BioC 3.2: CHECK report for SNPhood on oaxaca

Package: SNPhood

Version: 1.0.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.0.7.tar.gz

StartedAt: 2016-04-23 04:34:39 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:42:54 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 495.5 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_1.0.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SNPhood.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.0.7’
* 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 ... [31s/39s] 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 ... [137s/161s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
analyzeSNPhood         84.608  2.794 103.606
associateGenotypes      9.552  0.039   9.630
plotAllelicBiasResults  5.743  0.021   5.793
plotRegionCounts        4.701  0.072   7.248
* 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	84.608	2.794	103.606
annotation-methods	0.214	0.025	0.241
annotationBins	0.057	0.010	0.065
annotationBins2	0.349	0.006	2.004
annotationDatasets	0.055	0.001	0.056
annotationReadGroups	0.053	0.003	0.055
annotationRegions	0.087	0.001	0.088
associateGenotypes	9.552	0.039	9.630
bins-methods	0.051	0.001	0.052
collectFiles	0.058	0.001	0.059
convertToAllelicFractions	0.175	0.003	0.178
counts-method	0.225	0.002	0.227
datasets-methods	0.462	0.002	0.464
deleteDatasets	0.078	0.002	0.080
deleteReadGroups	0.104	0.002	0.105
deleteRegions	0.162	0.002	0.164
enrichment-methods	0.019	0.000	0.020
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.233	0.002	0.235
parameters-methods	0.006	0.001	0.008
plotAllelicBiasResults	5.743	0.021	5.793
plotAllelicBiasResultsOverview	1.812	0.008	4.102
plotAndCalculateCorrelationDatasets	0.263	0.004	0.282
plotAndCalculateWeakAndStrongGenotype	1.698	0.011	1.710
plotAndClusterMatrix	1.686	0.018	1.717
plotBinCounts	2.588	0.044	2.645
plotClusterAverage	0.603	0.005	0.610
plotGenotypesPerCluster	0.688	0.005	0.696
plotGenotypesPerSNP	0.405	0.004	0.418
plotRegionCounts	4.701	0.072	7.248
readGroups-methods	0.058	0.002	0.060
regions-methods	0.045	0.002	0.049
renameBins	0.106	0.003	0.110
renameDatasets	0.100	0.003	0.102
renameReadGroups	0.100	0.002	0.102
renameRegions	0.741	0.004	0.746
results	0.481	0.172	0.655
testForAllelicBiases	1.609	0.016	1.627