py*-scipy fail to upgrade to 0.12.0

[watsodw]

See logs

[mf2k (Frank Schima)]

I see the same issue. Mac OS X 10.8.3. Xcode 4.6.1.

$ port installed py27-scipy
The following ports are currently installed:
  py27-scipy @0.11.0_0+atlas+gcc47 (active)

[mf2k (Frank Schima)]

Complete log for py27-scipy.

[mf2k (Frank Schima)]

@david.w.watson: Most of the logs you submitted were not complete. Always clean the port before submitting the main.log.

[mf2k (Frank Schima)]

Cc Me!

[cooljeanius (Eric Gallager)]

mf2k, your error looks different from david.w.watson's. david.w.watson's ones all look like they have to do with this:

Symbol not found: _omp_get_num_threads

[mf2k (Frank Schima)]

Then that's the atlas bug, which seems to be fixed. See #37415.

@sean: Please look at my main.log attachment for this error:

:info:build               w,z,ifail,info = zhegvx(a,b,iu,[itype,jobz,uplo,il,lwork,overwrite_a,overwrite_b])
:info:build     Wrote C/API module "_flapack" to file "build/src.macosx-10.8-x86_64-2.7/build/src.macosx-10.8-x86_64-2.7/scipy/linalg/_flapackmodule.c"
:info:build     Fortran 77 wrappers are saved to "build/src.macosx-10.8-x86_64-2.7/build/src.macosx-10.8-x86_64-2.7/scipy/linalg/_flapack-f2pywrappers.f"
:info:build   adding 'build/src.macosx-10.8-x86_64-2.7/fortranobject.c' to sources.
:info:build   adding 'build/src.macosx-10.8-x86_64-2.7' to include_dirs.
:info:build   adding 'build/src.macosx-10.8-x86_64-2.7/build/src.macosx-10.8-x86_64-2.7/scipy/linalg/_flapack-f2pywrappers.f' to sources.
:info:build building extension "scipy.linalg._cblas" sources
:info:build from_template:> build/src.macosx-10.8-x86_64-2.7/cblas.pyf
:info:build error: cblas.pyf.src: No such file or directory

[sean@…]

Cc Me!

[os@…]

Weird. Had the same error message when I tried to upgrade scipy yesterday. After a port selfupdate and port clean py27-scipy this morning, it compiles.

[michaelld (Michael Dickens)]

Cc Me!

[mf2k (Frank Schima)]

Yes, seems to work for me now too.

@david.w.watson: Re-open the ticket and post a complete log for your primary python if this still is not working for you.

[stromnov (Andrey Stromnov)]

Some explanations: see r105087 and ​http://projects.scipy.org/scipy/ticket/1888

[stromnov (Andrey Stromnov)]

Cc Me!

[amicitas+macports@…]

I have just tried a "port selfupdate" and then a "port clean py27-scipy" followed by "port upgrade outdated" or "port upgrade py27-scipy". Still running into the same issue as reported here previously: "Symbol not found: _omp_get_num_threads".

I have attached the log file.

[amicitas+macports@…]

py27-scipy-main.log

[stromnov (Andrey Stromnov)]

It's a problem with yours numpy installation:

:info:build   File "/opt/macports/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/linalg/linalg.py", line 23, in <module>
121	:info:build     from numpy.linalg import lapack_lite
122	:info:build ImportError: dlopen(/opt/macports/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/linalg/lapack_lite.so, 2): Symbol not found: _omp_get_num_threads
123	:info:build   Referenced from: /opt/macports/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/linalg/lapack_lite.so
124	:info:build   Expected in: flat namespace
125	:info:build  in /opt/macports/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/linalg/lapack_lite.so

Please, try to reinstall py-numpy.

[michaelld (Michael Dickens)]

Any of the log files from "david.w.watson" and "amicitas+macports" -- the ones that include "from numpy.linalg import lapack_lite" failing: We're tracking that issue in ticket #37415. I would recommend you doing:

sudo port -f uninstall atlas pyXY-numpy pyXY-scipy
sudo port selfupdate
sudo port install atlas +variants
sudo port install pyXY-numpy +atlas +variants
sudo port install pyXY-scipy +atlas +variants

but replace "XY" by the correct python version, and "+variants" by your chosen variants (e.g., "+gcc47"). I'm pretty sure you need to start by reinstalling atlas, then numpy, then scipy, in that order. And, that you need to uninstall them first.

[michaelld (Michael Dickens)]

As for the "error: cblas.pyf.src: No such file or directory" issue: Is there a patch from that ticket that we can apply as a temporary measure to get scipy back working again?

[stromnov (Andrey Stromnov)]

Replying to michaelld@…:

As for the "error: cblas.pyf.src: No such file or directory" issue: Is there a patch from that ticket that we can apply as a temporary measure to get scipy back working again?

Patch already incorporated into source tarball (see comment:10).

[michaelld (Michael Dickens)]

Is the fix in the tarball we're using in the Portfile? If not, can we patch that tarball? Or, do folks think it is better waiting for 0.12.1 to come out which should contain the fix for this issue?

[stromnov (Andrey Stromnov)]

Yes, fix already in the tarball we're using (missing files were added to source tarball without revision bump, so-called "stealth update" at r105087, for more details see ​http://projects.scipy.org/scipy/ticket/1888).

[michaelld (Michael Dickens)]

Great; thanks! I think that takes care of the scipy issue; the rest is up to atlas and numpy (and, their respective tickets / issues).

[amicitas+macports@…]

For the _omp_get_num_threads issue.

The procedure suggested by @michaelld did not work, but I finally got py27-scipy to install doing the following:

sudo port -f uninstall atlas pyXY-numpy pyXY-scipy
sudo port selfupdate
sudo port install atlas +gcc46
sudo port install pyXY-numpy +atlas +gcc47
sudo port install pyXY-scipy +atlas +gcc47

The point here is that this did not work until I complied atlas using gcc46.

This is of course part of the numpy issue and not this scipy installer (see ​#37415).

[michaelld (Michael Dickens)]

I'm glad you got it working, even if my suggestion did not work. Did you install atlas, numpy, and scipy all using +gcc46? Or, did you mix and match which +gccXY for each port? We've had an issue in the past where folks have chosen different +gccXY variants and that didn't work well. I don't know if this will still be the case with all the compiler changes that have happened in the past few months.

[amicitas+macports@…]

In this particular case I used +gcc46 for atlas, and +gcc47 for numpy/scipy (I did this mostly as a way to isolate the problem a bit.) So far everything appears to be working without issue even with the mixed compiler versions.