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BioC 3.5: CHECK report for psichomics on veracruz2

This page was generated on 2017-08-16 13:35:09 -0400 (Wed, 16 Aug 2017).

Package 1026/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.2.1
Nuno Saraiva-Agostinho
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/psichomics
Last Changed Rev: 129177 / Revision: 131943
Last Changed Date: 2017-04-25 18:33:25 -0400 (Tue, 25 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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: 2017-08-16 06:48:57 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:52:18 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 201.6 seconds
RetCode: 0
Status:  OK 
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.2.1’
* 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

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
createGroupByAttribute0.0020.0000.002
createJunctionsTemplate0.0030.0000.004
diffAnalyses0.4220.0190.445
downloadFiles0.0000.0000.001
ensemblToUniprot0.1300.0010.373
filterGroups0.0010.0000.000
getDownloadsFolder000
getFirebrowseCohorts0.2330.0020.351
getFirebrowseDataTypes0.0180.0000.018
getFirebrowseDateFormat0.0010.0000.001
getFirebrowseDates0.0090.0010.085
getMatchingSamples0.0010.0000.002
getNumerics0.0040.0000.003
getPatientFromSample0.0010.0000.001
getSplicingEventTypes0.0000.0000.001
getValidEvents0.0040.0000.004
groupPerPatient0.0000.0000.001
groupPerSample0.0010.0000.001
hchart.survfit0.8640.0500.964
isFirebrowseUp0.0040.0000.043
labelBasedOnCutoff0.0160.0030.018
leveneTest0.0130.0020.017
listAllAnnotations0.0010.0000.001
listSplicingAnnotations000
loadAnnotation0.0010.0000.001
loadFirebrowseData0.0010.0000.000
loadLocalFiles0.0000.0000.001
missingDataModal0.0010.0000.001
optimalPSIcutoff0.1910.0100.206
parseFirebrowseMetadata0.0280.0020.235
parseMatsEvent0.0050.0000.006
parseMatsGeneric0.0290.0010.030
parseMisoAnnotation0.3320.0060.338
parseMisoEvent0.0050.0000.005
parseMisoEventID0.0060.0000.007
parseMisoGeneric0.0980.0010.100
parseMisoId0.0010.0010.001
parseSampleGroups0.0010.0000.001
parseSplicingEvent0.0020.0000.002
parseSuppaEvent0.0030.0000.003
parseSuppaGeneric0.0180.0000.019
parseUrlsFromFirebrowseResponse0.0120.0000.130
parseVastToolsEvent0.0050.0000.005
parseVastToolsSE0.0820.0010.083
performPCA0.0020.0000.003
plotDistribution0.3340.0120.355
plotPCA0.1830.0290.219
plotProtein0.0010.0000.000
plotSurvivalCurves0.0710.0120.083
plotTranscripts0.0130.0010.742
plotVariance0.0450.0120.058
prepareAnnotationFromEvents0.2600.0030.263
prepareFirebrowseArchives0.0000.0000.001
processSurvTerms0.0030.0000.003
psichomics000
quantifySplicing0.0190.0000.019
queryEnsembl0.0230.0010.691
queryEnsemblByEvent0.0470.0031.172
queryEnsemblByGene0.0670.0041.614
queryFirebrowseData0.0520.0010.315
queryPubMed0.0610.0020.319
queryUniprot0.4690.0031.226
readFile0.0010.0010.001
renameDuplicated0.0010.0000.001
survdiff.survTerms0.0070.0000.008
survfit.survTerms0.0250.0000.025
testSurvival0.0230.0010.023
textSuggestions0.0010.0000.000
trimWhitespace0.0000.0000.001