BioC 2.14: CHECK report for GWASTools on morelia

Package: GWASTools

Version: 1.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.10.1.tar.gz

StartedAt: 2014-10-07 23:24:58 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:30:42 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 343.6 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GWASTools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.10.1’
* 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 ... [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 ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  31.526  0.073  31.631
assocTestFisherExact  9.989  0.069  10.090
plinkUtils            5.777  0.064   5.845
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [131s/133s]
 [132s/133s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	1.375	0.052	1.496
BAFfromGenotypes	0.002	0.000	0.002
GdsGenotypeReader-class	0.066	0.007	0.182
GdsReader-class	0.029	0.003	0.032
GenotypeData-class	0.282	0.007	0.341
HLA	0.003	0.001	0.004
IntensityData-class	0.062	0.006	0.105
MatrixGenotypeReader-class	0.004	0.000	0.005
NcdfGenotypeReader-class	0.019	0.002	0.052
NcdfIntensityReader-class	0.021	0.001	0.022
NcdfReader-class	0.009	0.001	0.010
ScanAnnotationDataFrame-class	0.117	0.002	0.120
ScanAnnotationSQLite-class	0.090	0.007	0.097
SnpAnnotationDataFrame-class	0.137	0.003	0.140
SnpAnnotationSQLite-class	0.114	0.008	0.124
alleleFrequency	0.182	0.011	0.194
allequal	0.000	0.000	0.001
anomDetectBAF	1.080	0.010	1.091
anomDetectLOH	0.787	0.006	0.796
anomIdentifyLowQuality	0.888	0.012	0.901
anomSegStats	0.383	0.028	0.413
apartSnpSelection	0.115	0.004	0.119
assocTestCPH	4.941	0.012	4.959
assocTestFisherExact	9.989	0.069	10.090
assocTestRegression	31.526	0.073	31.631
batchTest	0.862	0.007	0.872
centromeres	0.003	0.000	0.004
chromIntensityPlot	0.118	0.008	0.126
convertNcdfGds	0.263	0.015	0.304
convertVcfGds	0.029	0.004	0.053
duplicateDiscordance	0.236	0.003	0.239
duplicateDiscordanceAcrossDatasets	1.847	0.021	1.868
duplicateDiscordanceProbability	0.001	0.000	0.001
findBAFvariance	0.519	0.009	0.529
gdsImputedDosage	2.023	0.048	2.249
gdsSubset	0.078	0.004	0.083
genoClusterPlot	0.346	0.027	0.448
genotypeToCharacter	0.002	0.000	0.001
getobj	0.002	0.001	0.002
gwasExactHW	0.161	0.005	0.167
hetByScanChrom	0.135	0.002	0.136
hetBySnpSex	0.120	0.002	0.123
ibdPlot	0.043	0.001	0.044
intensityOutliersPlot	0.429	0.011	0.450
manhattanPlot	0.009	0.001	0.010
meanIntensityByScanChrom	0.378	0.005	0.383
mendelErr	0.568	0.006	0.574
mendelList	0.016	0.000	0.016
missingGenotypeByScanChrom	0.170	0.003	0.173
missingGenotypeBySnpSex	0.120	0.004	0.124
ncdfAddData	1.178	0.032	1.250
ncdfCreate	0.035	0.003	0.038
ncdfImputedDosage	1.737	0.039	1.784
ncdfSetMissingGenotypes	0.061	0.002	0.065
ncdfSubset	0.066	0.003	0.068
pcaSnpFilters	0.003	0.001	0.003
pedigreeCheck	0.068	0.002	0.070
pedigreeDeleteDuplicates	0.009	0.000	0.010
pedigreeMaxUnrelated	0.121	0.002	0.123
pedigreePairwiseRelatedness	0.052	0.001	0.053
plinkToNcdf	3.437	0.028	3.488
plinkUtils	5.777	0.064	5.845
pseudoautoIntensityPlot	0.065	0.004	0.068
pseudoautosomal	0.003	0.001	0.003
qqPlot	0.022	0.001	0.023
qualityScoreByScan	0.264	0.007	0.271
qualityScoreBySnp	0.062	0.006	0.069
readWriteFirst	0.003	0.001	0.005
relationsMeanVar	0.002	0.000	0.002
saveas	0.001	0.001	0.002
simulateGenotypeMatrix	0.602	0.008	0.611
simulateIntensityMatrix	0.325	0.014	0.346
snpCorrelationPlot	0.006	0.000	0.006
snpStats	3.574	0.043	3.620