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Sébastien Durand

2005-Aug-03 20:29 UTC

[Rd] call fortran in R

Hello,

I used a mac G5, R.2.1.1, and G77 3.4.4 and I would like to use and  
call a fortran subroutine.
The trouble is that it seems I am not able to correctly load the  
compiled code.

Here is what I have done:

In the terminal this how I compiled my fortran code:

         R CMD SHLIB  ~/Desktop/Fortan_kmeans/kmeans3.f

There is the wrapper I have paste inside de kmeans3.f file:

         c THIS IS THE WRAPPER
               subroutine wrapper(n, p, nran, mat, ishort, w, z,
             + ntran, istand, k1, k2, iassign, iseed)
               integer n,p,kmax
               real*8 mat(n,p),sx(kmax,p),sx2(kmax,p),vect(p),
             +     xbar(kmax,p),var(kmax,p),mean(p),coord(10)
               real*8 D1,Dref,SSE,SSEref,Dvec(kmax),w(p),SST
               real*8 CH,CHr(kmax),SSEr(kmax),temp
               integer list(n),howmany(kmax),no(n),nobest(kmax)
               integer listr(kmax,n),howmanyr(kmax,kmax),nnitr(kmax)
               integer ishort(p)
               double precision kmeans,
               external kmeans

               call kmeans(n, p, nran, mat, ishort, w,
             + ntran, istand, k1, k2, iassign, iseed)
               end
             c THIS IS THE BEGINNING OF THE ORIGINAL FORTRAN CODE
               subroutine kmeans(n, p, nran, mat, ishort, w,
             + ntran, istand, k1, k2, iassign, iseed, CHr, SSEr)
              ......

Once compiled, in R, I get the following:

 > dyn.load("/Users/sebas/Desktop/Fortan_kmeans/K-means3.so")
 > getLoadedDLLs()
                                                                         
   Filename
1                                                                        
     base
2  /Library/Frameworks/R.framework/Resources/library/grDevices/libs/ 
grDevices.so
3          /Library/Frameworks/R.framework/Resources/library/stats/ 
libs/stats.so
4      /Library/Frameworks/R.framework/Resources/library/methods/libs/ 
methods.so
5   /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so

    Dynamic.Lookup
1           FALSE
2           FALSE
3           FALSE
4           FALSE
5            TRUE
 >
 > is.loaded(symbol.For("/Users/sebas/Desktop/Fortan_kmeans/ 
kmeans3.so"))
[1] FALSE
 > is.loaded(symbol.For("kmeans3"))
[1] FALSE
 > is.loaded(symbol.For("wrapper"))
[1] FALSE

Then whatever I write in .Fortran("",...), I always get :
Erreur in .Fortran("/Users/sebas/Desktop/Fortan_kmeans/kmeans3.so",...
:
     the function name "Fortran" is absent of the allocation table
     (this warning was translated from french)


So if anyone got a clue, please let me know.

I would be more than happy to find and understand what I am doing wrong!

Cheers
S?bastien Durand

Paul Roebuck

2005-Aug-03 22:07 UTC

head link

[Rd] call fortran in R

On Wed, 3 Aug 2005, =?iso-8859-1?Q?S=E9bastien_Durand_ wrote:
> I used a mac G5, R.2.1.1, and G77 3.4.4 and I would like to use and
> call a fortran subroutine.
> The trouble is that it seems I am not able to correctly load the
> compiled code.
>
> Here is what I have done:
>
> In the terminal this how I compiled my fortran code:
>
>          R CMD SHLIB  ~/Desktop/Fortan_kmeans/kmeans3.f
>
> There is the wrapper I have paste inside de kmeans3.f file:
>
>          c THIS IS THE WRAPPER
>                subroutine wrapper(n, p, nran, mat, ishort, w, z,
>              + ntran, istand, k1, k2, iassign, iseed)
>                integer n,p,kmax
>                real*8 mat(n,p),sx(kmax,p),sx2(kmax,p),vect(p),
>              +     xbar(kmax,p),var(kmax,p),mean(p),coord(10)
>                real*8 D1,Dref,SSE,SSEref,Dvec(kmax),w(p),SST
>                real*8 CH,CHr(kmax),SSEr(kmax),temp
>                integer list(n),howmany(kmax),no(n),nobest(kmax)
>                integer listr(kmax,n),howmanyr(kmax,kmax),nnitr(kmax)
>                integer ishort(p)
>                double precision kmeans,
>                external kmeans
>
>                call kmeans(n, p, nran, mat, ishort, w,
>              + ntran, istand, k1, k2, iassign, iseed)
>                end
>              c THIS IS THE BEGINNING OF THE ORIGINAL FORTRAN CODE
>                subroutine kmeans(n, p, nran, mat, ishort, w,
>              + ntran, istand, k1, k2, iassign, iseed, CHr, SSEr)
>               ......
>
> Once compiled, in R, I get the following:
>
>  > dyn.load("/Users/sebas/Desktop/Fortan_kmeans/K-means3.so")
>  > getLoadedDLLs()
>
>    Filename
> 1
>      base
> 2  /Library/Frameworks/R.framework/Resources/library/grDevices/libs/
> grDevices.so
> 3          /Library/Frameworks/R.framework/Resources/library/stats/
> libs/stats.so
> 4      /Library/Frameworks/R.framework/Resources/library/methods/libs/
> methods.so
> 5   /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so
>
>     Dynamic.Lookup
> 1           FALSE
> 2           FALSE
> 3           FALSE
> 4           FALSE
> 5            TRUE
>  >
>  > is.loaded(symbol.For("/Users/sebas/Desktop/Fortan_kmeans/
> kmeans3.so"))
> [1] FALSE
>  > is.loaded(symbol.For("kmeans3"))
> [1] FALSE
>  > is.loaded(symbol.For("wrapper"))
> [1] FALSE
>
> Then whatever I write in .Fortran("",...), I always get :
> Erreur in
.Fortran("/Users/sebas/Desktop/Fortan_kmeans/kmeans3.so",... :
>      the function name "Fortran" is absent of the allocation
table
>      (this warning was translated from french)
Shouldn't that be .Fortran("wrapper", <arglist>) or
something
to that effect? I'm surprised that a null string didn't
crash the program.

Might want to look into R's registration tables as well.
That way you might get some additional debugging help.

----------------------------------------------------------
SIGSIG -- signature too long (core dumped)

Sébastien Durand

2005-Aug-04 14:04 UTC

head link

[Rd] call fortran in R

Thanks for your help,

I had read those web pages already, and the post you referred to  
already.

So I will try to give more details to what I have done till now

First I must mention again that I am using a mac under tiger.  So I  
am using .so files.

My fortran file is called kmeans.f, and my subroutine or wrapper I  
named  it "wrapper"

There is my first line of code

     subroutine wrapper(n, p, nran, mat, ishort, w, z, ntran, istand,  
k1, k2, iassign, iseed)

In the terminal:
     R CMD SHLIB  ~/Desktop/Fortan_kmeans/kmeans3.fg77
         -fno-common  -g -O2 -c /Users/sebas/Desktop/Fortan_kmeans/ 
kmeans3.f -o /Users/sebas/Desktop/Fortan_kmeans/kmeans3.o
         gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/ 
local/lib -o
         /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so /Users/sebas/ 
Desktop/Fortan_kmeans/kmeans3.o
         -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c - 
lSystem -framework R

The files append to compile without any warnings.

In R:

 > dyn.load("/Users/sebas/Desktop/Fortan_kmeans/kmeans3.so")
 > getLoadedDLLs()

Filename
base                                                                     
            base
grDevices /Library/Frameworks/R.framework/Resources/library/grDevices/ 
libs/grDevices.so
stats             /Library/Frameworks/R.framework/Resources/library/ 
stats/libs/stats.so
methods       /Library/Frameworks/R.framework/Resources/library/ 
methods/libs/methods.so
kmeans3                                   /Users/sebas/Desktop/ 
Fortan_kmeans/kmeans3.so
           Dynamic.Lookup
base               FALSE
grDevices          FALSE
stats              FALSE
methods            FALSE
kmeans3             TRUE


Dyn.load seems to work since if I type in getLoadedDLLs()  I can see  
the link.

 > zozo=.Fortran(symbol.For("wrapper"),n=as.integer(n),
p=as.integer
(p), nran=as.integer(nran), mat=as.matrix(mat), ishort=as.vector 
(ishort), w=as.vector(w),ntran=as.integer(ntran), istand=as.integer 
(istand), k1=as.integer(k1), k2=as.integer(k2), iassign=as.integer 
(iassign), iseed=as.integer(iseed))
Erreur dans .Fortran(symbol.For("wrapper"), n = as.integer(n), p =  
as.integer(p),  :
     nom de fonction "Fortran" absent de la table d'allocation

Even so I am using in the name parameter of the .Fortran function,  
"wrapper", "kmeans3", "wrapper_" or
"kmeans3_"

I always get the same error call telling me that the fonction  
"Fortran" is not in the allocation table

That is where I am at now, it has been 4 days I am digging into docs  
but I haven't been able to find what I am doing wrong.

R is so great, I got tons of Fortran lines and subroutine to  
implement in R but I guess I am missing a little thing to make it  
work and now I really don't have a cue how to solve that problem.

Cheers

I will be anxiously waiting for any reply

Sébastien

>
> If I understand correctly, you used
> .Fortran("wrapper",....)
>
> The problem might be that the function name ("wrapper") was
changed
> in the
> compilation of the code! See the mail bellow for clues (a previous  
> post on
> R-help by Duncan Murdoch)
>
> Natalie Hawkins wrote:
> > Using R 2.0.1 on Windows XP, I am getting an error
> > msg:
> >
> > Error in .Fortran("conic", nxy = nxy, npt = npt, CP >
> cp, EP1 = ep1, EP2 = ep2,  :
> >
> > Fortran function name not in load table
> >
> > I am wondering if there is a way to see what function
> > names are in the load table?  Maybe the function name
> > has been altered?
>
> You need to look at the DLL to see what name it is exporting. I  
> believe
> R would be looking for "conic_".  If your Fortran compiler
doesn't
> append underscores, you'll get this error.
>
> You might want to look at this page
>
> http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/ 
> index.html#badname
>
> or this one
>
> http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/ 
> fortran.html
>
> for more help.
>
> Duncan Murdoch
	[[alternative HTML version deleted]]

Sébastien Durand

2005-Aug-04 14:24 UTC

head link

[Rd] call fortran in R

At the beginning I was not using symbol.For(), and whatever I add a  
"_" or not

e.g.:

.Fortran("wrapper",...

I get the same error

Sebastien


> You want to just say:
>
> .Fortran("wrapper", ...
>
> not
>
> .Fortran(symbol.For("wrapper"), ...
>
> Patrick Burns
> patrick@burns-stat.com
> +44 (0)20 8525 0696
> http://www.burns-stat.com
> (home of S Poetry and "A Guide for the Unwilling S User")
>
> Sébastien Durand wrote:
>
>
>> Thanks for your help,
>>
>> I had read those web pages already, and the post you referred to   
>> already.
>>
>> So I will try to give more details to what I have done till now
>>
>> First I must mention again that I am using a mac under tiger.  So  
>> I  am using .so files.
>>
>> My fortran file is called kmeans.f, and my subroutine or wrapper  
>> I  named  it "wrapper"
>>
>> There is my first line of code
>>
>>     subroutine wrapper(n, p, nran, mat, ishort, w, z, ntran,  
>> istand,  k1, k2, iassign, iseed)
>>
>> In the terminal:
>>     R CMD SHLIB  ~/Desktop/Fortan_kmeans/kmeans3.fg77
>>         -fno-common  -g -O2 -c /Users/sebas/Desktop/Fortan_kmeans/  
>> kmeans3.f -o /Users/sebas/Desktop/Fortan_kmeans/kmeans3.o
>>         gcc-3.3 -bundle -flat_namespace -undefined suppress -L/ 
>> usr/ local/lib -o
>>         /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so /Users/ 
>> sebas/ Desktop/Fortan_kmeans/kmeans3.o
>>         -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c -  
>> lSystem -framework R
>>
>> The files append to compile without any warnings.
>>
>> In R:
>>
>> >
dyn.load("/Users/sebas/Desktop/Fortan_kmeans/kmeans3.so")
>> > getLoadedDLLs()
>>
>> Filename
>> base                                                                  
>>                base
>> grDevices /Library/Frameworks/R.framework/Resources/library/ 
>> grDevices/ libs/grDevices.so
>> stats             /Library/Frameworks/R.framework/Resources/ 
>> library/ stats/libs/stats.so
>> methods       /Library/Frameworks/R.framework/Resources/library/  
>> methods/libs/methods.so
>> kmeans3                                   /Users/sebas/Desktop/  
>> Fortan_kmeans/kmeans3.so
>>           Dynamic.Lookup
>> base               FALSE
>> grDevices          FALSE
>> stats              FALSE
>> methods            FALSE
>> kmeans3             TRUE
>>
>>
>> Dyn.load seems to work since if I type in getLoadedDLLs()  I can  
>> see  the link.
>>
>> > zozo=.Fortran(symbol.For("wrapper"),n=as.integer(n),  
>> p=as.integer (p), nran=as.integer(nran), mat=as.matrix(mat),  
>> ishort=as.vector (ishort), w=as.vector(w),ntran=as.integer(ntran),  
>> istand=as.integer (istand), k1=as.integer(k1), k2=as.integer(k2),  
>> iassign=as.integer (iassign), iseed=as.integer(iseed))
>> Erreur dans .Fortran(symbol.For("wrapper"), n =
as.integer(n), p
>> =  as.integer(p),  :
>>     nom de fonction "Fortran" absent de la table
d'allocation
>>
>> Even so I am using in the name parameter of the .Fortran  
>> function,  "wrapper", "kmeans3",
"wrapper_" or "kmeans3_"
>>
>> I always get the same error call telling me that the fonction   
>> "Fortran" is not in the allocation table
>>
>> That is where I am at now, it has been 4 days I am digging into  
>> docs  but I haven't been able to find what I am doing wrong.
>>
>> R is so great, I got tons of Fortran lines and subroutine to   
>> implement in R but I guess I am missing a little thing to make it   
>> work and now I really don't have a cue how to solve that problem.
>>
>> Cheers
>>
>> I will be anxiously waiting for any reply
>>
>> Sébastien
>>
>>
>>
>>
>>> If I understand correctly, you used
>>> .Fortran("wrapper",....)
>>>
>>> The problem might be that the function name ("wrapper")
was
>>> changed  in the
>>> compilation of the code! See the mail bellow for clues (a  
>>> previous  post on
>>> R-help by Duncan Murdoch)
>>>
>>> Natalie Hawkins wrote:
>>>
>>>
>>>> Using R 2.0.1 on Windows XP, I am getting an error
>>>> msg:
>>>>
>>>> Error in .Fortran("conic", nxy = nxy, npt = npt, CP
>>>> cp, EP1 = ep1, EP2 = ep2,  :
>>>>
>>>> Fortran function name not in load table
>>>>
>>>> I am wondering if there is a way to see what function
>>>> names are in the load table?  Maybe the function name
>>>> has been altered?
>>>>
>>>>
>>> You need to look at the DLL to see what name it is exporting. I   
>>> believe
>>> R would be looking for "conic_".  If your Fortran
compiler doesn't
>>> append underscores, you'll get this error.
>>>
>>> You might want to look at this page
>>>
>>> http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/  
>>> index.html#badname
>>>
>>> or this one
>>>
>>> http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/  
>>> fortran.html
>>>
>>> for more help.
>>>
>>> Duncan Murdoch
>>>
>>>
>>
>>     [[alternative HTML version deleted]]
>>
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
>
	[[alternative HTML version deleted]]

Sébastien Durand

2005-Aug-04 15:05 UTC

head link

[Rd] call fortran in R

Ok,

Dear all,

I have state previously, I am using mac os X tiger on a g5, using the  
last version of R 2.1.1

When I type in the terminal

nm -g ~/Desktop/Fortan_kmeans/kmeans3.so
or
nm /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so | grep ' T '

Nothing appears on my screen

When I type

nm  ~/Desktop/Fortan_kmeans/kmeans3.so

this is what I get:

00000fe0 t __dyld_func_lookup
00000000 t __mh_bundle_header
00001000 d dyld__mh_bundle_header
00001008 s dyld_func_lookup_pointer
00001004 s dyld_lazy_symbol_binding_entry_point
00000fb0 t dyld_stub_binding_helper


By the way, yes I have tried
     is.loaded("wrapper") ?
And is always return FALSE

S.

Sébastien Durand

2005-Aug-04 15:25 UTC

head link

[Rd] call fortran in R

Dear all,

Since the command you ask me to type doesn't show anything
Here some more information, on my system and on the foo.so compiled file

I am using g77 version 3.4.4  Configured with: ../gcc/configure -- 
enable-threads=posix --enable-languages=f77

I am using gcc version 4.0.0 20041026 (Apple Computer, Inc. build 4061)
         Configured with: /private/var/tmp/gcc/gcc-4061.obj~8/src/ 
configure --disable-checking --prefix=/usr --mandir=/share/man -- 
enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^ 
+.-]*$/s/$/-4.0/
         --with-gxx-include-dir=/include/gcc/darwin/4.0/c++ -- 
build=powerpc-apple-darwin8 --host=powerpc-apple-darwin8 -- 
target=powerpc-apple-darwin8

I don't know if this can be of any help to you but there is again how  
I compile the foo.f

Double-G5:~ sebas$ R CMD SHLIB  ~/Desktop/Fortan_kmeans/kmeans3.f
         g77   -fno-common  -g -O2 -c /Users/sebas/Desktop/ 
Fortan_kmeans/kmeans3.f -o /Users/sebas/Desktop/Fortan_kmeans/kmeans3.o
         gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/ 
local/lib -o /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so /Users/ 
sebas/Desktop/Fortan_kmeans/kmeans3.o  -L/usr/local/lib/gcc/powerpc- 
apple-darwin6.8/3.4.2 -lg2c -lSystem -framework R


There is all the info about the foo.so file using nm -a option  
instead of -g:


Double-G5:~ sebas$ nm -a ~/Desktop/Fortan_kmeans/kmeans3.so
00000fe4 - 01 0114 SLINE
00000fb0 - 01 0000    SO
00000fd8 - 01 010d SLINE
00000fdc - 01 010e SLINE
00000fe0 - 01 010f SLINE
00000fec - 01 0116 SLINE
00000fe8 - 01 0115 SLINE
00001000 - 01 0000    SO
00001000 - 01 011b SLINE
00000ffc - 01 011a SLINE
00000ff8 - 01 0119 SLINE
00000fb4 - 01 0104 SLINE
00000fb8 - 01 0105 SLINE
00000fbc - 01 0106 SLINE
00000fc0 - 01 0107 SLINE
00000fc4 - 01 0108 SLINE
00000ff4 - 01 0118 SLINE
00000fc8 - 01 0109 SLINE
00000fcc - 01 010a SLINE
00000fd0 - 01 010b SLINE
00000fd4 - 01 010c SLINE
00000ff0 - 01 0117 SLINE
00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57//
00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57/bundle1.s
00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57/bundle1.s
00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57/bundle1.s
00000fb0 - 01 0000    SO /Users/sebas/
00000fb0 - 01 0000    SO /Users/sebas/Desktop/Fortan_kmeans/kmeans3.f
00000fb0 - 01 0000   SOL <built-in>
00000fb0 - 01 0000   SOL <command line>
00000fe0 t __dyld_func_lookup
00000fe0 - 01 0113   FUN __dyld_func_lookup:F3
00000000 - 00 0000  LSYM __g77_f2c_address:t(0,10)=*(0,11)=@s8;r 
(0,11);-128;127;
00000000 - 00 0000  LSYM __g77_f2c_complex:t(0,7)=R3;8;0;
00000000 - 00 0000  LSYM __g77_f2c_doublecomplex:t(0,6)=R3;16;0;
00000000 - 00 0000  LSYM __g77_f2c_doublereal:t(0,8)=r(0,0);8;0;
00000000 - 00 0000  LSYM __g77_f2c_flag:t(0,3)=r 
(0,3);-2147483648;2147483647;
00000000 - 00 0000  LSYM __g77_f2c_ftnint:t(0,1)=r 
(0,1);-2147483648;2147483647;
00000000 - 00 0000  LSYM __g77_f2c_ftnlen:t(0,2)=r 
(0,2);-2147483648;2147483647;
00000000 - 00 0000  LSYM __g77_f2c_integer:t(0,12)=r 
(0,12);-2147483648;2147483647;
00000000 - 00 0000  LSYM __g77_f2c_logical:t(0,4)=r 
(0,4);-2147483648;2147483647;
00000000 - 00 0000  LSYM __g77_f2c_longint:t(0,5)=@s64;r(0,5); 
001000000000000000000000;000777777777777777777777;
00000000 - 00 0000  LSYM __g77_f2c_real:t(0,9)=r(0,0);4;0;
00000000 t __mh_bundle_header
00000000 - 00 0000  LSYM byte:t(0,26)=@s8;r(0,26);-128;127;
00000000 - 00 0000  LSYM char:t(0,46)=@s8;r(0,46);0;255;
00000000 - 00 0000  LSYM char:t2=r2;0;127;
00000000 - 00 0000  LSYM complex double:t(0,31)=R3;16;0;
00000000 - 00 0000  LSYM complex float:t(0,32)=R3;8;0;
00000000 - 00 0000  LSYM complex int:t(0,33)=s8real:(0,34)=r 
(0,34);-2147483648;2147483647;,0,32;imag:(0,34),32,32;;
00000000 - 00 0000  LSYM complex long double:t(0,30)=R3;16;0;
00000000 - 00 0000  LSYM complex:t(0,14)=R3;8;0;
00000000 - 00 0000  LSYM double complex:t(0,13)=R3;16;0;
00000000 - 00 0000  LSYM double precision:t(0,15)=r(0,0);8;0;
00000000 - 00 0000  LSYM double:t(0,36)=r(0,34);8;0;
00001000 d dyld__mh_bundle_header
00001008 s dyld_func_lookup_pointer
00001004 s dyld_lazy_symbol_binding_entry_point
00000fb0 t dyld_stub_binding_helper
00000fb0 - 01 0103   FUN dyld_stub_binding_helper:F3
00000000 - 00 0000  LSYM float:t(0,37)=r(0,34);4;0;
00000000 - 00 0000   OPT gcc2_compiled.
00000000 - 00 0000  LSYM int:t(0,34)
00000000 - 00 0000  LSYM int:t1=r1;-2147483648;2147483647;
00000000 - 00 0000  LSYM integer4:t(0,22)=@s64;r(0,22); 
001000000000000000000000;000777777777777777777777;
00000000 - 00 0000  LSYM integer:t(0,28)=r(0,28);-2147483648;2147483647;
00000000 - 00 0000  LSYM logical2:t(0,19)=@s8;r(0,19);-128;127;
00000000 - 00 0000  LSYM logical3:t(0,18)=@s16;r(0,18);-32768;32767;
00000000 - 00 0000  LSYM logical4:t(0,17)=@s64;r(0,17); 
001000000000000000000000;000777777777777777777777;
00000000 - 00 0000  LSYM logical:t(0,20)=r(0,20);-2147483648;2147483647;
00000000 - 00 0000  LSYM long double:t(0,35)=r(0,34);8;0;
00000000 - 00 0000  LSYM long int:t(0,45)=r 
(0,45);-2147483648;2147483647;
00000000 - 00 0000  LSYM long long int:t(0,42)=@s64;r(0,42); 
001000000000000000000000;000777777777777777777777;
00000000 - 00 0000  LSYM long long unsigned int:t(0,41)=@s64;r(0,41); 
000000000000000000000000;001777777777777777777777;
00000000 - 00 0000  LSYM long unsigned int:t(0,43)=r(0,43); 
000000000000000000000000;000000000000037777777777;
00000000 - 00 0000  LSYM real:t(0,16)=r(0,0);4;0;
00000000 - 00 0000  LSYM short int:t(0,40)=@s16;r(0,40);-32768;32767;
00000000 - 00 0000  LSYM short unsigned int:t(0,39)=@s16;r(0,39); 
0;65535;
00000000 - 00 0000  LSYM signed char:t(0,11)
00000000 - 00 0000  LSYM unsigned byte:t(0,25)=@s8;r(0,25);0;255;
00000000 - 00 0000  LSYM unsigned char:t(0,38)=@s8;r(0,38);0;255;
00000000 - 00 0000  LSYM unsigned int:t(0,44)=r(0,44); 
000000000000000000000000;000000000000037777777777;
00000000 - 00 0000  LSYM unsigned word:t(0,23)=@s16;r(0,23);0;65535;
00000000 - 00 0000  LSYM unsigned4:t(0,21)=@s64;r(0,21); 
000000000000000000000000;001777777777777777777777;
00000000 - 00 0000  LSYM unsigned:t(0,27)=r(0,27); 
000000000000000000000000;000000000000037777777777;
00000000 - 00 0000  LSYM void:t(0,29)=(0,29)
00000000 - 00 0000  LSYM void:t3=3
00000000 - 00 0000  LSYM word:t(0,24)=@s16;r(0,24);-32768;32767;
00000fb0 - 01 0000    SO {standard input}
Double-G5:~ sebas$

S.

Sébastien Durand

2005-Aug-04 17:38 UTC

head link

[Rd] call fortran in R

Ok,  I am presently updating my system.

How do you set
      setenv gcc /usr/local/bin/gfortran.

Using bash.

Then I will the command to compile the foo.f file been the same!

I guess so

S.>
> also gcc 4061 is a bit old -- the tiger update in 10.4.2 was
> 50xx, i think, cvs is up to apple build 5217 and is now
> gcc-4.0.1.
>
> -- jan
>
> On Aug 4, 2005, at 8:25 , S?bastien Durand wrote:
>
>
>> Dear all,
>>
>> Since the command you ask me to type doesn't show anything
>> Here some more information, on my system and on the foo.so  
>> compiled file
>>
>> I am using g77 version 3.4.4  Configured with: ../gcc/configure --
>> enable-threads=posix --enable-languages=f77
>>
>> I am using gcc version 4.0.0 20041026 (Apple Computer, Inc. build  
>> 4061)
>>          Configured with: /private/var/tmp/gcc/gcc-4061.obj~8/src/
>> configure --disable-checking --prefix=/usr --mandir=/share/man --
>> enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^
>> +.-]*$/s/$/-4.0/
>>          --with-gxx-include-dir=/include/gcc/darwin/4.0/c++ --
>> build=powerpc-apple-darwin8 --host=powerpc-apple-darwin8 --
>> target=powerpc-apple-darwin8
>>
>> I don't know if this can be of any help to you but there is again
how
>> I compile the foo.f
>>
>> Double-G5:~ sebas$ R CMD SHLIB  ~/Desktop/Fortan_kmeans/kmeans3.f
>>          g77   -fno-common  -g -O2 -c /Users/sebas/Desktop/
>> Fortan_kmeans/kmeans3.f -o /Users/sebas/Desktop/Fortan_kmeans/ 
>> kmeans3.o
>>          gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/
>> local/lib -o /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so /Users/
>> sebas/Desktop/Fortan_kmeans/kmeans3.o  -L/usr/local/lib/gcc/powerpc-
>> apple-darwin6.8/3.4.2 -lg2c -lSystem -framework R
>>
>>
>> There is all the info about the foo.so file using nm -a option
>> instead of -g:
>>
>>
>> Double-G5:~ sebas$ nm -a ~/Desktop/Fortan_kmeans/kmeans3.so
>> 00000fe4 - 01 0114 SLINE
>> 00000fb0 - 01 0000    SO
>> 00000fd8 - 01 010d SLINE
>> 00000fdc - 01 010e SLINE
>> 00000fe0 - 01 010f SLINE
>> 00000fec - 01 0116 SLINE
>> 00000fe8 - 01 0115 SLINE
>> 00001000 - 01 0000    SO
>> 00001000 - 01 011b SLINE
>> 00000ffc - 01 011a SLINE
>> 00000ff8 - 01 0119 SLINE
>> 00000fb4 - 01 0104 SLINE
>> 00000fb8 - 01 0105 SLINE
>> 00000fbc - 01 0106 SLINE
>> 00000fc0 - 01 0107 SLINE
>> 00000fc4 - 01 0108 SLINE
>> 00000ff4 - 01 0118 SLINE
>> 00000fc8 - 01 0109 SLINE
>> 00000fcc - 01 010a SLINE
>> 00000fd0 - 01 010b SLINE
>> 00000fd4 - 01 010c SLINE
>> 00000ff0 - 01 0117 SLINE
>> 00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57//
>> 00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57/bundle1.s
>> 00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57/bundle1.s
>> 00000fb0 - 01 0000   SOL /SourceCache/Csu/Csu-57/bundle1.s
>> 00000fb0 - 01 0000    SO /Users/sebas/
>> 00000fb0 - 01 0000    SO /Users/sebas/Desktop/Fortan_kmeans/kmeans3.f
>> 00000fb0 - 01 0000   SOL <built-in>
>> 00000fb0 - 01 0000   SOL <command line>
>> 00000fe0 t __dyld_func_lookup
>> 00000fe0 - 01 0113   FUN __dyld_func_lookup:F3
>> 00000000 - 00 0000  LSYM __g77_f2c_address:t(0,10)=*(0,11)=@s8;r
>> (0,11);-128;127;
>> 00000000 - 00 0000  LSYM __g77_f2c_complex:t(0,7)=R3;8;0;
>> 00000000 - 00 0000  LSYM __g77_f2c_doublecomplex:t(0,6)=R3;16;0;
>> 00000000 - 00 0000  LSYM __g77_f2c_doublereal:t(0,8)=r(0,0);8;0;
>> 00000000 - 00 0000  LSYM __g77_f2c_flag:t(0,3)=r
>> (0,3);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM __g77_f2c_ftnint:t(0,1)=r
>> (0,1);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM __g77_f2c_ftnlen:t(0,2)=r
>> (0,2);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM __g77_f2c_integer:t(0,12)=r
>> (0,12);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM __g77_f2c_logical:t(0,4)=r
>> (0,4);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM __g77_f2c_longint:t(0,5)=@s64;r(0,5);
>> 001000000000000000000000;000777777777777777777777;
>> 00000000 - 00 0000  LSYM __g77_f2c_real:t(0,9)=r(0,0);4;0;
>> 00000000 t __mh_bundle_header
>> 00000000 - 00 0000  LSYM byte:t(0,26)=@s8;r(0,26);-128;127;
>> 00000000 - 00 0000  LSYM char:t(0,46)=@s8;r(0,46);0;255;
>> 00000000 - 00 0000  LSYM char:t2=r2;0;127;
>> 00000000 - 00 0000  LSYM complex double:t(0,31)=R3;16;0;
>> 00000000 - 00 0000  LSYM complex float:t(0,32)=R3;8;0;
>> 00000000 - 00 0000  LSYM complex int:t(0,33)=s8real:(0,34)=r
>> (0,34);-2147483648;2147483647;,0,32;imag:(0,34),32,32;;
>> 00000000 - 00 0000  LSYM complex long double:t(0,30)=R3;16;0;
>> 00000000 - 00 0000  LSYM complex:t(0,14)=R3;8;0;
>> 00000000 - 00 0000  LSYM double complex:t(0,13)=R3;16;0;
>> 00000000 - 00 0000  LSYM double precision:t(0,15)=r(0,0);8;0;
>> 00000000 - 00 0000  LSYM double:t(0,36)=r(0,34);8;0;
>> 00001000 d dyld__mh_bundle_header
>> 00001008 s dyld_func_lookup_pointer
>> 00001004 s dyld_lazy_symbol_binding_entry_point
>> 00000fb0 t dyld_stub_binding_helper
>> 00000fb0 - 01 0103   FUN dyld_stub_binding_helper:F3
>> 00000000 - 00 0000  LSYM float:t(0,37)=r(0,34);4;0;
>> 00000000 - 00 0000   OPT gcc2_compiled.
>> 00000000 - 00 0000  LSYM int:t(0,34)
>> 00000000 - 00 0000  LSYM int:t1=r1;-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM integer4:t(0,22)=@s64;r(0,22);
>> 001000000000000000000000;000777777777777777777777;
>> 00000000 - 00 0000  LSYM integer:t(0,28)=r 
>> (0,28);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM logical2:t(0,19)=@s8;r(0,19);-128;127;
>> 00000000 - 00 0000  LSYM logical3:t(0,18)=@s16;r(0,18);-32768;32767;
>> 00000000 - 00 0000  LSYM logical4:t(0,17)=@s64;r(0,17);
>> 001000000000000000000000;000777777777777777777777;
>> 00000000 - 00 0000  LSYM logical:t(0,20)=r 
>> (0,20);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM long double:t(0,35)=r(0,34);8;0;
>> 00000000 - 00 0000  LSYM long int:t(0,45)=r
>> (0,45);-2147483648;2147483647;
>> 00000000 - 00 0000  LSYM long long int:t(0,42)=@s64;r(0,42);
>> 001000000000000000000000;000777777777777777777777;
>> 00000000 - 00 0000  LSYM long long unsigned int:t(0,41)=@s64;r(0,41);
>> 000000000000000000000000;001777777777777777777777;
>> 00000000 - 00 0000  LSYM long unsigned int:t(0,43)=r(0,43);
>> 000000000000000000000000;000000000000037777777777;
>> 00000000 - 00 0000  LSYM real:t(0,16)=r(0,0);4;0;
>> 00000000 - 00 0000  LSYM short int:t(0,40)=@s16;r(0,40);-32768;32767;
>> 00000000 - 00 0000  LSYM short unsigned int:t(0,39)=@s16;r(0,39);
>> 0;65535;
>> 00000000 - 00 0000  LSYM signed char:t(0,11)
>> 00000000 - 00 0000  LSYM unsigned byte:t(0,25)=@s8;r(0,25);0;255;
>> 00000000 - 00 0000  LSYM unsigned char:t(0,38)=@s8;r(0,38);0;255;
>> 00000000 - 00 0000  LSYM unsigned int:t(0,44)=r(0,44);
>> 000000000000000000000000;000000000000037777777777;
>> 00000000 - 00 0000  LSYM unsigned word:t(0,23)=@s16;r(0,23);0;65535;
>> 00000000 - 00 0000  LSYM unsigned4:t(0,21)=@s64;r(0,21);
>> 000000000000000000000000;001777777777777777777777;
>> 00000000 - 00 0000  LSYM unsigned:t(0,27)=r(0,27);
>> 000000000000000000000000;000000000000037777777777;
>> 00000000 - 00 0000  LSYM void:t(0,29)=(0,29)
>> 00000000 - 00 0000  LSYM void:t3=3
>> 00000000 - 00 0000  LSYM word:t(0,24)=@s16;r(0,24);-32768;32767;
>> 00000fb0 - 01 0000    SO {standard input}
>> Double-G5:~ sebas$
>>
>> S.
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
>
> =========================================================> Jan de Leeuw,
11667 Steinhoff Rd, Frazier Park, CA 93225, 661-245-1725
> =========================================================>              
Und die Einen sind im Dunkeln
>                                      Und die Andern sind im Licht
>                                      Und man siehe die im Lichte
>                                      Die im Dunklen sieht man nicht
>                                                                        
>                                   Brecht
>
>
>
>

Bill Northcott

2005-Aug-05 07:56 UTC

head link

[Rd] call fortran in R

On 04/08/2005, at 8:00 PM, Sebastien Durand wrote:> I used a mac G5, R.2.1.1, and G77 3.4.4 and I would like to use and
> call a fortran subroutine.
> The trouble is that it seems I am not able to correctly load the
> compiled code.
.................
>      base
> 2  /Library/Frameworks/R.framework/Resources/library/grDevices/libs/
> grDevices.so
> 3          /Library/Frameworks/R.framework/Resources/library/stats/
> libs/stats.so
> 4      /Library/Frameworks/R.framework/Resources/library/methods/libs/
> methods.so
> 5   /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so
>
>     Dynamic.Lookup
> 1           FALSE
> 2           FALSE
> 3           FALSE
> 4           FALSE
> 5            TRUE
I really wish someone would make these issues clear in MacOS R  
documentation.

MacOS X 10.3 Panther uses gcc-3.3 as its default compiler.  The R  
binary is built with gcc-3.3 and g77 3.4 so that it will run on Panther.

MacOS X 10.4 Tiger uses gcc-4.00 as its default compiler.  This  
causes two problems.
1.  Fortran objects built with g77 cannot be linked with C/C++  
objects built with gcc-4.0.  So an R package with a mixture of C and  
Fortran code will very likely fail at some point.
2.  Even if you specifically invoke gcc-3.3 and g77 the code will  
still fail to link because it needs a symlink /usr/lib/ 
libcc_dynamic.dylib which points to libgcc.a.  This link is missing  
if the default gcc-4.0 is the selected compiler.  (It is missing  
because it does not work with gcc-4).

If you want to build Fortran source packages on Tiger using the R  
binary distribution, you need to to do
'sudo gcc_select 3.3'

That command will make gcc-3.3 the default compiler and reinstate the  
symlink, which recreates the environment in which the R binary was  
built.   You can always go back to gcc-4.0 with 'sudo gcc_select 4.0'.

Bill Northcott

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