BioC 3.4: CHECK report for SNPhood on morelia

Package: SNPhood

Version: 1.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.3.3.tar.gz

StartedAt: 2016-09-20 13:17:05 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:23:44 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 398.8 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_1.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.3.3’
* 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  7.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    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’
.createSNPhoodObject: no visible global function definition for ‘new’
.getMemoryProfile: no visible global function definition for
  ‘object.size’
.onAttach: no visible global function definition for ‘packageVersion’
plotAndSummarizeAllelicBiasTest: no visible global function definition
  for ‘geom_histogram’
show,SNPhood: no visible global function definition for ‘tail’
Undefined global functions or variables:
  geom_histogram new object.size packageVersion pp tail
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size", "packageVersion", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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         56.445  2.071  65.857
plotAllelicBiasResults 29.446  0.182  30.413
testForAllelicBiases   26.677  0.119  27.569
results                 3.017  3.038   6.116
* 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-3.4-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	56.445	2.071	65.857
annotation-methods	0.902	0.062	0.965
annotationBins	0.493	0.019	0.511
annotationBins2	0.634	0.043	2.351
annotationDatasets	0.795	0.008	0.803
annotationReadGroups	0.450	0.018	0.467
annotationRegions	0.455	0.031	0.485
associateGenotypes	4.833	0.085	4.949
bins-methods	0.530	0.042	0.572
changeObjectIntegrityChecking	0.536	0.029	0.565
collectFiles	0.028	0.000	0.029
convertToAllelicFractions	0.502	0.021	0.522
counts-method	0.557	0.030	0.588
datasets-methods	0.891	0.024	0.915
deleteDatasets	0.545	0.012	0.557
deleteReadGroups	0.452	0.025	0.477
deleteRegions	0.605	0.029	0.635
enrichment-methods	0.509	0.023	0.533
getDefaultParameterList	0.001	0.000	0.000
mergeReadGroups	0.548	0.021	0.571
parameters-methods	0.493	0.020	0.514
plotAllelicBiasResults	29.446	0.182	30.413
plotAllelicBiasResultsOverview	1.606	0.042	3.239
plotAndCalculateCorrelationDatasets	0.573	0.028	0.601
plotAndCalculateWeakAndStrongGenotype	1.252	0.040	1.296
plotAndClusterMatrix	1.159	0.042	1.208
plotBinCounts	2.260	0.031	2.295
plotClusterAverage	0.624	0.021	0.644
plotGenotypesPerCluster	0.867	0.049	0.918
plotGenotypesPerSNP	0.415	0.021	0.437
plotRegionCounts	2.505	0.050	4.830
readGroups-methods	0.133	0.012	0.145
regions-methods	0.484	0.030	0.514
renameBins	0.141	0.039	0.181
renameDatasets	0.448	0.037	0.486
renameReadGroups	0.138	0.034	0.172
renameRegions	0.580	0.038	0.618
results	3.017	3.038	6.116
testForAllelicBiases	26.677	0.119	27.569