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CHECK report for dupRadar on machv2

This page was generated on 2021-01-17 12:38:45 -0500 (Sun, 17 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE dupRadar PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 514/1931HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dupRadar 1.21.0
Sergi Sayols , Holger Klein
Snapshot Date: 2021-01-16 14:40:27 -0500 (Sat, 16 Jan 2021)
URL: https://git.bioconductor.org/packages/dupRadar
Branch: master
Last Commit: 0668896
Last Changed Date: 2020-10-27 11:08:08 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
riesling1 Windows Server 2019 Standard / x64 ...NOT SUPPORTED...
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: dupRadar
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dupRadar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dupRadar_1.21.0.tar.gz
StartedAt: 2021-01-17 00:10:48 -0500 (Sun, 17 Jan 2021)
EndedAt: 2021-01-17 00:11:50 -0500 (Sun, 17 Jan 2021)
EllapsedTime: 61.8 seconds
RetCode: 0
Status:  OK 
CheckDir: dupRadar.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dupRadar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dupRadar_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/dupRadar.Rcheck’
* using R Under development (unstable) (2021-01-06 r79800)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dupRadar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dupRadar’ version ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dupRadar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* 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
* 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-3.13-bioc/meat/dupRadar.Rcheck/00check.log’
for details.



Installation output

dupRadar.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dupRadar
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘dupRadar’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (dupRadar)

Tests output


Example timings

dupRadar.Rcheck/dupRadar-Ex.timings

nameusersystemelapsed
analyzeDuprates0.1240.0670.459
cumulativeDuprateBarplot0.1900.0400.231
duprateExpBoxplot0.2160.0290.245
duprateExpDensPlot1.3820.0891.473
duprateExpFit0.0470.0130.060
duprateExpIdentify0.4890.0210.513
duprateExpPlot0.1110.0150.127
expressionHist0.0330.0010.036
getDupMatStats0.0230.0010.024
getDynamicRange0.7030.1040.809
markDuplicates000
readcountExpBoxplot0.0730.0070.080