#22033: py26-scientific fails to build -----------------------------------------+---------------------------------- Reporter: singingwolfboy@… | Owner: adfernandes@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.8.1 Keywords: | Port: py26-scientific -----------------------------------------+---------------------------------- Comment(by adfernandes@…): Hmm... try re-syncing ports; py26-scientific should be at version 2.8 revision 1, now. -- Ticket URL: <http://trac.macports.org/ticket/22033#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS

#22033: py26-scientific fails to build -----------------------------------------+---------------------------------- Reporter: singingwolfboy@… | Owner: adfernandes@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.8.1 Keywords: | Port: py26-scientific -----------------------------------------+---------------------------------- Comment(by adfernandes@…): Okay - I just uninstalled, cleaned, and re-installed, without a problem. Which version and variant of netcdf do you have installed? The latest is 4.0.1 revision 7. If this version/revision is what you '''already''' have, can you please try re-installing netcdf with the `+netcdf4` variant? (It will install hdf5-18 as a dependency). Your build log indicates that there's something screwy with netcdf. (FYI - I know from other tickets that at least one other `py26-scientific` user has this running... but `netcdf` has been a sufficient pain that I'd really like to track this down!) -- Ticket URL: <http://trac.macports.org/ticket/22033#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS

#22033: py26-scientific fails to build -----------------------------------------+---------------------------------- Reporter: singingwolfboy@… | Owner: adfernandes@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.8.1 Keywords: | Port: py26-scientific -----------------------------------------+---------------------------------- Changes (by stromnov@…): * cc: stromnov@… (added) Comment: Please, try to build with debug flag (-d). Probably py26-scientific implicitly needs one of py26-numpy or py26-numeric installed. -- Ticket URL: <http://trac.macports.org/ticket/22033#comment:5> MacPorts <http://www.macports.org/> Ports system for Mac OS

#22033: py26-scientific fails to build -----------------------------------------+---------------------------------- Reporter: singingwolfboy@… | Owner: adfernandes@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.8.1 Keywords: | Port: py26-scientific -----------------------------------------+---------------------------------- Comment(by adfernandes@…): Replying to [comment:6 adfernandes@…]:

Replying to [comment:4 singingwolfboy@…]:

...

I went as far as uninstalling py26-scientific, netcdf, and hdf5-18, and reinstalling all of them. (For netcdf, I used both the "netcdf4" and "docs" variants). Same error message. Weird. Why would it work for you but not for me? Are you also running Leopard?

Yes - 10.5.8, latest dev tools, etc. The suggestion that perhaps py26-numpy or py26-numeric is required is implicitly required a good one; I've got them both.

Thanks for doing all those reinstalls, BTW. I've just checked my shared libraries for py26-scientific and get the following: {{{ Assam:ports andrew$ otool -L `port contents py26-scientific | fgrep .so` /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 /site-packages/Scientific/darwin/Scientific_affinitypropagation.so: /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 /site-packages/Scientific/darwin/Scientific_interpolation.so: /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 /site-packages/Scientific/darwin/Scientific_netcdf.so: /opt/local/lib/libnetcdf.6.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 /site-packages/Scientific/darwin/Scientific_numerics_package_id.so: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 /site-packages/Scientific/darwin/Scientific_vector.so: /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) }}} By the look of it, `Scientific_netcdf.so` is the only library that requires a non-system dylib, and only `/opt/local/lib/libnetcdf.6.dylib` at that. (Well, that's a runtime link dependency, but it would be weird if it had a build dependency on one of the other ports mentioned...!) -- Ticket URL: <http://trac.macports.org/ticket/22033#comment:7> MacPorts <http://www.macports.org/> Ports system for Mac OS

#22033: py26-scientific fails to build -----------------------------------------+---------------------------------- Reporter: singingwolfboy@… | Owner: adfernandes@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.8.1 Keywords: | Port: py26-scientific -----------------------------------------+---------------------------------- Comment(by adfernandes@…): Replying to [comment:8 singingwolfboy@…]:

Debug log is attached. I have py26-numeric installed, but not py26-numpy. Maybe that's the issue?

Thanks! Yes, your logs report the first error as {{{ running build_ext 1174 building 'Scientific_netcdf' extension 1175 creating build/temp.macosx-10.5-i386-2.6 1176 creating build/temp.macosx-10.5-i386-2.6/Src 1177 /usr/bin/gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py26-scientific/work/ScientificPython-2.8/Include -IInclude -I/opt/local/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 /site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Src/Scientific_netcdf.c -o build/temp.macosx-10.5-i386-2.6/Src/Scientific_netcdf.o -DNUMPY=1 1178 Src/Scientific_netcdf.c:14:31: error: numpy/arrayobject.h: No such file or directory 1179 In file included from Src/Scientific_netcdf.c:25: }}} When I locate the file in my system: {{{ Assam:~ andrew$ mdfind arrayobject.h | grep "numpy/arrayobject.h" /System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/arrayobject.h /opt/local/lib/python2.5/site- packages/numpy/core/include/numpy/arrayobject.h /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 /site-packages/numpy/core/include/numpy/arrayobject.h /Developer/SDKs/MacOSX10.5.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/arrayobject.h }}} So, yes, please try installing py26-numpy and see if the problem goes away. That would be nice if the problem was only an undeclared dependency. (I think this is a bug in py26-scientific, because the build docs say that numpy is not required.) -- Ticket URL: <http://trac.macports.org/ticket/22033#comment:9> MacPorts <http://www.macports.org/> Ports system for Mac OS

#22033: py26-scientific fails to build -----------------------------------------+---------------------------------- Reporter: singingwolfboy@… | Owner: adfernandes@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.8.1 Keywords: | Port: py26-scientific -----------------------------------------+---------------------------------- Comment(by stromnov@…): I'd just upload fixes for this ticket and some fixes for +mpi variant. -- Ticket URL: <http://trac.macports.org/ticket/22033#comment:11> MacPorts <http://www.macports.org/> Ports system for Mac OS

#22033: py26-scientific fails to build ------------------------------------------+--------------------------------- Reporter: singingwolfboy@… | Owner: adfernandes@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 1.8.1 Resolution: fixed | Keywords: Port: py26-scientific | ------------------------------------------+--------------------------------- Changes (by adfernandes@…): * status: new => closed * resolution: => fixed Comment: Thanks muchly - tested out fine. Committed in r59361. -- Ticket URL: <http://trac.macports.org/ticket/22033#comment:13> MacPorts <http://www.macports.org/> Ports system for Mac OS