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Make check error building R 2.6.1 under OS-X 10.4.11

5 messages · Simon Urbanek, Stephen Shiboski

Original
Stephen Shiboski
# 
Trying to build R 2.6.1 on a G5 imac running OS X 10.4.11. I am using  
Xcode 2.4.1 and the gfortran (4.2.1) from r.research.att.com/tools/.  
I am using following the configuration:

./configure --with-aqua --with-blas='-framework vecLib' --with-lapack  
--with-jpeglib --with-libpng


Builds fine, but make check fails as follows:

running code in 'd-p-q-r-tests.R' ...make[3]: *** [d-p-q-r- 
tests.Rout] Error 1
make[2]: *** [test-Specific] Error 2
make[1]: *** [test-all-basics] Error 1
make: *** [check] Error 2

Here's the error:

Error: dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf is not all TRUE
In addition: Warning message:
In dnbeta(x, shape1, shape2, ncp, log) : NaNs produced
Execution halted

I sucessfully built and checked 2.5.1 using the same set-up. The only  
thing that changed was the update to OS X 10.4.11 from 10.4.10.

It builds & checks fine on my Intel machine with the same Xcode and  
gfortran.

Any suggestions greatly appreciated. Thanks,

S Shiboski
Biostatistics
UC San Francisco
Simon Urbanek
#
On Dec 15, 2007, at 6:49 PM, Stephen Shiboski wrote:

            

      
      
      
    

        
The issue is known and appears to be a problem with a specific version  
of Apple's compilers generating incorrect ppc code. It goes away when  
you update to Apple's gcc 4.2 (or probably also when you revert to  
older compilers, although I didn't test that route specifically).

However, I'm surprised that 2.5.1 would work *if* you had exactly the  
same setup, because the dbeta source code didn't change since 2.5.1 at  
all. Are you 100% sure that you had exactly the same compiler versions  
as now?

Cheers,
Simon

  
  


  


      

    

    

      
      

        


  

        

      Stephen Shiboski
    

    

      
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Thanks a lot. I noticed that there is a binary for gcc 4.2.1  
(gcc-42-5531-darwin8.tar.gz) on the R developer's page. If this is  
the same as what Apple provides, I can install this.

I also noticed that the code for dbeta.c hadn't changed since 2.5.1.  
So, I just re-built 2.5.1 on the same machine and it makes & checks w/ 
o errors!

-S

        
On Dec 15, 2007, at 5:32 PM, Simon Urbanek wrote:

        

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Dec 15, 2007, at 10:47 PM, Stephen Shiboski wrote:

        

            

      
      
      
    

        
It is built from the same sources... (Apple doesn't provide gcc-4.2  
binaries for Mac OS X 10.4)

            

      
      
      
    

        
Ah, oh .. that is indeed interesting ... and does that build return  
all Inf for:
dbeta(0, 0.9, 2.2, ncp = rlnorm(100))

If so, then I shall have a closer look ...

Thanks,
Simon

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Stephen Shiboski
    

    

      
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Thanks Simon. I compiled both again last night on the same machine to  
make sure.

 From 2.5.1:

 > dbeta(0, 0.9, 2.2, ncp = rlnorm(100))
   [1] Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf  
Inf Inf Inf
  [19] Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf  
Inf Inf Inf
  [37] Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf  
Inf Inf Inf
  [55] Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf  
Inf Inf Inf
  [73] Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf  
Inf Inf Inf
  [91] Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf

 From 2.6.1:

 > dbeta(0, 0.9, 2.2, ncp = rlnorm(100))
   [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN  
NaN NaN NaN
  [19] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN  
NaN NaN NaN
  [37] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN  
NaN NaN NaN
  [55] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN  
NaN NaN NaN
  [73] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN  
NaN NaN NaN
  [91] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
Warning message:
In dnbeta(x, shape1, shape2, ncp, log) : NaNs produced

        
On Dec 16, 2007, at 6:21 AM, Simon Urbanek wrote: