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BioC 3.1: CHECK report for GWASTools on moscato2

This page was generated on 2015-10-09 09:29:27 -0700 (Fri, 09 Oct 2015).

Package 452/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWASTools 1.14.2
Stephanie M. Gogarten , Adrienne Stilp
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/GWASTools
Last Changed Rev: 109335 / Revision: 109384
Last Changed Date: 2015-10-07 16:11:28 -0700 (Wed, 07 Oct 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.14.2
Command: rm -rf GWASTools.buildbin-libdir GWASTools.Rcheck && mkdir GWASTools.buildbin-libdir GWASTools.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.14.2.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GWASTools.buildbin-libdir --install="check:GWASTools-install.out" --force-multiarch --no-vignettes --timings GWASTools_1.14.2.tar.gz
StartedAt: 2015-10-09 02:46:40 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:57:37 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 656.9 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.14.2.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GWASTools.buildbin-libdir --install="check:GWASTools-install.out" --force-multiarch --no-vignettes --timings GWASTools_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/GWASTools.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 'GWASTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GWASTools' version '1.14.2'
* 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 ... NOTE
'library' or 'require' call to 'snpStats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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' ... [58s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
vcfWrite            9.72   0.16    9.87
plinkUtils          5.18   0.01    5.53
BAFfromClusterMeans 1.66   0.03    5.32
** running examples for arch 'x64' ... [50s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 10.76   0.12   11.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R' [173s]
 [174s] OK
** running tests for arch 'x64' ...
  Running 'test.R' [193s]
 [193s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/GWASTools.Rcheck/00check.log'
for details.


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_1.14.2.zip
* DONE (GWASTools)

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

nameusersystemelapsed
BAFfromClusterMeans1.660.035.32
BAFfromGenotypes000
GdsGenotypeReader-class0.040.000.08
GdsIntensityReader-class0.030.000.03
GdsReader-class0.100.001.34
GenotypeData-class0.140.021.44
HLA0.010.000.01
IntensityData-class0.050.000.05
MatrixGenotypeReader-class0.020.000.01
NcdfGenotypeReader-class0.010.000.04
NcdfIntensityReader-class0.020.000.25
NcdfReader-class0.000.000.03
ScanAnnotationDataFrame-class0.070.000.14
ScanAnnotationSQLite-class0.070.000.06
SnpAnnotationDataFrame-class0.100.000.21
SnpAnnotationSQLite-class0.090.000.09
alleleFrequency0.170.020.19
allequal000
anomDetectBAF2.290.002.41
anomDetectLOH1.530.001.53
anomIdentifyLowQuality1.430.001.45
anomSegStats0.330.000.35
apartSnpSelection0.060.010.11
assocCoxPH0.370.000.37
assocRegression0.610.030.64
assocTestCPH0.020.000.02
assocTestFisherExact000
assocTestRegression000
batchTest1.510.141.65
centromeres000
chromIntensityPlot0.100.020.11
convertNcdfGds0.280.000.43
convertVcfGds0.050.000.07
createDataFile1.000.012.66
duplicateDiscordance0.560.000.57
duplicateDiscordanceAcrossDatasets0.140.000.14
duplicateDiscordanceProbability000
exactHWE0.170.020.18
findBAFvariance0.390.020.41
gdsSubset0.030.000.04
genoClusterPlot2.070.072.15
genotypeToCharacter000
getobj000
gwasExactHW000
hetByScanChrom0.160.000.15
hetBySnpSex0.240.000.23
ibdPlot0.040.000.05
imputedDosageFile1.760.024.57
intensityOutliersPlot0.460.030.48
manhattanPlot0.020.000.01
meanIntensityByScanChrom0.410.020.42
mendelErr1.090.011.11
mendelList000
missingGenotypeByScanChrom0.140.020.15
missingGenotypeBySnpSex0.120.000.13
ncdfSubset0.040.010.08
pasteSorted000
pcaSnpFilters000
pedigreeCheck0.050.000.05
pedigreeDeleteDuplicates000
pedigreeMaxUnrelated0.080.000.08
pedigreePairwiseRelatedness0.040.000.04
plinkToNcdf2.550.023.89
plinkUtils5.180.015.53
pseudoautoIntensityPlot0.170.000.17
pseudoautosomal0.000.020.01
qqPlot0.210.000.21
qualityScoreByScan0.430.000.43
qualityScoreBySnp0.080.000.08
readWriteFirst0.020.000.02
relationsMeanVar000
saveas0.010.000.01
setMissingGenotypes0.130.010.14
simulateGenotypeMatrix1.180.001.56
simulateIntensityMatrix0.160.000.17
snpCorrelationPlot0.010.000.02
snpStats0.800.020.83
vcfWrite9.720.169.87

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

nameusersystemelapsed
BAFfromClusterMeans1.920.062.06
BAFfromGenotypes000
GdsGenotypeReader-class0.060.000.07
GdsIntensityReader-class0.030.000.03
GdsReader-class0.110.020.29
GenotypeData-class0.300.030.39
HLA000
IntensityData-class0.100.000.09
MatrixGenotypeReader-class000
NcdfGenotypeReader-class0.030.000.03
NcdfIntensityReader-class0.040.000.05
NcdfReader-class0.020.000.02
ScanAnnotationDataFrame-class0.120.000.12
ScanAnnotationSQLite-class0.090.000.09
SnpAnnotationDataFrame-class0.180.000.17
SnpAnnotationSQLite-class0.140.010.16
alleleFrequency0.310.000.31
allequal000
anomDetectBAF2.490.002.50
anomDetectLOH1.390.001.39
anomIdentifyLowQuality1.260.021.28
anomSegStats0.320.000.33
apartSnpSelection0.080.020.09
assocCoxPH0.460.000.45
assocRegression1.130.011.16
assocTestCPH000
assocTestFisherExact000
assocTestRegression0.000.020.01
batchTest2.170.042.22
centromeres000
chromIntensityPlot0.110.040.14
convertNcdfGds0.430.010.48
convertVcfGds0.050.000.08
createDataFile0.680.030.78
duplicateDiscordance0.630.000.63
duplicateDiscordanceAcrossDatasets0.160.000.16
duplicateDiscordanceProbability000
exactHWE0.060.000.06
findBAFvariance0.480.000.48
gdsSubset0.050.000.05
genoClusterPlot2.200.032.76
genotypeToCharacter000
getobj000
gwasExactHW000
hetByScanChrom0.190.000.19
hetBySnpSex0.170.000.17
ibdPlot0.040.000.04
imputedDosageFile1.230.001.27
intensityOutliersPlot0.570.000.56
manhattanPlot0.030.000.03
meanIntensityByScanChrom0.610.000.61
mendelErr1.590.001.59
mendelList000
missingGenotypeByScanChrom0.150.010.17
missingGenotypeBySnpSex0.160.000.15
ncdfSubset0.060.000.07
pasteSorted000
pcaSnpFilters0.000.020.01
pedigreeCheck0.050.000.05
pedigreeDeleteDuplicates0.010.000.01
pedigreeMaxUnrelated0.10.00.1
pedigreePairwiseRelatedness0.040.000.04
plinkToNcdf3.090.003.12
plinkUtils4.850.034.89
pseudoautoIntensityPlot0.170.000.17
pseudoautosomal0.000.020.02
qqPlot0.20.00.2
qualityScoreByScan0.50.00.5
qualityScoreBySnp0.080.010.09
readWriteFirst0.020.000.02
relationsMeanVar000
saveas000
setMissingGenotypes0.120.020.30
simulateGenotypeMatrix1.140.011.15
simulateIntensityMatrix0.190.000.19
snpCorrelationPlot0.010.000.01
snpStats0.580.020.61
vcfWrite10.76 0.1211.03