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This page was generated on 2015-10-27 17:29:42 -0400 (Tue, 27 Oct 2015).
| Package 481/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| GWASTools 1.16.1 Stephanie M. Gogarten
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK |  | |||||
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | | |||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| Package: GWASTools |
| Version: 1.16.1 |
| Command: rm -rf GWASTools.buildbin-libdir GWASTools.Rcheck && mkdir GWASTools.buildbin-libdir GWASTools.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.16.1.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GWASTools.buildbin-libdir --install="check:GWASTools-install.out" --force-multiarch --no-vignettes --timings GWASTools_1.16.1.tar.gz |
| StartedAt: 2015-10-27 02:37:35 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 02:45:10 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 455.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GWASTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf GWASTools.buildbin-libdir GWASTools.Rcheck && mkdir GWASTools.buildbin-libdir GWASTools.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GWASTools.buildbin-libdir GWASTools_1.16.1.tar.gz >GWASTools.Rcheck\00install.out 2>&1 && cp GWASTools.Rcheck\00install.out GWASTools-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GWASTools.buildbin-libdir --install="check:GWASTools-install.out" --force-multiarch --no-vignettes --timings GWASTools_1.16.1.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GWASTools.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 'GWASTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GWASTools' version '1.16.1'
* 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 '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' ... [38s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
vcfWrite 7.61 0.19 7.8
** running examples for arch 'x64' ... [34s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
vcfWrite 8.56 0.15 8.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R' [123s]
[123s] OK
** running tests for arch 'x64' ...
Running 'test.R' [136s]
[137s] 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_1.16.1.zip * DONE (GWASTools)
GWASTools.Rcheck/examples_i386/GWASTools-Ex.timings:
| name | user | system | elapsed | |
| BAFfromClusterMeans | 1.50 | 0.04 | 2.17 | |
| BAFfromGenotypes | 0 | 0 | 0 | |
| GdsGenotypeReader-class | 0.03 | 0.02 | 0.10 | |
| GdsIntensityReader-class | 0.03 | 0.00 | 0.03 | |
| GdsReader-class | 0.05 | 0.01 | 0.26 | |
| GenotypeData-class | 0.09 | 0.05 | 0.19 | |
| HLA | 0 | 0 | 0 | |
| IntensityData-class | 0.02 | 0.01 | 0.03 | |
| MatrixGenotypeReader-class | 0 | 0 | 0 | |
| NcdfGenotypeReader-class | 0 | 0 | 0 | |
| NcdfIntensityReader-class | 0.00 | 0.00 | 0.17 | |
| NcdfReader-class | 0.01 | 0.00 | 0.02 | |
| ScanAnnotationDataFrame-class | 0.06 | 0.00 | 0.09 | |
| ScanAnnotationSQLite-class | 0.05 | 0.00 | 0.05 | |
| SnpAnnotationDataFrame-class | 0.04 | 0.01 | 0.21 | |
| SnpAnnotationSQLite-class | 0.08 | 0.00 | 0.08 | |
| alleleFrequency | 0.13 | 0.02 | 0.14 | |
| allequal | 0.01 | 0.00 | 0.01 | |
| anomDetectBAF | 2.17 | 0.00 | 2.30 | |
| anomDetectLOH | 1.19 | 0.01 | 1.20 | |
| anomIdentifyLowQuality | 0.97 | 0.00 | 0.97 | |
| anomSegStats | 0.3 | 0.0 | 0.3 | |
| apartSnpSelection | 0.06 | 0.00 | 0.06 | |
| assocCoxPH | 0.30 | 0.02 | 0.31 | |
| assocRegression | 0.54 | 0.00 | 0.55 | |
| batchTest | 1.35 | 0.08 | 1.42 | |
| centromeres | 0 | 0 | 0 | |
| chromIntensityPlot | 0.09 | 0.00 | 0.09 | |
| convertNcdfGds | 0.45 | 0.02 | 0.56 | |
| convertVcfGds | 0.05 | 0.02 | 0.11 | |
| createDataFile | 0.64 | 0.01 | 1.50 | |
| duplicateDiscordance | 0.57 | 0.00 | 0.58 | |
| duplicateDiscordanceAcrossDatasets | 0.19 | 0.00 | 0.18 | |
| duplicateDiscordanceProbability | 0 | 0 | 0 | |
| exactHWE | 0.19 | 0.02 | 0.21 | |
| findBAFvariance | 0.30 | 0.00 | 0.29 | |
| gdsSubset | 0.03 | 0.00 | 0.03 | |
| genoClusterPlot | 0.67 | 0.00 | 3.35 | |
| genotypeToCharacter | 0 | 0 | 0 | |
| getobj | 0 | 0 | 0 | |
| hetByScanChrom | 0.10 | 0.00 | 0.11 | |
| hetBySnpSex | 0.13 | 0.00 | 0.13 | |
| ibdPlot | 0.03 | 0.00 | 0.03 | |
| imputedDosageFile | 0.97 | 0.07 | 1.59 | |
| intensityOutliersPlot | 0.31 | 0.00 | 0.31 | |
| manhattanPlot | 0.03 | 0.00 | 0.03 | |
| meanIntensityByScanChrom | 0.31 | 0.00 | 0.32 | |
| mendelErr | 0.91 | 0.02 | 0.92 | |
| mendelList | 0 | 0 | 0 | |
| missingGenotypeByScanChrom | 0.11 | 0.00 | 0.11 | |
| missingGenotypeBySnpSex | 0.09 | 0.02 | 0.11 | |
| ncdfSubset | 0.03 | 0.00 | 0.03 | |
| pasteSorted | 0 | 0 | 0 | |
| pcaSnpFilters | 0.02 | 0.00 | 0.01 | |
| pedigreeCheck | 0.03 | 0.00 | 0.03 | |
| pedigreeDeleteDuplicates | 0 | 0 | 0 | |
| pedigreeMaxUnrelated | 0.05 | 0.00 | 0.05 | |
| pedigreePairwiseRelatedness | 0.01 | 0.00 | 0.02 | |
| plinkToNcdf | 1.47 | 0.00 | 1.68 | |
| plinkUtils | 2.72 | 0.01 | 2.73 | |
| pseudoautoIntensityPlot | 0.06 | 0.00 | 0.06 | |
| pseudoautosomal | 0 | 0 | 0 | |
| qqPlot | 0.11 | 0.00 | 0.11 | |
| qualityScoreByScan | 0.20 | 0.00 | 0.21 | |
| qualityScoreBySnp | 0.05 | 0.02 | 0.06 | |
| readWriteFirst | 0 | 0 | 0 | |
| relationsMeanVar | 0 | 0 | 0 | |
| saveas | 0 | 0 | 0 | |
| setMissingGenotypes | 0.09 | 0.00 | 0.09 | |
| simulateGenotypeMatrix | 0.64 | 0.00 | 0.64 | |
| simulateIntensityMatrix | 0.18 | 0.04 | 0.22 | |
| snpCorrelationPlot | 0.01 | 0.00 | 0.02 | |
| snpStats | 0.53 | 0.02 | 0.54 | |
| vcfWrite | 7.61 | 0.19 | 7.80 | |
GWASTools.Rcheck/examples_x64/GWASTools-Ex.timings:
| name | user | system | elapsed | |
| BAFfromClusterMeans | 1.13 | 0.05 | 1.17 | |
| BAFfromGenotypes | 0 | 0 | 0 | |
| GdsGenotypeReader-class | 0.01 | 0.01 | 0.03 | |
| GdsIntensityReader-class | 0.02 | 0.00 | 0.02 | |
| GdsReader-class | 0.06 | 0.00 | 0.06 | |
| GenotypeData-class | 0.14 | 0.02 | 0.15 | |
| HLA | 0 | 0 | 0 | |
| IntensityData-class | 0.05 | 0.00 | 0.05 | |
| MatrixGenotypeReader-class | 0 | 0 | 0 | |
| NcdfGenotypeReader-class | 0.01 | 0.00 | 0.01 | |
| NcdfIntensityReader-class | 0.02 | 0.00 | 0.02 | |
| NcdfReader-class | 0 | 0 | 0 | |
| ScanAnnotationDataFrame-class | 0.06 | 0.00 | 0.06 | |
| ScanAnnotationSQLite-class | 0.05 | 0.01 | 0.06 | |
| SnpAnnotationDataFrame-class | 0.07 | 0.00 | 0.08 | |
| SnpAnnotationSQLite-class | 0.08 | 0.00 | 0.08 | |
| alleleFrequency | 0.17 | 0.00 | 0.17 | |
| allequal | 0 | 0 | 0 | |
| anomDetectBAF | 1.46 | 0.02 | 1.47 | |
| anomDetectLOH | 0.86 | 0.00 | 0.86 | |
| anomIdentifyLowQuality | 0.95 | 0.03 | 0.98 | |
| anomSegStats | 0.42 | 0.02 | 0.44 | |
| apartSnpSelection | 0.06 | 0.00 | 0.06 | |
| assocCoxPH | 0.58 | 0.00 | 0.58 | |
| assocRegression | 0.76 | 0.00 | 0.76 | |
| batchTest | 1.33 | 0.10 | 1.44 | |
| centromeres | 0.02 | 0.00 | 0.02 | |
| chromIntensityPlot | 0.09 | 0.00 | 0.09 | |
| convertNcdfGds | 0.22 | 0.02 | 0.23 | |
| convertVcfGds | 0.05 | 0.00 | 0.05 | |
| createDataFile | 0.42 | 0.03 | 0.45 | |
| duplicateDiscordance | 0.44 | 0.03 | 0.47 | |
| duplicateDiscordanceAcrossDatasets | 0.12 | 0.00 | 0.13 | |
| duplicateDiscordanceProbability | 0 | 0 | 0 | |
| exactHWE | 0.17 | 0.00 | 0.17 | |
| findBAFvariance | 0.41 | 0.00 | 0.41 | |
| gdsSubset | 0.01 | 0.02 | 0.03 | |
| genoClusterPlot | 0.60 | 0.03 | 0.62 | |
| genotypeToCharacter | 0 | 0 | 0 | |
| getobj | 0 | 0 | 0 | |
| hetByScanChrom | 0.14 | 0.00 | 0.14 | |
| hetBySnpSex | 0.12 | 0.00 | 0.13 | |
| ibdPlot | 0.03 | 0.00 | 0.04 | |
| imputedDosageFile | 0.81 | 0.06 | 0.87 | |
| intensityOutliersPlot | 0.58 | 0.02 | 0.59 | |
| manhattanPlot | 0.03 | 0.00 | 0.04 | |
| meanIntensityByScanChrom | 0.55 | 0.01 | 0.56 | |
| mendelErr | 1.31 | 0.02 | 1.33 | |
| mendelList | 0.02 | 0.00 | 0.01 | |
| missingGenotypeByScanChrom | 0.12 | 0.00 | 0.13 | |
| missingGenotypeBySnpSex | 0.11 | 0.01 | 0.12 | |
| ncdfSubset | 0.03 | 0.00 | 0.03 | |
| pasteSorted | 0 | 0 | 0 | |
| pcaSnpFilters | 0.02 | 0.00 | 0.02 | |
| pedigreeCheck | 0.03 | 0.00 | 0.03 | |
| pedigreeDeleteDuplicates | 0.02 | 0.00 | 0.02 | |
| pedigreeMaxUnrelated | 0.06 | 0.00 | 0.06 | |
| pedigreePairwiseRelatedness | 0.05 | 0.00 | 0.04 | |
| plinkToNcdf | 1.76 | 0.02 | 1.79 | |
| plinkUtils | 2.78 | 0.08 | 2.86 | |
| pseudoautoIntensityPlot | 0.08 | 0.00 | 0.08 | |
| pseudoautosomal | 0.00 | 0.01 | 0.01 | |
| qqPlot | 0.11 | 0.00 | 0.11 | |
| qualityScoreByScan | 0.20 | 0.00 | 0.21 | |
| qualityScoreBySnp | 0.05 | 0.00 | 0.04 | |
| readWriteFirst | 0.01 | 0.00 | 0.02 | |
| relationsMeanVar | 0 | 0 | 0 | |
| saveas | 0 | 0 | 0 | |
| setMissingGenotypes | 0.06 | 0.00 | 0.06 | |
| simulateGenotypeMatrix | 0.52 | 0.00 | 0.52 | |
| simulateIntensityMatrix | 0.11 | 0.00 | 0.11 | |
| snpCorrelationPlot | 0.02 | 0.00 | 0.02 | |
| snpStats | 0.61 | 0.04 | 0.64 | |
| vcfWrite | 8.56 | 0.15 | 8.72 | |