Re: [Fink-users] Fwd: Re: problem installing scipy-py27
On 12/20/10 8:22 PM, Shaun Cutts wrote: Alexander, Removing that was all I needed -- thanks! Much less pain that I had feared. After simply removing, I couldn't use numpy, but remove/install of numpy fixed that, and then (after a self-update which I was due for) I was able to install scipy without moving anything in /usr/bin. Thanks again! -- Shaun I'm glad it was relatively simple. -- Alexander Hansen, Ph.D. Fink User Liaison -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] Fwd: Re: problem installing scipy-py27
Alexander, David, Thanks for the advice. I must have installed packages in the default locations ... which is often /usr/local/lib, but in some cases is /usr/lib. Rather than renaming /usr/lib, would renaming the individual libraries I have installed work? Is there a way to turn on diagnostics sufficient to see which dependencies might be causing scipy problems? (which ones it is finding somewhere besides /sw/lib?) Here are two candidates: $ ls /usr/lib/libatl* /usr/lib/libatlas.dylib $ ls /usr/lib/libbla* /usr/lib/libblas.dylib I do also have the fink version of altas installed: i atlas 3.9.11-1 Portably optimal linear algebra software From Alexander's advice: $ dpkg -p numpy-py27 | grep Version Version: 1.5.0-1 Also I do have /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg as well as /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info but when I link site-packages/numpy to the version in /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg, I get the same error. Again -- I'm grateful for any help. Thanks, -- Shaun On Dec 12, 2010, at 8:10 AM, David R. Morrison wrote: - Original Message Subject: Re: [Fink-users] problem installing scipy-py27 Date: Sun, 12 Dec 2010 02:06:28 -0500 From: Shaun Cutts sh...@cuttshome.net I do have some mathematical routines installed in /usr/lib ... I have used a convex optimization package, for instance, which required installing some other math libraries... but ... hopefully this isn't a mortal sin :) Is there a way to better diagnose what is going on and/or to tell fink to use only its versions of math libraries? It's not exactly a mortal sin, but it can cause problems. The way the linker in OS X is designed, it is extremely difficult if not impossible to hide things in /usr/lib or /usr/local/lib from the search paths used to locate libraries and headers (and presumably python-ish stuff as well). This is why fink chose to do its own installs in a separate location, and its also why we recommend against installing non-fink software in those locations. You say you have things in /usr/lib rather than /usr/local/lib? That makes this very difficult... If your only non-fink third party software was in /usr/local/lib, we could simply tell you to try mv /usr/local/lib /usr/local/lib.bak; fink install foo; mv /usr/local/lib.bak /usr/local/lib. However, you can't move /usr/lib out of the way like that, without breaking lots of stuff :( -- Dave -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] Fwd: Re: problem installing scipy-py27
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 12/20/10 11:15 AM, Shaun Cutts wrote: Alexander, David, Thanks for the advice. I must have installed packages in the default locations ... which is often /usr/local/lib, but in some cases is /usr/lib. Rather than renaming /usr/lib, would renaming the individual libraries I have installed work? Is there a way to turn on diagnostics sufficient to see which dependencies might be causing scipy problems? (which ones it is finding somewhere besides /sw/lib?) Here are two candidates: $ ls /usr/lib/libatl* /usr/lib/libatlas.dylib $ ls /usr/lib/libbla* /usr/lib/libblas.dylib I do also have the fink version of altas installed: i atlas 3.9.11-1 Portably optimal linear algebra software From Alexander's advice: $ dpkg -p numpy-py27 | grep Version Version: 1.5.0-1 Also I do have /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg as well as /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info but when I link site-packages/numpy to the version in /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg, I get the same error. Again -- I'm grateful for any help. Thanks, -- Shaun Let's make sure your Fink tree is clean, first. See what you get from dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info - -- Alexander Hansen, Ph.D. Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEUEARECAAYFAk0PgkIACgkQB8UpO3rKjQ/luQCY+lyLvKrMUjYPvbM4XDSPaoBm LQCgnavUdRYH8lYVhDoMjq8MqTOrU78= =pz5R -END PGP SIGNATURE- -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] Fwd: Re: problem installing scipy-py27
On 20/12/10 17:15 , Shaun Cutts wrote:
Alexander, David,
Thanks for the advice.
I must have installed packages in the default locations ... which is often
/usr/local/lib, but in some cases is /usr/lib.
If you really have 3rd party packages that install things into /usr/lib,
you should complain to the distributors. This is *very* bad style and
causes all sorts of problems. /usr/lib/ is reserved for Apple.
Rather than renaming /usr/lib, would renaming the individual libraries I have
installed work? Is there a way to turn on diagnostics sufficient to see which
dependencies might be causing scipy problems? (which ones it is finding
somewhere besides /sw/lib?)
Here are two candidates:
$ ls /usr/lib/libatl*
/usr/lib/libatlas.dylib
$ ls /usr/lib/libbla*
/usr/lib/libblas.dylib
These, however, are probably installed by the system. I see there
costabel% ls -l /usr/lib/lib{atlas,blas}*
lrwxr-xr-x 1 root wheel 112 Aug 15 2009 /usr/lib/libatlas.dylib -
../..//System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/libBLAS.dylib
lrwxr-xr-x 1 root wheel 112 Aug 15 2009 /usr/lib/libblas.dylib -
../..//System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/libBLAS.dylib
If something really tries to overwrite /usr/lib/libatlas.dylib, it risks
destroying the Accelerate framework, which can make your system unusable.
--
Martin
I do also have the fink version of altas installed:
i atlas 3.9.11-1 Portably optimal linear algebra
software
From Alexander's advice:
$ dpkg -p numpy-py27 | grep Version
Version: 1.5.0-1
Also I do have
/sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg as
well as /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info
but when I link site-packages/numpy to the version in
/sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg, I
get the same error.
Again -- I'm grateful for any help.
Thanks,
-- Shaun
On Dec 12, 2010, at 8:10 AM, David R. Morrison wrote:
- Original Message
Subject: Re: [Fink-users] problem installing scipy-py27
Date: Sun, 12 Dec 2010 02:06:28 -0500
From: Shaun Cuttssh...@cuttshome.net
I do have some mathematical routines installed in /usr/lib ... I have
used a convex optimization package, for instance, which required
installing some other math libraries... but ... hopefully this isn't a
mortal sin :) Is there a way to better diagnose what is going on and/or
to tell fink to use only its versions of math libraries?
It's not exactly a mortal sin, but it can cause problems.
The way the linker in OS X is designed, it is extremely difficult if not
impossible to hide things in /usr/lib or /usr/local/lib from the search
paths used to locate libraries and headers (and presumably python-ish stuff
as well). This is why fink chose to do its own installs in a separate
location, and its also why we recommend against installing non-fink software
in those locations.
You say you have things in /usr/lib rather than /usr/local/lib? That makes
this very difficult... If your only non-fink third party software was in
/usr/local/lib, we could simply tell you to try mv /usr/local/lib
/usr/local/lib.bak; fink install foo; mv /usr/local/lib.bak /usr/local/lib.
However, you can't move /usr/lib out of the way like that, without breaking
lots of stuff :(
-- Dave
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Re: [Fink-users] Fwd: Re: problem installing scipy-py27
Alexander, Let's make sure your Fink tree is clean, first. See what you get from dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info $$$ dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg dpkg: /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg not found. (despite the fact that this exists:) $$$ ll /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg total 0 drwxr-xr-x 9 root admin 306 Aug 13 18:09 EGG-INFO/ drwxr-xr-x 45 root admin 1530 Aug 13 18:09 numpy/ $$$ dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info numpy-py27: /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info Is this a problem for numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg? Should I purge and reinstall numpy? Gratefully, -- Shaun -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] Fwd: Re: problem installing scipy-py27
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 12/20/10 5:46 PM, Shaun Cutts wrote: Alexander, Let's make sure your Fink tree is clean, first. See what you get from dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info $$$ dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg dpkg: /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg not found. (despite the fact that this exists:) $$$ ll /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg total 0 drwxr-xr-x 9 root admin 306 Aug 13 18:09 EGG-INFO/ drwxr-xr-x 45 root admin 1530 Aug 13 18:09 numpy/ $$$ dpkg -S /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info numpy-py27: /sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info Is this a problem for numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg? Should I purge and reinstall numpy? Gratefully, -- Shaun You probably need to remove /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg . From your original posting, it looked like that is causing problems, and it's no longer in the database of files known in the Fink tree. - -- Alexander Hansen, Ph.D. Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk0P7WMACgkQB8UpO3rKjQ/WBACgoBsN9G+LEki/bEwKqgezvSuP mnIAnRmeMXl5dx9a2SQ31dHSLsJ2JiL2 =FZqY -END PGP SIGNATURE- -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] Fwd: Re: problem installing scipy-py27
Alexander, Removing that was all I needed -- thanks! Much less pain that I had feared. After simply removing, I couldn't use numpy, but remove/install of numpy fixed that, and then (after a self-update which I was due for) I was able to install scipy without moving anything in /usr/bin. Thanks again! -- Shaun You probably need to remove /sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg . From your original posting, it looked like that is causing problems, and it's no longer in the database of files known in the Fink tree. - -- Alexander Hansen, Ph.D. Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk0P7WMACgkQB8UpO3rKjQ/WBACgoBsN9G+LEki/bEwKqgezvSuP mnIAnRmeMXl5dx9a2SQ31dHSLsJ2JiL2 =FZqY -END PGP SIGNATURE- -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Fwd: Re: problem installing scipy-py27
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Not my package, and I don't do python, so back to the list and maintainer.
A couple of questions may help illuminate things a bit better.
What version of numpy-py27 is listed as currently installed on your
machine? You can get this from dpkg -p numpy-py27 | grep Version
And do you have
/sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg
on your system as well as
/sw/lib/python2.7/site-packages/numpy-1.5.0-py2.7.egg-info
- Original Message
Subject: Re: [Fink-users] problem installing scipy-py27
Date: Sun, 12 Dec 2010 02:06:28 -0500
From: Shaun Cutts sh...@cuttshome.net
To: Alexander Hansen alexanderk.han...@gmail.com
Alexander,
Thanks for the reply,
I temporarily moved /opt to /opt-x, which eliminated the reference to
it, but it still fails in the same way...
- --
...
/sw/bin/python2.7 setup.py build --fcompiler=gnu95
Warning: No configuration returned, assuming unavailable.blas_opt_info:
FOUND:
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
extra_compile_args = ['-msse3',
'-I/System/Library/Frameworks/vecLib.framework/Headers']
lapack_opt_info:
FOUND:
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
extra_compile_args = ['-msse3']
umfpack_info:
libraries umfpack not found in /usr/local/lib
libraries umfpack not found in /usr/lib
amd_info:
libraries amd not found in /usr/local/lib
libraries amd not found in /usr/lib
FOUND:
libraries = ['amd']
library_dirs = ['/sw/lib']
FOUND:
libraries = ['umfpack', 'amd']
library_dirs = ['/sw/lib']
...
[then still at bottom:]
numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s)
['/sw/lib/python2.7/site-packages/numpy-1.5.0b1-py2.7-macosx-10.6-i386.egg/numpy/core/lib/npy-pkg-config/npymath.ini']
-
I do have some mathematical routines installed in /usr/lib ... I have
used a convex optimization package, for instance, which required
installing some other math libraries... but ... hopefully this isn't a
mortal sin :) Is there a way to better diagnose what is going on and/or
to tell fink to use only its versions of math libraries?
I'll be grateful for any advice.
- -- Shaun
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.11 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAk0ExvsACgkQB8UpO3rKjQ++2ACglBQx8OETL4J+Yx/ZOZUQoJv/
pscAnj9f++RzlpQdHWgXYe7IrY8eQg51
=HrKL
-END PGP SIGNATURE-
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Re: [Fink-users] Fwd: Re: problem installing scipy-py27
- Original Message Subject: Re: [Fink-users] problem installing scipy-py27 Date: Sun, 12 Dec 2010 02:06:28 -0500 From: Shaun Cutts sh...@cuttshome.net I do have some mathematical routines installed in /usr/lib ... I have used a convex optimization package, for instance, which required installing some other math libraries... but ... hopefully this isn't a mortal sin :) Is there a way to better diagnose what is going on and/or to tell fink to use only its versions of math libraries? It's not exactly a mortal sin, but it can cause problems. The way the linker in OS X is designed, it is extremely difficult if not impossible to hide things in /usr/lib or /usr/local/lib from the search paths used to locate libraries and headers (and presumably python-ish stuff as well). This is why fink chose to do its own installs in a separate location, and its also why we recommend against installing non-fink software in those locations. You say you have things in /usr/lib rather than /usr/local/lib? That makes this very difficult... If your only non-fink third party software was in /usr/local/lib, we could simply tell you to try mv /usr/local/lib /usr/local/lib.bak; fink install foo; mv /usr/local/lib.bak /usr/local/lib. However, you can't move /usr/lib out of the way like that, without breaking lots of stuff :( -- Dave -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar functions, improved concurrency, built-in packages, OCI, SQL*Plus, data movement tools, best practices and more. http://p.sf.net/sfu/oracle-sfdev2dev ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
