BioC 2.13: CHECK report for GWASTools on zin1

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

* 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.

* 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)

name	user	system	elapsed
BAFfromClusterMeans	1.236	0.016	1.402
BAFfromGenotypes	0.008	0.000	0.008
GdsGenotypeReader-class	0.116	0.012	0.152
GdsReader-class	0.020	0.008	0.025
GenotypeData-class	0.216	0.000	0.306
HLA	0.004	0.000	0.004
IntensityData-class	0.064	0.000	0.086
MatrixGenotypeReader-class	0.016	0.000	0.017
NcdfGenotypeReader-class	0.024	0.004	0.028
NcdfIntensityReader-class	0.040	0.000	0.037
NcdfReader-class	0.072	0.000	0.076
ScanAnnotationDataFrame-class	0.092	0.000	0.091
ScanAnnotationSQLite-class	0.080	0.008	0.258
SnpAnnotationDataFrame-class	0.116	0.004	0.120
SnpAnnotationSQLite-class	0.096	0.004	0.432
alleleFrequency	0.148	0.004	0.151
allequal	0.004	0.000	0.004
anomDetectBAF	1.332	0.004	1.339
anomDetectLOH	0.924	0.004	0.925
anomIdentifyLowQuality	1.016	0.000	1.021
anomSegStats	0.392	0.012	0.403
apartSnpSelection	0.104	0.000	0.102
assocTestCPH	4.604	0.004	4.633
assocTestFisherExact	10.005	0.008	10.046
assocTestRegression	30.702	0.028	30.803
batchTest	0.680	0.012	0.691
centromeres	0.000	0.004	0.004
chromIntensityPlot	0.120	0.004	0.127
convertNcdfGds	0.324	0.012	0.348
convertVcfGds	0.108	0.004	0.113
duplicateDiscordance	0.208	0.004	0.214
duplicateDiscordanceAcrossDatasets	1.712	0.016	1.755
duplicateDiscordanceProbability	0.004	0.000	0.005
findBAFvariance	0.544	0.004	0.548
genoClusterPlot	0.292	0.008	0.322
genotypeToCharacter	0.000	0.004	0.003
getobj	0.004	0.000	0.002
gwasExactHW	0.160	0.000	0.159
hetByScanChrom	0.128	0.000	0.129
hetBySnpSex	0.104	0.004	0.111
ibdPlot	0.048	0.000	0.047
intensityOutliersPlot	0.360	0.008	0.373
manhattanPlot	0.012	0.000	0.012
meanIntensityByScanChrom	0.332	0.000	0.333
mendelErr	0.488	0.004	0.492
mendelList	0.020	0.000	0.018
missingGenotypeByScanChrom	0.140	0.000	0.138
missingGenotypeBySnpSex	0.100	0.000	0.101
ncdfAddData	0.628	0.012	1.248
ncdfCreate	0.032	0.004	0.127
ncdfImputedDosage	1.132	0.016	1.700
ncdfSetMissingGenotypes	0.136	0.004	0.287
ncdfSubset	0.064	0.000	0.150
pcaSnpFilters	0.000	0.004	0.002
pedigreeCheck	0.052	0.000	0.052
pedigreeDeleteDuplicates	0.012	0.000	0.010
pedigreeMaxUnrelated	0.088	0.004	0.095
pedigreePairwiseRelatedness	0.040	0.000	0.041
plinkToNcdf	2.532	0.004	2.750
plinkUtils	4.593	0.020	4.628
pseudoautoIntensityPlot	0.068	0.000	0.070
pseudoautosomal	0.004	0.000	0.005
qqPlot	0.036	0.000	0.033
qualityScoreByScan	0.216	0.012	0.233
qualityScoreBySnp	0.072	0.008	0.079
readWriteFirst	0.012	0.000	0.010
relationsMeanVar	0.004	0.000	0.004
saveas	0.008	0.000	0.005
simulateGenotypeMatrix	0.592	0.004	0.705
simulateIntensityMatrix	0.236	0.000	0.349
snpCorrelationPlot	0.004	0.000	0.006
snpStats	3.120	0.028	3.151