Multiple platform build/check report for BioC 3.10 - CHECK report for ggbio on tokay1

Package: ggbio

Version: 1.34.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ggbio_1.34.0.tar.gz

StartedAt: 2020-04-15 03:31:33 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:50:30 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 1136.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ggbio.Rcheck

Warnings: 4

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ggbio_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ggbio.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.34.0'
* 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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-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 ... WARNING
Codoc mismatches from documentation object 'geom_alignment':
\S4method{geom_alignment}{GRangesList}
  Code: function(data, ..., which = NULL, cds.rect.h = 0.25,
                 exon.rect.h = cds.rect.h, utr.rect.h = cds.rect.h/2,
                 xlab, ylab, main, facets = NULL, geom = "alignment",
                 stat = c("identity", "reduce"), range.geom = "rect",
                 gap.geom = "arrow", utr.geom = "rect", names.expr =
                 NULL, label = TRUE, label.color = "gray40", label.size
                 = 3, arrow.rate = 0.015, length = unit(0.1, "cm"))
  Docs: function(data, ..., which = NULL, cds.rect.h = 0.25,
                 exon.rect.h = cds.rect.h, utr.rect.h = cds.rect.h/2,
                 xlab, ylab, main, facets = NULL, geom = "alignment",
                 stat = c("identity", "reduce"), range.geom = "rect",
                 gap.geom = "arrow", utr.geom = "rect", names.expr =
                 NULL, label = TRUE, label.color = "gray40", arrow.rate
                 = 0.015, length = unit(0.1, "cm"))
  Argument names in code not in docs:
    label.size
  Mismatches in argument names:
    Position: 19 Code: label.size Docs: arrow.rate
    Position: 20 Code: arrow.rate Docs: length

* 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         104.65   2.27  107.80
geom_alignment-method    38.00   0.36   38.36
tracks                   28.94   0.03   28.97
layout_karyogram-method  17.69   0.02   17.70
ggplot-method            11.00   0.08   11.08
geom_arrow-method        10.21   0.01   10.22
plotRangesLinkedToData    9.38   0.10    9.47
stat_reduce-method        8.44   0.11    8.55
stat_aggregate-method     6.61   0.00    6.61
geom_segment-method       6.14   0.01    6.16
layout_circle-method      6.04   0.00    6.05
plotGrandLinear           5.42   0.01    5.44
stat_bin-method           5.36   0.00    5.36
geom_chevron-method       5.34   0.00    5.34
** 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            124.40   1.22  127.29
geom_alignment-method       43.74   0.50   44.33
tracks                      41.27   0.10   41.51
layout_karyogram-method     30.78   0.08   30.96
plotRangesLinkedToData      14.57   0.26   14.83
ggplot-method               14.08   0.04   14.19
stat_reduce-method          11.80   0.20   12.00
stat_aggregate-method       11.89   0.06   12.08
geom_arrow-method           10.83   0.02   10.84
layout_circle-method        10.75   0.02   10.76
plotGrandLinear              8.39   0.03    8.45
stat_bin-method              6.93   0.00    6.92
geom_chevron-method          6.64   0.02    6.66
stat_slice-method            5.28   0.03    5.31
geom_arrowrect-method        5.14   0.00    5.14
geom_segment-method          5.08   0.02    5.09
arrangeGrobByParsingLegend   4.89   0.19    5.08
* 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: 4 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/ggbio.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ggbio_1.34.0.tar.gz && rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggbio.buildbin-libdir ggbio_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ggbio_1.34.0.zip && rm ggbio_1.34.0.tar.gz ggbio_1.34.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1307k  100 1307k    0     0  16.1M      0 --:--:-- --:--:-- --:--:-- 17.2M

install for i386

* installing *source* package 'ggbio' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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-3.10-bioc/tmpdir/RtmpkjtHfN/R.INSTALLc6c7aea3dd5/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_1.34.0.zip
* DONE (ggbio)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ggbio' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  13.53    1.51   15.03


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  20.48    0.93   21.76

name	user	system	elapsed
arrangeGrobByParsingLegend	3.60	0.92	4.52
autoplot-method	104.65	2.27	107.80
geom_alignment-method	38.00	0.36	38.36
geom_arch-method	1.57	0.00	1.57
geom_arrow-method	10.21	0.01	10.22
geom_arrowrect-method	3.50	0.05	3.55
geom_bar-method	1.00	0.02	1.01
geom_chevron-method	5.34	0.00	5.34
geom_rect-method	3.86	0.03	3.89
geom_segment-method	6.14	0.01	6.16
ggbio-class	0	0	0
ggplot-method	11.00	0.08	11.08
layout_circle-method	6.04	0.00	6.05
layout_karyogram-method	17.69	0.02	17.70
plotFragLength	0	0	0
plotGrandLinear	5.42	0.01	5.44
plotRangesLinkedToData	9.38	0.10	9.47
plotSingleChrom	0	0	0
plotSpliceSum	0	0	0
plotStackedOverview	0	0	0
rescale-method	0.1	0.0	0.1
scale_fill_fold_change	0.53	0.00	0.53
scale_fill_giemsa	2.84	0.00	2.84
scale_x_sequnit	0.28	0.01	0.30
stat_aggregate-method	6.61	0.00	6.61
stat_bin-method	5.36	0.00	5.36
stat_coverage-method	2.80	0.02	2.81
stat_gene-method	0	0	0
stat_identity-method	2.85	0.04	2.90
stat_reduce-method	8.44	0.11	8.55
stat_slice-method	3.48	0.00	3.49
stat_stepping-method	3.39	0.00	3.39
stat_table-method	1.58	0.02	1.59
theme	2.13	0.00	2.13
tracks	28.94	0.03	28.97

name	user	system	elapsed
arrangeGrobByParsingLegend	4.89	0.19	5.08
autoplot-method	124.40	1.22	127.29
geom_alignment-method	43.74	0.50	44.33
geom_arch-method	1.66	0.01	1.67
geom_arrow-method	10.83	0.02	10.84
geom_arrowrect-method	5.14	0.00	5.14
geom_bar-method	1.41	0.01	1.43
geom_chevron-method	6.64	0.02	6.66
geom_rect-method	4.79	0.00	4.80
geom_segment-method	5.08	0.02	5.09
ggbio-class	0	0	0
ggplot-method	14.08	0.04	14.19
layout_circle-method	10.75	0.02	10.76
layout_karyogram-method	30.78	0.08	30.96
plotFragLength	0	0	0
plotGrandLinear	8.39	0.03	8.45
plotRangesLinkedToData	14.57	0.26	14.83
plotSingleChrom	0	0	0
plotSpliceSum	0	0	0
plotStackedOverview	0	0	0
rescale-method	0.14	0.02	0.16
scale_fill_fold_change	0.73	0.00	0.73
scale_fill_giemsa	4.05	0.00	4.05
scale_x_sequnit	0.48	0.00	0.48
stat_aggregate-method	11.89	0.06	12.08
stat_bin-method	6.93	0.00	6.92
stat_coverage-method	2.62	0.02	2.65
stat_gene-method	0	0	0
stat_identity-method	2.96	0.03	3.02
stat_reduce-method	11.8	0.2	12.0
stat_slice-method	5.28	0.03	5.31
stat_stepping-method	3.75	0.00	3.75
stat_table-method	2.07	0.00	2.06
theme	2.33	0.00	2.33
tracks	41.27	0.10	41.51

CHECK report for ggbio on tokay1

Summary

Command output

Installation output

Tests output

Example timings