BioC 3.4: CHECK report for psichomics on malbec1

Package: psichomics

Version: 1.0.8

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.0.8.tar.gz

StartedAt: 2017-04-15 00:34:05 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:36:56 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 170.3 seconds

RetCode: 0

Status:  OK

CheckDir: psichomics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.0.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/psichomics.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.8’
* 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	0.000	0.001
createJunctionsTemplate	0.000	0.000	0.003
diffAnalyses	0.076	0.008	0.084
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.064	0.004	0.290
filterGroups	0	0	0
getDownloadsFolder	0.004	0.000	0.001
getFirehoseCohorts	0.064	0.000	0.130
getFirehoseDataTypes	0.000	0.000	0.001
getFirehoseDateFormat	0	0	0
getFirehoseDates	0.016	0.004	0.078
getMatchingSamples	0.000	0.000	0.001
getNumerics	0.004	0.000	0.003
getPatientFromSample	0	0	0
getSplicingEventTypes	0	0	0
getValidEvents	0.004	0.000	0.004
groupPerPatient	0.000	0.000	0.001
groupPerSample	0.000	0.000	0.001
hchart.survfit	0.220	0.020	0.335
isFirehoseUp	0.004	0.000	0.034
labelBasedOnCutoff	0.000	0.000	0.002
leveneTest	0.012	0.000	0.010
listAllAnnotations	0	0	0
listSplicingAnnotations	0	0	0
loadAnnotation	0.000	0.000	0.001
loadFirehoseData	0.000	0.000	0.001
loadLocalFiles	0	0	0
missingDataModal	0	0	0
optimalPSIcutoff	0.104	0.000	0.106
parseFirehoseMetadata	0.072	0.004	0.430
parseMatsEvent	0.004	0.000	0.005
parseMatsGeneric	0.020	0.000	0.022
parseMisoAnnotation	0.144	0.004	0.147
parseMisoEvent	0.004	0.000	0.004
parseMisoEventID	0.004	0.000	0.007
parseMisoGeneric	0.040	0.000	0.038
parseMisoId	0	0	0
parseSampleGroups	0.000	0.000	0.001
parseSplicingEvent	0.004	0.000	0.002
parseSuppaEvent	0.004	0.000	0.005
parseSuppaGeneric	0.024	0.000	0.022
parseUrlsFromFirehoseResponse	0.028	0.000	0.145
parseVastToolsEvent	0.004	0.000	0.006
parseVastToolsSE	0.020	0.000	0.021
performPCA	0.004	0.000	0.003
plotDistribution	0.360	0.004	0.364
plotPCA	0.172	0.016	0.187
plotProtein	0	0	0
plotSurvivalCurves	0.080	0.004	0.082
plotTranscripts	0.028	0.000	0.562
plotVariance	0.056	0.004	0.063
prepareAnnotationFromEvents	0.172	0.004	0.179
prepareFirehoseArchives	0.000	0.000	0.001
processSurvTerms	0.000	0.000	0.003
psichomics	0.000	0.000	0.001
quantifySplicing	0.012	0.000	0.012
queryEnsembl	0.040	0.004	0.622
queryEnsemblByEvent	0.072	0.008	1.087
queryEnsemblByGene	0.08	0.00	1.45
queryFirehoseData	0.044	0.004	0.191
queryPubMed	0.172	0.016	0.465
queryUniprot	0.176	0.000	0.441
readFile	0.000	0.000	0.001
renameDuplicated	0	0	0
survdiff.survTerms	0.008	0.000	0.006
survfit.survTerms	0.024	0.000	0.025
testSurvival	0.02	0.00	0.02
textSuggestions	0.000	0.000	0.001
trimWhitespace	0.000	0.000	0.001