BioC 3.4: CHECK report for psichomics on morelia

Package: psichomics

Version: 1.0.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.0.8.tar.gz

StartedAt: 2017-04-15 06:32:18 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 06:35:34 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 196.0 seconds

RetCode: 0

Status:  OK

CheckDir: psichomics.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.0.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/psichomics.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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	0.001	0.000	0.001
createJunctionsTemplate	0.003	0.000	0.003
diffAnalyses	0.099	0.010	0.144
downloadFiles	0	0	0
ensemblToUniprot	0.020	0.003	0.369
filterGroups	0.000	0.000	0.001
getDownloadsFolder	0	0	0
getFirehoseCohorts	0.089	0.002	0.363
getFirehoseDataTypes	0.001	0.000	0.001
getFirehoseDateFormat	0	0	0
getFirehoseDates	0.010	0.001	0.278
getMatchingSamples	0.002	0.000	0.001
getNumerics	0.004	0.001	0.004
getPatientFromSample	0.001	0.000	0.001
getSplicingEventTypes	0	0	0
getValidEvents	0.004	0.000	0.005
groupPerPatient	0.001	0.001	0.001
groupPerSample	0.001	0.000	0.001
hchart.survfit	0.230	0.062	0.527
isFirehoseUp	0.004	0.000	0.139
labelBasedOnCutoff	0.001	0.000	0.001
leveneTest	0.009	0.001	0.008
listAllAnnotations	0.000	0.000	0.001
listSplicingAnnotations	0.001	0.000	0.000
loadAnnotation	0	0	0
loadFirehoseData	0.000	0.000	0.001
loadLocalFiles	0.000	0.000	0.001
missingDataModal	0.001	0.000	0.000
optimalPSIcutoff	0.101	0.001	0.102
parseFirehoseMetadata	0.036	0.002	0.720
parseMatsEvent	0.005	0.000	0.006
parseMatsGeneric	0.024	0.001	0.025
parseMisoAnnotation	0.156	0.005	0.330
parseMisoEvent	0.005	0.000	0.005
parseMisoEventID	0.006	0.001	0.007
parseMisoGeneric	0.049	0.001	0.050
parseMisoId	0.001	0.000	0.001
parseSampleGroups	0.002	0.000	0.001
parseSplicingEvent	0.003	0.000	0.004
parseSuppaEvent	0.006	0.000	0.007
parseSuppaGeneric	0.032	0.001	0.033
parseUrlsFromFirehoseResponse	0.021	0.000	0.340
parseVastToolsEvent	0.006	0.000	0.006
parseVastToolsSE	0.035	0.001	0.036
performPCA	0.003	0.000	0.002
plotDistribution	0.400	0.019	0.420
plotPCA	0.215	0.043	0.258
plotProtein	0	0	0
plotSurvivalCurves	0.087	0.015	0.102
plotTranscripts	0.018	0.001	0.745
plotVariance	0.074	0.018	0.093
prepareAnnotationFromEvents	0.204	0.005	0.209
prepareFirehoseArchives	0.001	0.000	0.001
processSurvTerms	0.022	0.000	0.022
psichomics	0	0	0
quantifySplicing	0.016	0.000	0.017
queryEnsembl	0.033	0.002	0.913
queryEnsemblByEvent	0.064	0.003	1.195
queryEnsemblByGene	0.076	0.004	1.745
queryFirehoseData	0.022	0.002	0.613
queryPubMed	0.090	0.002	0.602
queryUniprot	0.506	0.002	0.936
readFile	0.001	0.000	0.001
renameDuplicated	0.001	0.000	0.001
survdiff.survTerms	0.007	0.000	0.007
survfit.survTerms	0.018	0.001	0.019
testSurvival	0.013	0.000	0.014
textSuggestions	0.001	0.000	0.001
trimWhitespace	0.000	0.001	0.000