BioC 3.5: CHECK report for SNPhood on oaxaca

Package: SNPhood

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPhood_1.5.2.tar.gz

StartedAt: 2017-03-04 09:24:22 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:34:56 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 634.4 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_1.5.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.5.2’
* 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  8.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    4.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
* 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 ... OK
* 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’
Undefined global functions or variables:
  pp
* 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                  78.662  2.344 108.995
plotAllelicBiasResults          37.336  0.235  39.897
testForAllelicBiases            30.824  0.209  37.355
plotAndSummarizeAllelicBiasTest 30.494  0.223  34.215
plotFDRResults                  29.931  0.188  32.651
results                          3.973  3.898   7.876
associateGenotypes               6.131  0.113   6.275
plotRegionCounts                 3.759  0.206  12.907
plotAllelicBiasResultsOverview   3.489  0.131   8.457
annotationBins2                  1.589  0.143   6.765
* 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-3.5-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	78.662	2.344	108.995
annotation-methods	1.486	0.079	1.565
annotationBins	0.662	0.036	0.698
annotationBins2	1.589	0.143	6.765
annotationDatasets	0.719	0.032	0.884
annotationReadGroups	0.680	0.032	0.713
annotationRegions	0.715	0.041	0.757
associateGenotypes	6.131	0.113	6.275
bins-methods	0.69	0.03	0.72
changeObjectIntegrityChecking	0.777	0.055	0.833
collectFiles	0.144	0.001	0.146
convertToAllelicFractions	0.749	0.026	0.775
counts-method	0.842	0.028	0.870
datasets-methods	0.690	0.038	0.729
deleteDatasets	0.714	0.024	0.738
deleteReadGroups	0.717	0.034	0.752
deleteRegions	0.758	0.014	0.773
enrichment-methods	0.662	0.027	0.688
getDefaultParameterList	0.002	0.000	0.001
mergeReadGroups	0.726	0.031	0.756
parameters-methods	0.700	0.029	0.728
plotAllelicBiasResults	37.336	0.235	39.897
plotAllelicBiasResultsOverview	3.489	0.131	8.457
plotAndCalculateCorrelationDatasets	1.690	0.044	1.769
plotAndCalculateWeakAndStrongGenotype	1.445	0.084	1.534
plotAndClusterMatrix	1.523	0.077	1.607
plotAndSummarizeAllelicBiasTest	30.494	0.223	34.215
plotBinCounts	3.165	0.041	3.211
plotClusterAverage	1.053	0.045	1.099
plotFDRResults	29.931	0.188	32.651
plotGenotypesPerCluster	0.756	0.046	0.803
plotGenotypesPerSNP	1.104	0.083	1.190
plotRegionCounts	3.759	0.206	12.907
readGroups-methods	0.178	0.025	0.204
regions-methods	0.212	0.037	0.250
renameBins	0.777	0.053	0.831
renameDatasets	0.212	0.049	0.261
renameReadGroups	0.191	0.031	0.220
renameRegions	0.909	0.047	0.956
results	3.973	3.898	7.876
testForAllelicBiases	30.824	0.209	37.355