BioC 3.1: CHECK report for GWASTools on petty

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: 2015-10-08 23:37:29 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:46:39 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 550.5 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 GWASTools_1.14.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.14.2’
* 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 ... [16s/17s] 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 ... [59s/61s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
vcfWrite   14.657  0.362  15.033
plinkUtils  5.371  0.069   6.237
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [242s/251s]
 [242s/252s] 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	1.908	0.072	2.259
BAFfromGenotypes	0.002	0.000	0.003
GdsGenotypeReader-class	0.058	0.003	0.061
GdsIntensityReader-class	0.026	0.001	0.027
GdsReader-class	0.134	0.005	0.184
GenotypeData-class	0.318	0.009	0.411
HLA	0.003	0.001	0.005
IntensityData-class	0.111	0.003	0.113
MatrixGenotypeReader-class	0.007	0.000	0.007
NcdfGenotypeReader-class	0.019	0.001	0.037
NcdfIntensityReader-class	0.035	0.002	0.081
NcdfReader-class	0.012	0.002	0.032
ScanAnnotationDataFrame-class	0.162	0.002	0.174
ScanAnnotationSQLite-class	0.129	0.007	0.137
SnpAnnotationDataFrame-class	0.193	0.003	0.197
SnpAnnotationSQLite-class	0.173	0.012	0.393
alleleFrequency	0.356	0.005	0.361
allequal	0.002	0.000	0.002
anomDetectBAF	1.889	0.009	1.969
anomDetectLOH	1.056	0.006	1.063
anomIdentifyLowQuality	1.262	0.007	1.283
anomSegStats	0.481	0.045	0.570
apartSnpSelection	0.159	0.002	0.178
assocCoxPH	0.813	0.028	0.842
assocRegression	1.359	0.021	1.382
assocTestCPH	0.003	0.001	0.004
assocTestFisherExact	0.003	0.001	0.003
assocTestRegression	0.005	0.001	0.006
batchTest	2.124	0.036	2.166
centromeres	0.005	0.001	0.006
chromIntensityPlot	0.195	0.011	0.206
convertNcdfGds	0.465	0.027	0.526
convertVcfGds	0.059	0.006	0.078
createDataFile	0.758	0.035	0.977
duplicateDiscordance	0.767	0.005	0.772
duplicateDiscordanceAcrossDatasets	0.183	0.003	0.185
duplicateDiscordanceProbability	0.001	0.000	0.002
exactHWE	0.101	0.004	0.121
findBAFvariance	0.863	0.006	0.870
gdsSubset	0.053	0.005	0.058
genoClusterPlot	2.789	0.128	2.946
genotypeToCharacter	0.002	0.000	0.002
getobj	0.001	0.001	0.010
gwasExactHW	0.002	0.000	0.002
hetByScanChrom	0.284	0.002	0.286
hetBySnpSex	0.315	0.003	0.318
ibdPlot	0.077	0.002	0.082
imputedDosageFile	1.587	0.055	1.784
intensityOutliersPlot	0.833	0.006	0.840
manhattanPlot	0.027	0.002	0.030
meanIntensityByScanChrom	0.690	0.004	0.694
mendelErr	1.760	0.008	1.768
mendelList	0.014	0.001	0.014
missingGenotypeByScanChrom	0.253	0.002	0.255
missingGenotypeBySnpSex	0.223	0.002	0.224
ncdfSubset	0.082	0.004	0.113
pasteSorted	0.002	0.001	0.002
pcaSnpFilters	0.005	0.001	0.007
pedigreeCheck	0.086	0.002	0.087
pedigreeDeleteDuplicates	0.013	0.001	0.013
pedigreeMaxUnrelated	0.168	0.001	0.170
pedigreePairwiseRelatedness	0.071	0.001	0.073
plinkToNcdf	3.397	0.034	3.842
plinkUtils	5.371	0.069	6.237
pseudoautoIntensityPlot	0.097	0.003	0.101
pseudoautosomal	0.005	0.001	0.006
qqPlot	0.146	0.006	0.257
qualityScoreByScan	0.516	0.003	0.532
qualityScoreBySnp	0.079	0.009	0.089
readWriteFirst	0.005	0.001	0.006
relationsMeanVar	0.002	0.000	0.002
saveas	0.002	0.001	0.015
setMissingGenotypes	0.115	0.005	0.119
simulateGenotypeMatrix	0.776	0.019	0.810
simulateIntensityMatrix	0.183	0.026	0.240
snpCorrelationPlot	0.025	0.001	0.034
snpStats	1.264	0.035	1.301
vcfWrite	14.657	0.362	15.033