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CHECK report for SNPhood on celaya2

This page was generated on 2020-01-16 13:43:42 -0500 (Thu, 16 Jan 2020).

Package 1620/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.17.0
Christian Arnold
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/SNPhood
Branch: master
Last Commit: f8f7c1f
Last Changed Date: 2019-10-29 13:40:06 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SNPhood
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2020-01-16 09:04:24 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 09:21:49 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 1045.0 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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.17.0’
* 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 < >
   use the Contact field instead
* 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 (user + system) or elapsed time > 5s
                                   user system elapsed
plotAndSummarizeAllelicBiasTest 139.633 60.242  57.680
plotAllelicBiasResults          135.304 52.972  63.648
plotFDRResults                  132.642 54.541  57.829
testForAllelicBiases            131.700 54.310  58.036
analyzeSNPhood                  180.740  4.669 198.400
results                           9.766 12.546  22.355
annotationBins2                  11.839  0.221  16.105
associateGenotypes               11.503  0.183  11.705
renameRegions                     5.693  0.135   5.830
plotRegionCounts                  5.256  0.169  10.754
plotAllelicBiasResultsOverview    1.913  0.082   5.554
* 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-3.11-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/4.0/Resources/library’
* installing *source* package ‘SNPhood’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SNPhood)

Tests output


Example timings

SNPhood.Rcheck/SNPhood-Ex.timings

nameusersystemelapsed
analyzeSNPhood180.740 4.669198.400
annotation-methods0.4450.1860.631
annotationBins1.1800.0391.218
annotationBins211.839 0.22116.105
annotationDatasets0.2490.0780.346
annotationReadGroups0.2600.0570.316
annotationRegions1.2920.0391.332
associateGenotypes11.503 0.18311.705
bins-methods1.3600.0771.438
changeObjectIntegrityChecking0.2590.0720.331
collectFiles0.0450.0020.047
convertToAllelicFractions0.2600.0260.285
counts-method0.3960.0340.430
datasets-methods0.2570.0550.316
deleteDatasets1.2460.0401.286
deleteReadGroups0.2810.0610.342
deleteRegions0.2170.0330.249
enrichment-methods0.2690.0900.359
getDefaultParameterList0.0010.0010.001
mergeReadGroups0.3510.0490.399
parameters-methods1.2710.0791.351
plotAllelicBiasResults135.304 52.972 63.648
plotAllelicBiasResultsOverview1.9130.0825.554
plotAndCalculateCorrelationDatasets0.3720.0730.467
plotAndCalculateWeakAndStrongGenotype3.5130.1473.665
plotAndClusterMatrix1.7190.1941.921
plotAndSummarizeAllelicBiasTest139.633 60.242 57.680
plotBinCounts3.1530.0733.229
plotClusterAverage1.1060.0631.169
plotFDRResults132.642 54.541 57.829
plotGenotypesPerCluster1.0500.0761.127
plotGenotypesPerSNP0.7580.0230.782
plotRegionCounts 5.256 0.16910.754
readGroups-methods0.230.080.31
regions-methods0.2100.0840.296
renameBins0.2320.0860.318
renameDatasets0.2340.0830.316
renameReadGroups1.3980.0551.453
renameRegions5.6930.1355.830
results 9.76612.54622.355
testForAllelicBiases131.700 54.310 58.036