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Installing hexbin package (bioconductor)

5 messages · Michael Redmond, Byron Ellis, stefano iacus +1 more

Original
Hadley Wickham
# 
Has anyone had any luck installing the hexbin package from bioconductor?

Using gui and installing from binaries: library(hexbin) gives "Error
in library(hexbin) : 'hexbin' is not a valid package -- installed <
2.0.0?"

Using gui and installing from source: gives "make: g77: Command not
found" (and I do have g77)

Using command line and R CMD install: "
* Installing *source* package 'hexbin' ...
** libs
g77   -fno-common  -g -O2 -c hbin.f -o hbin.o
g77   -fno-common  -g -O2 -c hcell.f -o hcell.o
g77   -fno-common  -g -O2 -c herode.f -o herode.o
g77   -fno-common  -g -O2 -c hsm.f -o hsm.ogcc -bundle -flat_namespace
-undefined suppress -L/usr/local/lib -o hexbin.so hbin.o hcell.o
herode.o hsm.o  -L/usr/local/lib
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
-lg2c -lSystem -lcc_dynamic -framework R
ld: warning -L: directory name
(/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
ld: warning -L: directory name
(/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not
exist
ld: can't locate file for: -lfrtbegin"

Any suggestions?

Thanks,

Hadley
Michael Redmond
# 
Hadley,
Are you using the sourceforge version of g77 (rather than the fink 
version) as recommended in previous messages? I was getting errors 
similar to your:

ld: warning -L: directory name
(/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist

when I used fink and they went away with sourceforge.
Thanks
Mike
---
hadley wickham wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Byron Ellis
    

    

      
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Yup. I've built 1.1-4 (2004-10-27) from source without difficulty, 
though it doesn't pass CHECK apparently due to a (non-hexbin) related 
bug in the examples. However, the Release version seems to be 1.0 (and 
the download link broken at the moment). I'd recommend getting the 
Developer version of that package as the older hexbin packages were 
seriously broken in several ways---I think the difference between the 
two versions is the upgrade from S3/base to S4/grid that Martin 
Maechler & co. have been doing.

        
On Nov 9, 2004, at 11:53 AM, hadley wickham wrote:

        

            

      
      
      
    

        

      
      
    

        
---
Byron Ellis (ellis@stat.harvard.edu)
"Oook" -- The Librarian

  
  


  


      

    

    

      
      

        


  

        

      stefano iacus
    

    

      
      #
    

  


  

      
The problem with source compiling is because of wrong versiong of g77. 
Please read the Mac OS X Faq to get the latest and correct version of 
g77.

As for hexbin: it builds fine with this release of R for Mac OS X and 
related GUI (which I remember is just  a wrapper around command line 
R).

the other question is about 2.0 binaries for BioC. There was a wrong 
link to 1.9 packages instead of 2.0 packages in the macosx page on BioC 
(it was my fault as usual).

It is now fixed, so the package installer of R.app should now be able 
to get the correct version.

stefano

        
On Nov 9, 2004, at 8:53 PM, hadley wickham wrote:

        

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hadley Wickham
    

    

      
      #
    

  


  

      
Thanks to you all for your help.  I'll look into updating my version
of g77 and try getting the latest binary version.

Thanks again,

Hadley