BioC 3.4: CHECK report for SNPhood on zin1

Package: SNPhood

Version: 1.3.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SNPhood_1.3.3.tar.gz

StartedAt: 2016-09-20 12:45:43 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:52:13 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 389.6 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_1.3.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.3.3’
* 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         52.928  5.568  64.512
plotAllelicBiasResults 32.092  0.348  33.271
testForAllelicBiases   29.736  0.436  31.040
results                 3.352  2.136   5.491
plotRegionCounts        2.752  0.016   5.221
* 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	52.928	5.568	64.512
annotation-methods	1.076	0.068	1.147
annotationBins	0.564	0.008	0.572
annotationBins2	0.680	0.188	3.030
annotationDatasets	0.984	0.040	1.025
annotationReadGroups	0.556	0.004	0.557
annotationRegions	0.572	0.000	0.573
associateGenotypes	4.520	0.036	4.566
bins-methods	0.576	0.004	0.581
changeObjectIntegrityChecking	0.560	0.008	0.567
collectFiles	0.032	0.000	0.029
convertToAllelicFractions	0.596	0.004	0.599
counts-method	0.608	0.004	0.611
datasets-methods	0.956	0.004	0.961
deleteDatasets	0.568	0.000	0.566
deleteReadGroups	0.576	0.004	0.577
deleteRegions	0.588	0.000	0.587
enrichment-methods	0.564	0.004	0.569
getDefaultParameterList	0.000	0.000	0.001
mergeReadGroups	0.608	0.004	0.614
parameters-methods	0.564	0.004	0.566
plotAllelicBiasResults	32.092	0.348	33.271
plotAllelicBiasResultsOverview	1.568	0.008	3.389
plotAndCalculateCorrelationDatasets	0.648	0.000	0.650
plotAndCalculateWeakAndStrongGenotype	1.220	0.012	1.235
plotAndClusterMatrix	1.108	0.012	1.233
plotBinCounts	2.164	0.004	2.167
plotClusterAverage	0.612	0.004	0.614
plotGenotypesPerCluster	0.948	0.024	0.972
plotGenotypesPerSNP	0.400	0.304	0.703
plotRegionCounts	2.752	0.016	5.221
readGroups-methods	0.176	0.004	0.180
regions-methods	0.592	0.024	0.614
renameBins	0.168	0.012	0.183
renameDatasets	0.576	0.024	0.600
renameReadGroups	0.172	0.008	0.181
renameRegions	0.608	0.012	0.623
results	3.352	2.136	5.491
testForAllelicBiases	29.736	0.436	31.040