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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: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.4.2.tar.gz
StartedAt: 2013-03-25 02:03:46 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:08:12 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 266.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GWASTools.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  31.842  0.044  32.608
assocTestFisherExact 11.565  0.012  11.766
assocTestCPH          6.240  0.016   6.398
* 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
BAFfromClusterMeans1.5000.0561.912
BAFfromGenotypes0.0000.0000.001
GdsGenotypeReader-class0.1880.0080.239
GdsReader-class0.0280.0040.031
GenotypeData-class0.0560.0280.102
HLA0.0040.0000.004
IntensityData-class0.0760.0040.107
MatrixGenotypeReader-class0.0040.0000.003
NcdfGenotypeReader-class0.0200.0000.019
NcdfIntensityReader-class0.0200.0040.022
NcdfReader-class0.0080.0000.010
ScanAnnotationDataFrame-class0.1360.0000.136
ScanAnnotationSQLite-class0.1080.0000.125
SnpAnnotationDataFrame-class0.1560.0000.162
SnpAnnotationSQLite-class0.1360.0000.170
alleleFrequency0.1680.0120.183
allequal0.0000.0000.001
anomDetectBAF1.6040.0201.969
anomDetectLOH1.1000.0081.303
anomIdentifyLowQuality1.1560.0161.223
anomSegStats0.3680.0120.533
apartSnpSelection0.1040.0040.106
assocTestCPH6.2400.0166.398
assocTestFisherExact11.565 0.01211.766
assocTestRegression31.842 0.04432.608
batchTest0.7080.0080.787
centromeres0.0040.0000.004
chromIntensityPlot0.1200.0160.140
convertNcdfGds0.2800.0200.376
convertVcfGds0.0320.0080.058
duplicateDiscordance0.3360.0160.419
duplicateDiscordanceAcrossDatasets0.3720.0080.448
duplicateDiscordanceProbability0.0040.0000.001
findBAFvariance0.460.000.54
genoClusterPlot0.3400.0360.488
getobj000
gwasExactHW0.2120.0120.237
hetByScanChrom0.1400.0000.151
hetBySnpSex0.1440.0040.165
ibdPlot0.0560.0000.058
intensityOutliersPlot0.4520.0040.491
manhattanPlot0.0040.0040.007
meanIntensityByScanChrom0.3840.0000.384
mendelErr0.5200.0040.539
mendelList0.0160.0000.013
missingGenotypeByScanChrom0.1520.0040.165
missingGenotypeBySnpSex0.1080.0080.126
ncdfAddData0.6730.0120.850
ncdfCreate0.0400.0000.044
ncdfImputedDosage1.4400.0281.665
ncdfSetMissingGenotypes0.0600.0120.102
ncdfSubset0.0720.0080.079
pcaSnpFilters0.0080.0000.007
pedigreeCheck0.0160.0000.017
pedigreeClean0.0000.0000.006
pedigreeFindDuplicates0.0040.0000.007
pedigreePairwiseRelatedness0.0760.0000.075
plinkToNcdf2.4600.0282.587
plinkUtils2.7600.0362.798
pseudoautoIntensityPlot0.0640.0080.073
pseudoautosomal0.0040.0000.004
qqPlot0.0320.0000.033
qualityScoreByScan0.2640.0080.273
qualityScoreBySnp0.0960.0040.098
readWriteFirst0.0040.0000.005
relationsMeanVar0.0040.0000.002
saveas0.0040.0000.001
simulateGenotypeMatrix0.8680.0040.901
simulateIntensityMatrix0.3200.0080.347
snpCorrelationPlot0.0040.0000.005
snpStats4.5400.0564.808