Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for psichomics on tokay1

This page was generated on 2017-04-15 16:21:37 -0400 (Sat, 15 Apr 2017).

Package 964/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.0.8
Nuno Saraiva-Agostinho
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/psichomics
Last Changed Rev: 126837 / Revision: 128728
Last Changed Date: 2017-02-21 06:14:43 -0500 (Tue, 21 Feb 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: psichomics
Version: 1.0.8
Command: rm -rf psichomics.buildbin-libdir psichomics.Rcheck && mkdir psichomics.buildbin-libdir psichomics.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psichomics.buildbin-libdir psichomics_1.0.8.tar.gz >psichomics.Rcheck\00install.out 2>&1 && cp psichomics.Rcheck\00install.out psichomics-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=psichomics.buildbin-libdir --install="check:psichomics-install.out" --force-multiarch --no-vignettes --timings psichomics_1.0.8.tar.gz
StartedAt: 2017-04-15 00:13:19 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:17:47 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 267.9 seconds
RetCode: 0
Status:  OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf psichomics.buildbin-libdir psichomics.Rcheck && mkdir psichomics.buildbin-libdir psichomics.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psichomics.buildbin-libdir psichomics_1.0.8.tar.gz >psichomics.Rcheck\00install.out 2>&1 && cp psichomics.Rcheck\00install.out psichomics-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=psichomics.buildbin-libdir --install="check:psichomics-install.out" --force-multiarch --no-vignettes --timings psichomics_1.0.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/psichomics.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'psichomics/DESCRIPTION' ... OK
* this is package 'psichomics' version '1.0.8'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
hchart.survfit 0.45   0.06    5.29
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:


install for i386

* 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

install for x64

* installing *source* package 'psichomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psichomics' as psichomics_1.0.8.zip
* DONE (psichomics)

psichomics.Rcheck/examples_i386/psichomics-Ex.timings:

nameusersystemelapsed
createGroupByAttribute000
createJunctionsTemplate000
diffAnalyses0.110.020.12
downloadFiles000
ensemblToUniprot0.020.000.28
filterGroups000
getDownloadsFolder000
getFirehoseCohorts0.000.000.12
getFirehoseDataTypes000
getFirehoseDateFormat000
getFirehoseDates0.030.000.08
getMatchingSamples000
getNumerics000
getPatientFromSample000
getSplicingEventTypes0.020.000.02
getValidEvents000
groupPerPatient000
groupPerSample000
hchart.survfit0.450.065.29
isFirehoseUp0.000.000.03
labelBasedOnCutoff000
leveneTest0.020.000.02
listAllAnnotations000
listSplicingAnnotations000
loadAnnotation000
loadFirehoseData000
loadLocalFiles000
missingDataModal000
optimalPSIcutoff0.070.030.09
parseFirehoseMetadata0.060.000.19
parseMatsEvent000
parseMatsGeneric0.020.000.02
parseMisoAnnotation0.140.000.14
parseMisoEvent000
parseMisoEventID0.020.000.01
parseMisoGeneric0.030.000.04
parseMisoId000
parseSampleGroups000
parseSplicingEvent000
parseSuppaEvent000
parseSuppaGeneric0.030.000.03
parseUrlsFromFirehoseResponse0.010.000.11
parseVastToolsEvent0.020.000.01
parseVastToolsSE0.020.000.02
performPCA000
plotDistribution0.370.020.39
plotPCA0.200.061.22
plotProtein000
plotSurvivalCurves0.080.030.11
plotTranscripts0.020.000.61
plotVariance0.060.020.29
prepareAnnotationFromEvents0.190.000.19
prepareFirehoseArchives000
processSurvTerms0.010.000.02
psichomics000
quantifySplicing0.020.000.01
queryEnsembl0.010.000.63
queryEnsemblByEvent0.040.001.01
queryEnsemblByGene0.060.001.39
queryFirehoseData0.020.000.17
queryPubMed0.230.120.61
queryUniprot0.050.000.11
readFile000
renameDuplicated000
survdiff.survTerms000
survfit.survTerms0.010.000.02
testSurvival000
textSuggestions000
trimWhitespace000

psichomics.Rcheck/examples_x64/psichomics-Ex.timings:

nameusersystemelapsed
createGroupByAttribute000
createJunctionsTemplate0.010.000.01
diffAnalyses0.090.000.10
downloadFiles000
ensemblToUniprot0.000.020.23
filterGroups000
getDownloadsFolder000
getFirehoseCohorts0.040.000.08
getFirehoseDataTypes000
getFirehoseDateFormat000
getFirehoseDates0.030.000.08
getMatchingSamples000
getNumerics000
getPatientFromSample000
getSplicingEventTypes000
getValidEvents000
groupPerPatient000
groupPerSample000
hchart.survfit0.270.080.35
isFirehoseUp0.010.000.03
labelBasedOnCutoff000
leveneTest000
listAllAnnotations000
listSplicingAnnotations000
loadAnnotation000
loadFirehoseData000
loadLocalFiles000
missingDataModal000
optimalPSIcutoff0.110.000.11
parseFirehoseMetadata0.020.000.18
parseMatsEvent0.020.000.02
parseMatsGeneric0.030.000.03
parseMisoAnnotation0.140.000.14
parseMisoEvent0.010.000.02
parseMisoEventID000
parseMisoGeneric0.050.000.04
parseMisoId000
parseSampleGroups000
parseSplicingEvent000
parseSuppaEvent0.020.000.02
parseSuppaGeneric0.010.000.01
parseUrlsFromFirehoseResponse0.030.000.15
parseVastToolsEvent000
parseVastToolsSE0.030.000.03
performPCA000
plotDistribution0.460.021.07
plotPCA0.220.060.29
plotProtein000
plotSurvivalCurves0.090.020.11
plotTranscripts0.030.000.60
plotVariance0.080.000.47
prepareAnnotationFromEvents0.160.000.16
prepareFirehoseArchives000
processSurvTerms0.010.000.02
psichomics000
quantifySplicing0.020.000.01
queryEnsembl0.030.000.64
queryEnsemblByEvent0.060.000.97
queryEnsemblByGene0.060.001.34
queryFirehoseData0.030.010.19
queryPubMed0.240.050.50
queryUniprot0.030.000.11
readFile000
renameDuplicated000
survdiff.survTerms000
survfit.survTerms0.030.000.03
testSurvival0.010.000.01
textSuggestions000
trimWhitespace000