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Package 301/658HostnameOS / ArchBUILDCHECKBUILD BIN
GWASTools 1.5.9
Stephanie M. Gogarten
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GWASTools
Last Changed Rev: 74659 / Revision: 74774
Last Changed Date: 2013-03-21 12:58:50 -0700 (Thu, 21 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GWASTools
Version: 1.5.9
Command: E:\biocbld\bbs-2.12-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings GWASTools_1.5.9.tar.gz
StartedAt: 2013-03-25 02:56:05 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:00:17 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 251.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GWASTools.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-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 '1.5.9'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GWASTools' can be installed ... [9s] OK
* checking installed package size ... OK
* checking package 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
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [93s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
assocTestRegression  29.19   0.00   29.48
assocTestFisherExact  9.08   0.00    9.08
anomDetectBAF         2.70   0.00    5.34
BAFfromClusterMeans   1.09   0.03    6.16
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [42s]
 [43s] 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/GWASTools.Rcheck/00check.log'
for details.

GWASTools.Rcheck/00install.out:

* 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
   'Affymetrix.Rnw' using 'UTF-8' 
   'DataCleaning.Rnw' using 'UTF-8' 
   'Formats.Rnw' using 'UTF-8' 
   'VCF.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (GWASTools)

GWASTools.Rcheck/GWASTools-Ex.timings:

nameusersystemelapsed
BAFfromClusterMeans1.090.036.16
BAFfromGenotypes0.020.000.02
GdsGenotypeReader-class0.090.020.20
GdsReader-class0.040.000.04
GenotypeData-class0.330.050.48
HLA0.000.010.02
IntensityData-class0.110.021.53
MatrixGenotypeReader-class0.020.000.02
NcdfGenotypeReader-class0.050.000.08
NcdfIntensityReader-class0.060.000.06
NcdfReader-class0.030.000.03
ScanAnnotationDataFrame-class0.160.000.16
ScanAnnotationSQLite-class0.070.010.51
SnpAnnotationDataFrame-class0.130.000.16
SnpAnnotationSQLite-class0.110.021.24
alleleFrequency0.140.000.14
allequal000
anomDetectBAF2.700.005.34
anomDetectLOH1.610.001.60
anomIdentifyLowQuality1.480.022.64
anomSegStats0.500.000.55
apartSnpSelection0.110.000.11
assocTestCPH4.860.004.86
assocTestFisherExact9.080.009.08
assocTestRegression29.19 0.0029.48
batchTest0.710.000.72
centromeres0.000.010.02
chromIntensityPlot0.160.000.15
convertNcdfGds0.310.020.33
convertVcfGds0.030.000.04
duplicateDiscordance0.220.000.48
duplicateDiscordanceAcrossDatasets202
duplicateDiscordanceProbability0.000.000.02
findBAFvariance0.460.010.47
genoClusterPlot0.420.022.59
genotypeToCharacter000
getobj000
gwasExactHW0.170.000.17
hetByScanChrom0.140.000.14
hetBySnpSex0.130.000.12
ibdPlot0.050.000.05
intensityOutliersPlot0.390.000.84
manhattanPlot0.020.000.02
meanIntensityByScanChrom0.370.000.38
mendelErr0.480.000.49
mendelList0.010.000.01
missingGenotypeByScanChrom0.130.010.14
missingGenotypeBySnpSex0.110.000.11
ncdfAddData0.890.053.01
ncdfCreate0.070.000.06
ncdfImputedDosage1.650.022.46
ncdfSetMissingGenotypes0.060.000.06
ncdfSubset0.080.000.08
pcaSnpFilters000
pedigreeCheck0.060.000.06
pedigreeDeleteDuplicates0.010.000.02
pedigreeMaxUnrelated0.110.000.11
pedigreePairwiseRelatedness0.050.000.04
plinkToNcdf2.320.012.87
plinkUtils3.850.053.90
pseudoautoIntensityPlot0.140.010.15
pseudoautosomal000
qqPlot0.050.000.04
qualityScoreByScan0.220.000.24
qualityScoreBySnp0.060.020.07
readWriteFirst000
relationsMeanVar0.010.000.02
saveas0.020.000.01
simulateGenotypeMatrix0.950.000.95
simulateIntensityMatrix0.190.020.21
snpCorrelationPlot000
snpStats3.050.043.09