rpms/rpy/F-8 rpy-1.0.3-turn-off-debug.patch, NONE, 1.1 rpy-1.0.3-use-lapack.patch, NONE, 1.1 .cvsignore, 1.5, 1.6 rpy-1.0.1-FHSinclude.patch, 1.1, 1.2 rpy.spec, 1.27, 1.28 sources, 1.5, 1.6
José Abílio Oliveira Matos (jamatos)
fedora-extras-commits at redhat.com
Wed May 21 16:29:50 UTC 2008
Author: jamatos
Update of /cvs/pkgs/rpms/rpy/F-8
In directory cvs-int.fedora.redhat.com:/tmp/cvs-serv8158
Modified Files:
.cvsignore rpy-1.0.1-FHSinclude.patch rpy.spec sources
Added Files:
rpy-1.0.3-turn-off-debug.patch rpy-1.0.3-use-lapack.patch
Log Message:
* Wed May 21 2008 José Matos <jamatos[AT]fc.up.pt> - 1.0.3-1
- Update to 1.0.3
- Backport two patches from upstream (turn off debug and use the lapack version that R was compiled with)
rpy-1.0.3-turn-off-debug.patch:
--- NEW FILE rpy-1.0.3-turn-off-debug.patch ---
Revision: 517
http://rpy.svn.sourceforge.net/rpy/?rev=517&view=rev
Author: warnes
Date: 2008-05-14 10:10:57 -0700 (Wed, 14 May 2008)
Log Message:
-----------
Turn off debug build flag for default installs, add todo about Rlapack/lapack
Modified Paths:
--------------
trunk/rpy/setup.py
Modified: trunk/rpy/setup.py
===================================================================
--- trunk/rpy/setup.py 2008-05-14 17:05:47 UTC (rev 516)
+++ trunk/rpy/setup.py 2008-05-14 17:10:57 UTC (rev 517)
@@ -30,13 +30,14 @@
See the files INSTALL.UNIX and INSTALL.WINDOWS for more details.
"""
-DEBUG=True
+DEBUG=False
import os, os.path, sys, shutil, re
from distutils.core import setup, Extension
from distutils.sysconfig import *
from distutils.errors import *
import rpy_tools
+
if sys.platform=="win32":
import rpy_wintools
@@ -85,7 +86,7 @@
get_config_vars()['OPT'] = '-g -Wall'
else:
# to avoid strict prototypes errors from R includes
- get_config_vars()['OPT'] = '-DNDEBUG -g -O3 -Wall'
+ get_config_vars()['OPT'] = '-DNDEBUG -O3 -Wall'
# get the Python version
if sys.version[:3] >= '2.2':
rpy-1.0.3-use-lapack.patch:
--- NEW FILE rpy-1.0.3-use-lapack.patch ---
Revision: 523
http://rpy.svn.sourceforge.net/rpy/?rev=523&view=rev
Author: warnes
Date: 2008-05-14 11:31:21 -0700 (Wed, 14 May 2008)
Log Message:
-----------
Use the 'R CMD config LAPACK_LIBS' command to determin the appropriate link flags for lapack, instead of blindly assuming that '-L<RHOME>/lib -lRlapack' is the correct magic incantation.
Modified Paths:
--------------
trunk/rpy/rpy_tools.py
trunk/rpy/setup.py
Modified: trunk/rpy/rpy_tools.py
===================================================================
--- trunk/rpy/rpy_tools.py 2008-05-14 17:51:40 UTC (rev 522)
+++ trunk/rpy/rpy_tools.py 2008-05-14 18:31:21 UTC (rev 523)
@@ -143,3 +143,20 @@
% PYTHON_DIR )
return PYTHON_DIR
+
+def get_R_LAPACK_LIB_FLAGS(RHOME=get_R_HOME()):
+ """
+ Determine the necessary link arguments for lapack
+ """
+ rexec = os.path.join(RHOME, 'bin', 'R')
+ stat, output = getstatusoutput('"%s" CMD config LAPACK_LIBS' % rexec )
+ if stat or len(output)<=0:
+ raise RuntimeError("Couldn't execute the R interpreter" +
+ " `%s'.\n" % rexec )
+
+ LAPACK_LIB_FLAGS = output.strip()
+ if not LAPACK_LIB_FLAGS:
+ raise RuntimeError("Couldn't obtain LAPACK_LIBS information from output\n"
+ "of `R CMD config LAPACK_LIBS'.\n")
+
+ return LAPACK_LIB_FLAGS
Modified: trunk/rpy/setup.py
===================================================================
--- trunk/rpy/setup.py 2008-05-14 17:51:40 UTC (rev 522)
+++ trunk/rpy/setup.py 2008-05-14 18:31:21 UTC (rev 523)
@@ -150,23 +150,20 @@
library_dirs= r_libs
runtime_libs = r_libs
extra_compile_args=[]
- elif sys.platform=='osf1V5':
- include_dirs = [ os.path.join(RHOME.strip(), 'include'),
- 'src' ]
- libraries=['R','Rlapack']
- library_dirs = r_libs
- runtime_libs = r_libs
- extra_compile_args=["-shared"]
- source_files = source_files + ["src/setenv.c"]
+
else: # unix-like systems, this is known to work for Linux and Solaris
include_dirs = [ os.path.join(RHOME.strip(), 'include'),
'src', '/usr/share/R/include', "/usr/include/R"]
- libraries=['R','Rlapack']
library_dirs = r_libs
runtime_libs = r_libs
extra_compile_args=["-shared"]
source_files = source_files + ["src/setenv.c"]
+ libraries=['R']
+
+ # Ask R to tell us how to properly link against lapack
+ extra_compile_args += [ rpy_tools.get_R_LAPACK_LIB_FLAGS( RHOME ) ]
+
# Discover which array packages are present
try:
import numpy
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/rpy/F-8/.cvsignore,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- .cvsignore 4 Feb 2008 15:41:57 -0000 1.5
+++ .cvsignore 21 May 2008 16:28:48 -0000 1.6
@@ -1 +1 @@
-rpy-1.0.1.tar.gz
+rpy-1.0.3.tar.gz
rpy-1.0.1-FHSinclude.patch:
Index: rpy-1.0.1-FHSinclude.patch
===================================================================
RCS file: /cvs/pkgs/rpms/rpy/F-8/rpy-1.0.1-FHSinclude.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- rpy-1.0.1-FHSinclude.patch 4 Feb 2008 15:41:57 -0000 1.1
+++ rpy-1.0.1-FHSinclude.patch 21 May 2008 16:28:48 -0000 1.2
@@ -7,7 +7,7 @@
- include_dirs = [ os.path.join(RHOME.strip(), 'include'),
- 'src', '/usr/share/R/include' ]
+ include_dirs = [ os.path.join(RHOME.strip(), 'include'),
-+ 'src', '/usr/share/R/include', "/usr/include/R/"]
++ 'src', '/usr/share/R/include', "/usr/include/R"]
libraries=['R','Rlapack']
library_dirs = r_libs
runtime_libs = r_libs
Index: rpy.spec
===================================================================
RCS file: /cvs/pkgs/rpms/rpy/F-8/rpy.spec,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -r1.27 -r1.28
--- rpy.spec 14 May 2008 20:52:07 -0000 1.27
+++ rpy.spec 21 May 2008 16:28:48 -0000 1.28
@@ -3,16 +3,21 @@
%define rver 2.7.0
Name: rpy
Summary: Python interface to the R language
-Version: 1.0.1
-Release: 4%{?dist}
+Version: 1.0.3
+Release: 1%{?dist}
Url: http://rpy.sourceforge.net
Source: http://downloads.sf.net/%{name}/%{name}-%{version}.tar.gz
License: GPLv2+
Group: Development/Libraries
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+# The R headers are now in /usr/include/R (for F9+)
Patch0: rpy-1.0.1-FHSinclude.patch
+# Backported patches from development
+Patch1: rpy-1.0.3-turn-off-debug.patch
+Patch2: rpy-1.0.3-use-lapack.patch
-BuildRequires: R-devel = %{rver}, numpy, python-devel, texinfo, tetex
+BuildRequires: R-devel = %{rver}, numpy, python-devel, texinfo-tex, tetex
Requires: numpy
Requires: R = %{rver}
@@ -28,8 +33,9 @@
%prep
%setup -q
-# The R headers are now in /usr/include/R (for F9+)
%patch0
+%patch1 -p2
+%patch2 -p2
%build
env CFLAGS="$RPM_OPT_FLAGS" python setup.py build
@@ -68,11 +74,21 @@
%changelog
-* Wed May 14 2008 Tom "spot" Callaway <tcallawa at redhat.com> - 1.0.1-4
-- rebuild for R-2.7.0
+* Wed May 21 2008 José Matos <jamatos[AT]fc.up.pt> - 1.0.3-1
+- Update to 1.0.3
+- Backport two patches from upstream (turn off debug and use the lapack version that R was compiled with)
+
+* Wed May 14 2008 Tom "spot" Callaway <tcallawa at redhat.com> - 1.0.1-6
+- rebuild against R-2.7.0
+
+* Wed Feb 13 2008 José Matos <jamatos[AT]fc.up.pt> - 1.0.1-5
+- BR texinfo -> texinfo-tex
+
+* Wed Feb 13 2008 José Matos <jamatos[AT]fc.up.pt> - 1.0.1-4
+- Rebuild for gcc 4.3
-* Wed Mar 10 2008 Tom "spot" Callaway <tcallawa at redhat.com> - 1.0.1-3
-- rebuild for R-2.6.2
+* Fri Feb 8 2008 Tom "spot" Callaway <tcallawa at redhat.com> - 1.0.1-3
+- rebuild for R 2.6.2
* Mon Feb 4 2008 José Matos <jamatos[AT]fc.up.pt> - 1.0.1-2
- Sometimes _patch_'s guesses are not good enough. Redo patch to setup.py.
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/rpy/F-8/sources,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- sources 4 Feb 2008 15:41:57 -0000 1.5
+++ sources 21 May 2008 16:28:48 -0000 1.6
@@ -1 +1 @@
-3897e05e67230717396859bcc00a8768 rpy-1.0.1.tar.gz
+10fd4904f622e5647638817279933900 rpy-1.0.3.tar.gz
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