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: 2017-08-16 02:22:58 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:30:36 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 458.0 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 3.4.1 (2017-06-30)
* 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                  58.756  3.700  73.651
plotAllelicBiasResults          21.900  0.572  24.371
plotFDRResults                  18.392  0.596  20.806
plotAndSummarizeAllelicBiasTest 18.024  0.744  20.606
testForAllelicBiases            16.556  0.632  17.634
plotRegionCounts                 3.308  0.016   8.179
plotAllelicBiasResultsOverview   2.548  0.012   6.058
* 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	58.756	3.700	73.651
annotation-methods	1.464	0.076	1.542
annotationBins	0.708	0.020	0.728
annotationBins2	0.952	0.340	4.873
annotationDatasets	0.836	0.088	0.993
annotationReadGroups	0.760	0.000	0.761
annotationRegions	0.716	0.004	0.722
associateGenotypes	4.224	0.016	4.259
bins-methods	0.780	0.000	0.783
changeObjectIntegrityChecking	0.728	0.000	0.727
collectFiles	0.088	0.000	0.086
convertToAllelicFractions	0.224	0.000	0.225
counts-method	0.828	0.000	0.828
datasets-methods	0.168	0.000	0.168
deleteDatasets	0.692	0.004	0.698
deleteReadGroups	0.180	0.000	0.179
deleteRegions	0.216	0.012	0.229
enrichment-methods	0.184	0.008	0.190
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.764	0.004	0.767
parameters-methods	0.184	0.000	0.181
plotAllelicBiasResults	21.900	0.572	24.371
plotAllelicBiasResultsOverview	2.548	0.012	6.058
plotAndCalculateCorrelationDatasets	0.748	0.008	0.757
plotAndCalculateWeakAndStrongGenotype	1.048	0.012	1.061
plotAndClusterMatrix	1.296	0.004	1.301
plotAndSummarizeAllelicBiasTest	18.024	0.744	20.606
plotBinCounts	2.152	0.040	2.193
plotClusterAverage	1.256	0.008	1.263
plotFDRResults	18.392	0.596	20.806
plotGenotypesPerCluster	1.124	0.068	1.191
plotGenotypesPerSNP	0.424	0.004	0.429
plotRegionCounts	3.308	0.016	8.179
readGroups-methods	0.232	0.000	0.229
regions-methods	0.212	0.000	0.213
renameBins	0.812	0.000	0.810
renameDatasets	0.18	0.00	0.18
renameReadGroups	0.780	0.000	0.778
renameRegions	0.660	0.004	0.663
results	2.640	1.660	4.304
testForAllelicBiases	16.556	0.632	17.634