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: 2015-10-20 11:57:19 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 12:05:17 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 477.5 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_1.0.1.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 ... [31s/31s] 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 ... [146s/150s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
analyzeSNPhood         86.383  3.558  91.943
associateGenotypes      9.296  0.067   9.370
plotAllelicBiasResults  7.610  0.033   7.646
plotRegionCounts        4.345  0.027   5.108
* 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	86.383	3.558	91.943
annotation-methods	0.307	0.032	0.341
annotationBins	0.075	0.006	0.080
annotationBins2	0.618	0.008	1.179
annotationDatasets	0.073	0.000	0.074
annotationReadGroups	0.557	0.001	0.558
annotationRegions	0.094	0.003	0.097
associateGenotypes	9.296	0.067	9.370
bins-methods	0.583	0.004	0.586
collectFiles	0.081	0.001	0.082
convertToAllelicFractions	0.250	0.001	0.251
counts-method	0.357	0.008	0.364
datasets-methods	0.077	0.000	0.077
deleteDatasets	0.141	0.004	0.145
deleteReadGroups	0.149	0.002	0.150
deleteRegions	0.267	0.001	0.268
enrichment-methods	0.029	0.000	0.029
getDefaultParameterList	0.001	0.001	0.001
mergeReadGroups	0.309	0.003	0.312
parameters-methods	0.006	0.001	0.007
plotAllelicBiasResults	7.610	0.033	7.646
plotAllelicBiasResultsOverview	2.036	0.011	2.531
plotAndCalculateCorrelationDatasets	0.365	0.005	0.371
plotAndCalculateWeakAndStrongGenotype	1.662	0.019	1.681
plotAndClusterMatrix	2.091	0.020	2.116
plotBinCounts	3.168	0.053	3.225
plotClusterAverage	0.817	0.007	0.826
plotGenotypesPerCluster	1.334	0.006	1.340
plotGenotypesPerSNP	0.417	0.002	0.420
plotRegionCounts	4.345	0.027	5.108
readGroups-methods	0.078	0.001	0.080
regions-methods	0.067	0.004	0.071
renameBins	0.133	0.001	0.135
renameDatasets	0.169	0.002	0.172
renameReadGroups	0.126	0.001	0.127
renameRegions	0.771	0.001	0.772
results	0.688	0.227	1.140
testForAllelicBiases	1.984	0.004	1.987