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: 2017-10-18 01:38:51 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:41:59 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 188.5 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 3.4.2 (2017-09-28)
* 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	0.004	0.000	0.002
createJunctionsTemplate	0.000	0.004	0.003
diffAnalyses	0.436	0.000	0.435
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.476	0.008	0.717
filterGroups	0	0	0
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseCohorts	0.192	0.000	0.250
getFirebrowseDataTypes	0.020	0.004	0.024
getFirebrowseDateFormat	0	0	0
getFirebrowseDates	0.020	0.000	0.058
getMatchingSamples	0.000	0.000	0.002
getNumerics	0.000	0.000	0.003
getPatientFromSample	0.000	0.000	0.001
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	0.840	0.032	1.021
isFirebrowseUp	0.004	0.000	0.024
labelBasedOnCutoff	0.016	0.000	0.016
leveneTest	0.012	0.000	0.009
listAllAnnotations	0.000	0.000	0.001
listSplicingAnnotations	0	0	0
loadAnnotation	0.000	0.000	0.001
loadFirebrowseData	0	0	0
loadLocalFiles	0.000	0.000	0.001
missingDataModal	0	0	0
optimalPSIcutoff	0.488	0.000	0.486
parseFirebrowseMetadata	0.060	0.000	0.172
parseMatsEvent	0.004	0.000	0.006
parseMatsGeneric	0.020	0.000	0.021
parseMisoAnnotation	0.432	0.012	0.444
parseMisoEvent	0.004	0.000	0.004
parseMisoEventID	0.004	0.000	0.006
parseMisoGeneric	0.100	0.000	0.098
parseMisoId	0.000	0.000	0.001
parseSampleGroups	0.004	0.000	0.001
parseSplicingEvent	0.000	0.000	0.002
parseSuppaEvent	0.004	0.000	0.003
parseSuppaGeneric	0.016	0.000	0.017
parseUrlsFromFirebrowseResponse	0.032	0.000	0.103
parseVastToolsEvent	0.008	0.000	0.006
parseVastToolsSE	0.124	0.004	0.128
performPCA	0.004	0.000	0.004
plotDistribution	0.404	0.004	0.408
plotPCA	0.212	0.016	0.240
plotProtein	0	0	0
plotSurvivalCurves	0.076	0.004	0.083
plotTranscripts	0.032	0.000	0.841
plotVariance	0.048	0.008	0.055
prepareAnnotationFromEvents	0.300	0.004	0.307
prepareFirebrowseArchives	0	0	0
processSurvTerms	0.004	0.000	0.003
psichomics	0	0	0
quantifySplicing	0.02	0.00	0.02
queryEnsembl	0.040	0.000	0.546
queryEnsemblByEvent	0.052	0.000	1.479
queryEnsemblByGene	0.088	0.000	1.551
queryFirebrowseData	0.088	0.004	0.233
queryPubMed	0.172	0.008	0.514
queryUniprot	0.144	0.004	1.865
readFile	0.000	0.000	0.002
renameDuplicated	0.000	0.000	0.002
survdiff.survTerms	0.012	0.000	0.009
survfit.survTerms	0.036	0.000	0.035
testSurvival	0.028	0.000	0.026
textSuggestions	0.000	0.000	0.001
trimWhitespace	0.000	0.000	0.001