Skip to content

R-3.1.0 OSX Snow Leopard installs old binary

16 messages · Gábor Csárdi, Dan Tenenbaum, Simon Urbanek

Original
Simon Urbanek
#
On Apr 17, 2014, at 9:30 AM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

            

      
      
      
    

        
I think you may be misinterpreting - the is no binary for igraph 0.7 because it fails make check, so I don't see how "Downloading and installing the new binary by hand works fine." can be true.
The *source* is available so you can compile it from sources, but that's different that what you asked for which was to install the *binary*.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        
      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
      #
    

  


  

      
----- Original Message -----

            

      
      
      
    

        
The graph package is available:

http://www.bioconductor.org/packages/release/bioc/html/graph.html


...but maybe not installed on the CRAN build machine.

All of this would make more sense if the OP was using the Mavericks build of R because we don't yet have BioC binary packages for that, but his original sessionInfo() showed that he was using the Snow Leopard build.

            

      
      
      
    

        
I think they can. graph is in igraph's Suggests. If CRAN packages could not depend on BioC packages, I would imagine that igraph would be removed from CRAN until it got rid of that dependency.

Dan

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Apr 17, 2014, at 6:31 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

        

            

      
      
      
    

        
That is the 3.0 package. Sorry, my bad, the symlinks have not been switched from prerelease to release - my bad, now fixed.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Apr 17, 2014, at 7:42 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

        

            

      
      
      
    

        
No, the issue is that igraph suggests graph yet fails when it's not present. It should guard against failure is case it's not available. I didn't look at this particular case, but sometimes that is necessary to break infinite dependency loops.

Cheers,
Simon

  
  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Apr 17, 2014, at 9:24 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

        

            

      
      
      
    

        
The Suggests failure has nothing to do with BioC. Only packages listed in Depends/Imports are required for a package to work so there is no guarantee for any packages in Suggests to be available - hence the package should not break if they are not available - that's the whole point of Suggests. If you list it in Depends/Imports then it won't even get to the check if those packages are not available - it won't build at all. I didn't look at the dependencies in this particular case, but one reason to use Suggests is to break dependency loops: if A depends on B and B on A, then there is no way to install them, so typically A suggests B and B depends on A so that A can be installed and checked first without B and then B checked with A and finally A with B. If A breaks without B then it makes such bootstrapping impossible - we found some packages with this issue, that's why mentioned this - I don't know if that's the case with igraph or not.

As for BioC, the builds for BioC are independent of CRAN, so CRAN doesn't build BioC packages and thus their availability is subject to manual intervention - on the OS X build machine there is currently no automated way to track BioC packages, but we're working on it.

Cheers,
Simon

  
  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Apr 17, 2014, at 9:52 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

        

            

      
      
      
    

        
They cannot be installed together, R doesn't have a concept of "together" since it doesn't separate copying and parse/eval stages so you cannot "pre-install" the packages and then run them through R to create the binary. Therefore dependencies are always sequential.

            

      
      
      
    

        
No.

Cheers,
Simon

  
  


  


      

    

    

      
      

        
      

    

    

      
      

        
      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Apr 17, 2014, at 10:37 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:

        

            

      
      
      
    

        
Thanks. I have verified that graph is now available and igraph seems to pass check with it so it should be available tomorrow.

Cheers,
Simon

  
  


  


      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
      #
    

  


  

      
----- Original Message -----

            

      
      
      
    

        
Wrong. It's just the Mavericks binaries that are not yet available. Snow Leopard binaries are available.

Dan