math/R fails to build

[Rainer Hurling]

I have to set the following link, because R's configure is looking for 
pure name 'gfortran'

# ln -s /usr/local/bin/gfortran43 /usr/local/bin/gfortran

Hope this helps,
Rainer


On 14.01.2009 21:28 (UTC+1), Philipp Ost wrote:
> bf wrote:
>> --- On Tue, 1/13/09, Glen Barber <glen.j.barber at gmail.com> wrote:
>>
>>
>>> From: Glen Barber <glen.j.barber at gmail.com>
>>> Subject: Re: math/R fails to build
>>> To: "Philipp Ost" <pj at smo.de>
>>> Cc: bf2006a at yahoo.com, ports at freebsd.org
>>> Date: Tuesday, January 13, 2009, 8:03 PM
>>> On Tue, Jan 13, 2009 at 5:10 PM, Philipp Ost
>>> <pj at smo.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> math/R fails to build:
>>>> # make
>>>> [...]
>>>> cc -std=gnu99      -I. -I../../src/include
>>>
>>> -I../../src/include
>>>
>>>> -I/usr/local/include -DHAVE_CONFIG_H  -fpic  -O2
>>>
>>> -fno-strict-aliasing -pipe
>>>
>>>> -march=athlon-xp -c Rmain.c -o Rmain.o
>>>> cc -std=gnu99 -export-dynamic -L/usr/local/lib -o
>>>
>>> R.bin Rmain.o -L../../lib
>>>
>>>> -lR
>>>> /usr/local/lib/libblas.so.2: undefined reference to
>>>> `_gfortran_runtime_error_at'
>>>> *** Error code 1
>>>>
>>>> Stop in /usr/ports/math/R/work/R-2.8.1/src/main.
>>>> *** Error code 1
>>>>
>>>> Stop in /usr/ports/math/R/work/R-2.8.1/src/main.
>>>> *** Error code 1
>>>>
>>>> Stop in /usr/ports/math/R/work/R-2.8.1/src.
>>>> *** Error code 1
>>>>
>>>> Stop in /usr/ports/math/R/work/R-2.8.1.
>>>> *** Error code 1
>>>>
>>>> Stop in /usr/ports/math/R.
>>>> *** Error code 1
>>>>
>>>> Stop in /usr/ports/math/R.
>>>> #
>>>>
>>>> I run RELENG_7 as of 23 Dec. 2008 (on i386).
>>>>
>>>> Any hints? (Apart from rebuilding blas, which I did.
>>>
>>> It didn't solve the
>>>
>>>> problem)
>>>>
>>>
>>> Is it a safe assumption that you have recently updated your
>>> ports tree?
> 
> Yes
> 
> [...]
> 
>> There were recently some changes to
>> the organization of the Fortran-related
>> ports on FreeBSD.  The Fortran compiler
>> was added to the list of runtime
>> dependencies, as it should have been,
>> and the default Fortran compiler was
>> changed from gcc 4.2.x to 4.3.x.  As
>> Glen suggested, your problem may be
>> related.  Try updating your ports tree,
>> and then rebuilding blas, lapack,
>> and R, and see if it works.
> [...]
> 
> gcc43 is installed, ports tree is updated (as of ~20:00 MET today). I 
> did rebuild lapack and blas, then tried R again:
> # make
> [...]
> cc -std=gnu99      -I. -I../../src/include -I../../src/include 
> -I/usr/local/include -DHAVE_CONFIG_H  -fpic  -O2 -fno-strict-aliasing 
> -pipe -march=athlon-xp -c Rmain.c -o Rmain.o
> cc -std=gnu99 -export-dynamic -L/usr/local/lib -o R.bin Rmain.o 
> -L../../lib -lR
> /usr/bin/ld: warning: libgfortran.so.2, needed by 
> /usr/local/lib/libR.so, not found (try using -rpath or -rpath-link)
> /usr/local/lib/libblas.so.2: undefined reference to `_gfortran_st_write'
> /usr/local/lib/libblas.so.2: undefined reference to 
> `_gfortran_transfer_character'
> /usr/local/lib/libblas.so.2: undefined reference to 
> `_gfortran_st_write_done'
> /usr/local/lib/libblas.so.2: undefined reference to 
> `_gfortran_runtime_error_at'
> /usr/local/lib/libblas.so.2: undefined reference to 
> `_gfortran_transfer_integer'
> /usr/local/lib/libblas.so.2: undefined reference to 
> `_gfortran_stop_numeric'
> *** Error code 1
> 
> Stop in /usr/ports/math/R/work/R-2.8.1/src/main.
> *** Error code 1
> 
> Stop in /usr/ports/math/R/work/R-2.8.1/src/main.
> *** Error code 1
> 
> Stop in /usr/ports/math/R/work/R-2.8.1/src.
> *** Error code 1
> 
> Stop in /usr/ports/math/R/work/R-2.8.1.
> *** Error code 1
> 
> Stop in /usr/ports/math/R.
> *** Error code 1
> 
> Stop in /usr/ports/math/R.
> #
> 
> Seems like blas is to blame...
> 
> Here are some software version numbers:
> blas-1.0_3
> lapack-3.1.1_2
> gcc-4.3.3_20090108
> R-2.8.0
> 
> I haven't done any other other updates in the meantime (perl et. al.).
> If I have the time I will check and see if my 8.0-testbox has the same 
> problem (apart from being slow...).
> 
> Thanks for your time and help,
> Philipp
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