BioC 2.14: CHECK report for GWASTools on petty

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 22:26:19 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:35:24 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 545.5 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-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 ‘1.10.1’
* 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 ... [14s/14s] 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 ... [133s/138s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  52.619  0.157  55.079
assocTestFisherExact 16.484  0.139  16.823
plinkUtils            8.837  0.079   8.962
assocTestCPH          8.439  0.018   9.157
snpStats              6.313  0.103   6.428
plinkToNcdf           4.916  0.048   5.041
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [177s/186s]
 [177s/186s] 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	2.224	0.095	3.261
BAFfromGenotypes	0.003	0.001	0.003
GdsGenotypeReader-class	0.137	0.012	0.189
GdsReader-class	0.062	0.005	0.068
GenotypeData-class	0.492	0.023	0.566
HLA	0.004	0.000	0.005
IntensityData-class	0.114	0.010	0.206
MatrixGenotypeReader-class	0.009	0.001	0.009
NcdfGenotypeReader-class	0.028	0.002	0.050
NcdfIntensityReader-class	0.035	0.002	0.036
NcdfReader-class	0.015	0.001	0.017
ScanAnnotationDataFrame-class	0.206	0.004	0.222
ScanAnnotationSQLite-class	0.184	0.011	0.212
SnpAnnotationDataFrame-class	0.239	0.005	0.259
SnpAnnotationSQLite-class	0.220	0.013	0.239
alleleFrequency	0.313	0.013	0.332
allequal	0.001	0.000	0.002
anomDetectBAF	1.937	0.017	2.135
anomDetectLOH	1.388	0.008	1.398
anomIdentifyLowQuality	1.606	0.022	1.653
anomSegStats	0.653	0.063	0.721
apartSnpSelection	0.206	0.004	0.210
assocTestCPH	8.439	0.018	9.157
assocTestFisherExact	16.484	0.139	16.823
assocTestRegression	52.619	0.157	55.079
batchTest	1.466	0.018	1.492
centromeres	0.005	0.001	0.005
chromIntensityPlot	0.231	0.016	0.251
convertNcdfGds	0.474	0.025	0.505
convertVcfGds	0.056	0.006	0.082
duplicateDiscordance	0.418	0.007	0.432
duplicateDiscordanceAcrossDatasets	3.216	0.025	3.276
duplicateDiscordanceProbability	0.003	0.000	0.002
findBAFvariance	0.943	0.012	0.966
gdsImputedDosage	2.357	0.071	2.510
gdsSubset	0.141	0.008	0.153
genoClusterPlot	0.606	0.063	0.737
genotypeToCharacter	0.002	0.000	0.002
getobj	0.003	0.001	0.003
gwasExactHW	0.316	0.010	0.329
hetByScanChrom	0.268	0.002	0.277
hetBySnpSex	0.245	0.005	0.256
ibdPlot	0.086	0.002	0.092
intensityOutliersPlot	0.798	0.018	0.846
manhattanPlot	0.014	0.001	0.025
meanIntensityByScanChrom	0.633	0.006	0.640
mendelErr	1.015	0.011	1.035
mendelList	0.031	0.001	0.033
missingGenotypeByScanChrom	0.282	0.005	0.288
missingGenotypeBySnpSex	0.223	0.005	0.229
ncdfAddData	0.996	0.046	1.159
ncdfCreate	0.077	0.004	0.096
ncdfImputedDosage	2.059	0.061	2.149
ncdfSetMissingGenotypes	0.116	0.005	0.124
ncdfSubset	0.117	0.005	0.131
pcaSnpFilters	0.005	0.001	0.006
pedigreeCheck	0.109	0.002	0.115
pedigreeDeleteDuplicates	0.015	0.001	0.015
pedigreeMaxUnrelated	0.199	0.002	0.201
pedigreePairwiseRelatedness	0.092	0.002	0.094
plinkToNcdf	4.916	0.048	5.041
plinkUtils	8.837	0.079	8.962
pseudoautoIntensityPlot	0.148	0.008	0.157
pseudoautosomal	0.004	0.001	0.006
qqPlot	0.037	0.002	0.040
qualityScoreByScan	0.448	0.009	0.458
qualityScoreBySnp	0.237	0.017	0.255
readWriteFirst	0.007	0.002	0.009
relationsMeanVar	0.003	0.001	0.004
saveas	0.003	0.001	0.004
simulateGenotypeMatrix	0.972	0.014	0.995
simulateIntensityMatrix	0.430	0.019	0.464
snpCorrelationPlot	0.010	0.000	0.011
snpStats	6.313	0.103	6.428