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BioC 2.13: CHECK report for GWASTools on zin1

This page was generated on 2014-04-05 09:48:10 -0700 (Sat, 05 Apr 2014).

Package 336/750HostnameOS / ArchBUILDCHECKBUILD BIN
GWASTools 1.8.1
Stephanie M. Gogarten , Adrienne Stilp
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GWASTools
Last Changed Rev: 86824 / Revision: 88450
Last Changed Date: 2014-02-25 18:21:37 -0800 (Tue, 25 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GWASTools
Version: 1.8.1
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.8.1.tar.gz
StartedAt: 2014-04-05 01:47:05 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:50:37 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 211.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GWASTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GWASTools’ can be installed ... [6s/6s] 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Affymetrix.Rnw’, ‘DataCleaning.Rnw’, ‘Formats.Rnw’, ‘VCF.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [73s/76s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  30.702  0.028  30.803
assocTestFisherExact 10.005  0.008  10.046
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [34s/42s]
 [34s/42s] 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
BAFfromClusterMeans1.2360.0161.402
BAFfromGenotypes0.0080.0000.008
GdsGenotypeReader-class0.1160.0120.152
GdsReader-class0.0200.0080.025
GenotypeData-class0.2160.0000.306
HLA0.0040.0000.004
IntensityData-class0.0640.0000.086
MatrixGenotypeReader-class0.0160.0000.017
NcdfGenotypeReader-class0.0240.0040.028
NcdfIntensityReader-class0.0400.0000.037
NcdfReader-class0.0720.0000.076
ScanAnnotationDataFrame-class0.0920.0000.091
ScanAnnotationSQLite-class0.0800.0080.258
SnpAnnotationDataFrame-class0.1160.0040.120
SnpAnnotationSQLite-class0.0960.0040.432
alleleFrequency0.1480.0040.151
allequal0.0040.0000.004
anomDetectBAF1.3320.0041.339
anomDetectLOH0.9240.0040.925
anomIdentifyLowQuality1.0160.0001.021
anomSegStats0.3920.0120.403
apartSnpSelection0.1040.0000.102
assocTestCPH4.6040.0044.633
assocTestFisherExact10.005 0.00810.046
assocTestRegression30.702 0.02830.803
batchTest0.6800.0120.691
centromeres0.0000.0040.004
chromIntensityPlot0.1200.0040.127
convertNcdfGds0.3240.0120.348
convertVcfGds0.1080.0040.113
duplicateDiscordance0.2080.0040.214
duplicateDiscordanceAcrossDatasets1.7120.0161.755
duplicateDiscordanceProbability0.0040.0000.005
findBAFvariance0.5440.0040.548
genoClusterPlot0.2920.0080.322
genotypeToCharacter0.0000.0040.003
getobj0.0040.0000.002
gwasExactHW0.1600.0000.159
hetByScanChrom0.1280.0000.129
hetBySnpSex0.1040.0040.111
ibdPlot0.0480.0000.047
intensityOutliersPlot0.3600.0080.373
manhattanPlot0.0120.0000.012
meanIntensityByScanChrom0.3320.0000.333
mendelErr0.4880.0040.492
mendelList0.0200.0000.018
missingGenotypeByScanChrom0.1400.0000.138
missingGenotypeBySnpSex0.1000.0000.101
ncdfAddData0.6280.0121.248
ncdfCreate0.0320.0040.127
ncdfImputedDosage1.1320.0161.700
ncdfSetMissingGenotypes0.1360.0040.287
ncdfSubset0.0640.0000.150
pcaSnpFilters0.0000.0040.002
pedigreeCheck0.0520.0000.052
pedigreeDeleteDuplicates0.0120.0000.010
pedigreeMaxUnrelated0.0880.0040.095
pedigreePairwiseRelatedness0.0400.0000.041
plinkToNcdf2.5320.0042.750
plinkUtils4.5930.0204.628
pseudoautoIntensityPlot0.0680.0000.070
pseudoautosomal0.0040.0000.005
qqPlot0.0360.0000.033
qualityScoreByScan0.2160.0120.233
qualityScoreBySnp0.0720.0080.079
readWriteFirst0.0120.0000.010
relationsMeanVar0.0040.0000.004
saveas0.0080.0000.005
simulateGenotypeMatrix0.5920.0040.705
simulateIntensityMatrix0.2360.0000.349
snpCorrelationPlot0.0040.0000.006
snpStats3.1200.0283.151