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CHECK report for dupRadar on malbec1

This page was generated on 2021-01-22 11:51:16 -0500 (Fri, 22 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 517/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dupRadar 1.20.0
Sergi Sayols , Holger Klein
Snapshot Date: 2021-01-21 14:42:12 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/dupRadar
Branch: RELEASE_3_12
Last Commit: d9b9321
Last Changed Date: 2020-10-27 11:08:08 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dupRadar
Version: 1.20.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:dupRadar.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings dupRadar_1.20.0.tar.gz
StartedAt: 2021-01-22 01:39:54 -0500 (Fri, 22 Jan 2021)
EndedAt: 2021-01-22 01:40:40 -0500 (Fri, 22 Jan 2021)
EllapsedTime: 46.1 seconds
RetCode: 0
Status:  OK 
CheckDir: dupRadar.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:dupRadar.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings dupRadar_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/dupRadar.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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
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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/dupRadar.Rcheck/00check.log’
for details.



Installation output

dupRadar.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL dupRadar
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
analyzeDuprates0.0920.0040.218
cumulativeDuprateBarplot0.1680.0080.178
duprateExpBoxplot0.240.000.24
duprateExpDensPlot1.5040.0281.532
duprateExpFit0.0720.0080.077
duprateExpIdentify0.4760.0040.479
duprateExpPlot0.1160.0000.115
expressionHist0.0360.0040.040
getDupMatStats0.0320.0000.030
getDynamicRange0.8080.0000.811
markDuplicates000
readcountExpBoxplot0.0920.0000.092