BioC 3.3: CHECK report for SNPhood on linux2.bioconductor.org

Package: SNPhood

Version: 1.1.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.1.1.tar.gz

StartedAt: 2015-10-27 08:13:26 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:18:23 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 296.6 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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/19s] 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 ... [97s/99s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeSNPhood     59.021  1.615  60.860
associateGenotypes  5.212  0.000   5.212
* 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
  ‘/home/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	59.021	1.615	60.860
annotation-methods	0.205	0.032	0.236
annotationBins	0.073	0.000	0.073
annotationBins2	0.429	0.008	0.791
annotationDatasets	0.075	0.000	0.076
annotationReadGroups	0.451	0.000	0.452
annotationRegions	0.08	0.00	0.08
associateGenotypes	5.212	0.000	5.212
bins-methods	0.389	0.004	0.392
collectFiles	0.021	0.004	0.025
convertToAllelicFractions	0.129	0.000	0.129
counts-method	0.152	0.004	0.156
datasets-methods	0.045	0.000	0.045
deleteDatasets	0.074	0.000	0.074
deleteReadGroups	0.089	0.000	0.089
deleteRegions	0.149	0.000	0.148
enrichment-methods	0.014	0.000	0.014
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.236	0.000	0.235
parameters-methods	0.003	0.000	0.004
plotAllelicBiasResults	4.983	0.004	4.993
plotAllelicBiasResultsOverview	1.544	0.000	1.871
plotAndCalculateCorrelationDatasets	0.763	0.000	0.763
plotAndCalculateWeakAndStrongGenotype	1.520	0.008	1.528
plotAndClusterMatrix	1.778	0.004	1.783
plotBinCounts	1.761	0.004	1.765
plotClusterAverage	0.435	0.004	0.440
plotGenotypesPerCluster	0.908	0.000	0.910
plotGenotypesPerSNP	0.260	0.000	0.261
plotRegionCounts	3.818	0.004	4.312
readGroups-methods	0.063	0.000	0.066
regions-methods	0.075	0.000	0.074
renameBins	0.139	0.000	0.139
renameDatasets	0.15	0.00	0.15
renameReadGroups	0.137	0.000	0.137
renameRegions	0.775	0.000	0.775
results	0.553	0.088	0.644
testForAllelicBiases	1.097	0.000	1.097