BioC 3.3: CHECK report for SNPhood on zin2

Package: SNPhood

Version: 1.2.3

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.2.3.tar.gz

StartedAt: 2016-10-13 06:58:26 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:05:18 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 412.1 seconds

RetCode: 0

Status:  OK

CheckDir: SNPhood.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.2.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SNPhood.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.3’
* 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  6.6Mb
  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         60.652  3.312  70.441
plotAllelicBiasResults 32.613  0.408  37.374
testForAllelicBiases   31.191  0.369  32.363
results                 2.902  2.422   5.325
plotRegionCounts        2.884  0.011   5.561
* 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-3.3-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	60.652	3.312	70.441
annotation-methods	0.978	0.072	1.055
annotationBins	0.847	0.000	0.891
annotationBins2	0.628	0.197	2.677
annotationDatasets	0.546	0.040	0.654
annotationReadGroups	0.501	0.004	0.624
annotationRegions	0.511	0.000	0.521
associateGenotypes	4.641	0.008	4.907
bins-methods	0.515	0.016	0.601
changeObjectIntegrityChecking	0.513	0.012	0.524
collectFiles	0.027	0.004	0.030
convertToAllelicFractions	0.523	0.004	0.527
counts-method	0.558	0.000	0.600
datasets-methods	0.497	0.014	0.567
deleteDatasets	0.505	0.008	0.559
deleteReadGroups	0.878	0.003	0.937
deleteRegions	0.541	0.001	0.541
enrichment-methods	0.516	0.004	0.520
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.580	0.001	0.648
parameters-methods	0.512	0.001	0.574
plotAllelicBiasResults	32.613	0.408	37.374
plotAllelicBiasResultsOverview	1.693	0.044	3.993
plotAndCalculateCorrelationDatasets	0.646	0.005	0.721
plotAndCalculateWeakAndStrongGenotype	1.267	0.004	1.362
plotAndClusterMatrix	1.083	0.000	1.185
plotBinCounts	2.191	0.007	2.488
plotClusterAverage	1.019	0.000	1.202
plotGenotypesPerCluster	0.904	0.004	0.951
plotGenotypesPerSNP	0.410	0.003	0.460
plotRegionCounts	2.884	0.011	5.561
readGroups-methods	0.167	0.000	0.166
regions-methods	0.560	0.008	0.567
renameBins	0.173	0.008	0.180
renameDatasets	0.172	0.000	0.172
renameReadGroups	0.167	0.004	0.170
renameRegions	1.085	0.016	1.104
results	2.902	2.422	5.325
testForAllelicBiases	31.191	0.369	32.363