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BioC 3.5: CHECK report for Guitar on malbec2

This page was generated on 2017-08-16 13:16:58 -0400 (Wed, 16 Aug 2017).

Package 608/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Guitar 1.14.0
Jia Meng
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Guitar
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Guitar
Version: 1.14.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Guitar_1.14.0.tar.gz
StartedAt: 2017-08-15 23:43:32 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:47:10 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 217.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Guitar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Guitar_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Guitar.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
* 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
.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Guitar-package     12.980  0.048  13.036
GuitarPlot         10.360  0.008  10.377
combinedGuitarPlot  9.884  0.040   9.931
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/Guitar.Rcheck/00check.log’
for details.


Guitar.Rcheck/00install.out:

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

Guitar.Rcheck/Guitar-Ex.timings:

nameusersystemelapsed
BED12toGRangesList2.4720.0282.501
Guitar-package12.980 0.04813.036
GuitarPlot10.360 0.00810.377
combinedGuitarPlot9.8840.0409.931
getNeighborhood0.2640.0000.264
makeGuitarCoordsFromGRangesList0.4280.0000.428
makeGuitarCoordsFromTxDb2.7040.0122.747
narrowPeaktoGRanges0.0440.0000.046