BioC 3.6: CHECK report for SNPhood on malbec1

Package: SNPhood

Version: 1.7.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.7.1.tar.gz

StartedAt: 2017-08-16 02:31:04 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:38:46 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 461.5 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.7.1’
* 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  8.0Mb
  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                  59.636  3.788  74.851
plotAllelicBiasResults          22.392  0.560  24.486
plotAndSummarizeAllelicBiasTest 18.280  0.644  20.572
plotFDRResults                  17.144  0.600  19.671
testForAllelicBiases            16.704  0.564  18.917
plotAllelicBiasResultsOverview   2.776  0.056   6.041
plotRegionCounts                 2.036  0.020   7.169
annotationBins2                  0.952  0.336   5.141
* 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	59.636	3.788	74.851
annotation-methods	1.512	0.084	1.595
annotationBins	0.704	0.004	0.707
annotationBins2	0.952	0.336	5.141
annotationDatasets	0.788	0.096	0.941
annotationReadGroups	0.724	0.004	0.729
annotationRegions	0.172	0.000	0.174
associateGenotypes	4.096	0.016	4.124
bins-methods	0.208	0.000	0.210
changeObjectIntegrityChecking	0.704	0.000	0.708
collectFiles	0.088	0.000	0.090
convertToAllelicFractions	0.752	0.004	0.756
counts-method	0.844	0.004	0.848
datasets-methods	0.684	0.004	0.691
deleteDatasets	0.74	0.00	0.74
deleteReadGroups	0.740	0.000	0.739
deleteRegions	0.784	0.000	0.784
enrichment-methods	0.716	0.000	0.718
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.776	0.000	0.774
parameters-methods	0.176	0.000	0.175
plotAllelicBiasResults	22.392	0.560	24.486
plotAllelicBiasResultsOverview	2.776	0.056	6.041
plotAndCalculateCorrelationDatasets	1.392	0.004	1.398
plotAndCalculateWeakAndStrongGenotype	1.636	0.008	1.645
plotAndClusterMatrix	1.372	0.008	1.380
plotAndSummarizeAllelicBiasTest	18.280	0.644	20.572
plotBinCounts	2.208	0.048	2.254
plotClusterAverage	1.268	0.012	1.282
plotFDRResults	17.144	0.600	19.671
plotGenotypesPerCluster	0.520	0.008	0.530
plotGenotypesPerSNP	0.992	0.040	1.036
plotRegionCounts	2.036	0.020	7.169
readGroups-methods	0.180	0.000	0.178
regions-methods	0.744	0.000	0.743
renameBins	0.172	0.004	0.179
renameDatasets	0.744	0.000	0.744
renameReadGroups	0.164	0.000	0.165
renameRegions	1.252	0.000	1.250
results	1.916	1.656	3.574
testForAllelicBiases	16.704	0.564	18.917