Date: Wed, 14 Jan 2009 21:28:46 +0100 From: Philipp Ost <pj@smo.de> To: bf2006a@yahoo.com Cc: ports@freebsd.org, Glen Barber <glen.j.barber@gmail.com> Subject: Re: math/R fails to build Message-ID: <496E4AFE.2060803@smo.de> In-Reply-To: <365052.26421.qm@web39107.mail.mud.yahoo.com> References: <365052.26421.qm@web39107.mail.mud.yahoo.com>
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bf wrote: > --- On Tue, 1/13/09, Glen Barber <glen.j.barber@gmail.com> wrote: > > >>From: Glen Barber <glen.j.barber@gmail.com> >>Subject: Re: math/R fails to build >>To: "Philipp Ost" <pj@smo.de> >>Cc: bf2006a@yahoo.com, ports@freebsd.org >>Date: Tuesday, January 13, 2009, 8:03 PM >>On Tue, Jan 13, 2009 at 5:10 PM, Philipp Ost >><pj@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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