BioC 3.6: CHECK report for psichomics on malbec1

Package: psichomics

Version: 1.3.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.3.1.tar.gz

StartedAt: 2017-08-16 01:34:07 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:37:10 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 183.3 seconds

RetCode: 0

Status:  OK

CheckDir: psichomics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.3.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.3.1’
* 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 ‘psichomics’ 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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

* installing *source* package ‘psichomics’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (psichomics)

name	user	system	elapsed
createGroupByAttribute	0.004	0.000	0.002
createJunctionsTemplate	0.004	0.000	0.003
diffAnalyses	0.436	0.008	0.442
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.160	0.000	0.374
filterGroups	0.000	0.000	0.001
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseCohorts	0.288	0.000	0.337
getFirebrowseDataTypes	0.020	0.000	0.019
getFirebrowseDateFormat	0	0	0
getFirebrowseDates	0.016	0.000	0.051
getMatchingSamples	0.004	0.000	0.001
getNumerics	0.004	0.000	0.004
getPatientFromSample	0	0	0
getSplicingEventTypes	0.000	0.000	0.001
getValidEvents	0.004	0.000	0.005
groupPerPatient	0	0	0
groupPerSample	0.000	0.000	0.001
hchart.survfit	1.228	0.028	1.410
isFirebrowseUp	0.004	0.000	0.022
labelBasedOnCutoff	0.016	0.000	0.016
leveneTest	0.008	0.000	0.008
listAllAnnotations	0.004	0.000	0.002
listSplicingAnnotations	0	0	0
loadAnnotation	0	0	0
loadFirebrowseData	0	0	0
loadLocalFiles	0.000	0.000	0.001
missingDataModal	0	0	0
optimalPSIcutoff	0.2	0.0	0.2
parseFirebrowseMetadata	0.064	0.004	0.171
parseMatsEvent	0.004	0.000	0.006
parseMatsGeneric	0.020	0.000	0.019
parseMisoAnnotation	0.420	0.000	0.422
parseMisoEvent	0.004	0.000	0.005
parseMisoEventID	0.004	0.000	0.005
parseMisoGeneric	0.096	0.000	0.098
parseMisoId	0.000	0.000	0.001
parseSampleGroups	0.000	0.000	0.001
parseSplicingEvent	0.004	0.000	0.002
parseSuppaEvent	0.004	0.000	0.004
parseSuppaGeneric	0.016	0.000	0.017
parseUrlsFromFirebrowseResponse	0.028	0.000	0.307
parseVastToolsEvent	0.008	0.000	0.006
parseVastToolsSE	0.108	0.000	0.107
performPCA	0.004	0.000	0.003
plotDistribution	0.356	0.012	0.370
plotPCA	0.212	0.008	0.217
plotProtein	0.000	0.000	0.001
plotSurvivalCurves	0.084	0.000	0.084
plotTranscripts	0.024	0.000	0.716
plotVariance	0.052	0.004	0.053
prepareAnnotationFromEvents	0.312	0.000	0.314
prepareFirebrowseArchives	0.000	0.000	0.001
processSurvTerms	0.004	0.000	0.003
psichomics	0	0	0
quantifySplicing	0.024	0.000	0.021
queryEnsembl	0.036	0.000	0.656
queryEnsemblByEvent	0.072	0.004	1.184
queryEnsemblByGene	0.112	0.000	1.679
queryFirebrowseData	0.120	0.000	0.245
queryPubMed	0.120	0.008	0.477
queryUniprot	0.100	0.000	0.741
readFile	0.000	0.000	0.001
renameDuplicated	0.004	0.000	0.000
survdiff.survTerms	0.008	0.000	0.007
survfit.survTerms	0.028	0.000	0.028
testSurvival	0.024	0.000	0.023
textSuggestions	0.000	0.000	0.001
trimWhitespace	0.000	0.000	0.001