Package: SNPhood

Version: 1.8.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.8.0.tar.gz

StartedAt: 2018-04-12 03:01:58 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:09:29 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 450.6 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SNPhood.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 10.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    6.4Mb
* 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                  58.892  5.852  72.855
plotAllelicBiasResults          21.988  0.676  23.811
plotAndSummarizeAllelicBiasTest 18.092  0.704  19.925
plotFDRResults                  17.656  0.708  19.584
testForAllelicBiases            16.880  0.728  18.663
plotRegionCounts                 1.916  0.028   5.220
* 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
  ‘/home/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	58.892	5.852	72.855
annotation-methods	1.888	0.084	1.972
annotationBins	0.656	0.008	0.661
annotationBins2	0.908	0.296	3.909
annotationDatasets	0.724	0.112	0.869
annotationReadGroups	0.696	0.000	0.695
annotationRegions	0.688	0.008	0.695
associateGenotypes	4.104	0.008	4.133
bins-methods	1.176	0.008	1.186
changeObjectIntegrityChecking	0.660	0.004	0.665
collectFiles	0.080	0.000	0.081
convertToAllelicFractions	0.724	0.000	0.723
counts-method	0.772	0.004	0.778
datasets-methods	0.668	0.000	0.668
deleteDatasets	0.676	0.004	0.681
deleteReadGroups	0.680	0.004	0.682
deleteRegions	0.728	0.016	0.744
enrichment-methods	0.680	0.000	0.681
getDefaultParameterList	0.004	0.000	0.001
mergeReadGroups	0.712	0.004	0.717
parameters-methods	0.800	0.004	0.802
plotAllelicBiasResults	21.988	0.676	23.811
plotAllelicBiasResultsOverview	2.552	0.080	4.982
plotAndCalculateCorrelationDatasets	1.328	0.040	1.369
plotAndCalculateWeakAndStrongGenotype	1.612	0.004	1.616
plotAndClusterMatrix	1.236	0.012	1.247
plotAndSummarizeAllelicBiasTest	18.092	0.704	19.925
plotBinCounts	2.076	0.028	2.106
plotClusterAverage	0.700	0.024	0.728
plotFDRResults	17.656	0.708	19.584
plotGenotypesPerCluster	1.048	0.068	1.116
plotGenotypesPerSNP	0.900	0.004	0.904
plotRegionCounts	1.916	0.028	5.220
readGroups-methods	0.716	0.000	0.719
regions-methods	0.168	0.000	0.168
renameBins	0.688	0.004	0.694
renameDatasets	0.188	0.000	0.190
renameReadGroups	0.740	0.004	0.746
renameRegions	0.692	0.000	0.695
results	2.056	2.112	4.167
testForAllelicBiases	16.880	0.728	18.663