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BioC 3.5: CHECK report for psichomics on toluca2

This page was generated on 2017-04-23 14:42:17 -0400 (Sun, 23 Apr 2017).

Package 1022/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.1.10
Nuno Saraiva-Agostinho
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/psichomics
Last Changed Rev: 129045 / Revision: 129046
Last Changed Date: 2017-04-22 09:15:08 -0400 (Sat, 22 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK YES, new version is higher than in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK YES, new version is higher than in internal repository

Summary

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

Command output

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


* 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

psichomics.Rcheck/00install.out:

* 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)

psichomics.Rcheck/psichomics-Ex.timings:

nameusersystemelapsed
createGroupByAttribute0.0020.0000.001
createJunctionsTemplate0.0030.0010.004
diffAnalyses0.6910.0330.726
downloadFiles0.0000.0000.001
ensemblToUniprot1.0940.0041.352
filterGroups0.0010.0000.001
getDownloadsFolder0.0000.0010.001
getFirebrowseCohorts0.1750.0010.334
getFirebrowseDataTypes0.0330.0010.034
getFirebrowseDateFormat000
getFirebrowseDates0.0120.0010.167
getMatchingSamples0.0010.0000.002
getNumerics0.0040.0000.005
getPatientFromSample0.0010.0010.001
getSplicingEventTypes0.0000.0000.001
getValidEvents0.0060.0010.007
groupPerPatient0.0020.0000.002
groupPerSample0.0010.0000.001
hchart.survfit0.8320.0600.899
isFirebrowseUp0.0050.0000.081
labelBasedOnCutoff0.0210.0010.021
leveneTest0.0120.0000.012
listAllAnnotations0.0000.0000.001
listSplicingAnnotations0.0000.0000.001
loadAnnotation0.0010.0000.001
loadFirebrowseData0.0010.0000.000
loadLocalFiles0.0010.0000.000
missingDataModal0.0010.0000.000
optimalPSIcutoff0.2420.0010.243
parseFirebrowseMetadata0.0400.0030.442
parseMatsEvent0.0080.0000.008
parseMatsGeneric0.0330.0010.035
parseMisoAnnotation0.4610.0060.467
parseMisoEvent0.0050.0000.005
parseMisoEventID0.0060.0000.006
parseMisoGeneric0.1270.0010.127
parseMisoId0.0010.0000.001
parseSampleGroups0.0010.0000.001
parseSplicingEvent0.0040.0000.004
parseSuppaEvent0.0070.0010.007
parseSuppaGeneric0.0310.0010.031
parseUrlsFromFirebrowseResponse0.0180.0000.215
parseVastToolsEvent0.0080.0000.008
parseVastToolsSE0.1700.0010.171
performPCA0.0040.0000.004
plotDistribution0.5200.0180.540
plotPCA0.2780.0490.332
plotProtein0.0010.0010.001
plotSurvivalCurves0.1200.0180.138
plotTranscripts0.0210.0010.580
plotVariance0.0720.0160.089
prepareAnnotationFromEvents0.4700.0030.474
prepareFirebrowseArchives0.0010.0000.001
processSurvTerms0.0040.0000.004
psichomics0.0000.0000.001
quantifySplicing0.0320.0000.031
queryEnsembl0.0390.0010.668
queryEnsemblByEvent0.1050.0031.045
queryEnsemblByGene0.1130.0041.381
queryFirebrowseData0.0960.0010.438
queryPubMed0.0510.0020.274
queryUniprot0.5340.0021.011
readFile0.0010.0000.002
renameDuplicated0.0010.0000.002
survdiff.survTerms0.0100.0010.011
survfit.survTerms0.0330.0010.033
testSurvival0.0260.0010.026
textSuggestions0.0010.0000.001
trimWhitespace0.0010.0000.001