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CHECK report for ggbio on tokay2

This page was generated on 2018-10-17 08:35:50 -0400 (Wed, 17 Oct 2018).

Package 613/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.28.5
Michael Lawrence
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ggbio
Branch: RELEASE_3_7
Last Commit: 594521c
Last Changed Date: 2018-08-22 18:28:15 -0400 (Wed, 22 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ggbio
Version: 1.28.5
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ggbio_1.28.5.tar.gz
StartedAt: 2018-10-17 02:19:49 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:43:27 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1417.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ggbio_1.28.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ggbio.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.28.5'
* 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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-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' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
autoplot-method         131.16   1.92  134.50
geom_alignment-method    80.92   0.53   81.47
tracks                   40.42   0.02   40.43
layout_karyogram-method  21.86   0.07   21.96
stat_reduce-method       18.81   0.15   18.96
plotRangesLinkedToData   13.75   0.47   14.22
stat_aggregate-method    11.34   0.01   11.36
geom_arrow-method        10.96   0.02   10.96
stat_bin-method           8.41   0.00    8.42
ggplot-method             8.34   0.05    8.39
layout_circle-method      7.30   0.02    7.35
plotGrandLinear           6.18   0.05    6.27
stat_slice-method         5.38   0.00    5.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
autoplot-method            136.44   1.17  138.83
geom_alignment-method       71.19   0.31   71.53
tracks                      38.97   0.03   39.00
layout_karyogram-method     24.66   0.05   24.70
stat_reduce-method          15.48   0.11   15.59
geom_arrow-method           13.84   0.00   13.84
plotRangesLinkedToData      11.14   0.08   11.21
ggplot-method               10.77   0.06   10.82
stat_aggregate-method        8.83   0.01    8.84
layout_circle-method         8.15   0.02    8.17
plotGrandLinear              6.94   0.07    7.02
stat_bin-method              6.89   0.04    6.92
geom_chevron-method          6.19   0.01    6.20
stat_slice-method            5.89   0.02    5.91
geom_rect-method             5.67   0.00    5.67
arrangeGrobByParsingLegend   5.22   0.08    5.29
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ggbio.Rcheck/00check.log'
for details.



Installation output

ggbio.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ggbio_1.28.5.tar.gz && rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggbio.buildbin-libdir ggbio_1.28.5.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ggbio_1.28.5.zip && rm ggbio_1.28.5.tar.gz ggbio_1.28.5.zip
###
##############################################################################
##############################################################################


  % 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 1305k  100 1305k    0     0  17.5M      0 --:--:-- --:--:-- --:--:-- 19.3M

install for i386

* installing *source* package 'ggbio' ...
** 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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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-3.7-bioc/tmpdir/Rtmpm0zAuk/R.INSTALL2438392913b3/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
In R CMD INSTALL

install for x64

* installing *source* package 'ggbio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggbio' as ggbio_1.28.5.zip
* DONE (ggbio)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ggbio' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ggbio.Rcheck/tests_i386/test-all.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, lengths, 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 
  14.32    0.84   15.28 

ggbio.Rcheck/tests_x64/test-all.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, lengths, 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 
  15.85    0.51   16.70 

Example timings

ggbio.Rcheck/examples_i386/ggbio-Ex.timings

nameusersystemelapsed
arrangeGrobByParsingLegend3.700.213.91
autoplot-method131.16 1.92134.50
geom_alignment-method80.92 0.5381.47
geom_arch-method1.700.011.72
geom_arrow-method10.96 0.0210.96
geom_arrowrect-method3.900.003.91
geom_bar-method1.350.001.34
geom_chevron-method4.310.034.34
geom_rect-method4.360.024.37
geom_segment-method3.770.044.05
ggbio-class000
ggplot-method8.340.058.39
layout_circle-method7.300.027.35
layout_karyogram-method21.86 0.0721.96
plotFragLength000
plotGrandLinear6.180.056.27
plotRangesLinkedToData13.75 0.4714.22
plotSingleChrom000
plotSpliceSum000
plotStackedOverview000
rescale-method0.190.000.19
scale_fill_fold_change0.800.000.79
scale_fill_giemsa4.650.024.67
scale_x_sequnit0.630.000.63
stat_aggregate-method11.34 0.0111.36
stat_bin-method8.410.008.42
stat_coverage-method3.110.003.12
stat_gene-method000
stat_identity-method4.470.024.49
stat_reduce-method18.81 0.1518.96
stat_slice-method5.380.005.38
stat_stepping-method3.230.023.25
stat_table-method2.460.012.47
theme2.940.022.96
tracks40.42 0.0240.43

ggbio.Rcheck/examples_x64/ggbio-Ex.timings

nameusersystemelapsed
arrangeGrobByParsingLegend5.220.085.29
autoplot-method136.44 1.17138.83
geom_alignment-method71.19 0.3171.53
geom_arch-method2.410.032.44
geom_arrow-method13.84 0.0013.84
geom_arrowrect-method4.830.024.85
geom_bar-method1.870.021.89
geom_chevron-method6.190.016.20
geom_rect-method5.670.005.67
geom_segment-method3.910.003.91
ggbio-class0.010.000.02
ggplot-method10.77 0.0610.82
layout_circle-method8.150.028.17
layout_karyogram-method24.66 0.0524.70
plotFragLength0.010.000.02
plotGrandLinear6.940.077.02
plotRangesLinkedToData11.14 0.0811.21
plotSingleChrom000
plotSpliceSum000
plotStackedOverview000
rescale-method0.120.020.14
scale_fill_fold_change0.650.000.65
scale_fill_giemsa3.750.003.75
scale_x_sequnit0.460.000.46
stat_aggregate-method8.830.018.84
stat_bin-method6.890.046.92
stat_coverage-method3.460.033.50
stat_gene-method000
stat_identity-method4.070.044.11
stat_reduce-method15.48 0.1115.59
stat_slice-method5.890.025.91
stat_stepping-method3.210.033.23
stat_table-method2.670.032.70
theme2.690.002.69
tracks38.97 0.0339.00