bf wrote:
--- On Tue, 1/13/09, Glen Barber <[email protected]> wrote:
From: Glen Barber <[email protected]>
Subject: Re: math/R fails to build
To: "Philipp Ost" <[email protected]>
Cc: [email protected], [email protected]
Date: Tuesday, January 13, 2009, 8:03 PM
On Tue, Jan 13, 2009 at 5:10 PM, Philipp Ost
<[email protected]> 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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