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CHECK report for SNPhood on malbec2

This page was generated on 2018-10-17 08:28:11 -0400 (Wed, 17 Oct 2018).

Package 1397/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.10.0
Christian Arnold
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SNPhood
Branch: RELEASE_3_7
Last Commit: 894557e
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SNPhood
Version: 1.10.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SNPhood_1.10.0.tar.gz
StartedAt: 2018-10-16 03:52:22 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 03:59:43 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 441.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SNPhood_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/SNPhood.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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
analyzeSNPhood                  56.620  6.028  86.656
plotAllelicBiasResults          20.092  0.984  27.939
plotFDRResults                  17.576  0.956  20.727
plotAndSummarizeAllelicBiasTest 17.484  0.980  20.057
testForAllelicBiases            16.092  0.972  18.941
associateGenotypes               5.868  0.052   5.941
plotRegionCounts                 2.460  0.040   7.320
plotAllelicBiasResultsOverview   2.240  0.092   7.123
annotationBins2                  1.092  0.552   5.082
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/SNPhood.Rcheck/00check.log’
for details.



Installation output

SNPhood.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL SNPhood
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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
analyzeSNPhood56.620 6.02886.656
annotation-methods0.2320.0600.294
annotationBins0.2080.0480.253
annotationBins21.0920.5525.082
annotationDatasets0.2200.0400.314
annotationReadGroups0.8680.1601.029
annotationRegions0.1720.0000.175
associateGenotypes5.8680.0525.941
bins-methods0.1640.0200.185
changeObjectIntegrityChecking0.2120.0000.214
collectFiles0.0280.0000.026
convertToAllelicFractions0.1920.0000.194
counts-method0.2240.0040.231
datasets-methods0.1720.0000.175
deleteDatasets0.8320.0000.833
deleteReadGroups0.1800.0000.179
deleteRegions0.1960.0000.193
enrichment-methods0.1760.0000.177
getDefaultParameterList0.0040.0000.001
mergeReadGroups0.2080.0000.209
parameters-methods0.1720.0000.172
plotAllelicBiasResults20.092 0.98427.939
plotAllelicBiasResultsOverview2.2400.0927.123
plotAndCalculateCorrelationDatasets0.2280.0280.258
plotAndCalculateWeakAndStrongGenotype0.8760.0400.919
plotAndClusterMatrix1.5520.0241.579
plotAndSummarizeAllelicBiasTest17.484 0.98020.057
plotBinCounts2.4960.1122.610
plotClusterAverage0.7040.0160.721
plotFDRResults17.576 0.95620.727
plotGenotypesPerCluster0.4800.0280.512
plotGenotypesPerSNP1.2480.0921.342
plotRegionCounts2.460.047.32
readGroups-methods0.8840.0000.885
regions-methods0.1560.0040.159
renameBins0.1760.0000.179
renameDatasets0.1680.0040.171
renameReadGroups0.1920.0000.190
renameRegions0.8760.0040.881
results2.3202.0724.406
testForAllelicBiases16.092 0.97218.941