Package: SNPhood

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SNPhood_1.13.0.tar.gz

StartedAt: 2019-04-09 05:38:49 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:52:09 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 800.4 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 --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SNPhood_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.13.0’
* 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 ... OK
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
plotAllelicBiasResults          136.889 65.875  47.928
testForAllelicBiases            127.860 66.715  43.625
plotAndSummarizeAllelicBiasTest 127.398 66.067  44.466
plotFDRResults                  124.535 64.397  42.648
analyzeSNPhood                  106.056  3.841 123.932
results                           8.718 10.902  19.634
associateGenotypes                8.172  0.111   8.319
plotRegionCounts                  4.072  0.178   8.228
plotAllelicBiasResultsOverview    3.249  0.112   6.391
* 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-3.9-bioc/meat/SNPhood.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SNPhood
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SNPhood’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SNPhood)

name	user	system	elapsed
analyzeSNPhood	106.056	3.841	123.932
annotation-methods	0.321	0.167	0.488
annotationBins	1.228	0.054	1.281
annotationBins2	0.502	0.185	3.499
annotationDatasets	0.269	0.092	0.403
annotationReadGroups	0.199	0.032	0.230
annotationRegions	0.257	0.049	0.305
associateGenotypes	8.172	0.111	8.319
bins-methods	0.235	0.045	0.280
changeObjectIntegrityChecking	0.284	0.087	0.370
collectFiles	0.045	0.002	0.047
convertToAllelicFractions	0.202	0.052	0.255
counts-method	0.243	0.031	0.274
datasets-methods	0.168	0.041	0.209
deleteDatasets	0.242	0.044	0.287
deleteReadGroups	1.102	0.064	1.166
deleteRegions	0.259	0.068	0.327
enrichment-methods	0.249	0.054	0.303
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.298	0.040	0.338
parameters-methods	0.188	0.080	0.268
plotAllelicBiasResults	136.889	65.875	47.928
plotAllelicBiasResultsOverview	3.249	0.112	6.391
plotAndCalculateCorrelationDatasets	0.301	0.059	0.361
plotAndCalculateWeakAndStrongGenotype	1.507	0.137	1.645
plotAndClusterMatrix	1.308	0.098	1.408
plotAndSummarizeAllelicBiasTest	127.398	66.067	44.466
plotBinCounts	4.245	0.057	4.311
plotClusterAverage	1.115	0.062	1.182
plotFDRResults	124.535	64.397	42.648
plotGenotypesPerCluster	0.778	0.035	0.814
plotGenotypesPerSNP	1.546	0.085	1.632
plotRegionCounts	4.072	0.178	8.228
readGroups-methods	1.164	0.042	1.205
regions-methods	0.198	0.055	0.253
renameBins	0.227	0.079	0.306
renameDatasets	0.210	0.062	0.273
renameReadGroups	0.238	0.107	0.344
renameRegions	4.119	0.124	4.244
results	8.718	10.902	19.634
testForAllelicBiases	127.860	66.715	43.625