BioC 3.5: CHECK report for psichomics on malbec2

Package: psichomics

Version: 1.2.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.2.1.tar.gz

StartedAt: 2017-08-16 01:27:43 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:30:49 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 185.8 seconds

RetCode: 0

Status:  OK

CheckDir: psichomics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.2.1’
* 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	0.000	0.004	0.002
createJunctionsTemplate	0.004	0.000	0.003
diffAnalyses	0.44	0.00	0.44
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.184	0.000	0.419
filterGroups	0.004	0.000	0.000
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseCohorts	0.300	0.000	0.349
getFirebrowseDataTypes	0.024	0.000	0.025
getFirebrowseDateFormat	0.004	0.000	0.000
getFirebrowseDates	0.020	0.000	0.052
getMatchingSamples	0.000	0.000	0.001
getNumerics	0.004	0.000	0.004
getPatientFromSample	0	0	0
getSplicingEventTypes	0	0	0
getValidEvents	0.004	0.000	0.004
groupPerPatient	0.004	0.000	0.001
groupPerSample	0.000	0.000	0.001
hchart.survfit	1.028	0.028	1.186
isFirebrowseUp	0.004	0.000	0.020
labelBasedOnCutoff	0.012	0.000	0.015
leveneTest	0.008	0.000	0.008
listAllAnnotations	0	0	0
listSplicingAnnotations	0.000	0.000	0.001
loadAnnotation	0.000	0.000	0.001
loadFirebrowseData	0.000	0.000	0.001
loadLocalFiles	0.000	0.000	0.001
missingDataModal	0	0	0
optimalPSIcutoff	0.196	0.000	0.199
parseFirebrowseMetadata	0.056	0.004	0.154
parseMatsEvent	0.008	0.000	0.006
parseMatsGeneric	0.024	0.000	0.023
parseMisoAnnotation	0.368	0.000	0.366
parseMisoEvent	0.004	0.000	0.004
parseMisoEventID	0.004	0.000	0.006
parseMisoGeneric	0.104	0.000	0.105
parseMisoId	0.000	0.000	0.001
parseSampleGroups	0.000	0.000	0.001
parseSplicingEvent	0.004	0.000	0.002
parseSuppaEvent	0.000	0.004	0.003
parseSuppaGeneric	0.020	0.000	0.019
parseUrlsFromFirebrowseResponse	0.032	0.000	0.106
parseVastToolsEvent	0.008	0.000	0.006
parseVastToolsSE	0.100	0.000	0.102
performPCA	0.004	0.000	0.003
plotDistribution	0.360	0.004	0.365
plotPCA	0.220	0.004	0.223
plotProtein	0	0	0
plotSurvivalCurves	0.088	0.000	0.086
plotTranscripts	0.024	0.000	0.652
plotVariance	0.052	0.004	0.060
prepareAnnotationFromEvents	0.348	0.000	0.347
prepareFirebrowseArchives	0.004	0.000	0.002
processSurvTerms	0.008	0.000	0.006
psichomics	0.000	0.000	0.001
quantifySplicing	0.028	0.000	0.030
queryEnsembl	0.052	0.000	0.684
queryEnsemblByEvent	0.056	0.000	1.139
queryEnsemblByGene	0.084	0.000	1.698
queryFirebrowseData	0.116	0.000	0.441
queryPubMed	0.160	0.016	0.542
queryUniprot	0.132	0.000	0.707
readFile	0.004	0.000	0.002
renameDuplicated	0.000	0.000	0.001
survdiff.survTerms	0.008	0.000	0.009
survfit.survTerms	0.036	0.004	0.038
testSurvival	0.028	0.000	0.026
textSuggestions	0.004	0.000	0.001
trimWhitespace	0.000	0.000	0.001