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[Bioc-devel] affycoretools in devel failed to install

7 messages · Vojtech Kulvait, Dan Tenenbaum, James W. MacDonald +1 more

Original
Dan Tenenbaum
# 
----- Original Message -----
I don't think you do. In the latest version of affycoretools in devel, this issue has been fixed. Make sure you have the most recent version with

biocLite("affycoretools")

If you still have problems, please send the output of

sessionInfo()

Thanks,
Dan
James W. MacDonald
# 
Hi Vojtech,
On 7/25/2014 7:32 AM, Vojtech Kulvait wrote:
Cutting out just what you think is important from the output from 
biocLite isn't really helpful. Instead, please give us everything.

I cannot see how this has anything to do with affycoretools anyway. I 
don't import symbols2indices, nor do I call that function in any code in 
affycoretools. Plus, limma exports every function except those that 
begin with a period, so symbols2indices is for sure exported. And to top 
it all off, the build report for affycoretools is clean, except for some 
warnings I will have to clean up sometime 
(http://bioconductor.org/checkResults/devel/bioc-LATEST/affycoretools/zin1-checksrc.html)

If I were to make a haphazard guess, I would think your limma package 
install is borked somehow and you might be better off re-installing it.

Best,

Jim

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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On 07/25/2014 04:32 AM, Vojtech Kulvait wrote:

            

      
      
      
    

        
Hi Vojtech -- just to add to the advice, you can use

   BiocInstaller::biocValid()

to check your installation,

   BiocInstaller::biocLite()

to update your current packages.

Martin

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    
3 days later