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BioC 3.2: CHECK report for GWASTools on zin1

This page was generated on 2015-08-24 10:48:22 -0700 (Mon, 24 Aug 2015).

Package 467/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWASTools 1.15.14
Stephanie M. Gogarten , Adrienne Stilp
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GWASTools
Last Changed Rev: 106509 / Revision: 107696
Last Changed Date: 2015-07-16 17:05:55 -0700 (Thu, 16 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GWASTools
Version: 1.15.14
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.15.14.tar.gz
StartedAt: 2015-08-24 00:40:31 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:44:53 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 262.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GWASTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.15.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.15.14’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GWASTools’ can be installed ... [7s/8s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/34s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 8.138  0.148   8.288
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [124s/134s]
 [124s/134s] 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
* DONE

Status: 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
** testing if installed package can be loaded
* DONE (GWASTools)

GWASTools.Rcheck/GWASTools-Ex.timings:

nameusersystemelapsed
BAFfromClusterMeans1.2450.0241.301
BAFfromGenotypes0.0000.0000.001
GdsGenotypeReader-class0.0280.0000.030
GdsIntensityReader-class0.0140.0000.014
GdsReader-class0.0430.0080.110
GenotypeData-class0.1500.0070.258
HLA0.0010.0040.003
IntensityData-class0.0370.0040.039
MatrixGenotypeReader-class0.0020.0000.004
NcdfGenotypeReader-class0.0110.0000.016
NcdfIntensityReader-class0.0180.0000.024
NcdfReader-class0.0070.0000.007
ScanAnnotationDataFrame-class0.0730.0000.074
ScanAnnotationSQLite-class0.0530.0000.052
SnpAnnotationDataFrame-class0.0900.0000.091
SnpAnnotationSQLite-class0.0770.0000.077
alleleFrequency0.1940.0040.198
allequal0.0000.0000.001
anomDetectBAF1.4950.0041.497
anomDetectLOH0.9520.0000.951
anomIdentifyLowQuality0.9140.0090.921
anomSegStats0.2680.0040.273
apartSnpSelection0.0580.0030.075
assocCoxPH0.3630.0080.371
assocRegression0.6680.0040.700
batchTest1.2490.0681.326
centromeres0.0030.0000.003
chromIntensityPlot0.0830.0080.091
convertNcdfGds0.2340.0000.382
convertVcfGds0.0360.0080.072
createDataFile0.3910.0080.453
duplicateDiscordance0.4630.0120.477
duplicateDiscordanceAcrossDatasets0.1210.0000.121
duplicateDiscordanceProbability0.0010.0000.001
exactHWE0.0440.0040.048
findBAFvariance0.3980.0000.398
gdsSubset0.0320.0000.051
genoClusterPlot1.6030.0361.638
genotypeToCharacter0.0010.0000.001
getobj0.0010.0000.001
hetByScanChrom0.1430.0000.142
hetBySnpSex0.1470.0000.147
ibdPlot0.0350.0040.039
imputedDosageFile0.8900.0160.989
intensityOutliersPlot0.3830.0040.399
manhattanPlot0.0180.0000.018
meanIntensityByScanChrom0.3380.0000.341
mendelErr1.1630.0001.162
mendelList0.010.000.01
missingGenotypeByScanChrom0.1230.0000.123
missingGenotypeBySnpSex0.1180.0000.121
ncdfSubset0.0440.0000.117
pasteSorted0.0010.0000.000
pcaSnpFilters0.0030.0000.004
pedigreeCheck0.0430.0000.043
pedigreeDeleteDuplicates0.0070.0000.006
pedigreeMaxUnrelated0.2630.0000.263
pedigreePairwiseRelatedness0.0380.0000.038
plinkToNcdf1.7850.0162.040
plinkUtils2.8840.0162.903
pseudoautoIntensityPlot0.0510.0000.051
pseudoautosomal0.0030.0000.003
qqPlot0.1230.0000.124
qualityScoreByScan0.2170.0000.222
qualityScoreBySnp0.0400.0040.044
readWriteFirst0.0030.0000.007
relationsMeanVar0.0000.0000.001
saveas0.0010.0000.002
setMissingGenotypes0.0550.0080.074
simulateGenotypeMatrix0.4970.0000.590
simulateIntensityMatrix0.2800.0000.372
snpCorrelationPlot0.0160.0000.016
snpStats0.6570.0000.657
vcfWrite8.1380.1488.288