BioC 2.13: CHECK report for GWASTools on perceval

Package: GWASTools

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.8.1.tar.gz

StartedAt: 2014-04-05 01:56:09 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:01:40 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 330.1 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GWASTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [10s/11s] 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 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 ... [112s/115s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  46.511  0.987  48.724
assocTestFisherExact 15.342  0.473  16.285
assocTestCPH          6.453  0.040   6.607
plinkUtils            5.787  0.096   5.983
snpStats              5.671  0.169   5.948
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [54s/55s]
 [55s/56s] 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
  ‘/Users/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	1.966	0.095	2.137
BAFfromGenotypes	0.019	0.001	0.020
GdsGenotypeReader-class	0.274	0.020	0.330
GdsReader-class	0.050	0.010	0.061
GenotypeData-class	0.378	0.042	0.425
HLA	0.009	0.004	0.013
IntensityData-class	0.139	0.029	0.178
MatrixGenotypeReader-class	0.040	0.008	0.049
NcdfGenotypeReader-class	0.050	0.012	0.062
NcdfIntensityReader-class	0.079	0.012	0.092
NcdfReader-class	0.181	0.003	0.200
ScanAnnotationDataFrame-class	0.161	0.023	0.203
ScanAnnotationSQLite-class	0.151	0.024	0.184
SnpAnnotationDataFrame-class	0.204	0.016	0.222
SnpAnnotationSQLite-class	0.193	0.032	0.232
alleleFrequency	0.252	0.015	0.272
allequal	0.012	0.002	0.014
anomDetectBAF	1.419	0.029	1.468
anomDetectLOH	0.991	0.012	1.021
anomIdentifyLowQuality	1.172	0.020	1.204
anomSegStats	0.675	0.074	0.764
apartSnpSelection	0.162	0.005	0.168
assocTestCPH	6.453	0.040	6.607
assocTestFisherExact	15.342	0.473	16.285
assocTestRegression	46.511	0.987	48.724
batchTest	0.841	0.015	0.887
centromeres	0.011	0.004	0.016
chromIntensityPlot	0.191	0.020	0.226
convertNcdfGds	0.553	0.033	0.613
convertVcfGds	0.056	0.011	0.070
duplicateDiscordance	0.322	0.010	0.340
duplicateDiscordanceAcrossDatasets	2.330	0.036	2.403
duplicateDiscordanceProbability	0.011	0.002	0.014
findBAFvariance	0.697	0.021	0.732
genoClusterPlot	0.441	0.074	0.564
genotypeToCharacter	0.023	0.003	0.025
getobj	0.020	0.002	0.024
gwasExactHW	0.286	0.023	0.314
hetByScanChrom	0.182	0.007	0.217
hetBySnpSex	0.193	0.013	0.226
ibdPlot	0.078	0.004	0.086
intensityOutliersPlot	0.544	0.034	0.615
manhattanPlot	0.018	0.005	0.025
meanIntensityByScanChrom	0.433	0.010	0.446
mendelErr	0.602	0.017	0.632
mendelList	0.036	0.009	0.044
missingGenotypeByScanChrom	0.194	0.011	0.208
missingGenotypeBySnpSex	0.150	0.011	0.168
ncdfAddData	0.830	0.062	0.949
ncdfCreate	0.070	0.008	0.080
ncdfImputedDosage	1.769	0.097	1.913
ncdfSetMissingGenotypes	0.254	0.015	0.272
ncdfSubset	0.093	0.010	0.105
pcaSnpFilters	0.009	0.004	0.014
pedigreeCheck	0.087	0.018	0.106
pedigreeDeleteDuplicates	0.021	0.004	0.026
pedigreeMaxUnrelated	0.161	0.027	0.188
pedigreePairwiseRelatedness	0.077	0.011	0.088
plinkToNcdf	3.246	0.061	3.359
plinkUtils	5.787	0.096	5.983
pseudoautoIntensityPlot	0.130	0.017	0.150
pseudoautosomal	0.009	0.005	0.014
qqPlot	0.032	0.005	0.038
qualityScoreByScan	0.311	0.013	0.326
qualityScoreBySnp	0.099	0.015	0.115
readWriteFirst	0.018	0.005	0.023
relationsMeanVar	0.013	0.003	0.017
saveas	0.016	0.005	0.024
simulateGenotypeMatrix	0.999	0.043	1.061
simulateIntensityMatrix	0.376	0.043	0.431
snpCorrelationPlot	0.012	0.003	0.016
snpStats	5.671	0.169	5.948