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BioC 3.2: CHECK report for rcellminer on windows1.bioconductor.org

This page was generated on 2015-10-27 17:32:06 -0400 (Tue, 27 Oct 2015).

Package 850/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rcellminer 1.2.1
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/rcellminer
Last Changed Rev: 109881 / Revision: 109947
Last Changed Date: 2015-10-23 13:56:21 -0400 (Fri, 23 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rcellminer
Version: 1.2.1
Command: rm -rf rcellminer.buildbin-libdir rcellminer.Rcheck && mkdir rcellminer.buildbin-libdir rcellminer.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rcellminer.buildbin-libdir rcellminer_1.2.1.tar.gz >rcellminer.Rcheck\00install.out 2>&1 && cp rcellminer.Rcheck\00install.out rcellminer-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rcellminer.buildbin-libdir --install="check:rcellminer-install.out" --force-multiarch --no-vignettes --timings rcellminer_1.2.1.tar.gz
StartedAt: 2015-10-27 04:54:10 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:57:26 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 196.6 seconds
RetCode: 0
Status:  OK  
CheckDir: rcellminer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rcellminer.buildbin-libdir rcellminer.Rcheck && mkdir rcellminer.buildbin-libdir rcellminer.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rcellminer.buildbin-libdir rcellminer_1.2.1.tar.gz >rcellminer.Rcheck\00install.out 2>&1 && cp rcellminer.Rcheck\00install.out rcellminer-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rcellminer.buildbin-libdir --install="check:rcellminer-install.out" --force-multiarch --no-vignettes --timings rcellminer_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/rcellminer.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rcellminer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rcellminer' version '1.2.1'
* 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 'rcellminer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.9Mb
* 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
* 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 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
** running examples for arch 'x64' ... [11s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [47s]
 [47s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [54s]
 [54s] 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: 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/rcellminer.Rcheck/00check.log'
for details.


rcellminer.Rcheck/00install.out:


install for i386

* installing *source* package 'rcellminer' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'rcellminer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rcellminer' as rcellminer_1.2.1.zip
* DONE (rcellminer)

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

nameusersystemelapsed
compareFingerprints1.550.142.19
crossCors0.010.000.01
crossCorsSpearman000
getActivityRangeStats0.050.010.07
getColumnQuantiles000
getDrugActivityData0.010.000.01
getDrugActivityRange0.020.000.02
getDrugActivityRepeatData000
getDrugMoaList0.070.000.08
getDrugName000
getFeatureDataFromMatList2.320.112.47
getFingerprintList0.030.020.05
getMedSenLineActivity0.010.000.01
getMinDrugActivityRepeatCor0.020.000.02
getMoaStr0.250.030.28
getMoaToCompounds0.060.000.06
getMolDataMatrices0.220.050.27
getMolDataType000
getNumDrugActivityRepeats0.200.030.23
getNumMissingLines000
getRsd000
getSmiles000
hasMoa0.050.000.04
isPublic000
loadCellminerPlotInfo000
loadNciColorSet000
passRuleOf50.060.000.10
passRuleOf5FromNsc0.050.000.03
patternComparison0.180.030.22
plotCellMiner0.690.080.76
plotDrugActivityRepeats0.920.121.05
plotDrugSets0.080.020.09
plotStructures0.720.061.13
plotStructuresFromNscs0.310.020.27
rcdkplot0.100.000.07
removeMolDataType000
restrictFeatureMat000
rowCors000
runShinyApp000
runShinyComparePlots000
runShinyCompareStructures000
runShinyCompoundBrowser000
searchForNscs000
selectCorrelatedRows000
selectCorrelatedRowsFromMatrices0.020.000.01

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

nameusersystemelapsed
compareFingerprints2.280.131.73
crossCors000
crossCorsSpearman000
getActivityRangeStats0.040.000.05
getColumnQuantiles000
getDrugActivityData0.020.000.01
getDrugActivityRange0.020.000.02
getDrugActivityRepeatData000
getDrugMoaList0.060.010.08
getDrugName000
getFeatureDataFromMatList2.240.212.44
getFingerprintList0.200.000.06
getMedSenLineActivity0.020.000.02
getMinDrugActivityRepeatCor0.010.000.01
getMoaStr0.210.010.22
getMoaToCompounds0.040.000.06
getMolDataMatrices0.350.110.46
getMolDataType000
getNumDrugActivityRepeats0.010.000.01
getNumMissingLines000
getRsd000
getSmiles0.010.000.01
hasMoa0.030.000.04
isPublic000
loadCellminerPlotInfo0.020.000.01
loadNciColorSet000
passRuleOf50.090.020.05
passRuleOf5FromNsc0.050.010.01
patternComparison0.270.060.33
plotCellMiner0.710.190.91
plotDrugActivityRepeats0.490.210.69
plotDrugSets0.010.010.03
plotStructures1.430.141.26
plotStructuresFromNscs0.620.080.25
rcdkplot0.130.020.07
removeMolDataType000
restrictFeatureMat000
rowCors000
runShinyApp000
runShinyComparePlots000
runShinyCompareStructures000
runShinyCompoundBrowser000
searchForNscs000
selectCorrelatedRows000
selectCorrelatedRowsFromMatrices000