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CHECK report for Guitar on merida2

This page was generated on 2018-10-17 08:55:23 -0400 (Wed, 17 Oct 2018).

Package 666/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Guitar 1.18.0
Jia Meng
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Guitar
Branch: RELEASE_3_7
Last Commit: 6ac377f
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Guitar
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Guitar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Guitar_1.18.0.tar.gz
StartedAt: 2018-10-16 21:55:59 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:00:41 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 281.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Guitar.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:Guitar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Guitar_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Guitar.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Guitar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Guitar’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Rsamtools’ ‘GenomicFeatures’ ‘rtracklayer’ ‘GenomicAlignments’
  ‘GenomicRanges’ ‘ggplot2’ ‘grid’ ‘IRanges’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘Guitar’ 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 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
.makeFigure_fill: no visible global function definition for ‘pdf’
.makeFigure_fill: no visible global function definition for ‘dev.off’
.makeFigure_nofill: no visible global function definition for ‘pdf’
.makeFigure_nofill: no visible global function definition for ‘dev.off’
BED12toGRangesList: no visible global function definition for
  ‘read.table’
BED12toGRangesList: no visible global function definition for ‘head’
narrowPeaktoGRanges: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  dev.off head pdf read.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
combinedGuitarPlot       20.150  0.169  20.519
GuitarPlot               16.694  0.123  16.940
Guitar-package           16.323  0.174  16.628
makeGuitarCoordsFromTxDb  5.041  0.012   5.090
* 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-3.7-bioc/meat/Guitar.Rcheck/00check.log’
for details.



Installation output

Guitar.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Guitar
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Guitar’ ...
** R
** 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
* DONE (Guitar)

Tests output


Example timings

Guitar.Rcheck/Guitar-Ex.timings

nameusersystemelapsed
BED12toGRangesList2.7000.1542.876
Guitar-package16.323 0.17416.628
GuitarPlot16.694 0.12316.940
combinedGuitarPlot20.150 0.16920.519
getNeighborhood0.2710.0010.273
makeGuitarCoordsFromGRangesList0.8570.0030.868
makeGuitarCoordsFromTxDb5.0410.0125.090
narrowPeaktoGRanges0.0380.0010.039