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CHECK report for SNPhood on merida1

This page was generated on 2019-04-16 11:59:04 -0400 (Tue, 16 Apr 2019).

Package 1475/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.12.0
Christian Arnold
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/SNPhood
Branch: RELEASE_3_8
Last Commit: f6e5f8e
Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SNPhood
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SNPhood_1.12.0.tar.gz
StartedAt: 2019-04-16 02:53:46 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:04:09 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 622.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SNPhood_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SNPhood.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.12.0’
* 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 ... OK
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
plotAllelicBiasResults          119.512 78.830  41.293
plotFDRResults                  115.877 76.441  36.693
plotAndSummarizeAllelicBiasTest 109.781 81.021  36.806
testForAllelicBiases            116.063 65.242  35.779
analyzeSNPhood                   83.544  1.559  93.086
results                           5.725  5.585  11.416
associateGenotypes                7.080  0.082   7.257
plotRegionCounts                  3.069  0.064   5.789
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/SNPhood.Rcheck/00check.log’
for details.



Installation output

SNPhood.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SNPhood
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SNPhood’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPhood)

Tests output


Example timings

SNPhood.Rcheck/SNPhood-Ex.timings

nameusersystemelapsed
analyzeSNPhood83.544 1.55993.086
annotation-methods0.3650.1170.485
annotationBins0.2490.0380.291
annotationBins21.1800.0803.109
annotationDatasets0.1960.0130.240
annotationReadGroups0.9450.0340.986
annotationRegions0.9990.0511.064
associateGenotypes7.0800.0827.257
bins-methods0.2090.0130.224
changeObjectIntegrityChecking0.2610.0190.283
collectFiles0.0380.0010.042
convertToAllelicFractions0.8780.0390.924
counts-method0.2890.0470.338
datasets-methods0.2090.0260.239
deleteDatasets0.2040.0380.245
deleteReadGroups0.2640.0580.324
deleteRegions0.2430.0150.259
enrichment-methods0.9140.0350.952
getDefaultParameterList0.0010.0000.001
mergeReadGroups0.3200.0480.372
parameters-methods0.2490.0500.305
plotAllelicBiasResults119.512 78.830 41.293
plotAllelicBiasResultsOverview1.6460.0423.761
plotAndCalculateCorrelationDatasets1.1050.0431.161
plotAndCalculateWeakAndStrongGenotype1.0880.0691.176
plotAndClusterMatrix1.6630.0721.753
plotAndSummarizeAllelicBiasTest109.781 81.021 36.806
plotBinCounts2.7460.0582.828
plotClusterAverage1.7310.0321.787
plotFDRResults115.877 76.441 36.693
plotGenotypesPerCluster0.6740.0420.727
plotGenotypesPerSNP0.5520.0410.594
plotRegionCounts3.0690.0645.789
readGroups-methods0.2190.0200.239
regions-methods0.9380.0551.002
renameBins0.2120.0590.275
renameDatasets0.2240.0340.259
renameReadGroups0.2350.0390.279
renameRegions1.3580.0601.439
results 5.725 5.58511.416
testForAllelicBiases116.063 65.242 35.779