BioC 3.4: CHECK report for SNPhood on malbec1

Package: SNPhood

Version: 1.4.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.4.1.tar.gz

StartedAt: 2017-04-15 01:22:40 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:29:49 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 428.2 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SNPhood.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.1’
* 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         60.820  4.020  74.206
plotAllelicBiasResults 26.412  0.516  28.034
testForAllelicBiases   24.264  0.624  25.969
plotRegionCounts        2.960  0.060   6.795
* 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-3.4-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	60.820	4.020	74.206
annotation-methods	1.964	0.108	2.077
annotationBins	0.688	0.008	0.698
annotationBins2	1.008	0.364	3.909
annotationDatasets	0.772	0.064	0.880
annotationReadGroups	0.632	0.024	0.658
annotationRegions	0.656	0.004	0.662
associateGenotypes	4.364	0.008	4.389
bins-methods	0.688	0.008	0.698
changeObjectIntegrityChecking	0.660	0.004	0.661
collectFiles	0.040	0.000	0.039
convertToAllelicFractions	0.668	0.000	0.669
counts-method	0.716	0.004	0.722
datasets-methods	0.660	0.000	0.659
deleteDatasets	0.696	0.000	0.696
deleteReadGroups	1.248	0.000	1.246
deleteRegions	0.708	0.000	0.707
enrichment-methods	0.716	0.004	0.718
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.696	0.000	0.695
parameters-methods	0.648	0.016	0.666
plotAllelicBiasResults	26.412	0.516	28.034
plotAllelicBiasResultsOverview	1.912	0.088	3.993
plotAndCalculateCorrelationDatasets	0.740	0.004	0.743
plotAndCalculateWeakAndStrongGenotype	1.256	0.004	1.260
plotAndClusterMatrix	1.228	0.008	1.236
plotBinCounts	2.276	0.004	2.282
plotClusterAverage	1.148	0.004	1.153
plotGenotypesPerCluster	1.024	0.004	1.030
plotGenotypesPerSNP	0.956	0.004	0.959
plotRegionCounts	2.960	0.060	6.795
readGroups-methods	0.164	0.000	0.165
regions-methods	0.180	0.004	0.182
renameBins	0.656	0.008	0.662
renameDatasets	0.676	0.004	0.682
renameReadGroups	0.684	0.000	0.687
renameRegions	1.164	0.000	1.166
results	2.640	1.608	4.265
testForAllelicBiases	24.264	0.624	25.969