#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by mojca@…): While at it: may the following lines go away? {{{ CC="`${wxWidgets.wxconfig} --cc`" \ CXX="`${wxWidgets.wxconfig} --cxx`" \ LD="`${wxWidgets.wxconfig} --ld`" }}} Since the port depends on {{{wxWidgets}}} 2.9, I see no reason to change the compiler. The version 2.8 had problems with `clang`, but 2.9 should be fine with anything. -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by mojca@…): I can delete the lines myself, no need for another patch. However I'm getting: {{{ configure: error: Couldn't find lapack. }}} -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by mojca@…): To be more precise: {{{ checking for kernel... checking for fftw_malloc in -lfftw3... yes checking for dgemm_ in -latlas... no checking for dgemm_ in -llapack... no configure: error: Couldn't find lapack. }}} I do have a symlink {{{ /usr/lib/liblapack.dylib -> ../../System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib }}} but for some reason it wasn't found and the general policy of MacPorts is to try to be as independent of the system-provided libraries as possible. I thought that some port was supposed to provide the required libraries. My installation of atlas contains {{{ /opt/local/lib/libatlas.a /opt/local/lib/liblapack.a }}} (I don't know why the libraries are static), but the port doesn't seem to be satisfied with those either. Unrelated: did you even try to play with `PortGroup python 1.0` (or `python27`)? I have no problem committing the port as-is - it was probably "equally broken" earlier than it is now, but it would be nice to inspect why this happens. I'm on 10.7. Maybe different OS provides different functions and `dgemm_` happens to be absent on mine? -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by mojca@…): And here's the test from `config.log`: {{{ #ifdef __cplusplus extern "C" #endif char dgemm_ (); int main () { return dgemm_ (); ; return 0; } }}} built with {{{ /usr/bin/clang -o conftest -pipe -Os -arch x86_64 -fPIC -DWITH_PYTHON -L/opt/local/lib -Wl,-headerpad_max_install_names -headerpad_max_install_names -arch x86_64 conftest.c -llapack }}} I can reproduce the behaviour in an isolated environment and adding `-L/usr/lib` doesn't help in any way. Minimal example: {{{ clang conftest.c -llapack Undefined symbols for architecture x86_64: "_dgemm_", referenced from: _main in x-NjwmLU.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) }}} -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by christsc@…): OK, thanks for looking into this. Maybe there's a problem when MacPorts' lapack (/opt/local/lib/liblapack.a, which I don't have on my system) is installed? I'll try to reproduce this bug, fix it, and then update the Portfile accordingly. -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:11> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by christsc@…): Thanks again for your time. Not sure what's going on - some users are building on 10.6 without problems. At any rate, I will switch to MacPorts' atlas (which provides lapack) and post an update here as soon as it's ready. -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:13> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by mojca@…): The installation went fine after that. So I can apply the patch and commit and then you can take some time figuring out how exactly the different Mac OS X versions bundle lapack. The weird thing is also that `configure.ac` seems to test `-lblas` later on, but the program never reaches that point and configure throws an error earlier, not giving `-lblas` a chance. In the long term I would suggest creating a package for `lapack`/`blas` for MacPorts. In case it's relevant, here are a few warnings: {{{ ./abf/axon/AxAbfFio32/abfheadr.cpp:796:24: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign] int pFH = 0; pFH = pFH; ~~~ ^ ~~~ 1 warning generated. In file included from ./gui/doc.cpp:59: ./gui/./doc.h:94:67: warning: private field 'APPeak' is not used [-Wunused-private-field] base, APBase, baseSD, threshold, slopeForThreshold, peak, APPeak, tLoReal, tHiReal, t50LeftReal, t50RightReal, ^ ./gui/./doc.h:96:23: warning: private field 'APMaxRise' is not used [-Wunused-private-field] t50Y, APMaxT, APMaxRise, APMaxRiseT, APt50LeftReal, ^ 2 warnings generated. In file included from ./gui/childframe.cpp:64: ./gui/./childframe.h:214:17: warning: private field 'pTracesBoxSizer' is not used [-Wunused-private-field] wxBoxSizer *pTracesBoxSizer, *pChannelsBoxSizer; ^ ./gui/./childframe.h:214:35: warning: private field 'pChannelsBoxSizer' is not used [-Wunused-private-field] wxBoxSizer *pTracesBoxSizer, *pChannelsBoxSizer; ^ ./gui/./childframe.h:217:10: warning: private field 'firstResize' is not used [-Wunused-private-field] bool firstResize; ^ 3 warnings generated. In file included from ./gui/dlgs/smalldlgs.cpp:16: ./gui/dlgs/./smalldlgs.h:666:22: warning: private field 'm_srcDirPicker' is not used [-Wunused-private-field] wxDirPickerCtrl *m_srcDirPicker,*m_destDirPicker; ^ ./gui/dlgs/./smalldlgs.h:666:38: warning: private field 'm_destDirPicker' is not used [-Wunused-private-field] wxDirPickerCtrl *m_srcDirPicker,*m_destDirPicker; ^ ./gui/dlgs/./smalldlgs.h:667:17: warning: private field 'm_textCtrlSrcFilter' is not used [-Wunused-private-field] wxTextCtrl *m_textCtrlSrcFilter; ^ 3 warnings generated. In file included from ./pystf.cxx:66: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/arrayobject.h:15: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/ndarrayobject.h:17: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/ndarraytypes.h:1728: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" ^ In file included from ./pystf_wrap.cxx:3077: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/arrayobject.h:15: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/ndarrayobject.h:17: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/ndarraytypes.h:1728: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" ^ 1 warning generated. }}} -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:15> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by mojca@…): r110527. The buildbots succeed. Weird enough the configure step already succeeded at {{{ checking for dgemm_ in -latlas... yes }}} We can definitely discuss about a better/cleaner solution for the next release. And I still don't understand what is wrong with both of my machines. -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:17> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.8 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: closed Priority: Normal | Milestone: Component: ports | Version: Resolution: fixed | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Comment (by christsc@…): I've [https://code.google.com/p/stimfit/source/detail?r=1adb95de375a added a configure option to provide a custom LAPACK library] and [https://code.google.com/p/stimfit/source/detail?r=597dbe99a483 added a variant to use MacPorts atlas instead of system LAPACK]. The updated Portfile is available here: https://stimfit.googlecode.com/git/macosx/macports/science/stimfit/Portfile Should I submit a new ticket? -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:19> MacPorts <http://www.macports.org/> Ports system for OS X

#40317: stimfit @0.12.4_2: update 0.12.9 -------------------------+--------------------------------- Reporter: christsc@… | Owner: macports-tickets@… Type: update | Status: closed Priority: Normal | Milestone: Component: ports | Version: Resolution: fixed | Keywords: haspatch maintainer Port: stimfit | -------------------------+--------------------------------- Changes (by mojca@…): * status: reopened => closed * resolution: => fixed Comment: Committed in r110733. -- Ticket URL: <https://trac.macports.org/ticket/40317#comment:22> MacPorts <http://www.macports.org/> Ports system for OS X