BioC 3.6: CHECK report for SNPhood on veracruz1

Package: SNPhood

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.7.1.tar.gz

StartedAt: 2017-08-16 08:44:21 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:53:13 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 531.6 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SNPhood.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.1’
* 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                  69.434  1.275  80.255
plotAllelicBiasResults          29.644  0.128  32.176
plotAndSummarizeAllelicBiasTest 24.247  0.121  26.043
plotFDRResults                  23.389  0.108  25.477
testForAllelicBiases            22.083  0.112  23.925
results                          2.930  3.793   6.861
associateGenotypes               5.101  0.040   5.300
plotAllelicBiasResultsOverview   2.923  0.044   5.202
plotRegionCounts                 2.516  0.084   6.304
* 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	69.434	1.275	80.255
annotation-methods	1.340	0.068	1.451
annotationBins	0.657	0.030	0.704
annotationBins2	0.946	0.062	3.126
annotationDatasets	0.685	0.023	0.752
annotationReadGroups	0.688	0.026	0.749
annotationRegions	0.665	0.010	0.689
associateGenotypes	5.101	0.040	5.300
bins-methods	0.694	0.028	0.741
changeObjectIntegrityChecking	0.729	0.022	0.774
collectFiles	0.114	0.002	0.120
convertToAllelicFractions	0.747	0.020	0.802
counts-method	0.830	0.025	0.871
datasets-methods	0.167	0.014	0.188
deleteDatasets	0.692	0.031	0.748
deleteReadGroups	0.176	0.040	0.216
deleteRegions	0.244	0.031	0.286
enrichment-methods	0.178	0.017	0.200
getDefaultParameterList	0.001	0.000	0.001
mergeReadGroups	0.669	0.034	0.718
parameters-methods	0.158	0.036	0.204
plotAllelicBiasResults	29.644	0.128	32.176
plotAllelicBiasResultsOverview	2.923	0.044	5.202
plotAndCalculateCorrelationDatasets	1.401	0.029	1.478
plotAndCalculateWeakAndStrongGenotype	1.672	0.045	1.786
plotAndClusterMatrix	0.776	0.050	0.880
plotAndSummarizeAllelicBiasTest	24.247	0.121	26.043
plotBinCounts	2.715	0.028	2.819
plotClusterAverage	0.787	0.042	0.861
plotFDRResults	23.389	0.108	25.477
plotGenotypesPerCluster	0.666	0.037	0.732
plotGenotypesPerSNP	0.987	0.042	1.071
plotRegionCounts	2.516	0.084	6.304
readGroups-methods	0.155	0.020	0.184
regions-methods	0.691	0.051	0.759
renameBins	0.171	0.035	0.208
renameDatasets	0.173	0.028	0.205
renameReadGroups	0.177	0.019	0.200
renameRegions	1.276	0.031	1.360
results	2.930	3.793	6.861
testForAllelicBiases	22.083	0.112	23.925