Multiple platform build/check report for BioC 3.9 - CHECK report for ggbio on tokay2

Package: ggbio

Version: 1.32.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ggbio_1.32.0.tar.gz

StartedAt: 2019-10-16 04:03:21 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:21:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 1089.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ggbio.Rcheck

Warnings: 3

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ggbio_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.32.0'
* 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 whether package 'ggbio' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_aggregate-method.Rd:48: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:45: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:48: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:51: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:54: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:64: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:66: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:69: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:72: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:75: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:78: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:85: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
':::' 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:::rename_aes' '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'
ScalePlot: no visible binding for global variable 'y'
ScalePlot2: no visible binding for global variable 'breaks'
ScalePlot2: no visible binding for global variable 'yend'
ScalePlot2: no visible binding for global variable 'y.text'
getNR: no visible global function definition for 'se'
getNR: no visible global function definition for 'indexProbesProcessed'
getNR: no visible global function definition for 'coefs'
plotInter: no visible binding for global variable 'fe'
plotInter: no visible binding for global variable 'value'
plotInter2: no visible binding for global variable 'fe'
plotInter2: no visible binding for global variable 'value'
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 'y'
layout_karyogram,GRanges: no visible binding for global variable 'xend'
layout_karyogram,GRanges: no visible binding for global variable 'yend'
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 breaks coefs data eds fe fl
  gieStain ideoCyto indexProbesProcessed midpoint mt name read se
  stepping sts value variable x xend y y.text y2 yend yend2
Consider adding
  importFrom("utils", "data")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
autoplot-method         112.83   2.88  116.01
geom_alignment-method    43.17   0.27   43.44
tracks                   32.56   0.05   32.84
layout_karyogram-method  18.04   0.03   18.08
stat_reduce-method       11.52   0.20   11.74
geom_arrow-method        11.36   0.02   11.38
plotRangesLinkedToData   10.37   0.13   10.51
ggplot-method             8.86   0.06    8.92
stat_aggregate-method     6.43   0.03    6.46
stat_bin-method           6.11   0.00    6.12
layout_circle-method      5.39   0.05    5.44
plotGrandLinear           5.36   0.01    5.38
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
autoplot-method         106.36   1.19  107.67
geom_alignment-method    35.00   0.59   41.62
tracks                   30.42   0.05   30.48
layout_karyogram-method  17.08   0.02   17.09
plotRangesLinkedToData   11.46   0.06   11.51
geom_arrow-method         9.39   0.03    9.42
ggplot-method             9.20   0.03    9.24
stat_reduce-method        7.36   0.17    7.54
layout_circle-method      7.05   0.00    7.04
stat_aggregate-method     7.04   0.00    7.04
plotGrandLinear           6.56   0.06    6.63
geom_chevron-method       5.37   0.00    5.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ggbio_1.32.0.tar.gz && rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggbio.buildbin-libdir ggbio_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ggbio_1.32.0.zip && rm ggbio_1.32.0.tar.gz ggbio_1.32.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1305k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1305k  100 1305k    0     0  16.8M      0 --:--:-- --:--:-- --:--:-- 18.2M

install for i386

* installing *source* package 'ggbio' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
From .checkSubclasses(): subclass "GeneNameFilter" of class "AnnotationFilter" is not local and is not updated for new inheritance information currently; 
[where=, where2=]
From .checkSubclasses(): subclass "GeneNameFilter" of class "AnnotationFilter" is not local and is not updated for new inheritance information currently; 
[where=, where2=]
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
Creating a new generic function for 'geom_rect' in package 'ggbio'
Creating a new generic function for 'geom_segment' in package 'ggbio'
Creating a new generic function for 'geom_bar' in package 'ggbio'
Creating a new generic function for 'stat_identity' in package 'ggbio'
Creating a new generic function for 'stat_bin' in package 'ggbio'
** help
*** installing help indices
  converting help for package 'ggbio'
    finding HTML links ... done
    Grob-class                              html  
    Plot-class                              html  
    Tracked-class                           html  
    arrangeGrobByParsingLegend              html  
    autoplot-method                         html  
    finding level-2 HTML links ... done

    geom_alignment-method                   html  
    geom_arch-method                        html  
    geom_arrow-method                       html  
    geom_arrowrect-method                   html  
    geom_bar-method                         html  
    geom_chevron-method                     html  
    geom_rect-method                        html  
    geom_segment-method                     html  
    ggbio-class                             html  
    ggplot-method                           html  
    ggsave                                  html  
    layout_circle-method                    html  
    layout_karyogram-method                 html  
    nav                                     html  
    plotFragLength                          html  
    plotGrandLinear                         html  
    plotRangesLinkedToData                  html  
    plotSingleChrom                         html  
    plotSpliceSum                           html  
    plotStackedOverview                     html  
    rescale-method                          html  
    scale_fill_fold_change                  html  
    scale_fill_giemsa                       html  
    scale_x_sequnit                         html  
    stat_aggregate-method                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_aggregate-method.Rd:48: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    stat_bin-method                         html  
    stat_coverage-method                    html  
    stat_gene-method                        html  
    stat_identity-method                    html  
    stat_mismatch-method                    html  
    stat_reduce-method                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:45: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:48: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:51: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:54: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_reduce-method.Rd:64: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
    stat_slice-method                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:66: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:69: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:72: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:75: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:78: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpgXRqCR/R.INSTALL25707e1a7f8b/ggbio/man/stat_slice-method.Rd:85: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
    stat_stepping-method                    html  
    stat_table-method                       html  
    theme                                   html  
    tracks                                  html  
** 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

install for x64

* installing *source* package 'ggbio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggbio' as ggbio_1.32.0.zip
* DONE (ggbio)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ggbio' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("ggbio")
Loading required package: ggbio
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.15    1.34   17.50


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("ggbio")
Loading required package: ggbio
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.96    0.62   19.71

name	user	system	elapsed
arrangeGrobByParsingLegend	2.74	0.32	3.07
autoplot-method	112.83	2.88	116.01
geom_alignment-method	43.17	0.27	43.44
geom_arch-method	2.12	0.01	2.14
geom_arrow-method	11.36	0.02	11.38
geom_arrowrect-method	3.22	0.03	3.25
geom_bar-method	1.39	0.00	1.39
geom_chevron-method	4.09	0.01	4.11
geom_rect-method	3.20	0.02	3.22
geom_segment-method	3.44	0.05	3.48
ggbio-class	0	0	0
ggplot-method	8.86	0.06	8.92
layout_circle-method	5.39	0.05	5.44
layout_karyogram-method	18.04	0.03	18.08
plotFragLength	0	0	0
plotGrandLinear	5.36	0.01	5.38
plotRangesLinkedToData	10.37	0.13	10.51
plotSingleChrom	0	0	0
plotSpliceSum	0	0	0
plotStackedOverview	0	0	0
rescale-method	0.09	0.00	0.09
scale_fill_fold_change	0.5	0.0	0.5
scale_fill_giemsa	2.5	0.0	2.5
scale_x_sequnit	0.5	0.0	0.5
stat_aggregate-method	6.43	0.03	6.46
stat_bin-method	6.11	0.00	6.12
stat_coverage-method	2.28	0.01	2.30
stat_gene-method	0	0	0
stat_identity-method	3.29	0.02	3.31
stat_reduce-method	11.52	0.20	11.74
stat_slice-method	3.44	0.02	3.45
stat_stepping-method	2.64	0.01	2.65
stat_table-method	1.78	0.00	1.78
theme	2.17	0.00	2.17
tracks	32.56	0.05	32.84

name	user	system	elapsed
arrangeGrobByParsingLegend	4.64	0.06	4.70
autoplot-method	106.36	1.19	107.67
geom_alignment-method	35.00	0.59	41.62
geom_arch-method	1.53	0.03	1.57
geom_arrow-method	9.39	0.03	9.42
geom_arrowrect-method	3.19	0.05	3.23
geom_bar-method	1.5	0.0	1.5
geom_chevron-method	5.37	0.00	5.38
geom_rect-method	4.41	0.00	4.40
geom_segment-method	3.84	0.00	3.85
ggbio-class	0.02	0.00	0.01
ggplot-method	9.20	0.03	9.24
layout_circle-method	7.05	0.00	7.04
layout_karyogram-method	17.08	0.02	17.09
plotFragLength	0	0	0
plotGrandLinear	6.56	0.06	6.63
plotRangesLinkedToData	11.46	0.06	11.51
plotSingleChrom	0	0	0
plotSpliceSum	0	0	0
plotStackedOverview	0	0	0
rescale-method	0.09	0.02	0.11
scale_fill_fold_change	0.49	0.00	0.49
scale_fill_giemsa	2.61	0.01	2.62
scale_x_sequnit	0.31	0.00	0.32
stat_aggregate-method	7.04	0.00	7.04
stat_bin-method	4.75	0.00	4.75
stat_coverage-method	2.13	0.00	2.12
stat_gene-method	0	0	0
stat_identity-method	2.25	0.02	2.27
stat_reduce-method	7.36	0.17	7.54
stat_slice-method	3.69	0.00	3.68
stat_stepping-method	2.32	0.03	2.84
stat_table-method	1.52	0.00	1.51
theme	1.67	0.00	1.68
tracks	30.42	0.05	30.48

CHECK report for ggbio on tokay2

Summary

Command output

Installation output

Tests output

Example timings