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Package 238/514HostnameOS / ArchBUILDCHECKBUILD BIN
GWASTools 1.0.0
Stephanie Gogarten
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GWASTools
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GWASTools
Version: 1.0.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings GWASTools_1.0.0.tar.gz
StartedAt: 2012-03-24 01:45:53 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:48:45 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 172.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GWASTools.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-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 '1.0.0'
* 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 whether package 'GWASTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 for unstated 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

GWASTools.Rcheck/00install.out:

* installing *source* package 'GWASTools' ...
** R
** data
** 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 ...
*** tangling vignette sources ...
   'DataCleaning.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (GWASTools)

GWASTools.Rcheck/GWASTools-Ex.timings:

nameusersystemelapsed
BAFfromClusterMeans1.150.035.59
BAFfromGenotypes000
GenotypeData-class0.080.020.09
HLA000
IntensityData-class0.110.000.11
MatrixGenotypeReader-class000
NcdfGenotypeReader-class0.030.000.03
NcdfIntensityReader-class0.030.000.03
NcdfReader-class0.020.000.02
ScanAnnotationDataFrame-class0.090.000.09
ScanAnnotationSQLite-class0.130.000.67
SnpAnnotationDataFrame-class0.120.000.13
SnpAnnotationSQLite-class0.160.011.53
alleleFrequency0.200.020.22
allequal000
anomDetectBAF2.600.002.87
anomDetectLOH1.720.001.72
anomIdentifyLowQuality1.730.052.51
anomSegStats0.220.000.22
apartSnpSelection0.080.010.09
assocTestCPH5.620.005.62
assocTestRegression18.11 0.0018.11
batchTest0.640.000.64
centromeres000
chromIntensityPlot0.120.000.13
convertNcdfGds0.420.020.58
duplicateDiscordance0.060.000.72
duplicateDiscordanceAcrossDatasets0.530.010.56
duplicateDiscordanceProbability000
findBAFvariance0.590.000.59
genoClusterPlot0.330.050.38
getobj000
gwasExactHW0.170.000.17
hetByScanChrom0.130.000.12
hetBySnpSex0.110.020.13
ibdPlot0.030.000.04
intensityOutliersPlot0.390.000.39
manhattanPlot0.010.000.02
meanIntensityByScanChrom0.350.000.34
mendelErr0.470.000.47
mendelList0.040.000.05
missingGenotypeByScanChrom0.140.000.14
missingGenotypeBySnpSex0.110.010.12
ncdfAddData0.810.023.13
ncdfCreate0.030.000.03
ncdfSubset0.060.000.07
pedigreeCheck0.020.000.01
pedigreeClean000
pedigreeFindDuplicates0.010.000.02
pedigreePairwiseRelatedness0.020.000.01
pseudoautoIntensityPlot0.110.000.13
pseudoautosomal000
qqPlot0.040.000.05
qualityScoreByScan0.210.000.21
qualityScoreBySnp0.060.000.07
readWriteFirst0.00.00.7
relationsMeanVar000
saveas0.020.000.01
simulateGenotypeMatrix1.070.001.08
simulateIntensityMatrix0.310.000.31
snpCorrelationPlot0.020.000.02