BioC 3.3: CHECK report for SNPhood on morelia

Package: SNPhood

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.1.1.tar.gz

StartedAt: 2015-10-22 11:30:31 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 11:35:39 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 307.8 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_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.1.1’
* 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 ... [19s/20s] 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’
Undefined global functions or variables:
  Cluster Genotype SNP bin confLower confUpper datasetAndReadGroup pp
  type value valueTransf
* 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 ... [98s/102s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
analyzeSNPhood         57.753  2.023  62.122
associateGenotypes      6.903  0.022   7.033
plotAllelicBiasResults  5.110  0.015   5.134
* 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-3.3-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	57.753	2.023	62.122
annotation-methods	0.162	0.017	0.180
annotationBins	0.061	0.003	0.063
annotationBins2	0.289	0.004	1.059
annotationDatasets	0.039	0.001	0.041
annotationReadGroups	0.042	0.001	0.042
annotationRegions	0.064	0.000	0.064
associateGenotypes	6.903	0.022	7.033
bins-methods	0.056	0.001	0.057
collectFiles	0.045	0.001	0.047
convertToAllelicFractions	0.200	0.003	0.202
counts-method	0.213	0.001	0.216
datasets-methods	0.044	0.000	0.043
deleteDatasets	0.074	0.001	0.076
deleteReadGroups	0.105	0.000	0.105
deleteRegions	0.428	0.002	0.430
enrichment-methods	0.018	0.000	0.018
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.221	0.001	0.227
parameters-methods	0.007	0.001	0.007
plotAllelicBiasResults	5.110	0.015	5.134
plotAllelicBiasResultsOverview	2.116	0.034	2.671
plotAndCalculateCorrelationDatasets	0.294	0.003	0.332
plotAndCalculateWeakAndStrongGenotype	1.287	0.015	1.336
plotAndClusterMatrix	1.548	0.024	1.578
plotBinCounts	2.486	0.015	2.509
plotClusterAverage	0.899	0.004	0.905
plotGenotypesPerCluster	0.648	0.002	0.652
plotGenotypesPerSNP	0.277	0.003	0.280
plotRegionCounts	3.125	0.030	4.018
readGroups-methods	0.040	0.001	0.042
regions-methods	0.044	0.001	0.045
renameBins	0.079	0.000	0.079
renameDatasets	0.147	0.004	0.152
renameReadGroups	0.107	0.002	0.109
renameRegions	0.567	0.003	0.571
results	0.517	0.141	0.659
testForAllelicBiases	1.710	0.007	1.719