BioC 3.1: CHECK report for GWASTools on morelia

Package: GWASTools

Version: 1.14.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.14.2.tar.gz

StartedAt: 2015-10-09 02:53:18 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:59:02 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 344.2 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.14.2’
* 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 ... [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 ... NOTE
'library' or 'require' call to ‘snpStats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... [39s/40s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 9.403  0.602  10.015
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [172s/177s]
 [173s/177s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-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	1.264	0.094	1.548
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.038	0.002	0.065
GdsIntensityReader-class	0.013	0.001	0.014
GdsReader-class	0.052	0.006	0.126
GenotypeData-class	0.157	0.005	0.214
HLA	0.002	0.000	0.002
IntensityData-class	0.047	0.001	0.049
MatrixGenotypeReader-class	0.003	0.001	0.003
NcdfGenotypeReader-class	0.012	0.001	0.023
NcdfIntensityReader-class	0.023	0.001	0.036
NcdfReader-class	0.007	0.003	0.011
ScanAnnotationDataFrame-class	0.086	0.002	0.087
ScanAnnotationSQLite-class	0.052	0.004	0.056
SnpAnnotationDataFrame-class	0.125	0.003	0.127
SnpAnnotationSQLite-class	0.100	0.007	0.108
alleleFrequency	0.219	0.003	0.221
allequal	0	0	0
anomDetectBAF	1.097	0.015	1.135
anomDetectLOH	0.704	0.063	0.767
anomIdentifyLowQuality	0.806	0.083	0.890
anomSegStats	0.309	0.079	0.401
apartSnpSelection	0.080	0.011	0.103
assocCoxPH	0.475	0.008	0.483
assocRegression	0.842	0.029	0.872
assocTestCPH	0.002	0.000	0.002
assocTestFisherExact	0.001	0.000	0.001
assocTestRegression	0.003	0.000	0.004
batchTest	1.199	0.032	1.231
centromeres	0.003	0.000	0.003
chromIntensityPlot	0.108	0.007	0.115
convertNcdfGds	0.262	0.034	0.300
convertVcfGds	0.033	0.013	0.058
createDataFile	0.884	0.075	1.023
duplicateDiscordance	0.543	0.060	0.603
duplicateDiscordanceAcrossDatasets	0.167	0.003	0.171
duplicateDiscordanceProbability	0.001	0.000	0.002
exactHWE	0.063	0.006	0.087
findBAFvariance	0.481	0.042	0.523
gdsSubset	0.028	0.004	0.033
genoClusterPlot	1.717	0.164	1.900
genotypeToCharacter	0.001	0.000	0.002
getobj	0.001	0.001	0.002
gwasExactHW	0.001	0.000	0.002
hetByScanChrom	0.203	0.012	0.215
hetBySnpSex	0.183	0.004	0.187
ibdPlot	0.030	0.000	0.032
imputedDosageFile	1.421	0.129	1.785
intensityOutliersPlot	0.514	0.068	0.583
manhattanPlot	0.018	0.002	0.020
meanIntensityByScanChrom	0.346	0.009	0.355
mendelErr	1.420	0.082	1.503
mendelList	0.009	0.001	0.009
missingGenotypeByScanChrom	0.187	0.047	0.234
missingGenotypeBySnpSex	0.160	0.005	0.165
ncdfSubset	0.051	0.002	0.071
pasteSorted	0.000	0.000	0.001
pcaSnpFilters	0.004	0.001	0.004
pedigreeCheck	0.035	0.001	0.036
pedigreeDeleteDuplicates	0.006	0.000	0.006
pedigreeMaxUnrelated	0.096	0.001	0.097
pedigreePairwiseRelatedness	0.048	0.001	0.050
plinkToNcdf	2.323	0.200	2.619
plinkUtils	3.612	0.268	3.882
pseudoautoIntensityPlot	0.063	0.010	0.074
pseudoautosomal	0.003	0.001	0.004
qqPlot	0.080	0.013	0.094
qualityScoreByScan	0.341	0.006	0.361
qualityScoreBySnp	0.042	0.004	0.047
readWriteFirst	0.003	0.001	0.003
relationsMeanVar	0.001	0.000	0.001
saveas	0.001	0.001	0.002
setMissingGenotypes	0.069	0.003	0.073
simulateGenotypeMatrix	0.474	0.020	0.496
simulateIntensityMatrix	0.230	0.013	0.252
snpCorrelationPlot	0.017	0.001	0.018
snpStats	0.563	0.015	0.591
vcfWrite	9.403	0.602	10.015