BioC 3.5: CHECK report for SNPhood on toluca2

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: 2017-04-23 10:09:31 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:19:56 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 624.9 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 r72187)
* 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                        85.014  1.741  93.867
plotAllelicBiasResults                38.007  0.225  39.065
plotAndSummarizeAllelicBiasTest       31.545  0.205  32.761
plotFDRResults                        30.882  0.176  31.772
testForAllelicBiases                  29.627  0.203  30.552
results                                3.836  3.902   7.769
associateGenotypes                     5.810  0.065   5.911
plotAndCalculateWeakAndStrongGenotype  5.508  0.084   5.624
plotAllelicBiasResultsOverview         3.327  0.114   6.543
plotRegionCounts                       3.238  0.180   5.209
* 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	85.014	1.741	93.867
annotation-methods	1.447	0.089	1.541
annotationBins	0.674	0.031	0.712
annotationBins2	1.103	0.126	2.519
annotationDatasets	0.668	0.022	0.725
annotationReadGroups	0.662	0.019	0.682
annotationRegions	0.676	0.035	0.712
associateGenotypes	5.810	0.065	5.911
bins-methods	0.713	0.031	0.745
changeObjectIntegrityChecking	0.714	0.050	0.769
collectFiles	0.130	0.001	0.132
convertToAllelicFractions	0.743	0.028	0.772
counts-method	0.827	0.025	0.856
datasets-methods	0.696	0.034	0.732
deleteDatasets	0.690	0.023	0.715
deleteReadGroups	0.667	0.027	0.698
deleteRegions	0.765	0.017	0.789
enrichment-methods	0.697	0.023	0.720
getDefaultParameterList	0.001	0.000	0.001
mergeReadGroups	0.724	0.030	0.756
parameters-methods	0.704	0.023	0.729
plotAllelicBiasResults	38.007	0.225	39.065
plotAllelicBiasResultsOverview	3.327	0.114	6.543
plotAndCalculateCorrelationDatasets	1.682	0.037	1.732
plotAndCalculateWeakAndStrongGenotype	5.508	0.084	5.624
plotAndClusterMatrix	1.007	0.050	1.069
plotAndSummarizeAllelicBiasTest	31.545	0.205	32.761
plotBinCounts	2.520	0.023	2.570
plotClusterAverage	1.515	0.027	1.549
plotFDRResults	30.882	0.176	31.772
plotGenotypesPerCluster	1.245	0.080	1.331
plotGenotypesPerSNP	0.518	0.032	0.553
plotRegionCounts	3.238	0.180	5.209
readGroups-methods	0.163	0.009	0.172
regions-methods	0.173	0.038	0.211
renameBins	0.716	0.041	0.760
renameDatasets	0.196	0.039	0.239
renameReadGroups	0.190	0.025	0.221
renameRegions	0.895	0.024	0.931
results	3.836	3.902	7.769
testForAllelicBiases	29.627	0.203	30.552