[R-SIG-Mac] Compiling 2.5.1 on OSX Panther (James Kyle)

[James Kyle]

This seems to be the problem area:

> ld: common symbols not allowed with MH_DYLIB output format with the  
> -multi_module option
> /usr/local/lib/libg2c.a(err.o) definition of common _f__cblank  
> (size 4)
> /usr/local/lib/libg2c.a(fmt.o) definition of common _f__cnt (size 40)
> /usr/local/lib/libg2c.a(fmt.o) definition of common f(char,  *)  
> (size 4)
> /usr/local/lib/libg2c.a(err.o) definition of common f(char, long *,  
> short __restrict) (size 4)
> /usr/local/lib/libg2c.a(err.o) definition of common _f__cursor  
> (size 4)
>

It goes on to list the other common symbols found in libg2c.a.  
libg2c.a is a library provided by the g77 libraries.

So I checked out "$ man ld" to find out about this pesky - 
multi_module option and also poked around and found some references  
to MH_DYLIB and some other interesting options like -undefined.

Particularly, under the heading TWO-LEVEL AND FLAT NAMESPACES, three  
paragraphs down we see the default for static link editor is - 
twolevel_namespace which requires that all undefined references be  
satisfied at static link time. Also, the ability to suppress these  
errors is disabled (-undefined suppress).

I assume that what's going on is some of the global variables in /usr/ 
local/lib/libg2c.a are defined but not instantiated. So they need to  
be explicitly set as externs or set to some default value. Since the  
ability to suppress errors isn't available when compiling the  
libRlapack.dylib, then it must be changed in libg2c.a....that entails  
recompiling gfortran.


I'm not clear on why the same code compiles on 10.4 unless gfortran  
4.x. doesn't do this. Anyway, I downloaded the 3.4.2 gcc source and  
looked for err.c with f__cblank var declared (the first error):

> /usr/local/lib/libg2c.a(err.o) definition of common _f__cblank  
> (size 4)

It seems there were some major changes in fortran between 3.x and 4.x  
as the above variables don't exist and even directory structures are  
different. For example, f__cblank and f__cnt don't exist in 4.x. Nor  
does the libf2c directory where libg2c.a is compiled in 3.x.

That's a wrap for  me today, but I'll try to compile a version of  
libg2c.a without the common symbol errors on Monday.

As always, if any developers or those more familiar with the code  
base would like to chime in and direct, correct, refute, or suggest.  
It'd be very appreciated.


-james kyle
On Aug 10, 2007, at 7:14 AM, Ulf Martin wrote:

> Hi
>
> James R. Milks schrieb:
>> You can find the compiled version of R 2.5.1 for OS 10.4.4 or higher
>> at http://cran.r-project.org/bin/macosx/.  I try not to get into
>> compiling myself as I've had pretty bad luck with doing compilations.
>
> I think the problem is, that the binaries are for OS 10.4.x = "Tiger",
> they don't work on 10.3.y = "Panther". So this tip won't help. Two  
> month
> ago I also tried to compile the new R version (2.5.0 then) on Panther
> without success. So I am still hanging around with R 2.4.1. :-(
>
> Just a guess, as I have no idea what's really going on: The  
> compilation
> fails making lapack stuff. Now, since lapack is a Fortran 77  
> package the
> problem might have something to do with this?! (My compilation also
> failed at this point.)
>
>> On Aug 9, 2007, at 3:04 PM, krunk7 at gmail.com wrote:
>>>
>>> I'm attempting to compile R 2.5.1 on OSX Panther and have run into
>>> some issues. First off, if anyone has a link to a binary build of
>>> 2.5.1 for Panther I have no issue going that route.
>>>
>>> -) gcc version 3.3 20030304 (Apple Computer, Inc. build 1666)
>>> -) g77 version 3.4.2
>>> -) ./configure --with-blas='-framework vecLib' --with-lapack
>>> R_PAPERSIZE=letter F77=g77
>>>
>>> When first seeing the build issues, I wanted to verify that I have
>>> the necessary basic environment. I grabbed the 2.2.1 sources, which
>>> are the latest version available with a binary for Panther, and they
>>> compiled without a hitch.
>>>
>>> The error appears in the lapack module when building
>>> libRlapack.dylib. Error output is:
>>>
>>>> make[4]: Entering directory `/opt/sandbox/R-2.5.1/src/modules/ 
>>>> lapack'
>>>> gcc -std=gnu99 -dynamiclib -L/sw/lib -L/usr/local/lib -o
>>>> libRlapack.dylib dlamch.o dlapack0.o dlapack1.o dlapack2.o
>>>> dlapack3.o dlapack4.o cmplx.o -install_name libRlapack.dylib -
>>>> compatibility_version 2.5.0 -current_version 2.5.1  -
>>>> headerpad_max_install_names  -L/usr/local/lib/gcc/powerpc-apple-
>>>> darwin6.8/3.4.2 -lg2c -L../../../lib -lR
>>>> /usr/bin/libtool: internal link edit command failedld: warning
>>>> multiple definitions of symbol _z_abs/usr/local/lib/libg2c.a
>>>> (z_abs.o) definition of _z_abs in section (__TEXT,__text)../../../
>>>> lib/libR.dylib(z_abs.o) definition of _z_absld: warning multiple
>>>> definitions of symbol _f__cabs/usr/local/lib/libg2c.a(cabs.o)
>>>> definition of _f__cabs in section (__TEXT,__text)../../../lib/
>>>> libR.dylib(cabs.o) definition of _f__cabsld: common symbols not
>>>> allowed with MH_DYLIB output format with the -multi_module option/
>>>> usr/local/lib/libg2c.a(err.o) definition of common _f__cblank (size
>>>> 4)/usr/local/lib/libg2c.a(fmt.o) definition of common _f__cnt (size
>>>> 40)/usr/local/lib/libg2c.a(fmt.o) definition of common f(char,  *)
>>>> (size 4)/usr/local/lib/libg2c.a(err.o) definition of common f(char,
>>>> long *, short __restrict) (size 4)/usr/local/lib/libg2c.a(err.o)
>>>> definition of common _f__cursor (size 4)/usr/local/lib/libg2c.a
>>>> (err.o) definition of common _f__doed (size 4)/usr/local/lib/
>>>> libg2c.a(err.o) definition of common _f__doend (size 4)/usr/local/
>>>> lib/libg2c.a(err.o) definition of common _f__doned (size 4)/usr/
>>>> local/lib/libg2c.a(err.o) definition of common _f__dorevert (size
>>>> 4)/usr/local/lib/libg2c.a(err.o) definition of common _f__elist
>>>> (size 4)/usr/local/lib/libg2c.a(err.o) definition of common
>>>> _f__fmtbuf (size 4)/usr/local/lib/libg2c.a(err.o) definition of
>>>> common _f__fmtlen (size 4)/usr/local/lib/libg2c.a(err.o) definition
>>>> of common _f__init (size 4)/usr/local/lib/libg2c.a(fmt.o)
>>>> definition of common _f__nonl (size 4)/usr/local/lib/libg2c.a
>>>> (fmt.o) definition of common _f__parenlvl (size 4)/usr/local/lib/
>>>> libg2c.a(fmt.o) definition of common f(char *) (size 4)/usr/local/
>>>> lib/libg2c.a(fmt.o) definition of common _f__ret (size 40)/usr/
>>>> local/lib/libg2c.a(fmt.o) definition of common _f__revloc (size 4)/
>>>> usr/local/lib/libg2c.a(fmt.o) definition of common f(long double,
>>>> *) (size 4)/usr/local/lib/libg2c.a(err.o) definition of common
>>>> _f__scale (size 4)/usr/local/lib/libg2c.a(fmt.o) definition of
>>>> common _f__workdone (size 4)/usr/local/lib/libg2c.a(err.o)
>>>> definition of common _f__units (size 4800)/usr/local/lib/libg2c.a
>>>> (err.o) definition of common f(char, float) (size 4)/usr/local/lib/
>>>> libg2c.a(err.o) definition of common _f__curunit (size 4)/usr/ 
>>>> local/
>>>> lib/libg2c.a(err.o) definition of common _f__donewrec (size 4)/usr/
>>>> local/lib/libg2c.a(err.o) definition of common _f__external (size
>>>> 4)/usr/local/lib/libg2c.a(err.o) definition of common _f__formatted
>>>> (size 4)/usr/local/lib/libg2c.a(err.o) definition of common
>>>> _f__hiwater (size 4)/usr/local/lib/libg2c.a(err.o) definition of
>>>> common _f__putn (size 4)/usr/local/lib/libg2c.a(err.o) definition
>>>> of common _f__reading (size 4)/usr/local/lib/libg2c.a(err.o)
>>>> definition of common _f__recpos (size 4)/usr/local/lib/libg2c.a
>>>> (err.o) definition of common _f__sequential (size 4)/usr/local/lib/
>>>> libg2c.a(err.o) definition of common _f__getn (size 4)/usr/local/
>>>> lib/libg2c.a(err.o) definition of common _f__icptr (size 4)/usr/
>>>> local/lib/libg2c.a(err.o) definition of common f(short, void, int,
>>>> char) (size 4)
>>>> make[4]: *** [libRlapack.dylib] Error 1  make[4]: Leaving directory
>>>> `/opt/sandbox/R-2.5.1/src/modules/lapack'make[3]: *** [R] Error
>>>> 2make[3]: Leaving directory `/opt/sandbox/R-2.5.1/src/modules/
>>>> lapack'make[2]: *** [R] Error 1make[2]: Leaving directory `/opt/
>>>> sandbox/R-2.5.1/src/modules'make[1]: *** [R] Error 1make[1]:
>>>> Leaving directory `/opt/sandbox/R-2.5.1/src'make: *** [R] Error 1
>
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