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Package 258/554 | Hostname | OS / Arch | BUILD | CHECK | BUILD BIN | ||||
GWASTools 1.2.0 Stephanie M. Gogarten
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |||||
puck5 | Linux (Ubuntu 12.04) / 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 |
Package: GWASTools |
Version: 1.2.0 |
Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.2.0.tar.gz |
StartedAt: 2012-04-01 01:34:32 -0700 (Sun, 01 Apr 2012) |
EndedAt: 2012-04-01 01:37:13 -0700 (Sun, 01 Apr 2012) |
EllapsedTime: 161.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GWASTools.Rcheck |
Warnings: 0 |
* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/GWASTools.Rcheck' * using R version 2.15.0 RC (2012-03-22 r58802) * using platform: x86_64-unknown-linux-gnu (64-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 '1.2.0' * 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 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 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:
name | user | system | elapsed | |
BAFfromClusterMeans | 0.948 | 0.028 | 1.186 | |
BAFfromGenotypes | 0 | 0 | 0 | |
GenotypeData-class | 0.068 | 0.004 | 0.102 | |
HLA | 0.000 | 0.004 | 0.019 | |
IntensityData-class | 0.048 | 0.000 | 0.073 | |
MatrixGenotypeReader-class | 0.004 | 0.000 | 0.002 | |
NcdfGenotypeReader-class | 0.008 | 0.008 | 0.020 | |
NcdfIntensityReader-class | 0.02 | 0.00 | 0.02 | |
NcdfReader-class | 0.008 | 0.000 | 0.010 | |
ScanAnnotationDataFrame-class | 0.108 | 0.004 | 0.125 | |
ScanAnnotationSQLite-class | 0.084 | 0.004 | 0.351 | |
SnpAnnotationDataFrame-class | 0.116 | 0.008 | 0.142 | |
SnpAnnotationSQLite-class | 0.096 | 0.004 | 0.538 | |
alleleFrequency | 0.120 | 0.004 | 0.139 | |
allequal | 0 | 0 | 0 | |
anomDetectBAF | 1.468 | 0.000 | 1.508 | |
anomDetectLOH | 0.836 | 0.008 | 0.872 | |
anomIdentifyLowQuality | 0.984 | 0.012 | 1.034 | |
anomSegStats | 0.180 | 0.004 | 0.227 | |
apartSnpSelection | 0.100 | 0.000 | 0.116 | |
assocTestCPH | 4.312 | 0.004 | 4.337 | |
assocTestRegression | 25.326 | 0.000 | 25.350 | |
batchTest | 0.704 | 0.004 | 0.733 | |
centromeres | 0.004 | 0.000 | 0.021 | |
chromIntensityPlot | 0.076 | 0.004 | 0.101 | |
convertNcdfGds | 0.264 | 0.012 | 0.316 | |
duplicateDiscordance | 0.172 | 0.000 | 0.193 | |
duplicateDiscordanceAcrossDatasets | 0.320 | 0.020 | 0.394 | |
duplicateDiscordanceProbability | 0.000 | 0.000 | 0.001 | |
findBAFvariance | 0.464 | 0.000 | 0.481 | |
genoClusterPlot | 0.284 | 0.016 | 0.324 | |
getobj | 0 | 0 | 0 | |
gwasExactHW | 0.164 | 0.000 | 0.186 | |
hetByScanChrom | 0.124 | 0.000 | 0.127 | |
hetBySnpSex | 0.104 | 0.000 | 0.121 | |
ibdPlot | 0.044 | 0.004 | 0.067 | |
intensityOutliersPlot | 0.340 | 0.000 | 0.355 | |
manhattanPlot | 0.008 | 0.000 | 0.006 | |
meanIntensityByScanChrom | 0.288 | 0.000 | 0.291 | |
mendelErr | 0.384 | 0.008 | 0.407 | |
mendelList | 0.036 | 0.000 | 0.052 | |
missingGenotypeByScanChrom | 0.128 | 0.012 | 0.154 | |
missingGenotypeBySnpSex | 0.088 | 0.004 | 0.112 | |
ncdfAddData | 0.552 | 0.004 | 0.981 | |
ncdfCreate | 0.028 | 0.004 | 0.173 | |
ncdfSetMissingGenotypes | 0.060 | 0.000 | 0.291 | |
ncdfSubset | 0.072 | 0.000 | 0.197 | |
pcaSnpFilters | 0.004 | 0.000 | 0.019 | |
pedigreeCheck | 0.012 | 0.000 | 0.008 | |
pedigreeClean | 0.000 | 0.000 | 0.003 | |
pedigreeFindDuplicates | 0.004 | 0.000 | 0.006 | |
pedigreePairwiseRelatedness | 0.024 | 0.000 | 0.027 | |
plinkToNcdf | 1.732 | 0.004 | 2.027 | |
plinkUtils | 2.080 | 0.036 | 2.137 | |
pseudoautoIntensityPlot | 0.052 | 0.004 | 0.088 | |
pseudoautosomal | 0.000 | 0.004 | 0.018 | |
qqPlot | 0.028 | 0.000 | 0.029 | |
qualityScoreByScan | 0.200 | 0.004 | 0.224 | |
qualityScoreBySnp | 0.072 | 0.000 | 0.073 | |
readWriteFirst | 0.004 | 0.000 | 0.006 | |
relationsMeanVar | 0.00 | 0.00 | 0.01 | |
saveas | 0.000 | 0.000 | 0.001 | |
simulateGenotypeMatrix | 0.616 | 0.000 | 0.781 | |
simulateIntensityMatrix | 0.244 | 0.004 | 0.387 | |
snpCorrelationPlot | 0.004 | 0.000 | 0.002 | |