BioC 3.3: CHECK report for SNPhood on oaxaca

Package: SNPhood

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.2.3.tar.gz

StartedAt: 2016-10-13 06:27:53 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:36:37 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 524.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SNPhood.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.3’
* 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  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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
analyzeSNPhood         79.794  2.363  88.532
plotAllelicBiasResults 40.208  0.137  41.805
testForAllelicBiases   37.107  0.152  38.039
results                 3.260  3.818   7.087
associateGenotypes      6.417  0.045   6.547
plotRegionCounts        3.867  0.060   6.175
* 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	79.794	2.363	88.532
annotation-methods	1.021	0.054	1.078
annotationBins	0.858	0.026	0.890
annotationBins2	0.681	0.068	2.387
annotationDatasets	0.510	0.021	0.531
annotationReadGroups	0.512	0.025	0.538
annotationRegions	0.499	0.020	0.518
associateGenotypes	6.417	0.045	6.547
bins-methods	0.533	0.018	0.550
changeObjectIntegrityChecking	0.530	0.018	0.548
collectFiles	0.047	0.001	0.048
convertToAllelicFractions	0.508	0.017	0.524
counts-method	0.602	0.021	0.623
datasets-methods	0.472	0.014	0.486
deleteDatasets	0.504	0.019	0.524
deleteReadGroups	0.898	0.020	0.920
deleteRegions	0.546	0.017	0.564
enrichment-methods	0.542	0.021	0.565
getDefaultParameterList	0.001	0.000	0.001
mergeReadGroups	0.567	0.021	0.589
parameters-methods	0.522	0.023	0.546
plotAllelicBiasResults	40.208	0.137	41.805
plotAllelicBiasResultsOverview	2.115	0.037	3.850
plotAndCalculateCorrelationDatasets	0.633	0.016	0.651
plotAndCalculateWeakAndStrongGenotype	1.477	0.035	1.516
plotAndClusterMatrix	1.360	0.033	1.398
plotBinCounts	2.917	0.033	2.955
plotClusterAverage	1.243	0.026	1.269
plotGenotypesPerCluster	1.120	0.042	1.165
plotGenotypesPerSNP	0.521	0.015	0.538
plotRegionCounts	3.867	0.060	6.175
readGroups-methods	0.162	0.010	0.174
regions-methods	0.549	0.023	0.572
renameBins	0.180	0.023	0.203
renameDatasets	0.179	0.018	0.199
renameReadGroups	0.173	0.020	0.193
renameRegions	1.275	0.032	1.307
results	3.260	3.818	7.087
testForAllelicBiases	37.107	0.152	38.039