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CHECK report for dupRadar on veracruz1

This page was generated on 2018-04-12 13:41:36 -0400 (Thu, 12 Apr 2018).

Package 395/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dupRadar 1.8.0
Sergi Sayols , Holger Klein
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/dupRadar
Branch: RELEASE_3_6
Last Commit: 028d5af
Last Changed Date: 2017-10-30 12:40:57 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: dupRadar
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dupRadar_1.8.0.tar.gz
StartedAt: 2018-04-12 03:08:39 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:09:05 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 25.3 seconds
RetCode: 0
Status:  OK 
CheckDir: dupRadar.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dupRadar_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/dupRadar.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.0’
* 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 ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    4.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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-3.6-bioc/meat/dupRadar.Rcheck/00check.log’
for details.



Installation output

dupRadar.Rcheck/00install.out

* installing *source* package ‘dupRadar’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dupRadar)

Tests output


Example timings

dupRadar.Rcheck/dupRadar-Ex.timings

nameusersystemelapsed
analyzeDuprates0.2840.0800.420
cumulativeDuprateBarplot0.2240.0300.263
duprateExpBoxplot0.1740.0120.193
duprateExpDensPlot1.3170.0761.434
duprateExpFit0.0690.0160.087
duprateExpIdentify0.1320.0110.147
duprateExpPlot0.1470.0230.179
expressionHist0.0260.0020.029
getDupMatStats0.0210.0020.023
getDynamicRange0.5140.0950.620
markDuplicates0.0010.0000.001
readcountExpBoxplot0.0620.0120.076