BioC 3.5: CHECK report for SNPhood on veracruz2

Package: SNPhood

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.6.1.tar.gz

StartedAt: 2017-10-18 09:15:28 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:24:45 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 557.6 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_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SNPhood.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.6.1’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    4.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
* 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 ... OK
* 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’
Undefined global functions or variables:
  pp
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
analyzeSNPhood                  73.544  1.631  83.978
plotAllelicBiasResults          31.560  0.266  33.596
plotAndSummarizeAllelicBiasTest 24.432  0.190  26.188
plotFDRResults                  24.084  0.202  26.141
testForAllelicBiases            23.998  0.194  25.770
results                          3.121  4.167   7.477
associateGenotypes               5.329  0.066   5.584
plotAllelicBiasResultsOverview   2.986  0.036   5.106
plotRegionCounts                 2.424  0.088   5.782
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	73.544	1.631	83.978
annotation-methods	1.468	0.082	1.599
annotationBins	0.710	0.033	0.759
annotationBins2	1.027	0.062	2.998
annotationDatasets	0.668	0.027	0.738
annotationReadGroups	0.672	0.022	0.708
annotationRegions	0.644	0.028	0.686
associateGenotypes	5.329	0.066	5.584
bins-methods	0.701	0.025	0.746
changeObjectIntegrityChecking	0.736	0.040	0.788
collectFiles	0.118	0.003	0.123
convertToAllelicFractions	0.699	0.022	0.730
counts-method	0.821	0.026	0.862
datasets-methods	0.688	0.012	0.717
deleteDatasets	0.690	0.023	0.728
deleteReadGroups	0.714	0.020	0.747
deleteRegions	0.797	0.019	0.865
enrichment-methods	0.748	0.024	0.790
getDefaultParameterList	0.001	0.000	0.001
mergeReadGroups	0.826	0.013	0.857
parameters-methods	0.736	0.029	0.787
plotAllelicBiasResults	31.560	0.266	33.596
plotAllelicBiasResultsOverview	2.986	0.036	5.106
plotAndCalculateCorrelationDatasets	1.615	0.040	1.704
plotAndCalculateWeakAndStrongGenotype	1.946	0.065	2.062
plotAndClusterMatrix	0.935	0.063	1.038
plotAndSummarizeAllelicBiasTest	24.432	0.190	26.188
plotBinCounts	2.748	0.051	2.896
plotClusterAverage	0.870	0.044	0.935
plotFDRResults	24.084	0.202	26.141
plotGenotypesPerCluster	0.691	0.057	0.774
plotGenotypesPerSNP	1.086	0.047	1.166
plotRegionCounts	2.424	0.088	5.782
readGroups-methods	0.161	0.019	0.182
regions-methods	0.686	0.051	0.760
renameBins	0.173	0.035	0.218
renameDatasets	0.175	0.029	0.217
renameReadGroups	0.177	0.023	0.209
renameRegions	1.428	0.041	1.499
results	3.121	4.167	7.477
testForAllelicBiases	23.998	0.194	25.770