWhippetDataSet	0.073	0.571	0.645
readWhippetJNCfiles	0.032	0.290	0.365
readWhippetPSIfiles	0.018	0.290	0.366
removeDuplicateTranscripts	0.362	0.012	0.376
removeSameExon	0.294	0.013	0.306
removeVersion	0.000	0.000	0.001
reorderExonNumbers	0.291	0.023	0.316
replaceJunction	2.689	0.757	3.445
skipExonInTranscript	2.090	0.819	2.923
summariseExonTypes	2.187	0.009	2.196
transcriptChangeSummary	1.865	0.537	2.403
whippetTranscriptChangeSummary	13.020	0.563	13.586