Re: eigen
On Mar 21, 2014, at 19:38, René J.V. Bertin wrote: >> Have you contacted the developers of eigen about whether this change is >> correct? > > No. But I'm planning to have a deeper look into this. Took me a while but today I ran `make test` on the modified code, and that completed just fine. R. ___ macports-users mailing list macports-users@lists.macosforge.org https://lists.macosforge.org/mailman/listinfo/macports-users
Re: eigen
Hello Ryan, On Mar 21, 2014, at 18:45, Ryan Schmidt wrote: > I can confirm that this now builds on Mavericks. However, I am not a C++ > developer so I cannot say whether the change you have made is correct. How > did you come to this solution? Here: http://stackoverflow.com/questions/767477/template-specialization-for-static-member-functions-howto > Have you contacted the developers of eigen about whether this change is > correct? No. But I'm planning to have a deeper look into this. R. ___ macports-users mailing list macports-users@lists.macosforge.org https://lists.macosforge.org/mailman/listinfo/macports-users
Re: eigen
On Mar 21, 2014, at 08:05, René J.V. Bertin wrote: > On Mar 20, 2014, at 17:41, Nicolas Pavillon wrote: > >> I may have expressed myself incorrectly, but the compatibility mode of >> eigen3 does not reduce the amount of options of calligra. provides full >> support, apart from some modules which are not supported. It is thus a >> yes/no case, where either you can use the compatibility mode if you are not >> using the unsupported modules, or you have to adjust your code. > > Exactly, and that's not something I'm very much interested in testing in > something that's not a stable release :) > > Anyway, I figured out why eigen 2 doesn't build with clang. Apparently a C++ > specialisation error in a single file. I'm not sure I understood it > completely, but googling the error led me to a very simple solution that > allows the build to complete (hopefully without introducing any regressions). > A patch file and modified Portfile are attached to this message. Thanks. I submitted a ticket for this problem for you: https://trac.macports.org/ticket/42969 I generated a unified diff of your Portfile changes, removing the lines you had commented out, and also converted your contextual diff to a unified one. I can confirm that this now builds on Mavericks. However, I am not a C++ developer so I cannot say whether the change you have made is correct. How did you come to this solution? Have you contacted the developers of eigen about whether this change is correct? ___ macports-users mailing list macports-users@lists.macosforge.org https://lists.macosforge.org/mailman/listinfo/macports-users
Re: eigen
On Mar 20, 2014, at 17:41, Nicolas Pavillon wrote: > I may have expressed myself incorrectly, but the compatibility mode of eigen3 > does not reduce the amount of options of calligra. provides full support, > apart from some modules which are not supported. It is thus a yes/no case, > where either you can use the compatibility mode if you are not using the > unsupported modules, or you have to adjust your code. Exactly, and that's not something I'm very much interested in testing in something that's not a stable release :) Anyway, I figured out why eigen 2 doesn't build with clang. Apparently a C++ specialisation error in a single file. I'm not sure I understood it completely, but googling the error led me to a very simple solution that allows the build to complete (hopefully without introducing any regressions). A patch file and modified Portfile are attached to this message. >> [snip] but the applications I tested seemed functional enough. The suite is >> well too complicated to assert if it's "completely working", aside from what >> the unit tests say… > > Well, if you get something which is working satisfyingly, I would encourage > you to attach your Portfile to the ticket #37579. Calligra is still not an > official port of Macports, so if there is something working, it would be nice > to have it committed. Heh, for the moment I don't have anything like a Portfile, neither for Calligra nor for the 2 or 3 dependencies I had to install outside of MacPorts ... but who knows. In any case I'll post an update when I think things are ripe. I hope the build process will be as standard as possible (and strive to get any adaptations accepted upstream) so making a Portfile ought to be easy enough for anyone accustomed to do so. R. patch-QrInstantiations.cpp.txt.diff Description: Binary data Portfile Description: Binary data ___ macports-users mailing list macports-users@lists.macosforge.org https://lists.macosforge.org/mailman/listinfo/macports-users
Re: eigen
Hello, >> More generally, it is also possible to use eigen3 in compatibility mode, >> which works for most modules. I could use this for example in Kstars to keep >> to the port to build. > > I'll have a look at that, but I prefer to have the maximum of optional > components available. I started out trying to build without GLEW, but > realised rather quickly that the code hadn't been tested for a while in its > absence. And in fact, the only true issue I had until now was probably > introduced by (or was at least concurrent with) not building the gmic > extension for Krita. I may have expressed myself incorrectly, but the compatibility mode of eigen3 does not reduce the amount of options of calligra. It provides full support, apart from some modules which are not supported. It is thus a yes/no case, where either you can use the compatibility mode if you are not using the unsupported modules, or you have to adjust your code. For what I tested in the past with Calligra’s Portfile, it is possible to use the compatibility mode. > [snip] but the applications I tested seemed functional enough. The suite is > well too complicated to assert if it's "completely working", aside from what > the unit tests say… Well, if you get something which is working satisfyingly, I would encourage you to attach your Portfile to the ticket #37579. Calligra is still not an official port of Macports, so if there is something working, it would be nice to have it committed. Cheers, Nicolas ___ macports-users mailing list macports-users@lists.macosforge.org https://lists.macosforge.org/mailman/listinfo/macports-users
Re: eigen
Hello, On Wednesday March 19 2014 09:00:50 you wrote: > > In fact, I'm more interested in eigen 2, required by Calligra … > I do not remember the specific reason why eigen2 cannot build on Mavericks, > but in the case of calligra (which is not an official port, by the way, there > is only a tentative port in a ticket to my knowledge), eigen2 is an optional > dependency, not a required one. So if you are referring to the ticket #37579, > you can remove the dependency eigen2 and try to build in this way. But note > that there are other issues too. I looked a little bit at it some time ago, > but could not reach a completely working program to then commit the Portfile. I'm working on Calligra git/master (0.9.0 pre-alpha) following the official build instructions and product set, and until now I have been rather surprised at how well things worked. Of course I had to install a certain number of packages in /opt/local, as well as tweak a cmake file or two, only about 70% of the unit tests succeeded, but the applications I tested seemed functional enough. The suite is well too complicated to assert if it's "completely working", aside from what the unit tests say... > More generally, it is also possible to use eigen3 in compatibility mode, > which works for most modules. I could use this for example in Kstars to keep > to the port to build. I'll have a look at that, but I prefer to have the maximum of optional components available. I started out trying to build without GLEW, but realised rather quickly that the code hadn't been tested for a while in its absence. And in fact, the only true issue I had until now was probably introduced by (or was at least concurrent with) not building the gmic extension for Krita. R. ___ macports-users mailing list macports-users@lists.macosforge.org https://lists.macosforge.org/mailman/listinfo/macports-users
eigen
On Mar 18, 2014, at 12:14, Vincent Habchi wrote: > Le 18 mars 2014 à 12:01, René J.V. Bertin a écrit : > >> A bit OT, but is clang the reason libeigen doesn't currently build on OS X >> 10.9? > > Er… I think eigen3 was building fine with clang, except the BLAS part which > requires a Fortran compiler. In fact, I'm more interested in eigen 2, required by Calligra ... R. ___ macports-users mailing list macports-users@lists.macosforge.org https://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
On Mon, Dec 17, 2012 at 3:46 PM, Amy Anderson wrote:
> Hi macport users,
>
> I am trying to run this script in python and the script is now working with
> the test data (eigen problem solved) but when I input my own data to be
> called by script I got the following errors.
>
> [moriaht-5:~/Desktop/pyClusterROI] moriah% python pyClusterROI_test.py
> tcorr connectivity subject2002.nii
>
> Traceback (most recent call last):
> File "pyClusterROI_test.py", line 89, in
> make_local_connectivity_tcorr( infiles[i], maskname, outname, 0.5 )
> File
> "/Users/moriah/Desktop/pyClusterROI/make_local_connectivity_tcorr.py", line
> 114, in make_local_connectivity_tcorr
> msk=csc_matrix((range(1,m+1),(iv,zeros(m))),shape=(prod(sz[1:]),1))
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/compressed.py",
> line 44, in __init__
> other = self.__class__( coo_matrix(arg1, shape=shape) )
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/coo.py",
> line 188, in __init__
> self._check()
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/sparse/coo.py",
> line 220, in _check
> raise ValueError('row index exceedes matrix dimensions')
> ValueError: row index exceedes matrix dimensions
>
>
> I was wondering if anyone might know what this error might mean or how to
> fix it?
Off the top of my head, no ideas besides the obvious "the index is
larger than the number of rows in the matrix" from the error message.
Since this error is coming from make_local_connectivity_tcorr, you'll
have to the authors of pyClusterROI.py to look into it, or better yet,
use a newer script (if available) from http://nipy.sourceforge.net.
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Re: running script error (eigen symmetric)
Hi macport users,
I am trying to run this script in python and the script is now working with
the test data (eigen problem solved) but when I input my own data to be
called by script I got the following errors.
[moriaht-5:~/Desktop/pyClusterROI] moriah% python pyClusterROI_test.py
tcorr connectivity subject2002.nii
Traceback (most recent call last):
File "pyClusterROI_test.py", line 89, in
make_local_connectivity_tcorr( infiles[i], maskname, outname, 0.5 )
File "/Users/moriah/Desktop/pyClusterROI/make_local_connectivity_tcorr.py",
line 114, in make_local_connectivity_tcorr
msk=csc_matrix((range(1,m+1),(iv,zeros(m))),shape=(prod(sz[1:]),1))
File "/opt/local/Library/Frameworks/Python.framework/
Versions/2.6/lib/python2.6/site-packages/scipy/sparse/compressed.py", line
44, in __init__
other = self.__class__( coo_matrix(arg1, shape=shape) )
File "/opt/local/Library/Frameworks/Python.framework/
Versions/2.6/lib/python2.6/site-packages/scipy/sparse/coo.py", line 188, in
__init__
self._check()
File "/opt/local/Library/Frameworks/Python.framework/
Versions/2.6/lib/python2.6/site-packages/scipy/sparse/coo.py", line 220, in
_check
raise ValueError('row index exceedes matrix dimensions')
ValueError: row index exceedes matrix dimensions
I was wondering if anyone might know what this error might mean or how to
fix it?
On Tue, Dec 4, 2012 at 3:49 PM, Sean Farley
wrote:
> On Mon, Dec 3, 2012 at 10:35 AM, Amy Anderson wrote:
> > Dear macports-users,
> >
> > I am a new macports, python, and scipy user and I am looking for some
> help
> > to troubleshoot an error I have been getting when trying to run a script
> in
> > python. The script I am trying to run is called pyCluster ROI and it
> needs
> > python, pynifti, scipy, and numpy to run. I have installed all these
> > programs successfully using macports on Mac OS 10.8.
> >
> >
> > I unarchived the scripts and ran the test script getting this error:
> >
> > $ python pyClusterROI_test.py
> >
> > Traceback (most recent call last):
> >
> > File "pyClusterROI_test.py", line 48, in
> >
> > from make_local_connectivity_scorr import *
> >
> > File
> >
> "/Users/matthewnye/Downloads/pyClusterROI/make_local_connectivity_scorr.py",
> > line 40, in
> >
> > from scipy.sparse.linalg.eigen.arpack import eigen_symmetric
> >
> > ImportError: cannot import name eigen_symmetric
> >
> >
> > I have been trying to hunt down what this error may be and it seems that
> > older versions of scipy might have used
> > ‘scipy.sparse.linalg.eigen.arpack.eigen symmetric()’ where as new
> versions
> > it has been renamed as "scipy.sparse.linalg.eigen.arpack.eigs()."
> >
> >
> > Does anyone know what might be causing this error or if it is a version
> > problem, is there any way to get an older version of scipy through
> macports?
> > Also I have considered installing all these modules through a manual
> install
> > but since i am a novice user I did not want to attempt that if there was
> a
> > potentially simpler solution.
>
> Woah, woah, woah now. Let's not go down the (more difficult) rabbit
> hole of installing an older version of a port. For this issue, there
> is a much easier solution (so please undo all the installations of an
> older scipy, etc.). After scipy 0.9.0, the function 'eigen_symmetric'
> was renamed to 'eigsh'. All you have to do is run,
>
> $ perl -i -pe 's,eigen_symmetric,eigsh,g' *.py
>
> in the pyClusterROI directory and you should get much further along.
> Alternatively, attached is a patch if you would prefer that, which you
> can run with,
>
> $ patch -p1 < /path/to/eigen_symmetric.patch
>
> For reference, I'm able to get to script to run on the test data and
> produce subject{1,2,…,etc.}.nii.gz. Also, as a bonus, I was able to
> get this pyClusterROI thing to work with the newer nibabel (which
> replaces pynifty [macports devs:I'll create a ticket later today to
> file these]). You can use the attached nibabel.patch to try it out.
>
> Though, judging by the age of this script, you might find a suitable
> replacement here (which is also where the pynifti replacement lives),
>
> http://nipy.sourceforge.net
>
> Hope that helps!
>
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Re: running script error (eigen symmetric)
On Mon, Dec 3, 2012 at 10:35 AM, Amy Anderson wrote:
> Dear macports-users,
>
> I am a new macports, python, and scipy user and I am looking for some help
> to troubleshoot an error I have been getting when trying to run a script in
> python. The script I am trying to run is called pyCluster ROI and it needs
> python, pynifti, scipy, and numpy to run. I have installed all these
> programs successfully using macports on Mac OS 10.8.
>
>
> I unarchived the scripts and ran the test script getting this error:
>
> $ python pyClusterROI_test.py
>
> Traceback (most recent call last):
>
> File "pyClusterROI_test.py", line 48, in
>
> from make_local_connectivity_scorr import *
>
> File
> "/Users/matthewnye/Downloads/pyClusterROI/make_local_connectivity_scorr.py",
> line 40, in
>
> from scipy.sparse.linalg.eigen.arpack import eigen_symmetric
>
> ImportError: cannot import name eigen_symmetric
>
>
> I have been trying to hunt down what this error may be and it seems that
> older versions of scipy might have used
> ‘scipy.sparse.linalg.eigen.arpack.eigen symmetric()’ where as new versions
> it has been renamed as "scipy.sparse.linalg.eigen.arpack.eigs()."
>
>
> Does anyone know what might be causing this error or if it is a version
> problem, is there any way to get an older version of scipy through macports?
> Also I have considered installing all these modules through a manual install
> but since i am a novice user I did not want to attempt that if there was a
> potentially simpler solution.
Woah, woah, woah now. Let's not go down the (more difficult) rabbit
hole of installing an older version of a port. For this issue, there
is a much easier solution (so please undo all the installations of an
older scipy, etc.). After scipy 0.9.0, the function 'eigen_symmetric'
was renamed to 'eigsh'. All you have to do is run,
$ perl -i -pe 's,eigen_symmetric,eigsh,g' *.py
in the pyClusterROI directory and you should get much further along.
Alternatively, attached is a patch if you would prefer that, which you
can run with,
$ patch -p1 < /path/to/eigen_symmetric.patch
For reference, I'm able to get to script to run on the test data and
produce subject{1,2,…,etc.}.nii.gz. Also, as a bonus, I was able to
get this pyClusterROI thing to work with the newer nibabel (which
replaces pynifty [macports devs:I'll create a ticket later today to
file these]). You can use the attached nibabel.patch to try it out.
Though, judging by the age of this script, you might find a suitable
replacement here (which is also where the pynifti replacement lives),
http://nipy.sourceforge.net
Hope that helps!
eigen_symmetric.patch
Description: Binary data
nibabel.patch
Description: Binary data
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Re: running script error (eigen symmetric)
On Dec 3, 2012, at 14:59, Amy Anderson wrote: > I tried installing py27-scikits-umfpack and got this error. > main.log is attached also. > > sudo port install > could not read "/Users/moriah/Desktop/Portfile": permission denied > Please see the log file for port py-scikits-umfpack for details: > > /opt/local/var/macports/logs/_Users_moriah_Desktop/py-scikits-umfpack/main.log > To report a bug, follow the instructions in the guide: > http://guide.macports.org/#project.tickets You will need to put the portfile somewhere where MacPorts can read it. Ever since the gsoc08-privileges branch was merged into MacPorts, locations in your home directory are no longer a good place, unless you use chmod to change the permissions of your home directory to allow the macports user to look inside it. ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
I tried installing py27-scikits-umfpack and got this error. main.log is attached also. sudo port install could not read "/Users/moriah/Desktop/Portfile": permission denied Please see the log file for port py-scikits-umfpack for details: /opt/local/var/macports/logs/_Users_moriah_Desktop/py-scikits-umfpack/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets On Mon, Dec 3, 2012 at 3:40 PM, Ryan Schmidt wrote: > / main.log Description: Binary data ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
On Dec 3, 2012, at 14:35, Amy Anderson wrote: > I have attached the main.log file. I can cut and paste it if that is better, > but it had quite a lot of content. The relevant lines seem to be: :info:build swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i :info:build swig -python -I/opt/local/include -I/opt/local/include -I/opt/local/include -o build/src.macosx-10.7-x86_64-2.4/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.macosx-10.7-x86_64-2.4/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:192: Error: Unable to find '/opt/local/include/ufsparse/umfpack.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:193: Error: Unable to find '/opt/local/include/ufsparse/umfpack_solve.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:194: Error: Unable to find '/opt/local/include/ufsparse/umfpack_defaults.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:195: Error: Unable to find '/opt/local/include/ufsparse/umfpack_triplet_to_col.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:196: Error: Unable to find '/opt/local/include/ufsparse/umfpack_col_to_triplet.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:197: Error: Unable to find '/opt/local/include/ufsparse/umfpack_transpose.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:198: Error: Unable to find '/opt/local/include/ufsparse/umfpack_scale.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:200: Error: Unable to find '/opt/local/include/ufsparse/umfpack_report_symbolic.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:201: Error: Unable to find '/opt/local/include/ufsparse/umfpack_report_numeric.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:202: Error: Unable to find '/opt/local/include/ufsparse/umfpack_report_info.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:203: Error: Unable to find '/opt/local/include/ufsparse/umfpack_report_control.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:215: Error: Unable to find '/opt/local/include/ufsparse/umfpack_symbolic.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:216: Error: Unable to find '/opt/local/include/ufsparse/umfpack_numeric.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:225: Error: Unable to find '/opt/local/include/ufsparse/umfpack_free_symbolic.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:226: Error: Unable to find '/opt/local/include/ufsparse/umfpack_free_numeric.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:248: Error: Unable to find '/opt/local/include/ufsparse/umfpack_get_lunz.h' :info:build scipy/sparse/linalg/dsolve/umfpack/umfpack.i:272: Error: Unable to find '/opt/local/include/ufsparse/umfpack_get_numeric.h' :info:build error: command 'swig' failed with exit status 1 Sounds like maybe you need the old py-scikits-umfpack (or, for python 2.6, py27-scikits-umfpack) port. This became part of py-scipy at some point after version 0.7. ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
On Dec 3, 2012, at 13:47, Amy Anderson wrote: > Is this the log info you needed: > > mdworker(61946) deny file-write-create > /opt/local/var/macports/home/Library/Preferences/com.apple.LaunchServices.plist.lockfile > () > No; the file identified by the command "port logfile" run in the appropriate port's directory. It is named "main.log". > Also I need to install scipy 0.7 to work with a script that uses calls > eigen-symmetric, it was changed in versions 0.9 and after. can I install > scipy 0.7 to work with python 2.7? The earliest version of the py27-scipy port was 0.8.0: http://trac.macports.org/browser/trunk/dports/python/py27-scipy/Portfile?rev=73540 You can download that port, then edit it to change the version and checksums to match 0.7. ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
Is this the log info you needed: mdworker(61946) deny file-write-create /opt/local/var/macports/home/Library/Preferences/com.apple.LaunchServices.plist.lockfile () Process: mdworker [61946] Path: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Support/mdworker Load Address:0x100535000 Identifier: mdworker Version: ??? (???) Code Type: X86-64 (Native) Parent Process: launchd [61944] Date/Time: 2012-12-03 14:40:53.265 -0500 OS Version: Mac OS X 10.7.5 (11G56) Report Version: 7 Backtrace: 0 libsystem_kernel.dylib0x7fff8d9d6ad2 __open + 10 1 libmdworker.dylib 0x0001005b5dd5 mdworker_open + 149 2 CoreFoundation0x7fff885b8188 -[CFXPreferencesPropertyListSourceSynchronizer _openLockFile:force:] + 24 3 CoreFoundation0x7fff884e3297 -[CFXPreferencesPropertyListSourceSynchronizer synchronize] + 295 4 CoreFoundation0x7fff884e2f9c -[CFXPreferencesPropertyListSource synchronize] + 108 5 CoreFoundation0x7fff884e23a6 ___CFXPreferencesSynchronize_block_invoke_1 + 54 6 CoreFoundation0x7fff884e2360 CFXPREFS_SYNC_LOCKED_block_invoke_1 + 32 7 libdispatch.dylib 0x7fff8f117c75 _dispatch_barrier_sync_f_invoke + 33 8 CoreFoundation0x7fff884e2313 CFPreferencesSynchronize + 323 9 LaunchServices0x7fff8e494e1a LSHandlerPref::CopyHandlers() + 154 10 LaunchServices0x7fff8e438838 _LSContextInit + 502 11 LaunchServices0x7fff8e4a9a9e _UTTypeCopyPedigree + 23 12 mdworker 0x0001005573b0 13 mdworker 0x00010053a54b 14 mdworker 0x00010053830e 15 mdworker 0x00010053d9b6 16 libdispatch.dylib 0x7fff8f117c75 _dispatch_barrier_sync_f_invoke + 33 17 mdworker 0x0001005381c1 18 mdworker 0x000100542071 19 libsystem_c.dylib 0x7fff911348bf _pthread_start + 335 20 libsystem_c.dylib 0x7fff91137b75 thread_start + 13 Binary Images: 0x100535000 -0x100588fff mdworker (??? - ???) <054C2D9C-0315-35AB-A9F7-1CC9050486AD> /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/mdworker 0x1005b5000 -0x1005b5fff libmdworker.dylib (??? - ???) <75CC0C0A-040A-3063-8217-BD2D0864BA6C> /System/Library/Frameworks/CoreServices.framework/Frameworks/Metadata.framework/Versions/A/Support/libmdworker.dylib 0x7fff8849a000 - 0x7fff8866eff7 com.apple.CoreFoundation (6.7.2 - 635.21) <62A3402E-A4E7-391F-AD20-1EF20236CE1B> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x7fff8d9c - 0x7fff8d9e0fff libsystem_kernel.dylib (1699.32.7 - compatibility 1.0.0) <66C9F9BD-C7B3-30D4-B1A0-03C8A6392351> /usr/lib/system/libsystem_kernel.dylib 0x7fff8e43 - 0x7fff8e4d1fff com.apple.LaunchServices (480.39 - 480.39) <677E5B34-215E-3615-AC10-BED60DC460FD> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices 0x7fff8f114000 - 0x7fff8f122fff libdispatch.dylib (187.10.0 - compatibility 1.0.0) <8E03C652-922A-3399-93DE-9EA0CBFA0039> /usr/lib/system/libdispatch.dylib 0x7fff910e6000 - 0x7fff911c3fef libsystem_c.dylib (763.13.0 - compatibility 1.0.0) <41B43515-2806-3FBC-ACF1-A16F35B7E290> /usr/lib/system/libsystem_c.dylib Also I need to install scipy 0.7 to work with a script that uses calls eigen-symmetric, it was changed in versions 0.9 and after. can I install scipy 0.7 to work with python 2.7? On Mon, Dec 3, 2012 at 2:37 PM, Ryan Schmidt wrote: > > On Dec 3, 2012, at 13:23, Amy Anderson wrote: > > > Thank you. I tried installing an older version of scipy (0.7) following > the directions on your link provided below and got the following error. > > > > ---> Building py-scipy > > Error: org.macports.build for port py-scipy returned: command execution > failed > > To report a bug, follow the instructions in the guide: > > http://guide.macports.org/#project.tickets > > Error: Processing of port py-scipy failed > > > > Do you have any idea how to fix this error or why it is happening? > > We would need to see the contents of failing port's main.log file. > > But you probably should not be using Python 2.4 anymore; it is very old. > Please try using Python 2.7, in this case by using the py27-scipy port > instead. > > > ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
On Dec 3, 2012, at 2:23 PM, Amy Anderson wrote: > Thank you. I tried installing an older version of scipy (0.7) following the > directions on your link provided below and got the following error. > > ---> Building py-scipy > Error: org.macports.build for port py-scipy returned: command execution failed > To report a bug, follow the instructions in the guide: > http://guide.macports.org/#project.tickets > Error: Processing of port py-scipy failed > > Do you have any idea how to fix this error or why it is happening? Did the output say anything about a log? We'll need to see its contents in order to help. Alternately, run the following from the directory where you downloaded the old Portfile, and paste the output: sudo port clean py-scipy sudo port -d install vq ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
On Dec 3, 2012, at 13:23, Amy Anderson wrote: > Thank you. I tried installing an older version of scipy (0.7) following the > directions on your link provided below and got the following error. > > ---> Building py-scipy > Error: org.macports.build for port py-scipy returned: command execution failed > To report a bug, follow the instructions in the guide: > http://guide.macports.org/#project.tickets > Error: Processing of port py-scipy failed > > Do you have any idea how to fix this error or why it is happening? We would need to see the contents of failing port's main.log file. But you probably should not be using Python 2.4 anymore; it is very old. Please try using Python 2.7, in this case by using the py27-scipy port instead. ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
Thank you. I tried installing an older version of scipy (0.7) following the directions on your link provided below and got the following error. ---> Building py-scipy Error: org.macports.build for port py-scipy returned: command execution failed To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port py-scipy failed Do you have any idea how to fix this error or why it is happening? On Mon, Dec 3, 2012 at 11:44 AM, Jeremy Lavergne wrote: > Actually, this anchor on the page will get you half down to the sections > relevant to you. > https://trac.macports.org/wiki/howto/InstallingOlderPort#Installation > > ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
Re: running script error (eigen symmetric)
> I have been trying to hunt down what this error may be and it seems that > older versions of scipy might have used > ‘scipy.sparse.linalg.eigen.arpack.eigen symmetric()’ where as new versions > it has been renamed as "scipy.sparse.linalg.eigen.arpack.eigs()." > > Does anyone know what might be causing this error or if it is a version > problem, is there any way to get an older version of scipy through macports? Check out this link for installing older versions of a given port: https://trac.macports.org/wiki/howto/InstallingOlderPort ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
running script error (eigen symmetric)
Dear macports-users, I am a new macports, python, and scipy user and I am looking for some help to troubleshoot an error I have been getting when trying to run a script in python. The script I am trying to run is called pyCluster ROI and it needs python, pynifti, scipy, and numpy to run. I have installed all these programs successfully using macports on Mac OS 10.8. I unarchived the scripts and ran the test script getting this error: $ python pyClusterROI_test.py Traceback (most recent call last): File "pyClusterROI_test.py", line 48, in from make_local_connectivity_scorr import * File "/Users/matthewnye/Downloads/pyClusterROI/make_local_connectivity_scorr.py", line 40, in from scipy.sparse.linalg.eigen.arpack import eigen_symmetric ImportError: cannot import name eigen_symmetric I have been trying to hunt down what this error may be and it seems that older versions of scipy might have used ‘scipy.sparse.linalg.eigen.arpack.eigen symmetric()’ where as new versions it has been renamed as " scipy.sparse.linalg.eigen.arpack.eigs()." Does anyone know what might be causing this error or if it is a version problem, is there any way to get an older version of scipy through macports? Also I have considered installing all these modules through a manual install but since i am a novice user I did not want to attempt that if there was a potentially simpler solution. Thank you for any help you can give. -Amy ___ macports-users mailing list macports-users@lists.macosforge.org http://lists.macosforge.org/mailman/listinfo/macports-users
