BioC 3.2: CHECK report for SNPhood on oaxaca

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: 2015-10-27 08:04:15 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:11:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 410.7 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 (2015-08-14)
* 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 ‘1.0.1’
* 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 ... [27s/27s] 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 ... [122s/128s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeSNPhood     77.240  2.252  83.289
associateGenotypes  6.562  0.032   6.615
plotRegionCounts    4.278  0.022   5.112
* 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	77.240	2.252	83.289
annotation-methods	0.157	0.018	0.175
annotationBins	0.042	0.003	0.045
annotationBins2	0.385	0.005	0.950
annotationDatasets	0.056	0.001	0.057
annotationReadGroups	0.043	0.001	0.043
annotationRegions	0.339	0.001	0.340
associateGenotypes	6.562	0.032	6.615
bins-methods	0.041	0.002	0.042
collectFiles	0.045	0.001	0.045
convertToAllelicFractions	0.178	0.004	0.182
counts-method	0.163	0.001	0.165
datasets-methods	0.041	0.001	0.042
deleteDatasets	0.356	0.002	0.358
deleteReadGroups	0.082	0.001	0.084
deleteRegions	0.213	0.001	0.214
enrichment-methods	0.018	0.000	0.018
getDefaultParameterList	0.001	0.000	0.002
mergeReadGroups	0.243	0.001	0.245
parameters-methods	0.004	0.000	0.004
plotAllelicBiasResults	4.468	0.036	4.522
plotAllelicBiasResultsOverview	1.500	0.009	1.997
plotAndCalculateCorrelationDatasets	0.229	0.003	0.272
plotAndCalculateWeakAndStrongGenotype	1.145	0.024	1.168
plotAndClusterMatrix	1.477	0.015	1.496
plotBinCounts	2.315	0.010	2.329
plotClusterAverage	0.552	0.007	0.559
plotGenotypesPerCluster	0.981	0.005	0.987
plotGenotypesPerSNP	0.373	0.005	0.377
plotRegionCounts	4.278	0.022	5.112
readGroups-methods	0.065	0.001	0.066
regions-methods	0.057	0.003	0.060
renameBins	0.155	0.010	0.165
renameDatasets	0.119	0.002	0.121
renameReadGroups	0.123	0.001	0.124
renameRegions	0.827	0.008	0.837
results	0.636	0.193	0.830
testForAllelicBiases	1.785	0.007	1.794