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BioC 3.4: CHECK report for GWASTools on tokay1

This page was generated on 2017-04-15 16:16:56 -0400 (Sat, 15 Apr 2017).

Package 577/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWASTools 1.20.0
Stephanie M. Gogarten , Adrienne Stilp
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/GWASTools
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GWASTools
Version: 1.20.0
Command: rm -rf GWASTools.buildbin-libdir GWASTools.Rcheck && mkdir GWASTools.buildbin-libdir GWASTools.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.20.0.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GWASTools.buildbin-libdir --install="check:GWASTools-install.out" --force-multiarch --no-vignettes --timings GWASTools_1.20.0.tar.gz
StartedAt: 2017-04-14 22:55:07 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:03:58 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 530.7 seconds
RetCode: 0
Status:  OK  
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GWASTools.buildbin-libdir GWASTools.Rcheck && mkdir GWASTools.buildbin-libdir GWASTools.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.20.0.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GWASTools.buildbin-libdir --install="check:GWASTools-install.out" --force-multiarch --no-vignettes --timings GWASTools_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/GWASTools.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 'GWASTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GWASTools' version '1.20.0'
* 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 'GWASTools' 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
* 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' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
vcfWrite  7.2   0.23    7.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
vcfWrite 9.37    0.3    9.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  Running 'test.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

GWASTools.Rcheck/00install.out:


install for i386

* installing *source* package 'GWASTools' ...
** 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 'GWASTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GWASTools' as GWASTools_1.20.0.zip
* DONE (GWASTools)

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

nameusersystemelapsed
BAFfromClusterMeans0.700.031.40
BAFfromGenotypes000
GdsGenotypeReader-class0.030.000.05
GdsIntensityReader-class000
GdsReader-class0.030.000.16
GenotypeData-class0.110.020.15
HLA000
IntensityData-class0.010.010.03
MatrixGenotypeReader-class000
NcdfGenotypeReader-class0.020.000.14
NcdfIntensityReader-class0.020.000.20
NcdfReader-class0.010.000.04
ScanAnnotationDataFrame-class0.050.020.09
ScanAnnotationSQLite-class0.050.010.06
SnpAnnotationDataFrame-class0.100.000.25
SnpAnnotationSQLite-class0.150.020.16
alleleFrequency0.120.020.14
allequal000
anomDetectBAF1.690.011.92
anomDetectLOH1.170.031.20
anomIdentifyLowQuality1.020.021.04
anomSegStats0.270.010.28
apartSnpSelection0.10.00.2
assocCoxPH0.540.000.55
assocRegression0.820.000.81
batchTest1.420.111.53
centromeres000
chromIntensityPlot0.070.030.09
convertNcdfGds0.210.040.28
createDataFile0.440.072.00
duplicateDiscordance0.360.030.39
duplicateDiscordanceAcrossDatasets0.110.000.11
duplicateDiscordanceProbability000
exactHWE0.360.020.38
findBAFvariance0.270.000.26
gdsSubset0.010.020.03
genoClusterPlot0.690.033.07
genotypeToCharacter000
getobj000
hetByScanChrom0.10.00.1
hetBySnpSex0.110.000.11
ibdPlot0.500.010.51
imputedDosageFile2.060.442.99
intensityOutliersPlot0.300.020.31
manhattanPlot0.030.000.03
meanIntensityByScanChrom0.260.000.26
mendelErr0.860.000.86
mendelList0.020.000.02
missingGenotypeByScanChrom0.090.000.09
missingGenotypeBySnpSex0.080.000.08
pasteSorted000
pcaSnpFilters0.020.000.02
pedigreeCheck0.030.000.03
pedigreeDeleteDuplicates000
pedigreeMaxUnrelated0.060.000.06
pedigreePairwiseRelatedness0.030.000.03
plinkUtils2.690.042.74
pseudoautoIntensityPlot0.080.000.07
pseudoautosomal0.010.000.02
qqPlot0.130.000.13
qualityScoreByScan0.150.000.15
qualityScoreBySnp0.030.020.05
readWriteFirst000
relationsMeanVar0.000.010.01
saveas000
setMissingGenotypes0.040.020.05
simulateGenotypeMatrix0.840.020.86
snpCorrelationPlot0.020.000.02
snpStats0.560.000.57
vcfWrite7.200.237.44

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

nameusersystemelapsed
BAFfromClusterMeans0.810.030.87
BAFfromGenotypes000
GdsGenotypeReader-class0.030.000.03
GdsIntensityReader-class0.010.000.02
GdsReader-class0.030.000.03
GenotypeData-class0.190.020.21
HLA0.000.010.01
IntensityData-class0.030.020.05
MatrixGenotypeReader-class0.010.000.01
NcdfGenotypeReader-class0.040.000.14
NcdfIntensityReader-class0.030.000.04
NcdfReader-class0.010.000.01
ScanAnnotationDataFrame-class0.110.000.11
ScanAnnotationSQLite-class0.110.000.11
SnpAnnotationDataFrame-class0.140.000.14
SnpAnnotationSQLite-class0.130.030.16
alleleFrequency0.170.030.20
allequal000
anomDetectBAF1.360.001.36
anomDetectLOH0.920.000.92
anomIdentifyLowQuality0.910.000.91
anomSegStats0.320.000.33
apartSnpSelection0.080.000.07
assocCoxPH0.380.020.39
assocRegression0.650.010.68
batchTest1.190.081.26
centromeres000
chromIntensityPlot0.110.000.11
convertNcdfGds0.250.020.27
createDataFile0.500.010.52
duplicateDiscordance0.480.020.50
duplicateDiscordanceAcrossDatasets0.130.000.12
duplicateDiscordanceProbability000
exactHWE0.150.000.16
findBAFvariance0.280.010.30
gdsSubset0.020.000.04
genoClusterPlot0.670.020.69
genotypeToCharacter000
getobj0.020.000.02
hetByScanChrom0.110.000.11
hetBySnpSex0.10.00.1
ibdPlot0.220.000.22
imputedDosageFile1.380.261.68
intensityOutliersPlot0.330.020.34
manhattanPlot0.010.000.02
meanIntensityByScanChrom0.310.000.31
mendelErr0.930.010.94
mendelList0.010.000.02
missingGenotypeByScanChrom0.110.000.11
missingGenotypeBySnpSex0.110.000.10
pasteSorted000
pcaSnpFilters0.020.000.02
pedigreeCheck0.010.020.03
pedigreeDeleteDuplicates0.020.000.02
pedigreeMaxUnrelated0.080.000.08
pedigreePairwiseRelatedness0.030.000.03
plinkUtils2.930.012.95
pseudoautoIntensityPlot0.080.000.08
pseudoautosomal000
qqPlot0.080.000.08
qualityScoreByScan0.180.020.20
qualityScoreBySnp0.050.000.05
readWriteFirst000
relationsMeanVar000
saveas000
setMissingGenotypes0.060.000.06
simulateGenotypeMatrix0.830.000.83
snpCorrelationPlot0.000.010.02
snpStats0.660.000.69
vcfWrite9.370.309.67