Hi everyone,

I am using the newest version of R and trying to install ggbio, here is my problem:

> biocLite("ggbio")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘ggbio’
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 1259k  100 1259k    0     0  1057k      0  0:00:01  0:00:01 --:--:-- 1057k
* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘grid::arrow’ when loading ‘GGally’
Warning: replacing previous import by ‘grid::unit’ when loading ‘GGally’
Warning: replacing previous import by ‘ggplot2::unit’ when loading ‘ggbio’
Warning: replacing previous import by ‘ggplot2::arrow’ when loading ‘ggbio’
Warning: replacing previous import by ‘BiocGenerics::Position’ when loading ‘ggbio’
Creating a new generic function for ‘rescale’ in package ‘ggbio’
Creating a new generic function for ‘xlim’ in package ‘ggbio’
Creating a generic function for ‘print’ from package ‘base’ in package ‘ggbio’
Warning: 'eval' is deprecated.
Use 'plotIdeogram' instead.
See help("Deprecated")
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : 
  arguments (environment) after '...' in the generic must appear in the method, in the same place at the end of the argument list
Error : unable to load R code in package ‘ggbio’
ERROR: lazy loading failed for package ‘ggbio’
* removing ‘/usr/local/lib/R/3.2/site-library/ggbio’

The downloaded source packages are in
    ‘/private/var/folders/gb/vd06k92974n6yp3bshy0rh9w0000gn/T/RtmpynGNyF/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ggbio’ had non-zero exit status

The output of session information:

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin15.2.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicRanges_1.22.2 GenomeInfoDb_1.6.1   IRanges_2.4.6        S4Vectors_0.8.5     
[5] BiocGenerics_0.16.1  edgeR_3.12.0         limma_3.26.3         BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 XVector_0.10.0  tools_3.2.3   

I can reproduce this and I am not sure what the answer is but if you install the binary it should work:

biocLite("ggbio", type="binary")

Hi,

I've got the exact same problem, using the R version of Ubuntu 16.04.

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          2.3                         
year           2015                        
month          12                          
day            10                          
svn rev        69752                       
language       R                           
version.string R version 3.2.3 (2015-12-10)
nickname       Wooden Christmas-Tree  

binary install is not supported for this version...

I also tried to install ggplot2 1.0.1, but then I get a message, that I should install ggplot >= 2.0.0.

I had a similar problem and could solve it by updating all my Bioclient packages. You can do this by typing: 

biocLite("BiocUpgrade")

I'm not sure, what the cause for the problem was, but I could imagine, that some functions in old packages were deprecated.