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BioC 3.4: CHECK report for GWASTools on moscato1

This page was generated on 2016-09-21 03:43:53 -0700 (Wed, 21 Sep 2016).

Package 561/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWASTools 1.19.3
Stephanie M. Gogarten , Adrienne Stilp
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GWASTools
Last Changed Rev: 120344 / Revision: 121152
Last Changed Date: 2016-08-22 11:52:10 -0700 (Mon, 22 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.19.3
Command: rm -rf GWASTools.buildbin-libdir GWASTools.Rcheck && mkdir GWASTools.buildbin-libdir GWASTools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.19.3.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out && D:\biocbld\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_1.19.3.tar.gz
StartedAt: 2016-09-20 10:12:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:22:41 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 592.9 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.19.3.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out  && D:\biocbld\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_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/GWASTools.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.19.3'
* 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        8.52   0.17    8.75
genoClusterPlot 0.77   0.04    5.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
vcfWrite 8.63   0.12    8.75
* 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
Creating a generic function for 'open' from package 'base' in package 'GWASTools'
Creating a generic function for 'close' from package 'base' in package 'GWASTools'
** 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_1.19.3.zip
* DONE (GWASTools)

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

nameusersystemelapsed
BAFfromClusterMeans0.650.061.84
BAFfromGenotypes000
GdsGenotypeReader-class0.040.000.15
GdsIntensityReader-class0.010.020.03
GdsReader-class0.080.000.48
GenotypeData-class0.300.000.38
HLA0.010.000.01
IntensityData-class0.030.000.04
MatrixGenotypeReader-class0.020.000.01
NcdfGenotypeReader-class0.010.000.19
NcdfIntensityReader-class0.020.000.17
NcdfReader-class0.000.000.09
ScanAnnotationDataFrame-class0.060.000.19
ScanAnnotationSQLite-class0.050.000.05
SnpAnnotationDataFrame-class0.080.000.90
SnpAnnotationSQLite-class0.070.000.08
alleleFrequency0.160.000.16
allequal000
anomDetectBAF1.900.012.20
anomDetectLOH1.250.001.24
anomIdentifyLowQuality1.140.001.64
anomSegStats0.260.051.10
apartSnpSelection0.080.000.13
assocCoxPH0.360.010.37
assocRegression0.700.000.71
batchTest1.500.031.52
centromeres000
chromIntensityPlot0.100.000.09
convertNcdfGds0.400.002.58
createDataFile0.630.053.06
duplicateDiscordance0.530.000.53
duplicateDiscordanceAcrossDatasets0.140.000.14
duplicateDiscordanceProbability000
exactHWE0.170.000.17
findBAFvariance0.350.000.34
gdsSubset0.010.020.04
genoClusterPlot0.770.045.92
genotypeToCharacter000
getobj000
hetByScanChrom0.140.000.14
hetBySnpSex0.120.000.13
ibdPlot0.560.020.58
imputedDosageFile1.600.263.04
intensityOutliersPlot0.370.000.37
manhattanPlot0.030.000.03
meanIntensityByScanChrom0.410.000.41
mendelErr1.090.001.11
mendelList0.010.000.01
missingGenotypeByScanChrom0.110.000.11
missingGenotypeBySnpSex0.110.000.11
pasteSorted000
pcaSnpFilters000
pedigreeCheck0.050.000.05
pedigreeDeleteDuplicates000
pedigreeMaxUnrelated0.080.000.08
pedigreePairwiseRelatedness0.040.000.04
plinkUtils3.550.023.56
pseudoautoIntensityPlot0.110.000.11
pseudoautosomal0.000.020.01
qqPlot0.150.000.16
qualityScoreByScan0.220.000.78
qualityScoreBySnp0.030.010.05
readWriteFirst000
relationsMeanVar0.020.000.01
saveas000
setMissingGenotypes0.040.000.05
simulateGenotypeMatrix0.880.000.89
snpCorrelationPlot0.010.000.01
snpStats0.720.020.78
vcfWrite8.520.178.75

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

nameusersystemelapsed
BAFfromClusterMeans0.550.050.63
BAFfromGenotypes000
GdsGenotypeReader-class0.030.000.03
GdsIntensityReader-class0.010.000.01
GdsReader-class0.050.000.05
GenotypeData-class0.280.000.28
HLA0.020.000.02
IntensityData-class0.040.000.04
MatrixGenotypeReader-class000
NcdfGenotypeReader-class0.050.020.53
NcdfIntensityReader-class0.020.000.02
NcdfReader-class000
ScanAnnotationDataFrame-class0.080.000.08
ScanAnnotationSQLite-class0.040.030.08
SnpAnnotationDataFrame-class0.110.000.11
SnpAnnotationSQLite-class0.090.000.09
alleleFrequency0.160.000.16
allequal000
anomDetectBAF1.890.031.92
anomDetectLOH1.140.001.14
anomIdentifyLowQuality1.090.021.10
anomSegStats0.310.000.32
apartSnpSelection0.070.000.08
assocCoxPH0.540.000.59
assocRegression0.930.000.94
batchTest1.450.081.53
centromeres0.000.010.02
chromIntensityPlot0.080.020.09
convertNcdfGds0.380.000.48
createDataFile0.540.020.56
duplicateDiscordance0.50.00.5
duplicateDiscordanceAcrossDatasets0.140.000.14
duplicateDiscordanceProbability0.020.000.02
exactHWE0.170.000.17
findBAFvariance0.530.000.53
gdsSubset0.020.000.01
genoClusterPlot0.730.040.92
genotypeToCharacter000
getobj000
hetByScanChrom0.140.000.14
hetBySnpSex0.120.000.12
ibdPlot0.270.000.27
imputedDosageFile1.430.171.62
intensityOutliersPlot0.410.000.40
manhattanPlot0.010.000.01
meanIntensityByScanChrom0.390.000.39
mendelErr0.980.011.00
mendelList0.020.000.02
missingGenotypeByScanChrom0.120.000.12
missingGenotypeBySnpSex0.090.020.11
pasteSorted000
pcaSnpFilters0.020.000.01
pedigreeCheck0.050.000.05
pedigreeDeleteDuplicates000
pedigreeMaxUnrelated0.110.000.11
pedigreePairwiseRelatedness0.070.000.08
plinkUtils3.530.003.76
pseudoautoIntensityPlot0.110.000.10
pseudoautosomal0.000.020.02
qqPlot0.140.000.14
qualityScoreByScan0.220.010.23
qualityScoreBySnp0.030.020.05
readWriteFirst000
relationsMeanVar0.000.010.02
saveas000
setMissingGenotypes0.060.000.06
simulateGenotypeMatrix0.780.020.79
snpCorrelationPlot0.020.000.02
snpStats0.400.050.45
vcfWrite8.630.128.75