BioC 3.5: CHECK report for SNPhood on malbec2

Package: SNPhood

Version: 1.6.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.6.1.tar.gz

StartedAt: 2017-10-18 02:36:06 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:43:44 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 457.8 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SNPhood.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.1’
* 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  8.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    3.8Mb
* 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                  61.084  3.692  72.786
plotAllelicBiasResults          23.004  0.652  24.837
plotFDRResults                  18.068  0.640  19.877
plotAndSummarizeAllelicBiasTest 17.876  0.712  19.716
testForAllelicBiases            16.376  0.620  18.189
plotRegionCounts                 2.848  0.008   6.644
plotAllelicBiasResultsOverview   2.752  0.060   5.134
* 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-3.5-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	61.084	3.692	72.786
annotation-methods	1.488	0.064	1.550
annotationBins	0.700	0.008	0.708
annotationBins2	1.052	0.420	3.727
annotationDatasets	0.820	0.088	0.943
annotationReadGroups	0.720	0.004	0.721
annotationRegions	0.688	0.004	0.693
associateGenotypes	4.312	0.024	4.358
bins-methods	0.724	0.008	0.736
changeObjectIntegrityChecking	0.748	0.008	0.759
collectFiles	0.092	0.000	0.091
convertToAllelicFractions	0.828	0.004	0.831
counts-method	0.84	0.00	0.84
datasets-methods	0.708	0.000	0.706
deleteDatasets	0.748	0.004	0.752
deleteReadGroups	0.188	0.004	0.191
deleteRegions	0.772	0.000	0.774
enrichment-methods	0.164	0.012	0.177
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.224	0.004	0.229
parameters-methods	0.176	0.000	0.177
plotAllelicBiasResults	23.004	0.652	24.837
plotAllelicBiasResultsOverview	2.752	0.060	5.134
plotAndCalculateCorrelationDatasets	1.448	0.008	1.454
plotAndCalculateWeakAndStrongGenotype	1.768	0.016	1.784
plotAndClusterMatrix	1.256	0.012	1.271
plotAndSummarizeAllelicBiasTest	17.876	0.712	19.716
plotBinCounts	2.144	0.028	2.175
plotClusterAverage	0.644	0.008	0.655
plotFDRResults	18.068	0.640	19.877
plotGenotypesPerCluster	0.516	0.004	0.524
plotGenotypesPerSNP	0.420	0.000	0.421
plotRegionCounts	2.848	0.008	6.644
readGroups-methods	0.164	0.008	0.172
regions-methods	0.168	0.000	0.169
renameBins	0.180	0.012	0.194
renameDatasets	0.748	0.000	0.751
renameReadGroups	0.176	0.000	0.173
renameRegions	1.236	0.000	1.238
results	2.000	1.512	3.514
testForAllelicBiases	16.376	0.620	18.189