Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 257/553HostnameOS / ArchBUILDCHECKBUILD BIN
GWASTools 1.2.1
Stephanie M. Gogarten
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/GWASTools
Last Changed Rev: 67010 / Revision: 69725
Last Changed Date: 2012-06-25 14:57:49 -0700 (Mon, 25 Jun 2012)
lamb2 Linux (openSUSE 11.4) / 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: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.2.1.tar.gz
StartedAt: 2012-09-24 00:32:19 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:36:17 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 237.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/GWASTools.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GWASTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GWASTools' version '1.2.1'
* 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 whether package 'GWASTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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
** installing vignettes
   'DataCleaning.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (GWASTools)

GWASTools.Rcheck/GWASTools-Ex.timings:

nameusersystemelapsed
BAFfromClusterMeans1.6530.2742.108
BAFfromGenotypes0.0000.0000.001
GenotypeData-class0.0860.0120.142
HLA0.0020.0010.003
IntensityData-class0.0660.0160.106
MatrixGenotypeReader-class0.0030.0000.004
NcdfGenotypeReader-class0.0160.0030.019
NcdfIntensityReader-class0.0210.0030.024
NcdfReader-class0.0080.0020.011
ScanAnnotationDataFrame-class0.1350.0070.142
ScanAnnotationSQLite-class0.1200.0150.143
SnpAnnotationDataFrame-class0.1620.0100.173
SnpAnnotationSQLite-class0.1250.0150.152
alleleFrequency0.2420.0230.267
allequal0.0000.0000.001
anomDetectBAF2.1520.0452.241
anomDetectLOH1.7310.0331.765
anomIdentifyLowQuality1.7440.0711.856
anomSegStats0.2820.0310.313
apartSnpSelection0.1830.0070.190
assocTestCPH8.0050.0168.021
assocTestRegression36.461 0.03136.493
batchTest0.7700.0220.793
centromeres0.0030.0010.004
chromIntensityPlot0.1040.0110.115
convertNcdfGds0.4990.0780.735
duplicateDiscordance0.3350.0260.364
duplicateDiscordanceAcrossDatasets0.5280.0300.559
duplicateDiscordanceProbability0.0010.0000.001
findBAFvariance0.6330.0390.672
genoClusterPlot0.4030.0620.479
getobj0.0010.0010.003
gwasExactHW0.2500.0210.271
hetByScanChrom0.1770.0060.183
hetBySnpSex0.1620.0210.186
ibdPlot0.0940.0040.098
intensityOutliersPlot0.5570.0460.626
manhattanPlot0.0070.0020.009
meanIntensityByScanChrom0.4420.0330.476
mendelErr0.5470.0360.582
mendelList0.0500.0040.054
missingGenotypeByScanChrom0.1640.0060.170
missingGenotypeBySnpSex0.1270.0120.139
ncdfAddData0.7880.1000.985
ncdfCreate0.0400.0060.050
ncdfSetMissingGenotypes0.0910.0090.119
ncdfSubset0.1240.0060.136
pcaSnpFilters0.0040.0010.005
pedigreeCheck0.0140.0000.015
pedigreeClean0.0050.0000.005
pedigreeFindDuplicates0.0110.0000.012
pedigreePairwiseRelatedness0.0480.0010.049
plinkToNcdf3.5120.1913.736
plinkUtils3.1630.1903.363
pseudoautoIntensityPlot0.0950.0100.108
pseudoautosomal0.0030.0010.004
qqPlot0.0380.0030.042
qualityScoreByScan0.2870.0370.324
qualityScoreBySnp0.0930.0230.119
readWriteFirst0.0030.0030.006
relationsMeanVar0.0020.0010.002
saveas0.0010.0010.002
simulateGenotypeMatrix0.8530.0500.912
simulateIntensityMatrix0.3780.0740.471
snpCorrelationPlot0.0030.0000.003