BioC 3.5: CHECK report for psichomics on veracruz2

Package: psichomics

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.2.1.tar.gz

StartedAt: 2017-10-18 07:35:43 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:38:44 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 181.0 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_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/psichomics.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.1’
* 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	0.002	0.000	0.002
createJunctionsTemplate	0.003	0.001	0.003
diffAnalyses	0.399	0.013	0.417
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.134	0.002	0.374
filterGroups	0.001	0.000	0.000
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseCohorts	1.709	0.008	1.840
getFirebrowseDataTypes	0.016	0.000	0.016
getFirebrowseDateFormat	0.000	0.000	0.001
getFirebrowseDates	0.009	0.001	0.082
getMatchingSamples	0.002	0.000	0.002
getNumerics	0.003	0.000	0.004
getPatientFromSample	0.001	0.000	0.001
getSplicingEventTypes	0.001	0.000	0.000
getValidEvents	0.004	0.001	0.004
groupPerPatient	0.000	0.000	0.001
groupPerSample	0.001	0.000	0.001
hchart.survfit	0.636	0.041	0.693
isFirebrowseUp	0.004	0.000	0.040
labelBasedOnCutoff	0.012	0.000	0.011
leveneTest	0.008	0.001	0.008
listAllAnnotations	0.000	0.000	0.001
listSplicingAnnotations	0.000	0.000	0.001
loadAnnotation	0	0	0
loadFirebrowseData	0	0	0
loadLocalFiles	0	0	0
missingDataModal	0.000	0.000	0.001
optimalPSIcutoff	0.422	0.002	0.429
parseFirebrowseMetadata	0.027	0.002	0.228
parseMatsEvent	0.004	0.001	0.005
parseMatsGeneric	0.020	0.002	0.022
parseMisoAnnotation	0.351	0.022	0.374
parseMisoEvent	0.004	0.000	0.004
parseMisoEventID	0.006	0.001	0.005
parseMisoGeneric	0.089	0.001	0.091
parseMisoId	0.001	0.000	0.000
parseSampleGroups	0.001	0.000	0.002
parseSplicingEvent	0.003	0.000	0.003
parseSuppaEvent	0.004	0.001	0.003
parseSuppaGeneric	0.020	0.001	0.020
parseUrlsFromFirebrowseResponse	0.012	0.000	0.129
parseVastToolsEvent	0.005	0.000	0.005
parseVastToolsSE	0.093	0.001	0.095
performPCA	0.003	0.000	0.002
plotDistribution	0.366	0.016	0.389
plotPCA	0.219	0.035	0.267
plotProtein	0.001	0.000	0.001
plotSurvivalCurves	0.087	0.013	0.102
plotTranscripts	0.013	0.001	0.861
plotVariance	0.043	0.014	0.057
prepareAnnotationFromEvents	0.302	0.004	0.308
prepareFirebrowseArchives	0.001	0.000	0.000
processSurvTerms	0.003	0.000	0.003
psichomics	0.000	0.000	0.001
quantifySplicing	0.023	0.000	0.024
queryEnsembl	0.025	0.002	0.583
queryEnsemblByEvent	0.050	0.003	1.425
queryEnsemblByGene	0.067	0.003	1.605
queryFirebrowseData	0.054	0.001	0.306
queryPubMed	0.055	0.003	0.318
queryUniprot	0.116	0.002	2.198
readFile	0.001	0.001	0.001
renameDuplicated	0.001	0.000	0.000
survdiff.survTerms	0.006	0.000	0.007
survfit.survTerms	0.022	0.001	0.022
testSurvival	0.013	0.001	0.014
textSuggestions	0.000	0.000	0.001
trimWhitespace	0.000	0.000	0.001