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

Package: ggbio

Version: 1.31.1

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_1.31.1.tar.gz

StartedAt: 2019-02-09 03:07:50 -0500 (Sat, 09 Feb 2019)

EndedAt: 2019-02-09 03:28:44 -0500 (Sat, 09 Feb 2019)

EllapsedTime: 1253.9 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_1.31.1.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck'
* using R Under development (unstable) (2019-01-10 r75962)
* 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 '1.31.1'
* 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:
  Warning: subclass "GeneNameFilter" of class "AnnotationFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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         99.24   2.48  105.70
tracks                  46.25   0.00   46.25
geom_alignment-method   37.00   0.39   37.39
layout_karyogram-method 25.02   0.06   25.08
plotRangesLinkedToData  14.65   0.10   14.75
geom_arrow-method       11.36   0.03   11.39
ggplot-method           10.77   0.05   10.81
stat_aggregate-method    9.75   0.03    9.79
stat_reduce-method       8.84   0.14    8.99
stat_bin-method          8.41   0.04    8.43
layout_circle-method     8.08   0.00    8.08
plotGrandLinear          7.28   0.03    7.31
geom_chevron-method      5.64   0.05    5.69
stat_slice-method        5.52   0.00    5.51
** 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         88.94   0.95   90.06
geom_alignment-method   38.16   0.36   38.54
tracks                  36.52   0.08   36.60
layout_karyogram-method 19.69   0.04   19.72
plotRangesLinkedToData  12.91   0.20   14.06
geom_arrow-method       12.33   0.01   12.34
stat_aggregate-method   12.21   0.04   12.25
stat_reduce-method       8.34   0.09    8.44
ggplot-method            7.17   0.03    7.20
stat_bin-method          6.88   0.00    6.87
layout_circle-method     6.22   0.02    6.24
plotGrandLinear          5.75   0.01    5.76
geom_chevron-method      5.64   0.02    5.66
geom_arrowrect-method    5.01   0.03    5.05
* 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_1.31.1.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_1.31.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ggbio_1.31.1.zip && rm ggbio_1.31.1.tar.gz ggbio_1.31.1.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1305k  100 1305k    0     0  18.5M      0 --:--:-- --:--:-- --:--:-- 20.2M

install for i386

* installing *source* package 'ggbio' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: subclass "GeneNameFilter" of class "AnnotationFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "GeneNameFilter" of class "AnnotationFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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/RtmpqANlat/R.INSTALL2480247229a2/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

install for x64

* installing *source* package 'ggbio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggbio' as ggbio_1.31.1.zip
* DONE (ggbio)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ggbio' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-01-10 r75962) -- "Unsuffered Consequences"
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, colMeans, colSums, 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, rowMeans, rowSums,
    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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.93    1.07   14.98


R Under development (unstable) (2019-01-10 r75962) -- "Unsuffered Consequences"
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, colMeans, colSums, 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, rowMeans, rowSums,
    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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  16.10    0.57   16.67

name	user	system	elapsed
arrangeGrobByParsingLegend	4.29	0.23	4.73
autoplot-method	99.24	2.48	105.70
geom_alignment-method	37.00	0.39	37.39
geom_arch-method	2.41	0.02	2.42
geom_arrow-method	11.36	0.03	11.39
geom_arrowrect-method	3.96	0.00	3.96
geom_bar-method	1.65	0.00	1.64
geom_chevron-method	5.64	0.05	5.69
geom_rect-method	4.69	0.04	4.73
geom_segment-method	3.54	0.03	3.56
ggbio-class	0.01	0.00	0.02
ggplot-method	10.77	0.05	10.81
layout_circle-method	8.08	0.00	8.08
layout_karyogram-method	25.02	0.06	25.08
plotFragLength	0	0	0
plotGrandLinear	7.28	0.03	7.31
plotRangesLinkedToData	14.65	0.10	14.75
plotSingleChrom	0	0	0
plotSpliceSum	0	0	0
plotStackedOverview	0	0	0
rescale-method	0.17	0.00	0.17
scale_fill_fold_change	0.72	0.00	0.72
scale_fill_giemsa	4.34	0.01	4.36
scale_x_sequnit	0.39	0.00	0.39
stat_aggregate-method	9.75	0.03	9.79
stat_bin-method	8.41	0.04	8.43
stat_coverage-method	3.11	0.00	3.11
stat_gene-method	0	0	0
stat_identity-method	3.17	0.00	3.17
stat_reduce-method	8.84	0.14	8.99
stat_slice-method	5.52	0.00	5.51
stat_stepping-method	3.10	0.01	3.11
stat_table-method	2.41	0.05	2.46
theme	3.42	0.00	3.43
tracks	46.25	0.00	46.25

name	user	system	elapsed
arrangeGrobByParsingLegend	4.22	0.13	4.35
autoplot-method	88.94	0.95	90.06
geom_alignment-method	38.16	0.36	38.54
geom_arch-method	2.25	0.02	2.26
geom_arrow-method	12.33	0.01	12.34
geom_arrowrect-method	5.01	0.03	5.05
geom_bar-method	1.94	0.03	1.97
geom_chevron-method	5.64	0.02	5.66
geom_rect-method	3.97	0.03	4.00
geom_segment-method	3.02	0.01	3.03
ggbio-class	0.01	0.00	0.02
ggplot-method	7.17	0.03	7.20
layout_circle-method	6.22	0.02	6.24
layout_karyogram-method	19.69	0.04	19.72
plotFragLength	0	0	0
plotGrandLinear	5.75	0.01	5.76
plotRangesLinkedToData	12.91	0.20	14.06
plotSingleChrom	0	0	0
plotSpliceSum	0	0	0
plotStackedOverview	0	0	0
rescale-method	0.16	0.00	0.16
scale_fill_fold_change	0.56	0.00	0.56
scale_fill_giemsa	3.87	0.00	3.88
scale_x_sequnit	0.54	0.00	0.53
stat_aggregate-method	12.21	0.04	12.25
stat_bin-method	6.88	0.00	6.87
stat_coverage-method	2.65	0.00	2.66
stat_gene-method	0	0	0
stat_identity-method	3.61	0.01	3.65
stat_reduce-method	8.34	0.09	8.44
stat_slice-method	4.61	0.02	4.63
stat_stepping-method	2.86	0.00	2.85
stat_table-method	2.18	0.00	2.18
theme	2.4	0.0	2.4
tracks	36.52	0.08	36.60

CHECK report for ggbio on tokay2

Summary

Command output

Installation output

Tests output

Example timings