BioC 3.5: CHECK report for psichomics on oaxaca

Package: psichomics

Version: 1.1.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.1.8.tar.gz

StartedAt: 2017-03-04 07:25:05 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:28:39 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 213.7 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_1.1.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.1.8’
* 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	0.002
createJunctionsTemplate	0.003	0.000	0.004
diffAnalyses	0.795	0.052	0.877
downloadFiles	0.001	0.000	0.000
ensemblToUniprot	0.368	0.004	0.759
filterGroups	0.001	0.000	0.000
getDownloadsFolder	0.001	0.000	0.001
getFirehoseCohorts	0.198	0.002	0.493
getFirehoseDataTypes	0.001	0.000	0.001
getFirehoseDateFormat	0	0	0
getFirehoseDates	0.012	0.000	0.304
getMatchingSamples	0.001	0.000	0.002
getNumerics	0.005	0.000	0.004
getPatientFromSample	0.001	0.000	0.001
getSplicingEventTypes	0.000	0.000	0.001
getValidEvents	0.006	0.000	0.007
groupPerPatient	0.002	0.000	0.001
groupPerSample	0.001	0.000	0.002
hchart.survfit	0.788	0.062	1.237
isFirehoseUp	0.005	0.000	0.150
labelBasedOnCutoff	0.023	0.000	0.024
leveneTest	0.015	0.000	0.015
listAllAnnotations	0.001	0.000	0.001
listSplicingAnnotations	0	0	0
loadAnnotation	0.001	0.000	0.000
loadFirehoseData	0.000	0.000	0.001
loadLocalFiles	0.001	0.000	0.000
missingDataModal	0.001	0.000	0.001
optimalPSIcutoff	0.252	0.001	0.253
parseFirehoseMetadata	0.036	0.002	0.778
parseMatsEvent	0.009	0.001	0.010
parseMatsGeneric	0.037	0.001	0.038
parseMisoAnnotation	0.560	0.005	0.565
parseMisoEvent	0.005	0.001	0.005
parseMisoEventID	0.007	0.000	0.007
parseMisoGeneric	0.128	0.001	0.131
parseMisoId	0.001	0.000	0.002
parseSampleGroups	0.002	0.000	0.002
parseSplicingEvent	0.034	0.000	0.034
parseSuppaEvent	0.007	0.000	0.007
parseSuppaGeneric	0.035	0.001	0.037
parseUrlsFromFirehoseResponse	0.016	0.001	0.370
parseVastToolsEvent	0.01	0.00	0.01
parseVastToolsSE	0.149	0.001	0.151
performPCA	0.004	0.000	0.004
plotDistribution	0.514	0.024	0.538
plotPCA	0.310	0.053	0.363
plotProtein	0	0	0
plotSurvivalCurves	0.131	0.020	0.151
plotTranscripts	0.017	0.000	0.824
plotVariance	0.056	0.018	0.074
prepareAnnotationFromEvents	0.576	0.005	0.582
prepareFirehoseArchives	0.001	0.001	0.001
processSurvTerms	0.005	0.000	0.006
psichomics	0.001	0.000	0.000
quantifySplicing	0.031	0.000	0.032
queryEnsembl	0.037	0.002	0.981
queryEnsemblByEvent	0.074	0.004	1.384
queryEnsemblByGene	0.099	0.004	1.928
queryFirehoseData	0.106	0.001	0.728
queryPubMed	0.107	0.004	0.664
queryUniprot	0.516	0.002	0.955
readFile	0.002	0.000	0.002
renameDuplicated	0.001	0.000	0.002
survdiff.survTerms	0.011	0.001	0.011
survfit.survTerms	0.036	0.001	0.038
testSurvival	0.025	0.001	0.025
textSuggestions	0.001	0.000	0.002
trimWhitespace	0.001	0.000	0.001