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CHECK report for nucleR on veracruz1

This page was generated on 2018-04-12 13:34:28 -0400 (Thu, 12 Apr 2018).

Package 953/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.10.0
Ricard Illa
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/nucleR
Branch: RELEASE_3_6
Last Commit: 4fe65b8
Last Changed Date: 2017-10-30 12:39:35 -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  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: nucleR
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nucleR_2.10.0.tar.gz
StartedAt: 2018-04-12 07:08:57 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:12:04 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 187.1 seconds
RetCode: 0
Status:  OK 
CheckDir: nucleR.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 nucleR_2.10.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/nucleR.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 ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘2.10.0’
* 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 ‘nucleR’ 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 ... 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 ... NOTE
.buildGRSingle: no visible binding for global variable ‘rname’
.buildGRSingle: no visible binding for global variable ‘qwidth’
Undefined global functions or variables:
  qwidth rname
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/nucleR.Rcheck/00check.log’
for details.



Installation output

nucleR.Rcheck/00install.out

* installing *source* package ‘nucleR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nucleR)

Tests output


Example timings

nucleR.Rcheck/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.0840.0020.085
coverage.rpm0.7310.0180.769
export.bed0.0010.0000.002
export.wig0.0010.0000.002
filterFFT0.4090.0230.445
fragmentLenDetect1.1730.0381.233
mergeCalls0.7500.0020.766
nucleR-package0.6230.0080.652
pcKeepCompDetect0.2260.0060.239
peakDetection0.3510.0050.371
peakScoring0.1040.0030.110
plotPeaks0.2590.0030.268
processReads0.1450.0040.152
processTilingArray0.0010.0000.001
syntheticNucMap0.6190.0110.643