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Question: Error when install ggbio
0
gravatar for syrttgump
23 months ago by
syrttgump20
United States
syrttgump20 wrote:

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   
 
ADD COMMENTlink modified 22 months ago by RandomAcessStoredProgram0 • written 23 months ago by syrttgump20
1
gravatar for Dan Tenenbaum
23 months ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

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")

 

ADD COMMENTlink written 23 months ago by Dan Tenenbaum ♦♦ 8.2k

Thanks for your quick reply! It seems no Mac version binary has been provided: "type 'binary' is not supported on this platform"

ADD REPLYlink written 23 months ago by syrttgump20

Thanks for your quick reply! It seems no Mac version binary has been provided: "type 'binary' is not supported on this platform"

ADD REPLYlink written 23 months ago by syrttgump20

Hmm, did you build R from source or get it from a non-standard place (like brew)?

If you built R from source on your Mac, then you won't be able to install binary packages. But the binary is available, I just installed it successfully with the command above. It's also on the ggbio landing page.

 

ADD REPLYlink written 23 months ago by Dan Tenenbaum ♦♦ 8.2k

I install my R from brew. So should I get R using binary from the official website?

ADD REPLYlink written 23 months ago by syrttgump20

I recommend it. 

I am told that the problem is that ggbio has not been upgraded to work with the newest ggplot2; so another workaround for you is to install the previous version of ggplot2 (1.0.1) from https://cran.r-project.org/src/contrib/Archive/ggplot2/ . But you should really install the officially supported R.

 

ADD REPLYlink written 23 months ago by Dan Tenenbaum ♦♦ 8.2k

Got it. I will do it as you said. Thank you for your reply!

Yes. I installed official version R and it can work now. Best.

ADD REPLYlink modified 23 months ago • written 23 months ago by syrttgump20
0
gravatar for Hoeze
22 months ago by
Hoeze0
Hoeze0 wrote:

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.

 
ADD COMMENTlink modified 22 months ago • written 22 months ago by Hoeze0
0
gravatar for RandomAcessStoredProgram
22 months ago by

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. 

 

ADD COMMENTlink written 22 months ago by RandomAcessStoredProgram0

> biocLite("BiocUpgrade")      
Fehler: Bioconductor version 3.2 cannot be upgraded with R version 3.2.3

 

EDIT:

Anyway, this problem seems to be solved, I could install it with 'biocLite("ggbio")'

ADD REPLYlink modified 22 months ago • written 22 months ago by Hoeze0

It's important to distinguish between updating and upgrading. Updating = installing the latest version of every package within the version of Bioconductor that you are currently using (e.g. BioC 3.2, the current release). Upgrading = installing a more recent version of Bioconductor (e.g. installing BioC 3.2 if you were using an old BioC version). For the former just call biocLite() with no arguments. For the latter call biocLite("BiocUpgrade"). The former never requires an upgrade of R itself but the latter sometimes does. If you're already running the current BioC release (which you are), trying to upgrade does not really make sense and won't work. IMO it would help if biocLite("BiocUpgrade") was displaying something like:

    you're already running the latest version of Bioconductor (3.2)

rather than the current message which is a little bit obscure/misleading...

H.

ADD REPLYlink written 22 months ago by Hervé Pagès ♦♦ 13k
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