BioC 3.0: CHECK report for GWASTools on oaxaca

Package: GWASTools

Version: 1.12.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.12.2.tar.gz

StartedAt: 2015-04-10 00:24:26 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:32:21 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 474.8 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_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GWASTools.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.2’
* 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 ... 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 ... [9s/10s] 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 ... NOTE
ibdAreasDraw: no visible binding for global variable ‘relationsMeanVar’
ibdAssignRelatedness: no visible binding for global variable
  ‘relationsMeanVar’
ibdPlot: no visible binding for global variable ‘relationsMeanVar’
* 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 ... [102s/114s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  34.121  0.070  38.263
vcfWrite             14.756  0.329  16.889
assocTestFisherExact 10.455  0.077  11.586
assocTestCPH          5.315  0.012   5.403
plinkUtils            5.077  0.047   5.803
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [162s/226s]
 [162s/227s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	1.449	0.045	1.659
BAFfromGenotypes	0.001	0.001	0.002
GdsGenotypeReader-class	0.029	0.002	0.092
GdsIntensityReader-class	0.024	0.001	0.025
GdsReader-class	0.052	0.008	0.164
GenotypeData-class	0.230	0.009	0.300
HLA	0.003	0.000	0.003
IntensityData-class	0.058	0.004	0.076
MatrixGenotypeReader-class	0.005	0.001	0.005
NcdfGenotypeReader-class	0.020	0.002	0.045
NcdfIntensityReader-class	0.026	0.002	0.047
NcdfReader-class	0.010	0.001	0.067
ScanAnnotationDataFrame-class	0.100	0.003	0.126
ScanAnnotationSQLite-class	0.077	0.005	0.084
SnpAnnotationDataFrame-class	0.131	0.002	0.134
SnpAnnotationSQLite-class	0.113	0.006	0.146
alleleFrequency	0.316	0.006	0.342
allequal	0.001	0.000	0.001
anomDetectBAF	1.113	0.006	1.165
anomDetectLOH	0.789	0.005	0.794
anomIdentifyLowQuality	1.007	0.010	1.022
anomSegStats	0.406	0.059	0.514
apartSnpSelection	0.122	0.003	0.143
assocTestCPH	5.315	0.012	5.403
assocTestFisherExact	10.455	0.077	11.586
assocTestRegression	34.121	0.070	38.263
batchTest	1.760	0.017	1.815
centromeres	0.002	0.001	0.004
chromIntensityPlot	0.118	0.013	0.147
convertNcdfGds	0.558	0.022	0.630
convertVcfGds	0.038	0.005	0.100
createDataFile	1.069	0.030	1.249
duplicateDiscordance	0.783	0.008	0.883
duplicateDiscordanceAcrossDatasets	0.163	0.002	0.186
duplicateDiscordanceProbability	0.001	0.000	0.002
findBAFvariance	0.549	0.005	0.620
gdsImputedDosage	0.003	0.000	0.004
gdsSubset	0.032	0.004	0.039
genoClusterPlot	2.169	0.085	2.547
genotypeToCharacter	0.001	0.000	0.002
getobj	0.001	0.000	0.002
gwasExactHW	0.176	0.005	0.210
hetByScanChrom	0.263	0.002	0.285
hetBySnpSex	0.216	0.005	0.238
ibdPlot	0.050	0.001	0.060
imputedDosageFile	2.022	0.037	2.392
intensityOutliersPlot	0.652	0.005	0.743
manhattanPlot	0.020	0.001	0.026
meanIntensityByScanChrom	0.597	0.003	0.682
mendelErr	1.639	0.012	1.890
mendelList	0.015	0.001	0.017
missingGenotypeByScanChrom	0.254	0.003	0.269
missingGenotypeBySnpSex	0.186	0.005	0.191
ncdfAddData	0.005	0.001	0.005
ncdfCreate	0.001	0.000	0.001
ncdfImputedDosage	0.003	0.000	0.003
ncdfSetMissingGenotypes	0.001	0.000	0.001
ncdfSubset	0.072	0.002	0.085
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.003	0.000	0.004
pedigreeCheck	0.061	0.001	0.063
pedigreeDeleteDuplicates	0.01	0.00	0.01
pedigreeMaxUnrelated	0.107	0.001	0.107
pedigreePairwiseRelatedness	0.052	0.001	0.056
plinkToNcdf	3.328	0.039	3.891
plinkUtils	5.077	0.047	5.803
pseudoautoIntensityPlot	0.077	0.004	0.087
pseudoautosomal	0.003	0.001	0.003
qqPlot	0.089	0.003	0.102
qualityScoreByScan	0.401	0.005	0.472
qualityScoreBySnp	0.156	0.006	0.192
readWriteFirst	0.006	0.002	0.017
relationsMeanVar	0.002	0.000	0.002
saveas	0.002	0.001	0.003
setMissingGenotypes	0.072	0.004	0.083
simulateGenotypeMatrix	0.583	0.009	0.686
simulateIntensityMatrix	0.337	0.010	1.198
snpCorrelationPlot	0.018	0.001	0.020
snpStats	3.643	0.048	4.126
vcfWrite	14.756	0.329	16.889