BioC 3.6: CHECK report for psichomics on veracruz1

Package: psichomics

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.3.1.tar.gz

StartedAt: 2017-08-16 07:05:05 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:08:19 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 193.3 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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.3.1’
* 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	0.001	0.003
diffAnalyses	0.413	0.013	0.429
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.147	0.001	0.405
filterGroups	0.000	0.000	0.001
getDownloadsFolder	0.001	0.000	0.001
getFirebrowseCohorts	0.116	0.001	0.233
getFirebrowseDataTypes	0.016	0.000	0.019
getFirebrowseDateFormat	0.001	0.000	0.001
getFirebrowseDates	0.009	0.001	0.086
getMatchingSamples	0.002	0.000	0.002
getNumerics	0.004	0.000	0.004
getPatientFromSample	0.001	0.001	0.001
getSplicingEventTypes	0.001	0.000	0.001
getValidEvents	0.004	0.000	0.004
groupPerPatient	0.001	0.001	0.001
groupPerSample	0.001	0.000	0.002
hchart.survfit	0.971	0.067	1.092
isFirebrowseUp	0.004	0.000	0.044
labelBasedOnCutoff	0.011	0.000	0.010
leveneTest	0.010	0.001	0.017
listAllAnnotations	0.000	0.000	0.001
listSplicingAnnotations	0.000	0.000	0.001
loadAnnotation	0	0	0
loadFirebrowseData	0.001	0.001	0.001
loadLocalFiles	0.000	0.000	0.001
missingDataModal	0.001	0.000	0.001
optimalPSIcutoff	0.172	0.001	0.184
parseFirebrowseMetadata	0.040	0.003	0.245
parseMatsEvent	0.006	0.000	0.007
parseMatsGeneric	0.017	0.001	0.018
parseMisoAnnotation	0.382	0.005	0.397
parseMisoEvent	0.005	0.000	0.005
parseMisoEventID	0.005	0.001	0.006
parseMisoGeneric	0.112	0.002	0.122
parseMisoId	0.001	0.000	0.001
parseSampleGroups	0.001	0.000	0.001
parseSplicingEvent	0.002	0.000	0.002
parseSuppaEvent	0.004	0.000	0.004
parseSuppaGeneric	0.021	0.001	0.022
parseUrlsFromFirebrowseResponse	0.012	0.000	0.142
parseVastToolsEvent	0.007	0.001	0.009
parseVastToolsSE	0.109	0.001	0.116
performPCA	0.002	0.000	0.003
plotDistribution	0.369	0.015	0.395
plotPCA	0.218	0.038	0.270
plotProtein	0.001	0.000	0.001
plotSurvivalCurves	0.079	0.014	0.093
plotTranscripts	0.016	0.001	0.731
plotVariance	0.051	0.015	0.069
prepareAnnotationFromEvents	0.347	0.004	0.357
prepareFirebrowseArchives	0	0	0
processSurvTerms	0.003	0.000	0.003
psichomics	0	0	0
quantifySplicing	0.019	0.000	0.028
queryEnsembl	0.028	0.002	0.732
queryEnsemblByEvent	0.048	0.003	1.073
queryEnsemblByGene	0.090	0.004	1.583
queryFirebrowseData	0.057	0.002	0.315
queryPubMed	0.038	0.002	0.286
queryUniprot	0.479	0.003	1.121
readFile	0.001	0.000	0.001
renameDuplicated	0.001	0.000	0.001
survdiff.survTerms	0.012	0.001	0.013
survfit.survTerms	0.025	0.001	0.026
testSurvival	0.018	0.000	0.019
textSuggestions	0.000	0.000	0.001
trimWhitespace	0.001	0.001	0.000