BioC 3.5: CHECK report for psichomics on toluca2

Package: psichomics

Version: 1.1.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.1.10.tar.gz

StartedAt: 2017-04-23 08:17:55 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:21:41 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 226.2 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_1.1.10.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 r72187)
* 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 ‘1.1.10’
* 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	0.001
createJunctionsTemplate	0.003	0.001	0.004
diffAnalyses	0.691	0.033	0.726
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	1.094	0.004	1.352
filterGroups	0.001	0.000	0.001
getDownloadsFolder	0.000	0.001	0.001
getFirebrowseCohorts	0.175	0.001	0.334
getFirebrowseDataTypes	0.033	0.001	0.034
getFirebrowseDateFormat	0	0	0
getFirebrowseDates	0.012	0.001	0.167
getMatchingSamples	0.001	0.000	0.002
getNumerics	0.004	0.000	0.005
getPatientFromSample	0.001	0.001	0.001
getSplicingEventTypes	0.000	0.000	0.001
getValidEvents	0.006	0.001	0.007
groupPerPatient	0.002	0.000	0.002
groupPerSample	0.001	0.000	0.001
hchart.survfit	0.832	0.060	0.899
isFirebrowseUp	0.005	0.000	0.081
labelBasedOnCutoff	0.021	0.001	0.021
leveneTest	0.012	0.000	0.012
listAllAnnotations	0.000	0.000	0.001
listSplicingAnnotations	0.000	0.000	0.001
loadAnnotation	0.001	0.000	0.001
loadFirebrowseData	0.001	0.000	0.000
loadLocalFiles	0.001	0.000	0.000
missingDataModal	0.001	0.000	0.000
optimalPSIcutoff	0.242	0.001	0.243
parseFirebrowseMetadata	0.040	0.003	0.442
parseMatsEvent	0.008	0.000	0.008
parseMatsGeneric	0.033	0.001	0.035
parseMisoAnnotation	0.461	0.006	0.467
parseMisoEvent	0.005	0.000	0.005
parseMisoEventID	0.006	0.000	0.006
parseMisoGeneric	0.127	0.001	0.127
parseMisoId	0.001	0.000	0.001
parseSampleGroups	0.001	0.000	0.001
parseSplicingEvent	0.004	0.000	0.004
parseSuppaEvent	0.007	0.001	0.007
parseSuppaGeneric	0.031	0.001	0.031
parseUrlsFromFirebrowseResponse	0.018	0.000	0.215
parseVastToolsEvent	0.008	0.000	0.008
parseVastToolsSE	0.170	0.001	0.171
performPCA	0.004	0.000	0.004
plotDistribution	0.520	0.018	0.540
plotPCA	0.278	0.049	0.332
plotProtein	0.001	0.001	0.001
plotSurvivalCurves	0.120	0.018	0.138
plotTranscripts	0.021	0.001	0.580
plotVariance	0.072	0.016	0.089
prepareAnnotationFromEvents	0.470	0.003	0.474
prepareFirebrowseArchives	0.001	0.000	0.001
processSurvTerms	0.004	0.000	0.004
psichomics	0.000	0.000	0.001
quantifySplicing	0.032	0.000	0.031
queryEnsembl	0.039	0.001	0.668
queryEnsemblByEvent	0.105	0.003	1.045
queryEnsemblByGene	0.113	0.004	1.381
queryFirebrowseData	0.096	0.001	0.438
queryPubMed	0.051	0.002	0.274
queryUniprot	0.534	0.002	1.011
readFile	0.001	0.000	0.002
renameDuplicated	0.001	0.000	0.002
survdiff.survTerms	0.010	0.001	0.011
survfit.survTerms	0.033	0.001	0.033
testSurvival	0.026	0.001	0.026
textSuggestions	0.001	0.000	0.001
trimWhitespace	0.001	0.000	0.001