##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Gviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Gviz_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Gviz.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.51.0’
* package encoding: UTF-8
* 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 ‘Gviz’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   2.5Mb
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AlignmentsTrack-class.Rd: IRanges-class, GRanges-class, panel.grid
  AnnotationTrack-class.Rd: IRanges-class, GRanges-class, panel.grid
  BiomartGeneRegionTrack-class.Rd: Mart-class, getBM, GRanges-class,
    IRanges-class, panel.grid
  CustomTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  DataTrack-class.Rd: IRanges-class, panel.loess, panel.bwplot,
    horizonplot, GRanges-class, panel.grid
  GdObject-class.Rd: GRanges-class, IRanges-class, panel.grid
  GeneRegionTrack-class.Rd: IRanges-class, GRanges-class, panel.grid
  GenomeAxisTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  HighlightTrack-class.Rd: IRanges-class, GRanges-class, panel.grid
  IdeogramTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  NumericTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  OverlayTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  RangeTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  ReferenceTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  SequenceTrack-class.Rd: DNAStringSet-class, DNAString-class,
    BSgenome-class, GRanges-class, IRanges-class, panel.grid
  StackedTrack-class.Rd: GRanges-class, IRanges-class, panel.grid
  settings.Rd: panel.grid, panel.xyplot, panel.bwplot, horizonplot,
    panel.loess
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
AlignmentsTrack-class 14.386  0.699  15.588
AnnotationTrack-class  8.809  0.185   9.210
GeneRegionTrack-class  7.371  0.096   7.666
plotTracks             5.124  0.037   5.321
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.21-bioc/meat/Gviz.Rcheck/00check.log’
for details.