Package: SNPhood

Version: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2020-04-15 05:49:53 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:02:24 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 751.0 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SNPhood.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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 < >
   use the Contact field instead
* 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          132.253 92.522  50.897
testForAllelicBiases            127.366 93.378  46.087
plotFDRResults                  130.499 87.237  48.441
plotAndSummarizeAllelicBiasTest 127.913 74.742  48.299
analyzeSNPhood                  123.339  2.495 135.452
results                           5.589  5.465  11.238
annotationBins2                   8.821  0.128  12.094
associateGenotypes                8.557  0.077   8.721
plotRegionCounts                  4.140  0.116   8.004
* 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-3.10-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
** 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	123.339	2.495	135.452
annotation-methods	0.379	0.094	0.482
annotationBins	0.193	0.015	0.209
annotationBins2	8.821	0.128	12.094
annotationDatasets	0.160	0.022	0.183
annotationReadGroups	0.187	0.014	0.203
annotationRegions	0.192	0.016	0.210
associateGenotypes	8.557	0.077	8.721
bins-methods	0.223	0.032	0.258
changeObjectIntegrityChecking	0.943	0.038	0.994
collectFiles	0.035	0.001	0.037
convertToAllelicFractions	0.281	0.031	0.313
counts-method	1.027	0.027	1.061
datasets-methods	0.978	0.026	1.012
deleteDatasets	0.229	0.022	0.253
deleteReadGroups	0.216	0.009	0.226
deleteRegions	0.245	0.026	0.275
enrichment-methods	1.006	0.028	1.045
getDefaultParameterList	0.000	0.001	0.001
mergeReadGroups	0.294	0.029	0.327
parameters-methods	0.216	0.033	0.258
plotAllelicBiasResults	132.253	92.522	50.897
plotAllelicBiasResultsOverview	1.587	0.060	3.747
plotAndCalculateCorrelationDatasets	1.088	0.063	1.182
plotAndCalculateWeakAndStrongGenotype	0.982	0.077	1.066
plotAndClusterMatrix	0.889	0.053	0.951
plotAndSummarizeAllelicBiasTest	127.913	74.742	48.299
plotBinCounts	2.789	0.048	2.897
plotClusterAverage	1.888	0.056	1.974
plotFDRResults	130.499	87.237	48.441
plotGenotypesPerCluster	0.700	0.051	0.761
plotGenotypesPerSNP	0.672	0.064	0.738
plotRegionCounts	4.140	0.116	8.004
readGroups-methods	0.188	0.031	0.222
regions-methods	0.210	0.070	0.281
renameBins	0.204	0.036	0.241
renameDatasets	0.232	0.049	0.285
renameReadGroups	0.223	0.032	0.256
renameRegions	4.089	0.080	4.208
results	5.589	5.465	11.238
testForAllelicBiases	127.366	93.378	46.087