BioC 3.5: CHECK report for psichomics on veracruz2

Package: psichomics

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.2.1.tar.gz

StartedAt: 2017-08-16 06:48:57 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:52:18 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 201.6 seconds

RetCode: 0

Status:  OK

CheckDir: psichomics.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/psichomics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ 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 ‘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	0.002	0.000	0.002
createJunctionsTemplate	0.003	0.000	0.004
diffAnalyses	0.422	0.019	0.445
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.130	0.001	0.373
filterGroups	0.001	0.000	0.000
getDownloadsFolder	0	0	0
getFirebrowseCohorts	0.233	0.002	0.351
getFirebrowseDataTypes	0.018	0.000	0.018
getFirebrowseDateFormat	0.001	0.000	0.001
getFirebrowseDates	0.009	0.001	0.085
getMatchingSamples	0.001	0.000	0.002
getNumerics	0.004	0.000	0.003
getPatientFromSample	0.001	0.000	0.001
getSplicingEventTypes	0.000	0.000	0.001
getValidEvents	0.004	0.000	0.004
groupPerPatient	0.000	0.000	0.001
groupPerSample	0.001	0.000	0.001
hchart.survfit	0.864	0.050	0.964
isFirebrowseUp	0.004	0.000	0.043
labelBasedOnCutoff	0.016	0.003	0.018
leveneTest	0.013	0.002	0.017
listAllAnnotations	0.001	0.000	0.001
listSplicingAnnotations	0	0	0
loadAnnotation	0.001	0.000	0.001
loadFirebrowseData	0.001	0.000	0.000
loadLocalFiles	0.000	0.000	0.001
missingDataModal	0.001	0.000	0.001
optimalPSIcutoff	0.191	0.010	0.206
parseFirebrowseMetadata	0.028	0.002	0.235
parseMatsEvent	0.005	0.000	0.006
parseMatsGeneric	0.029	0.001	0.030
parseMisoAnnotation	0.332	0.006	0.338
parseMisoEvent	0.005	0.000	0.005
parseMisoEventID	0.006	0.000	0.007
parseMisoGeneric	0.098	0.001	0.100
parseMisoId	0.001	0.001	0.001
parseSampleGroups	0.001	0.000	0.001
parseSplicingEvent	0.002	0.000	0.002
parseSuppaEvent	0.003	0.000	0.003
parseSuppaGeneric	0.018	0.000	0.019
parseUrlsFromFirebrowseResponse	0.012	0.000	0.130
parseVastToolsEvent	0.005	0.000	0.005
parseVastToolsSE	0.082	0.001	0.083
performPCA	0.002	0.000	0.003
plotDistribution	0.334	0.012	0.355
plotPCA	0.183	0.029	0.219
plotProtein	0.001	0.000	0.000
plotSurvivalCurves	0.071	0.012	0.083
plotTranscripts	0.013	0.001	0.742
plotVariance	0.045	0.012	0.058
prepareAnnotationFromEvents	0.260	0.003	0.263
prepareFirebrowseArchives	0.000	0.000	0.001
processSurvTerms	0.003	0.000	0.003
psichomics	0	0	0
quantifySplicing	0.019	0.000	0.019
queryEnsembl	0.023	0.001	0.691
queryEnsemblByEvent	0.047	0.003	1.172
queryEnsemblByGene	0.067	0.004	1.614
queryFirebrowseData	0.052	0.001	0.315
queryPubMed	0.061	0.002	0.319
queryUniprot	0.469	0.003	1.226
readFile	0.001	0.001	0.001
renameDuplicated	0.001	0.000	0.001
survdiff.survTerms	0.007	0.000	0.008
survfit.survTerms	0.025	0.000	0.025
testSurvival	0.023	0.001	0.023
textSuggestions	0.001	0.000	0.000
trimWhitespace	0.000	0.000	0.001