BioC 3.5: CHECK report for Guitar on malbec2

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

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

* 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)

name	user	system	elapsed
BED12toGRangesList	2.472	0.028	2.501
Guitar-package	12.980	0.048	13.036
GuitarPlot	10.360	0.008	10.377
combinedGuitarPlot	9.884	0.040	9.931
getNeighborhood	0.264	0.000	0.264
makeGuitarCoordsFromGRangesList	0.428	0.000	0.428
makeGuitarCoordsFromTxDb	2.704	0.012	2.747
narrowPeaktoGRanges	0.044	0.000	0.046