BioC 3.4: CHECK report for SNPhood on morelia

Package: SNPhood

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.4.1.tar.gz

StartedAt: 2017-04-15 08:20:11 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:29:24 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 553.6 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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SNPhood.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.1’
* 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  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                 77.682  2.220 109.266
plotAllelicBiasResults         37.661  0.186  40.167
testForAllelicBiases           34.184  0.178  36.963
results                         3.641  3.618   7.290
associateGenotypes              5.663  0.039   5.730
plotRegionCounts                3.585  0.169  10.858
plotAllelicBiasResultsOverview  2.193  0.120   7.507
* 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	77.682	2.220	109.266
annotation-methods	1.180	0.076	1.257
annotationBins	0.620	0.034	0.654
annotationBins2	0.855	0.129	4.957
annotationDatasets	0.616	0.016	0.755
annotationReadGroups	0.493	0.019	0.513
annotationRegions	0.610	0.022	0.634
associateGenotypes	5.663	0.039	5.730
bins-methods	0.631	0.024	0.656
changeObjectIntegrityChecking	0.616	0.036	0.651
collectFiles	0.041	0.001	0.042
convertToAllelicFractions	0.616	0.018	0.635
counts-method	0.746	0.020	0.768
datasets-methods	0.603	0.018	0.622
deleteDatasets	0.567	0.018	0.584
deleteReadGroups	0.620	0.019	0.639
deleteRegions	0.662	0.011	0.674
enrichment-methods	0.632	0.020	0.652
getDefaultParameterList	0.001	0.000	0.001
mergeReadGroups	0.745	0.031	0.779
parameters-methods	0.611	0.027	0.640
plotAllelicBiasResults	37.661	0.186	40.167
plotAllelicBiasResultsOverview	2.193	0.120	7.507
plotAndCalculateCorrelationDatasets	0.670	0.029	0.700
plotAndCalculateWeakAndStrongGenotype	1.504	0.046	1.555
plotAndClusterMatrix	1.366	0.039	1.416
plotBinCounts	3.148	0.033	3.228
plotClusterAverage	1.267	0.030	1.298
plotGenotypesPerCluster	1.042	0.030	1.074
plotGenotypesPerSNP	1.001	0.033	1.037
plotRegionCounts	3.585	0.169	10.858
readGroups-methods	0.168	0.020	0.188
regions-methods	0.644	0.028	0.671
renameBins	0.635	0.032	0.667
renameDatasets	0.196	0.021	0.217
renameReadGroups	0.652	0.032	0.685
renameRegions	0.849	0.052	0.903
results	3.641	3.618	7.290
testForAllelicBiases	34.184	0.178	36.963