Package: Guitar

Version: 1.20.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Guitar.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Guitar_1.20.1.tar.gz

StartedAt: 2019-04-16 00:31:50 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:37:01 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 310.5 seconds

RetCode: 0

Status:  OK

CheckDir: Guitar.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Guitar.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Guitar_1.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Guitar.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.20.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
combinedGuitarPlot       23.200  0.028  24.424
Guitar-package           20.992  0.032  22.321
GuitarPlot               19.364  0.016  20.942
makeGuitarCoordsFromTxDb  5.932  0.004   6.548
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/Guitar.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Guitar
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

name	user	system	elapsed
BED12toGRangesList	2.140	0.136	2.330
Guitar-package	20.992	0.032	22.321
GuitarPlot	19.364	0.016	20.942
combinedGuitarPlot	23.200	0.028	24.424
getNeighborhood	0.332	0.000	0.382
makeGuitarCoordsFromGRangesList	1.024	0.000	1.072
makeGuitarCoordsFromTxDb	5.932	0.004	6.548
narrowPeaktoGRanges	0.044	0.000	0.101