Package: SNPhood

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.8.0.tar.gz

StartedAt: 2018-04-12 09:47:50 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 09:56:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 535.7 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SNPhood.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 11.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    7.5Mb
* 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                  67.946  0.817  77.295
plotAllelicBiasResults          28.847  0.119  30.505
plotAndSummarizeAllelicBiasTest 24.214  0.113  26.220
testForAllelicBiases            23.823  0.140  25.520
plotFDRResults                  22.656  0.164  24.223
results                          4.709  4.779   9.670
plotRegionCounts                 3.039  0.062   6.065
plotAllelicBiasResultsOverview   2.772  0.030   5.080
* 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-3.6-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	67.946	0.817	77.295
annotation-methods	1.357	0.084	1.466
annotationBins	0.643	0.017	0.665
annotationBins2	0.955	0.073	3.369
annotationDatasets	0.622	0.014	0.674
annotationReadGroups	0.639	0.024	0.676
annotationRegions	0.645	0.024	0.689
associateGenotypes	4.701	0.048	4.855
bins-methods	0.630	0.015	0.659
changeObjectIntegrityChecking	0.614	0.016	0.642
collectFiles	0.101	0.001	0.107
convertToAllelicFractions	0.652	0.020	0.683
counts-method	0.733	0.019	0.768
datasets-methods	0.584	0.013	0.598
deleteDatasets	0.597	0.018	0.624
deleteReadGroups	0.593	0.023	0.617
deleteRegions	0.666	0.020	0.690
enrichment-methods	0.584	0.012	0.598
getDefaultParameterList	0.001	0.000	0.001
mergeReadGroups	0.663	0.017	0.687
parameters-methods	0.586	0.011	0.599
plotAllelicBiasResults	28.847	0.119	30.505
plotAllelicBiasResultsOverview	2.772	0.030	5.080
plotAndCalculateCorrelationDatasets	1.556	0.015	1.603
plotAndCalculateWeakAndStrongGenotype	1.783	0.040	1.884
plotAndClusterMatrix	1.326	0.039	1.397
plotAndSummarizeAllelicBiasTest	24.214	0.113	26.220
plotBinCounts	2.650	0.029	2.745
plotClusterAverage	1.248	0.012	1.283
plotFDRResults	22.656	0.164	24.223
plotGenotypesPerCluster	1.159	0.028	1.213
plotGenotypesPerSNP	0.476	0.036	0.524
plotRegionCounts	3.039	0.062	6.065
readGroups-methods	0.169	0.034	0.205
regions-methods	0.682	0.028	0.733
renameBins	0.177	0.038	0.220
renameDatasets	0.200	0.028	0.238
renameReadGroups	0.185	0.024	0.213
renameRegions	0.858	0.045	0.933
results	4.709	4.779	9.670
testForAllelicBiases	23.823	0.140	25.520