Package: Pviz

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pviz_1.20.0.tar.gz

StartedAt: 2020-04-15 04:51:23 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:56:47 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 324.1 seconds

RetCode: 0

Status:  OK

CheckDir: Pviz.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pviz_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Pviz.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pviz’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘Pviz’ 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
.makeParMapping: no visible global function definition for
  'assignInNamespace'
drawGD,ProbeTrack: no visible global function definition for
  'pushViewport'
drawGD,ProbeTrack: no visible global function definition for 'viewport'
drawGD,ProbeTrack: no visible global function definition for
  'popViewport'
drawGD,ProbeTrack: no visible global function definition for 'unit'
drawGD,ProbeTrack: no visible global function definition for 'gpar'
drawGD,ProbeTrack: no visible global function definition for
  'convertWidth'
drawGD,ProbeTrack: no visible global function definition for
  'stringWidth'
drawGD,ProbeTrack: no visible global function definition for
  'stringHeight'
drawGD,ProbeTrack: no visible global function definition for
  'grid.text'
drawGD,ProbeTrack: no visible global function definition for
  'grid.rect'
drawGD,ProbeTrack: no visible global function definition for
  'dataViewport'
drawGD,ProbeTrack : <anonymous>: no visible global function definition
  for 'grid.rect'
drawGD,ProbeTrack : <anonymous>: no visible global function definition
  for 'gpar'
drawGD,ProbeTrack : <anonymous>: no visible global function definition
  for 'grid.text'
drawGD,ProteinAxisTrack: no visible global function definition for
  'pushViewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  'dataViewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  'convertHeight'
drawGD,ProteinAxisTrack: no visible global function definition for
  'stringHeight'
drawGD,ProteinAxisTrack: no visible global function definition for
  'popViewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  '.getGapPos'
drawGD,ProteinAxisTrack: no visible global function definition for
  'gaps'
drawGD,ProteinAxisTrack: no visible global function definition for
  'viewport'
drawGD,ProteinAxisTrack: no visible global function definition for
  'grid.segments'
drawGD,ProteinAxisTrack: no visible global function definition for
  'gpar'
drawGD,ProteinAxisTrack: no visible global function definition for
  'coord2ext'
drawGD,ProteinAxisTrack: no visible global function definition for
  'grid.text'
drawGD,ProteinAxisTrack: no visible global function definition for
  'convertWidth'
drawGD,ProteinAxisTrack: no visible global function definition for
  'stringWidth'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'pushViewport'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'dataViewport'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'gpar'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'popViewport'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'convertUnit'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'stringWidth'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'grid.lines'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'unit'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'grid.text'
drawGD,ProteinSequenceTrack: no visible global function definition for
  'grid.rect'
Undefined global functions or variables:
  .getGapPos assignInNamespace convertHeight convertUnit convertWidth
  coord2ext dataViewport gaps gpar grid.lines grid.rect grid.segments
  grid.text popViewport pushViewport stringHeight stringWidth unit
  viewport
Consider adding
  importFrom("utils", "assignInNamespace")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ProbeTrack 6.656  0.128   6.969
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/Pviz.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pviz
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Pviz’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Pviz.Rnw’ 
** 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 (Pviz)

name	user	system	elapsed
ATrack	4.690	0.174	4.924
CladeTrack	1.230	0.049	1.285
DTrack	0.153	0.004	0.157
ProbeTrack	6.656	0.128	6.969
ProteinAxisTrack	0.820	0.005	0.827
ProteinSequenceTrack	0.446	0.008	0.462
plot_clade	2.276	0.033	2.383
plot_inter	1.384	0.417	1.212