BioC 3.0: CHECK report for GWASTools on perceval

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 02:35:47 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:43:34 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 466.6 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_1.12.2.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-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 ‘1.12.2’
* 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 ... [11s/19s] 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 ... [111s/115s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  34.792  0.154  34.967
vcfWrite             19.860  0.640  20.562
assocTestFisherExact 10.612  0.214  10.841
snpStats              5.311  0.113   5.431
assocTestCPH          5.273  0.010   5.283
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [167s/197s]
 [168s/197s] 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	1.906	0.072	2.568
BAFfromGenotypes	0.001	0.000	0.002
GdsGenotypeReader-class	0.030	0.003	0.066
GdsIntensityReader-class	0.023	0.002	0.026
GdsReader-class	0.073	0.012	0.534
GenotypeData-class	0.254	0.016	0.687
HLA	0.003	0.001	0.003
IntensityData-class	0.073	0.004	0.077
MatrixGenotypeReader-class	0.004	0.001	0.005
NcdfGenotypeReader-class	0.016	0.002	0.019
NcdfIntensityReader-class	0.027	0.003	0.145
NcdfReader-class	0.009	0.002	0.093
ScanAnnotationDataFrame-class	0.133	0.004	0.189
ScanAnnotationSQLite-class	0.110	0.012	0.213
SnpAnnotationDataFrame-class	0.140	0.005	0.147
SnpAnnotationSQLite-class	0.126	0.012	0.311
alleleFrequency	0.338	0.008	0.349
allequal	0.001	0.000	0.001
anomDetectBAF	1.324	0.011	1.337
anomDetectLOH	0.950	0.008	0.960
anomIdentifyLowQuality	1.123	0.010	1.142
anomSegStats	0.398	0.058	0.524
apartSnpSelection	0.147	0.004	0.151
assocTestCPH	5.273	0.010	5.283
assocTestFisherExact	10.612	0.214	10.841
assocTestRegression	34.792	0.154	34.967
batchTest	2.143	0.029	2.183
centromeres	0.003	0.001	0.003
chromIntensityPlot	0.146	0.016	0.175
convertNcdfGds	0.559	0.024	0.664
convertVcfGds	0.039	0.006	0.064
createDataFile	0.518	0.044	0.673
duplicateDiscordance	0.905	0.011	0.917
duplicateDiscordanceAcrossDatasets	0.169	0.002	0.172
duplicateDiscordanceProbability	0.002	0.000	0.002
findBAFvariance	0.618	0.008	0.627
gdsImputedDosage	0.003	0.001	0.004
gdsSubset	0.053	0.007	0.071
genoClusterPlot	2.304	0.164	3.079
genotypeToCharacter	0.002	0.000	0.002
getobj	0.002	0.002	0.016
gwasExactHW	0.218	0.006	0.233
hetByScanChrom	0.266	0.002	0.269
hetBySnpSex	0.263	0.005	0.269
ibdPlot	0.055	0.001	0.063
imputedDosageFile	1.870	0.073	2.111
intensityOutliersPlot	0.705	0.012	0.726
manhattanPlot	0.022	0.003	0.041
meanIntensityByScanChrom	0.625	0.006	0.631
mendelErr	1.628	0.020	1.658
mendelList	0.016	0.001	0.016
missingGenotypeByScanChrom	0.299	0.005	0.304
missingGenotypeBySnpSex	0.195	0.004	0.199
ncdfAddData	0.004	0.001	0.005
ncdfCreate	0.000	0.000	0.001
ncdfImputedDosage	0.003	0.001	0.003
ncdfSetMissingGenotypes	0.001	0.001	0.001
ncdfSubset	0.078	0.006	0.117
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.000	0.004
pedigreeCheck	0.063	0.001	0.065
pedigreeDeleteDuplicates	0.01	0.00	0.01
pedigreeMaxUnrelated	0.126	0.002	0.128
pedigreePairwiseRelatedness	0.055	0.002	0.057
plinkToNcdf	2.945	0.040	3.120
plinkUtils	4.579	0.078	4.681
pseudoautoIntensityPlot	0.085	0.005	0.099
pseudoautosomal	0.002	0.001	0.003
qqPlot	0.113	0.006	0.138
qualityScoreByScan	0.427	0.006	0.434
qualityScoreBySnp	0.069	0.012	0.082
readWriteFirst	0.004	0.002	0.015
relationsMeanVar	0.002	0.000	0.003
saveas	0.002	0.001	0.014
setMissingGenotypes	0.081	0.006	0.102
simulateGenotypeMatrix	0.586	0.017	0.687
simulateIntensityMatrix	0.388	0.021	0.478
snpCorrelationPlot	0.020	0.002	0.034
snpStats	5.311	0.113	5.431
vcfWrite	19.860	0.640	20.562

BioC 3.0: CHECK report for GWASTools on perceval

Summary

Command output