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Package 282/609HostnameOS / ArchBUILDCHECKBUILD BIN
GWASTools 1.4.2
Stephanie M. Gogarten
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/GWASTools
Last Changed Rev: 73098 / Revision: 74773
Last Changed Date: 2013-02-02 16:49:37 -0800 (Sat, 02 Feb 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GWASTools
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.4.2.tar.gz
StartedAt: 2013-03-24 23:57:31 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-25 00:01:39 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 248.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GWASTools.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.4.2'
* 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 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  29.246  0.114  29.887
assocTestFisherExact 10.610  0.040  10.729
assocTestCPH          5.602  0.026   5.691
* 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
**  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
BAFfromClusterMeans1.4500.2911.864
BAFfromGenotypes000
GdsGenotypeReader-class0.0720.0150.135
GdsReader-class0.0290.0080.039
GenotypeData-class0.1330.0120.151
HLA0.0020.0010.004
IntensityData-class0.0600.0120.076
MatrixGenotypeReader-class0.0030.0010.004
NcdfGenotypeReader-class0.0180.0050.024
NcdfIntensityReader-class0.0230.0060.029
NcdfReader-class0.0090.0020.011
ScanAnnotationDataFrame-class0.2030.0060.209
ScanAnnotationSQLite-class0.0930.0140.109
SnpAnnotationDataFrame-class0.1400.0060.151
SnpAnnotationSQLite-class0.1210.0170.140
alleleFrequency0.1380.0200.160
allequal0.0010.0000.001
anomDetectBAF1.6750.0441.768
anomDetectLOH1.2050.0291.248
anomIdentifyLowQuality1.2170.0671.291
anomSegStats0.4170.0590.523
apartSnpSelection0.1320.0070.140
assocTestCPH5.6020.0265.691
assocTestFisherExact10.610 0.04010.729
assocTestRegression29.246 0.11429.887
batchTest0.7180.0330.807
centromeres0.0020.0010.003
chromIntensityPlot0.1380.0160.157
convertNcdfGds0.3230.0730.447
convertVcfGds0.0520.0190.074
duplicateDiscordance0.2230.0300.262
duplicateDiscordanceAcrossDatasets0.4420.0390.496
duplicateDiscordanceProbability0.0020.0010.001
findBAFvariance0.5610.0450.624
genoClusterPlot0.3580.0650.443
getobj0.0010.0020.002
gwasExactHW0.2160.0210.238
hetByScanChrom0.2210.0100.232
hetBySnpSex0.1340.0230.164
ibdPlot0.0550.0030.058
intensityOutliersPlot0.4320.0520.499
manhattanPlot0.0070.0010.009
meanIntensityByScanChrom0.3650.0380.406
mendelErr0.4820.0450.535
mendelList0.0130.0010.013
missingGenotypeByScanChrom0.1520.0060.159
missingGenotypeBySnpSex0.1180.0150.134
ncdfAddData0.6340.1330.817
ncdfCreate0.0400.0060.051
ncdfImputedDosage1.1720.1151.438
ncdfSetMissingGenotypes0.0720.0110.090
ncdfSubset0.0720.0060.080
pcaSnpFilters0.0030.0010.005
pedigreeCheck0.0190.0010.021
pedigreeClean0.0020.0010.003
pedigreeFindDuplicates0.0090.0000.010
pedigreePairwiseRelatedness0.0750.0030.088
plinkToNcdf2.1800.2082.604
plinkUtils2.4020.2292.702
pseudoautoIntensityPlot0.0840.0160.107
pseudoautosomal0.0020.0010.004
qqPlot0.0270.0040.031
qualityScoreByScan0.2450.0450.297
qualityScoreBySnp0.0730.0270.104
readWriteFirst0.0030.0030.006
relationsMeanVar0.0020.0010.002
saveas0.0020.0010.005
simulateGenotypeMatrix0.6070.0670.694
simulateIntensityMatrix0.3360.0870.456
snpCorrelationPlot0.0040.0000.005
snpStats4.4480.1974.720