problems building rpy in linking, appreciate advice?
John Owens
john_owens at yahoo.com
Sat Apr 28 08:08:37 PDT 2007
Greetings, I'm trying to write a port for rpy, a python
set of bindings for R. I'm attaching the build log below.
Basically the problem is that it's trying to link to a
dynamic library "libRblas.dylib" that is clearly in the
right place (/opt/local/lib/R/lib/libRblas.dylib) and whose
directory is explicitly specified with -L. (LD_LIBRARY_PATH
didn't help either.)
Suggestions?
This is my first port of this type - it seemed to figure out
all sorts of stuff automatically (like to run setup.py). I
didn't really have much in the portfile (I'll attach it
at the bottom).
JDO
movenpick 539$ file /opt/local/lib/R/lib/libRblas.dylib
/opt/local/lib/R/lib/libRblas.dylib: Mach-O dynamically linked shared library ppc
movenpick 540$ sudo port -d install rpy
DEBUG: Found port in file:///Users/jowens/Documents/src/dports/python/rpy
DEBUG: Changing to port directory: /Users/jowens/Documents/src/dports/
python/rpy
DEBUG: Requested variant powerpc is not provided by port rpy.
DEBUG: Requested variant darwin is not provided by port rpy.
DEBUG: Requested variant macosx is not provided by port rpy.
DEBUG: Found port in
file:///opt/local/var/db/dports/sources/rsync.rsync.darwinports.org_dpupdate
_dports/lang/python24
DEBUG: Changing to port directory:
/opt/local/var/db/dports/sources/rsync.rsync.darwinports.org_dpupdate_dports
/lang/python24
DEBUG: Searching for dependency: python24
DEBUG: Found Dependency: receipt exists for python24
DEBUG: Found port in
file:///opt/local/var/db/dports/sources/rsync.rsync.darwinports.org_dpupdate
_dports/math/R
DEBUG: Changing to port directory:
/opt/local/var/db/dports/sources/rsync.rsync.darwinports.org_dpupdate_
dports/math/R
DEBUG: Searching for dependency: R
DEBUG: Found Dependency: receipt exists for R
DEBUG: Found port in
file:///opt/local/var/db/dports/sources/rsync.rsync.darwinports.org_
dpupdate_dports/lang/python24
DEBUG: Searching for dependency: python24
DEBUG: Found Dependency: receipt exists for python24
DEBUG: Skipping completed com.apple.main (rpy)
DEBUG: Skipping completed com.apple.fetch (rpy)
DEBUG: Skipping completed com.apple.checksum (rpy)
DEBUG: Skipping completed com.apple.extract (rpy)
DEBUG: Skipping completed com.apple.patch (rpy)
DEBUG: Skipping completed com.apple.configure (rpy)
---> Building rpy with target build
DEBUG: Executing com.apple.build (rpy)
DEBUG: Environment:
DEBUG: Assembled command: 'cd
"/opt/local/var/db/dports/build/_Users_jowens_Documents_src_dports_python
_rpy/work/rpy-1.0-RC2"
&& /opt/local/bin/python2.4 setup.py build'
RHOMES= []
Setting RHOMES to ['/opt/local/lib/R']
### Using R verion 2.5.0 installed at /opt/local/lib/R ###
RHOME= /opt/local/lib/R
copying src/rpymodule.c -> src/rpymodule2050.c
copying src/R_eval.c -> src/R_eval2050.c
copying src/io.c -> src/io2050.c
running build
running build_py
running build_ext
building '_rpy2050' extension
/usr/bin/gcc-4.0 -bundle -undefined dynamic_lookup
build/temp.darwin-8.9.0-Power_Macintosh-2.4/src/rpymodule2050.o
build/temp.darwin-8.9.0-Power_Macintosh-2.4/src/R_eval2050.o
build/temp.darwin-8.9.0-Power_Macintosh-2.4/src/io2050.o
-L/opt/local/lib/R/bin
-L/opt/local/lib/R/lib -L/opt/local/lib/R/bin
-L/opt/local/lib/R/lib -lR -o
build/lib.darwin-8.9.0-Power_Macintosh-2.4/_rpy2050.so
/usr/bin/ld: warning can't open dynamic library: libRblas.dylib
referenced from:
/opt/local/lib/R/lib/libR.dylib (checking for undefined symbols may
be affected)
(No such file or directory, errno = 2)
/usr/bin/ld: Undefined symbols:
_dgemm_ referenced from libR expected to be defined in libRblas.dylib
_dsyrk_ referenced from libR expected to be defined in libRblas.dylib
_zgemm_ referenced from libR expected to be defined in libRblas.dylib
_dcopy_ referenced from libR expected to be defined in libRblas.dylib
_dtrsm_ referenced from libR expected to be defined in libRblas.dylib
_daxpy_ referenced from libR expected to be defined in libRblas.dylib
_dswap_ referenced from libR expected to be defined in libRblas.dylib
_ddot_ referenced from libR expected to be defined in libRblas.dylib
_dasum_ referenced from libR expected to be defined in libRblas.dylib
_dscal_ referenced from libR expected to be defined in libRblas.dylib
_dnrm2_ referenced from libR expected to be defined in libRblas.dylib
_drot_ referenced from libR expected to be defined in libRblas.dylib
_drotg_ referenced from libR expected to be defined in libRblas.dylib
collect2: ld returned 1 exit status
error: command '/usr/bin/gcc-4.0' failed with exit status 1
Error: Target com.apple.build returned: shell command " cd
"/opt/local/var/db/dports/build/_Users_jowens_Documents_src_dports_
python_rpy/work/rpy-1.0-RC2"
&& /opt/local/bin/python2.4 setup.py build " returned error 1
Command output: RHOMES= []
Setting RHOMES to ['/opt/local/lib/R']
### Using R verion 2.5.0 installed at /opt/local/lib/R ###
RHOME= /opt/local/lib/R
copying src/rpymodule.c -> src/rpymodule2050.c
copying src/R_eval.c -> src/R_eval2050.c
copying src/io.c -> src/io2050.c
running build
running build_py
running build_ext
building '_rpy2050' extension
/usr/bin/gcc-4.0 -bundle -undefined dynamic_lookup
build/temp.darwin-8.9.0-Power_Macintosh-2.4/src/rpymodule2050.o
build/temp.darwin-8.9.0-Power_Macintosh-2.4/src/R_eval2050.o
build/temp.darwin-8.9.0-Power_Macintosh-2.4/src/io2050.o
-L/opt/local/lib/R/bin
-L/opt/local/lib/R/lib -L/opt/local/lib/R/bin -L/opt/local/lib/R/lib -lR -o
build/lib.darwin-8.9.0-Power_Macintosh-2.4/_rpy2050.so
/usr/bin/ld: warning can't open dynamic library: libRblas.dylib
referenced from:
/opt/local/lib/R/lib/libR.dylib (checking for undefined symbols
may be affected)
(No such file or directory, errno = 2)
/usr/bin/ld: Undefined symbols:
_dgemm_ referenced from libR expected to be defined in libRblas.dylib
_dsyrk_ referenced from libR expected to be defined in libRblas.dylib
_zgemm_ referenced from libR expected to be defined in libRblas.dylib
_dcopy_ referenced from libR expected to be defined in libRblas.dylib
_dtrsm_ referenced from libR expected to be defined in libRblas.dylib
_daxpy_ referenced from libR expected to be defined in libRblas.dylib
_dswap_ referenced from libR expected to be defined in libRblas.dylib
_ddot_ referenced from libR expected to be defined in libRblas.dylib
_dasum_ referenced from libR expected to be defined in libRblas.dylib
_dscal_ referenced from libR expected to be defined in libRblas.dylib
_dnrm2_ referenced from libR expected to be defined in libRblas.dylib
_drot_ referenced from libR expected to be defined in libRblas.dylib
_drotg_ referenced from libR expected to be defined in libRblas.dylib
collect2: ld returned 1 exit status
error: command '/usr/bin/gcc-4.0' failed with exit status 1
Warning: the following items did not execute (for rpy): com.apple.activate
com.apple.build com.apple.destroot com.apple.install
Error: Status 1 encountered during processing.
# $Id: Portfile $
PortSystem 1.0
PortGroup python24 1.0
name rpy
version 1.0-RC2
revision 1
categories python
platforms darwin
maintainers nomaintainer at macports.org
description Python interface to the R Programming Language
long_description RPy is a very simple, yet robust, Python interface to the R
Programming Language. It can manage all kinds of R objects and can execute
arbitrary R functions (including the graphic functions).
homepage http://rpy.sourceforge.net
master_sites sourceforge:rpy
distname rpy-${version}
checksums sha1 f3d19253f4f6bd903794b2f9d66ce55a7aa510d1
depends_lib-append port:R port:python24
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