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BioC 2.14: CHECK report for GWASTools on moscato2

This page was generated on 2014-10-08 08:54:17 -0700 (Wed, 08 Oct 2014).

Package 377/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWASTools 1.10.1
Stephanie M. Gogarten , Adrienne Stilp
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GWASTools
Last Changed Rev: 89359 / Revision: 95116
Last Changed Date: 2014-04-22 14:21:06 -0700 (Tue, 22 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: GWASTools
Version: 1.10.1
Command: E:\biocbld\bbs-2.14-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings GWASTools_1.10.1.tar.gz
StartedAt: 2014-10-08 02:00:26 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:05:42 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 315.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   E:\biocbld\bbs-2.14-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings GWASTools_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/GWASTools.Rcheck'
* using R version 3.1.1 (2014-07-10)
* 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 '1.10.1'
* 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 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 ... [10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 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 files in 'vignettes' ... OK
* checking examples ... [86s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
assocTestRegression  25.28   0.00   25.31
assocTestFisherExact  7.89   0.00    7.90
BAFfromClusterMeans   1.22   0.05    6.88
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [111s]
 [111s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-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
** testing if installed package can be loaded
* DONE (GWASTools)

GWASTools.Rcheck/GWASTools-Ex.timings:

nameusersystemelapsed
BAFfromClusterMeans1.220.056.88
BAFfromGenotypes000
GdsGenotypeReader-class0.050.000.21
GdsReader-class0.010.010.03
GenotypeData-class0.190.000.28
HLA000
IntensityData-class0.070.001.80
MatrixGenotypeReader-class000
NcdfGenotypeReader-class0.000.000.17
NcdfIntensityReader-class0.040.000.03
NcdfReader-class000
ScanAnnotationDataFrame-class0.070.000.09
ScanAnnotationSQLite-class0.080.000.53
SnpAnnotationDataFrame-class0.100.020.16
SnpAnnotationSQLite-class0.090.001.71
alleleFrequency0.130.000.14
allequal000
anomDetectBAF2.340.004.54
anomDetectLOH1.530.001.53
anomIdentifyLowQuality1.500.012.32
anomSegStats0.420.020.44
apartSnpSelection0.140.000.14
assocTestCPH3.950.033.98
assocTestFisherExact7.890.007.90
assocTestRegression25.28 0.0025.31
batchTest0.620.030.65
centromeres000
chromIntensityPlot0.150.000.14
convertNcdfGds0.260.000.28
convertVcfGds0.020.000.05
duplicateDiscordance0.150.020.17
duplicateDiscordanceAcrossDatasets1.590.031.62
duplicateDiscordanceProbability000
findBAFvariance0.40.00.4
gdsImputedDosage1.350.031.66
gdsSubset0.060.010.07
genoClusterPlot0.330.022.53
genotypeToCharacter000
getobj000
gwasExactHW0.110.020.13
hetByScanChrom0.100.000.11
hetBySnpSex0.110.000.11
ibdPlot0.050.020.06
intensityOutliersPlot0.330.000.66
manhattanPlot0.010.000.01
meanIntensityByScanChrom0.280.010.30
mendelErr0.390.000.39
mendelList0.020.000.02
missingGenotypeByScanChrom0.120.000.12
missingGenotypeBySnpSex0.080.020.09
ncdfAddData0.790.011.75
ncdfCreate0.040.000.03
ncdfImputedDosage1.180.021.48
ncdfSetMissingGenotypes0.050.000.05
ncdfSubset0.060.000.06
pcaSnpFilters000
pedigreeCheck0.060.000.06
pedigreeDeleteDuplicates000
pedigreeMaxUnrelated0.100.000.09
pedigreePairwiseRelatedness0.040.000.05
plinkToNcdf2.250.013.20
plinkUtils3.810.024.06
pseudoautoIntensityPlot0.110.000.11
pseudoautosomal000
qqPlot0.050.000.05
qualityScoreByScan0.20.00.2
qualityScoreBySnp0.060.000.06
readWriteFirst0.020.000.02
relationsMeanVar000
saveas000
simulateGenotypeMatrix0.930.030.97
simulateIntensityMatrix0.170.020.19
snpCorrelationPlot000
snpStats3.090.033.12