##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Pviz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Pviz_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Pviz.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Pviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pviz’ version ‘1.43.0’
* 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 code 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
.makeParMapping: no visible global function definition for
  'assignInNamespace'
plot_clade: no visible global function definition for 'tail'
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 tail unit
  viewport
Consider adding
  importFrom("utils", "assignInNamespace", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'ATrack.Rd':
  ‘GdObject’

Missing link(s) in Rd file 'DTrack.Rd':
  ‘GdObject’

Missing link(s) in Rd file 'ProbeTrack.Rd':
  ‘GdObject’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ATrack.Rd: AnnotationTrack, GdObject
  DTrack.Rd: DataTrack, GdObject
  ProbeTrack.Rd: GdObject
  ProteinAxisTrack.Rd: GenomeAxisTrack
  ProteinSequenceTrack.Rd: SequenceTrack, DisplayPars
  plot_clade.Rd: plotTracks
  plot_inter.Rd: plotTracks
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Pviz.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Pviz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Pviz’ ...
** this is package ‘Pviz’ version ‘1.43.0’
** 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 (Pviz)