BioC 3.3: CHECK report for SNPhood on morelia

Package: SNPhood

Version: 1.1.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.1.10.tar.gz

StartedAt: 2016-04-21 07:44:20 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:52:21 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 480.9 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_1.1.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SNPhood.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.1.10’
* 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 ... [32s/33s] OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
* 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’
.getMemoryProfile: no visible global function definition for
  ‘object.size’
.onAttach: no visible global function definition for ‘packageVersion’
show,SNPhood: no visible global function definition for ‘tail’
Undefined global functions or variables:
  object.size packageVersion pp tail
Consider adding
  importFrom("utils", "object.size", "packageVersion", "tail")
to your NAMESPACE file.
* 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 ... [192s/207s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
analyzeSNPhood         70.586  1.887  80.398
plotAllelicBiasResults 36.099  0.129  37.071
testForAllelicBiases   33.327  0.145  34.335
results                 3.240  3.687   6.933
associateGenotypes      5.827  0.036   5.949
plotRegionCounts        3.545  0.060   5.898
* 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-3.3-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	70.586	1.887	80.398
annotation-methods	1.056	0.066	1.123
annotationBins	0.537	0.031	0.569
annotationBins2	0.742	0.055	2.375
annotationDatasets	0.504	0.019	0.525
annotationReadGroups	0.482	0.015	0.498
annotationRegions	0.545	0.018	0.565
associateGenotypes	5.827	0.036	5.949
bins-methods	0.542	0.018	0.561
changeObjectIntegrityChecking	0.501	0.024	0.524
collectFiles	0.042	0.001	0.043
convertToAllelicFractions	0.525	0.017	0.541
counts-method	0.541	0.020	0.561
datasets-methods	0.166	0.029	0.195
deleteDatasets	0.546	0.027	0.575
deleteReadGroups	0.535	0.020	0.556
deleteRegions	0.551	0.014	0.566
enrichment-methods	0.565	0.014	0.582
getDefaultParameterList	0.001	0.001	0.002
mergeReadGroups	0.622	0.027	0.650
parameters-methods	0.565	0.022	0.588
plotAllelicBiasResults	36.099	0.129	37.071
plotAllelicBiasResultsOverview	2.243	0.037	3.820
plotAndCalculateCorrelationDatasets	0.196	0.012	0.208
plotAndCalculateWeakAndStrongGenotype	1.023	0.033	1.061
plotAndClusterMatrix	1.197	0.033	1.263
plotBinCounts	2.710	0.026	2.765
plotClusterAverage	1.392	0.025	1.443
plotGenotypesPerCluster	1.082	0.021	1.106
plotGenotypesPerSNP	0.456	0.014	0.472
plotRegionCounts	3.545	0.060	5.898
readGroups-methods	0.122	0.010	0.132
regions-methods	0.172	0.024	0.195
renameBins	0.146	0.020	0.166
renameDatasets	0.184	0.022	0.206
renameReadGroups	0.168	0.020	0.189
renameRegions	1.368	0.036	1.407
results	3.240	3.687	6.933
testForAllelicBiases	33.327	0.145	34.335