Package: Guitar

Version: 2.0.0

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_2.0.0.tar.gz

StartedAt: 2019-10-16 03:33:09 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:40:43 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 454.1 seconds

RetCode: 0

Status:  OK

CheckDir: Guitar.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Guitar.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GenomicFeatures', 'rtracklayer', 'AnnotationDbi', 'GenomicRanges',
  'magrittr', 'ggplot2', 'knitr', 'dplyr'
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 15.8Mb
  sub-directories of 1Mb or more:
    extdata  15.7Mb
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘knitr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘GenomicRanges:::get_out_of_bound_index’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extractComponent: no visible binding for global variable ‘gene_id’
.generate_guitar_coordinates: no visible global function definition for
  ‘makeGuitarCoordsFromTxDb’
.generate_guitar_coordinates: no visible binding for global variable
  ‘noBins’
Undefined global functions or variables:
  gene_id makeGuitarCoordsFromTxDb noBins
* 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
GuitarPlot                  44.730  3.818  52.351
GRangesListmapToTranscripts 19.941  0.662  22.222
samplePoints                18.861  0.286  20.718
normalize                   16.057  0.161  16.325
makeGuitarTxdb              14.510  0.264  14.812
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Guitar.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Guitar
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Guitar’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Guitar)

name	user	system	elapsed
GRangesListmapToTranscripts	19.941	0.662	22.222
GuitarPlot	44.730	3.818	52.351
makeGuitarTxdb	14.510	0.264	14.812
normalize	16.057	0.161	16.325
samplePoints	18.861	0.286	20.718