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This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).

CHECK results for SNPhood on nebbiolo1

To the developers/maintainers of the SNPhood package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SNPhood.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1801/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.22.0  (landing page)
Christian Arnold
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: RELEASE_3_13
git_last_commit: 562991f
git_last_commit_date: 2021-05-19 12:16:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SNPhood
Version: 1.22.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SNPhood_1.22.0.tar.gz
StartedAt: 2021-10-14 11:41:03 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:50:29 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 565.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SNPhood_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/SNPhood.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.22.0’
* 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 LazyData ... 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
analyzeSNPhood                  104.926  6.606 112.281
plotAllelicBiasResults           29.964  0.205  28.302
plotFDRResults                   28.519  1.330  27.936
testForAllelicBiases             28.309  1.225  28.017
plotAndSummarizeAllelicBiasTest  27.930  0.677  27.095
results                           2.811 10.402  13.213
annotationBins2                  12.165  0.091  12.299
associateGenotypes                6.780  0.020   6.801
* 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-3.13-bioc/meat/SNPhood.Rcheck/00check.log’
for details.



Installation output

SNPhood.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SNPhood
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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
analyzeSNPhood104.926 6.606112.281
annotation-methods0.2760.1160.392
annotationBins0.1720.0360.208
annotationBins212.165 0.09112.299
annotationDatasets0.1560.0320.188
annotationReadGroups0.1700.0120.182
annotationRegions0.1890.0080.197
associateGenotypes6.7800.0206.801
bins-methods0.1830.0200.203
changeObjectIntegrityChecking0.2110.0360.247
collectFiles0.0320.0040.036
convertToAllelicFractions1.3380.0001.338
counts-method0.230.040.27
datasets-methods0.1730.0120.185
deleteDatasets0.1970.0040.201
deleteReadGroups0.2070.0240.232
deleteRegions0.2230.0040.226
enrichment-methods0.2050.0000.205
getDefaultParameterList0.0010.0000.001
mergeReadGroups0.2100.0160.225
parameters-methods0.1780.0160.194
plotAllelicBiasResults29.964 0.20528.302
plotAllelicBiasResultsOverview0.8960.0400.937
plotAndCalculateCorrelationDatasets1.4210.0921.513
plotAndCalculateWeakAndStrongGenotype0.6270.0320.659
plotAndClusterMatrix0.5440.0160.560
plotAndSummarizeAllelicBiasTest27.930 0.67727.095
plotBinCounts1.1210.1601.282
plotClusterAverage0.5130.0360.548
plotFDRResults28.519 1.33027.936
plotGenotypesPerCluster0.5060.0320.538
plotGenotypesPerSNP0.3450.0200.365
plotRegionCounts1.7200.0481.768
readGroups-methods0.1900.0120.201
regions-methods0.1730.0040.177
renameBins1.2610.1521.413
renameDatasets0.1640.0280.192
renameReadGroups0.1750.0200.194
renameRegions3.7110.0603.772
results 2.81110.40213.213
testForAllelicBiases28.309 1.22528.017