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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggbio_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ggbio.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.48.0’
* 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 ‘ggbio’ 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': 'ggplot2:::set_last_plot'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
  'ggplot2:::rescale01'
  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
.combineNames: no visible binding for global variable
  '.layout_circle.stats'
Ideogram: no visible global function definition for 'data'
Ideogram: no visible binding for global variable 'ideoCyto'
getNR: no visible global function definition for 'se'
getNR: no visible global function definition for 'indexProbesProcessed'
getNR: no visible global function definition for 'coefs'
scale_x_sequnit: no visible binding for global variable '.x'
autoplot,ExpressionSet: no visible binding for global variable
  'variable'
autoplot,RangedSummarizedExperiment: no visible binding for global
  variable 'variable'
autoplot,VCF: no visible binding for global variable 'stepping'
autoplot,VCF: no visible binding for global variable 'value'
autoplot,VRanges: no visible binding for global variable 'midpoint'
autoplot,Views: no visible binding for global variable 'x'
autoplot,Views: no visible binding for global variable 'value'
geom_alignment,BamFile: no visible binding for global variable 'fl'
geom_alignment,BamFile: no visible binding for global variable
  'stepping'
height,GGbio: no visible binding for global variable 'mt'
height,Tracked: no visible binding for global variable 'mt'
height,gg: no visible binding for global variable 'mt'
layout_karyogram,GRanges: no visible binding for global variable
  'gieStain'
layout_karyogram,GRanges: no visible binding for global variable 'x'
layout_karyogram,GRanges: no visible binding for global variable 'xend'
layout_karyogram,GRanges: no visible binding for global variable 'y2'
layout_karyogram,GRanges: no visible binding for global variable
  'yend2'
layout_karyogram,GRanges: no visible binding for global variable 'name'
plotFragLength,character-GRanges: no visible binding for global
  variable '.fragLength'
plotSpliceSum,character-EnsDb: possible error in GRangesFilter(which,
  condition = "overlapping"): unused argument (condition =
  "overlapping")
stat_mismatch,GRanges: no visible binding for global variable 'sts'
stat_mismatch,GRanges: no visible binding for global variable 'eds'
stat_mismatch,GRanges: no visible binding for global variable 'read'
Undefined global functions or variables:
  .fragLength .layout_circle.stats .x coefs data eds fl gieStain
  ideoCyto indexProbesProcessed midpoint mt name read se stepping sts
  value variable x xend y2 yend2
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) autoplot-method.Rd:445: Escaped LaTeX specials: \~
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '+' and siglist 'Tracks,ANY'
  generic '+' and siglist 'Tracks,Tracks'
  generic '+' and siglist 'Tracks,cartesian'
  generic '+' and siglist 'Tracks,position_c'
  generic '+' and siglist 'Tracks,theme'
  generic '+' and siglist 'Tracks,zoom'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'geom_alignment':
\S4method{geom_alignment}{GRanges}
  Code: function(data, ..., xlab, ylab, main, facets = NULL, stat =
                 c("stepping", "identity"), range.geom = c("rect",
                 "arrowrect"), gap.geom = c("chevron", "arrow",
                 "segment"), rect.height = NULL, group.selfish = TRUE)
  Docs: function(data, ..., xlab, ylab, main, facets = NULL, stat =
                 c("stepping", "identity"), range.geom = c("rect",
                 "arrowrect"), gap.geom = c("chevron", "arrow",
                 "segment"), rect.height = NULL, group.selfish = TRUE,
                 label = TRUE)
  Argument names in docs not in code:
    label

Codoc mismatches from documentation object 'ggsave':
ggsave
  Code: function(filename, plot = last_plot(), device = NULL, path =
                 NULL, scale = 1, width = NA, height = NA, units =
                 c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...)
  Docs: function(filename, plot = last_plot(), device =
                 default_device(filename), path = NULL, scale = 1,
                 width = par("din")[1], height = par("din")[2], units =
                 c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...)
  Mismatches in argument default values:
    Name: 'device' Code: NULL Docs: default_device(filename)
    Name: 'width' Code: NA Docs: par("din")[1]
    Name: 'height' Code: NA Docs: par("din")[2]

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
autoplot-method            181.236  3.508 294.310
geom_alignment-method       66.562  1.691  93.269
tracks                      51.890  0.340  68.448
layout_karyogram-method     37.576  0.274  47.473
plotRangesLinkedToData      21.058  0.285  28.063
stat_reduce-method          16.784  0.296  23.485
ggplot-method               16.418  0.205  20.759
stat_aggregate-method       16.133  0.140  21.022
layout_circle-method        14.122  0.092  17.258
plotGrandLinear             12.636  0.233  16.594
geom_arrow-method           12.410  0.272  18.969
geom_chevron-method         10.469  0.104  13.842
stat_bin-method              9.977  0.084  12.651
geom_arrowrect-method        7.907  0.124  12.226
geom_rect-method             7.097  0.067   9.173
geom_segment-method          6.748  0.052   8.434
stat_slice-method            6.258  0.097   8.286
stat_identity-method         6.167  0.143   8.582
scale_fill_giemsa            6.098  0.050   7.923
arrangeGrobByParsingLegend   5.641  0.317   7.616
stat_stepping-method         5.520  0.055   7.234
stat_coverage-method         4.948  0.077   6.479
geom_arch-method             4.100  0.103   5.879
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/ggbio.Rcheck/00check.log’
for details.