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BioC 3.1: CHECK report for PhenStat on moscato2

This page was generated on 2015-10-09 09:30:52 -0700 (Fri, 09 Oct 2015).

Package 716/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.2.0
Natasha Karp
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/PhenStat
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: PhenStat
Version: 2.2.0
Command: rm -rf PhenStat.buildbin-libdir PhenStat.Rcheck && mkdir PhenStat.buildbin-libdir PhenStat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PhenStat.buildbin-libdir PhenStat_2.2.0.tar.gz >PhenStat.Rcheck\00install.out 2>&1 && cp PhenStat.Rcheck\00install.out PhenStat-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=PhenStat.buildbin-libdir --install="check:PhenStat-install.out" --force-multiarch --no-vignettes --timings PhenStat_2.2.0.tar.gz
StartedAt: 2015-10-09 04:47:41 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:51:04 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 202.6 seconds
RetCode: 0
Status:  OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PhenStat.buildbin-libdir PhenStat.Rcheck && mkdir PhenStat.buildbin-libdir PhenStat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PhenStat.buildbin-libdir PhenStat_2.2.0.tar.gz >PhenStat.Rcheck\00install.out 2>&1 && cp PhenStat.Rcheck\00install.out PhenStat-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=PhenStat.buildbin-libdir --install="check:PhenStat-install.out" --force-multiarch --no-vignettes --timings PhenStat_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/PhenStat.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PhenStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PhenStat' version '2.2.0'
* 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 'PhenStat' 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' ... [40s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qqplotRotatedResiduals 6.07   0.06    6.13
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qqplotRotatedResiduals 6.18   0.04    6.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [3s]
 [3s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [3s]
 [3s] 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

PhenStat.Rcheck/00install.out:


install for i386

* installing *source* package 'PhenStat' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'PhenStat' ...
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'PhenStat' as PhenStat_2.2.0.zip
* DONE (PhenStat)

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

nameusersystemelapsed
FisherExactTest0.340.000.34
LRDataset0.110.000.11
PhenList-class0.280.000.28
PhenList0.30.00.3
PhenTestResult-class2.190.062.24
PhenTestResult1.450.091.55
RRTest0.120.000.12
TFDataset0.420.000.42
boxplotResidualBatch1.250.101.35
boxplotSexGenotype0.110.000.10
boxplotSexGenotypeBatch0.190.010.21
boxplotSexGenotypeBatchAdjusted0.110.000.11
categoricalBarplot0.310.020.32
checkDataset0.060.000.07
classificationTag1.260.081.34
determiningLambda1.050.031.07
dim0.060.000.07
finalLRModel0.420.010.43
finalModel1.180.001.19
finalTFModel1.050.001.04
htestPhenStat-class0.230.000.23
modelFormula000
modelFormulaLR000
parserOutputSummary1.270.001.27
parserOutputSummaryLR0.420.020.43
parserOutputTFSummary0.150.000.16
plotResidualPredicted1.220.001.22
printLROutput0.520.000.51
printTabStyle000
qqplotGenotype1.190.001.18
qqplotRandomEffects1.430.001.44
qqplotRotatedResiduals6.070.066.13
recommendMethod0.360.000.36
reverseTransformValues000
scatterplotGenotypeWeight0.140.000.14
scatterplotSexGenotypeBatch0.120.000.13
startLRModel0.520.000.51
startModel1.730.001.74
startTFModel0.640.000.64
summaryOutput1.330.001.32
testDataset2.600.002.61
testFinalLRModel0.420.010.43
testFinalModel1.380.001.38
transformValues000
vectorOutput1.370.001.37
vectorOutputMatrices0.20.00.2

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

nameusersystemelapsed
FisherExactTest0.390.000.39
LRDataset0.100.000.09
PhenList-class0.250.000.25
PhenList0.250.010.27
PhenTestResult-class1.810.001.81
PhenTestResult1.810.041.84
RRTest0.110.000.11
TFDataset0.450.000.45
boxplotResidualBatch1.250.001.25
boxplotSexGenotype0.110.000.11
boxplotSexGenotypeBatch0.370.000.37
boxplotSexGenotypeBatchAdjusted0.090.000.10
categoricalBarplot0.220.000.21
checkDataset0.050.000.05
classificationTag1.200.011.22
determiningLambda0.750.020.76
dim0.050.000.05
finalLRModel0.420.000.43
finalModel1.400.001.41
finalTFModel0.800.000.79
htestPhenStat-class0.20.00.2
modelFormula000
modelFormulaLR000
parserOutputSummary1.310.001.33
parserOutputSummaryLR0.570.000.57
parserOutputTFSummary0.210.000.21
plotResidualPredicted1.40.01.4
printLROutput0.450.000.45
printTabStyle000
qqplotGenotype1.380.001.37
qqplotRandomEffects1.240.001.25
qqplotRotatedResiduals6.180.046.22
recommendMethod0.430.000.44
reverseTransformValues000
scatterplotGenotypeWeight0.160.000.16
scatterplotSexGenotypeBatch0.130.000.12
startLRModel0.390.000.39
startModel2.150.052.20
startTFModel1.030.021.04
summaryOutput1.410.001.40
testDataset2.570.002.58
testFinalLRModel0.420.010.44
testFinalModel1.360.031.38
transformValues000
vectorOutput1.580.001.58
vectorOutputMatrices0.210.000.22