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Convergence problem in GLMM

3 messages · Richard O'Keefe, Brian Ripley

Original
Richard O'Keefe
# 
I was trying to install some more packages and ran into a problem
I hadn't seen before.

Version:

    platform sparc-sun-solaris2.9
    arch     sparc               
    os       solaris2.9          
    system   sparc, solaris2.9   
    status                       
    major    2                   
    minor    0.1                 
    year     2004                
    month    11                  
    day      15                  
    language R                   

Fortran compilers available to me:

    f77: Sun WorkShop 6 update 2 FORTRAN 77 5.3 2001/05/15
    f90: Sun WorkShop 6 update 2 Fortran 95 6.2 2001/05/15
    f95: Sun WorkShop 6 update 2 Fortran 95 6.2 2001/05/15

Package:

    gam

    In fact I didn't ask for this one specifically, I had
    "dependencies=TRUE" in a call to install.packages().

Problem:

    Following the installation instructions for R, I had selected F95
    as my Fortran compiler.

    The f95 compiler complained about nearly every line of
    gam/src/bsplvd.f

    From the error messages as displayed on the screen, I could see no
    reason for complaint.  However, looking at the file with a text
    editor immediately revealed the problem.  The files

	bsplvd.f	bvalue.f	bvalus.f	loessf.f
	qsbart.f	sgram.f		sinerp.f	sslvrg.f
	stxwx.f

    all use CR-LF line termination.  The files

	linear.f	lo.f		splsm.f

    all use LF line termination expected on UNIX.

    It turns out that the g77 and f77 compilers don't mind CR at the
    end of a line, but f90 and f95 hate them like poison.

    Removing the CRs makes f90 and f95 happy again.

Second-order problem:

    I know how to fix the immediate problem.  What I don't know is how
    to intervene in the installation process.  What I need to do is
	- get and unpack files (steps normally done by install.packages)
	- make changes (remove CR, edit configuration, whatever)
	- resume whatever install.packages normally does
Brian Ripley
# 
What did this have to do with GLMM?  I've changed the subject line.
On Wed, 24 Nov 2004, Richard A. O'Keefe wrote:

            

      
      
      
    

        
We've seen it for C, and test it for C in R CMD check.  I think we should 
check C++ and Fortran files too.

            

      
      
      
    

        
BTW, in that version of Sun Workshop f90 and f95 are the same compiler, 
and in later versions so is f77.  (I think these compilers are on version 
9 now.)  Even in version 7, there is no problem with line endings.

I did get a warning:

       call dchdc(a,p,p,work,jpvt,job,info)
                                      ^
"linear.f", Line = 408, Column = 38: WARNING: Procedure "DCHDC" is defined 
at line 194 (linear.f).  Illegal association of array actual argument with 
scalar dummy argument "INFO".

which seems genuine (make it info(1) in the call).

            

      
      
      
    

        
- Use install.packages(destdir=) to retain the tarballs which are 
downloaded.

- Unpack the package tarball, make changes.

- Run R CMD INSTALL on the changed sources.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
I added a check for CRLF termination of Fortran and C++ source files to R
CMD check and found potential problems in packages

BsMD
MCMCpack (C++)
asypow
aws
bayesSurv (C++)
eha
fBasics/fOptions/fSeries
gam
mclust
ncomplete
noverlap
pan
rrcov
subselect (C++)
survrec

I'd be interested to know if C++ gives your problems too.  (Sun cc used to 
object to CRLF, but does not in Forte 7.)  I don't think I've ever tried 
one of the above before on Solaris, but had no CRLF problems with Forte 7, 
just plenty of other problems in MCMCpack and bayesSurv.  Could you please 
try installing subselect.

        
On Wed, 24 Nov 2004, Prof Brian Ripley wrote: