BioC 3.2: CHECK report for SNPhood on perceval

Package: SNPhood

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.0.1.tar.gz

StartedAt: 2015-11-10 09:40:48 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:48:05 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 436.8 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.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 SNPhood_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SNPhood.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.0.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SNPhood’ can be installed ... [29s/29s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcBinomTestVector: no visible binding for global variable ‘pp’
.plotClusterAverage: no visible binding for global variable ‘value’
.plotClusterAverage: no visible binding for global variable ‘Cluster’
.plotRegionFeatures: no visible binding for global variable ‘value’
.plotRegionFeatures: no visible binding for global variable
  ‘datasetAndReadGroup’
plotAllelicBiasResults: no visible binding for global variable ‘bin’
plotAllelicBiasResults: no visible binding for global variable ‘value’
plotAllelicBiasResults: no visible binding for global variable
  ‘confLower’
plotAllelicBiasResults: no visible binding for global variable
  ‘confUpper’
plotAllelicBiasResults: no visible binding for global variable
  ‘valueTransf’
plotBinCounts: no visible binding for global variable ‘bin’
plotBinCounts: no visible binding for global variable ‘value’
plotGenotypesPerCluster: no visible binding for global variable ‘type’
plotGenotypesPerCluster: no visible binding for global variable ‘value’
plotGenotypesPerCluster: no visible binding for global variable
  ‘Genotype’
plotGenotypesPerSNP: no visible binding for global variable ‘SNP’
plotGenotypesPerSNP: no visible binding for global variable ‘value’
plotGenotypesPerSNP: no visible binding for global variable ‘Genotype’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [133s/137s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
analyzeSNPhood         77.699  3.444  82.730
associateGenotypes      8.913  0.044   8.971
plotAllelicBiasResults  6.878  0.017   6.897
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/SNPhood.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPhood’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPhood)

name	user	system	elapsed
analyzeSNPhood	77.699	3.444	82.730
annotation-methods	0.242	0.027	0.268
annotationBins	0.069	0.006	0.074
annotationBins2	0.436	0.007	0.911
annotationDatasets	0.069	0.000	0.069
annotationReadGroups	0.518	0.001	0.518
annotationRegions	0.091	0.002	0.093
associateGenotypes	8.913	0.044	8.971
bins-methods	0.544	0.004	0.547
collectFiles	0.080	0.001	0.082
convertToAllelicFractions	0.211	0.001	0.211
counts-method	0.293	0.007	0.300
datasets-methods	0.065	0.000	0.065
deleteDatasets	0.122	0.004	0.125
deleteReadGroups	0.149	0.002	0.151
deleteRegions	0.243	0.001	0.245
enrichment-methods	0.024	0.001	0.025
getDefaultParameterList	0.002	0.000	0.001
mergeReadGroups	0.294	0.003	0.298
parameters-methods	0.006	0.000	0.008
plotAllelicBiasResults	6.878	0.017	6.897
plotAllelicBiasResultsOverview	1.910	0.019	2.372
plotAndCalculateCorrelationDatasets	0.326	0.004	0.331
plotAndCalculateWeakAndStrongGenotype	1.537	0.008	1.545
plotAndClusterMatrix	1.999	0.014	2.017
plotBinCounts	2.916	0.054	2.971
plotClusterAverage	1.193	0.005	1.199
plotGenotypesPerCluster	0.788	0.005	0.792
plotGenotypesPerSNP	0.435	0.005	0.440
plotRegionCounts	3.939	0.025	4.759
readGroups-methods	0.064	0.000	0.064
regions-methods	0.092	0.001	0.094
renameBins	0.133	0.003	0.137
renameDatasets	0.144	0.001	0.145
renameReadGroups	0.140	0.003	0.143
renameRegions	0.749	0.002	0.750
results	0.614	0.188	0.802
testForAllelicBiases	1.815	0.003	1.819