Can't install scipy from svn (caused by ndimage)
Hi all, I cannot build/install scipy from svn. Here is the output of python setup.py install ... Lib/ndimage/src/ni_morphology.c: In function ‘NI_BinaryErosion’: Lib/ndimage/src/ni_morphology.c:101: warning: implicit declaration of function ‘NA_OFFSETDATA’ Lib/ndimage/src/ni_morphology.c:101: warning: cast to pointer from integer of different size Lib/ndimage/src/ni_morphology.c:110: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:128: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:129: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c: In function ‘NI_BinaryErosion2’: Lib/ndimage/src/ni_morphology.c:313: warning: cast to pointer from integer of different size Lib/ndimage/src/ni_morphology.c:340: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:354: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:370: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:467: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:468: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c: In function ‘NI_DistanceTransformBruteForce’: Lib/ndimage/src/ni_morphology.c:513: warning: pointer/integer type mismatch in conditional expression Lib/ndimage/src/ni_morphology.c:517: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:523: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:531: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:554: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c: In function ‘NI_DistanceTransformOnePass’: Lib/ndimage/src/ni_morphology.c:681: warning: cast to pointer from integer of different size Lib/ndimage/src/ni_morphology.c:691: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:709: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c: In function ‘NI_EuclideanFeatureTransform’: Lib/ndimage/src/ni_morphology.c:921: warning: pointer/integer type mismatch in conditional expression Lib/ndimage/src/ni_morphology.c:923: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c:924: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_morphology.c: At top level: /usr/lib64/python2.4/site-packages/numpy/core/include/numpy/__multiarray_api.h:944: warning: ‘_import_array’ defined but not used gcc: Lib/ndimage/src/ni_support.c Lib/ndimage/src/ni_support.c: In function ‘NI_InitLineBuffer’: Lib/ndimage/src/ni_support.c:147: warning: implicit declaration of function ‘NA_OFFSETDATA’ Lib/ndimage/src/ni_support.c:147: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_support.c: At top level: /usr/lib64/python2.4/site-packages/numpy/core/include/numpy/__multiarray_api.h:944: warning: ‘_import_array’ defined but not used gcc: Lib/ndimage/src/ni_fourier.c Lib/ndimage/src/ni_fourier.c: In function ‘NI_FourierFilter’: Lib/ndimage/src/ni_fourier.c:190: warning: implicit declaration of function ‘NA_OFFSETDATA’ Lib/ndimage/src/ni_fourier.c:190: warning: initialization makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:315: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:316: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:366: error: ‘npy_complex32’ undeclared (first use in this function) Lib/ndimage/src/ni_fourier.c:366: error: (Each undeclared identifier is reported only once Lib/ndimage/src/ni_fourier.c:366: error: for each function it appears in.) Lib/ndimage/src/ni_fourier.c:366: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:366: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:367: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:367: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:373: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:373: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:374: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:374: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:401: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:401: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:402: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:402: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c: In function ‘NI_FourierShift’: Lib/ndimage/src/ni_fourier.c:441: warning: initialization makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:497: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:498: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:524: error: ‘npy_complex32’ undeclared (first use in this function) Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:531: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:531: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:532: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:532: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c: In function ‘NI_FourierFilter’: Lib/ndimage/src/ni_fourier.c:190: warning: implicit declaration of function ‘NA_OFFSETDATA’ Lib/ndimage/src/ni_fourier.c:190: warning: initialization makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:315: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:316: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:366: error: ‘npy_complex32’ undeclared (first use in this function) Lib/ndimage/src/ni_fourier.c:366: error: (Each undeclared identifier is reported only once Lib/ndimage/src/ni_fourier.c:366: error: for each function it appears in.) Lib/ndimage/src/ni_fourier.c:366: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:366: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:367: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:367: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:373: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:373: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:374: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:374: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:401: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:401: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:402: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:402: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c: In function ‘NI_FourierShift’: Lib/ndimage/src/ni_fourier.c:441: warning: initialization makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:497: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:498: warning: assignment makes pointer from integer without a cast Lib/ndimage/src/ni_fourier.c:524: error: ‘npy_complex32’ undeclared (first use in this function) Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:524: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:525: error: ‘struct <anonymous>’ has no member named ‘i’ Lib/ndimage/src/ni_fourier.c:531: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:531: error: syntax error before ‘)’ token Lib/ndimage/src/ni_fourier.c:532: error: ‘struct <anonymous>’ has no member named ‘r’ Lib/ndimage/src/ni_fourier.c:532: error: ‘struct <anonymous>’ has no member named ‘i’ error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC -ILib/ndimage/src -I/usr/lib64/python2.4/site-packages/numpy/core/include -I/usr/lib64/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c Lib/ndimage/src/ni_fourier.c -o build/temp.linux-x86_64-2.4/Lib/ndimage/src/ni_fourier.o" failed with exit status 1 Nils
On Thu, Mar 29, 2007 at 09:08:25AM +0200, Nils Wagner wrote:
I cannot build/install scipy from svn. Here is the output of
python setup.py install
Sorry, Nils, I'm just moving around parts of ndimage. I'll be done soon. Cheers Stéfan
Stefan van der Walt wrote:
On Thu, Mar 29, 2007 at 09:08:25AM +0200, Nils Wagner wrote:
I cannot build/install scipy from svn. Here is the output of
python setup.py install
Sorry, Nils, I'm just moving around parts of ndimage. I'll be done soon.
Cheers Stéfan _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
Hi Stéfan, Now python setup.py install works fine for me, but I get a segfault running scipy.test(1) on a 64-bit machine using
scipy.__version__ '0.5.3.dev2888'
Here is a backtrace Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 46912509653888 (LWP 6350)] PyArray_NewFromDescr (subtype=0x2aaaabf1dee0, descr=0x2aaaabf20140, nd=1, dims=0x2, strides=0x0, data=0x0, flags=0, obj=0x0) at arrayobject.c:5318 5318 if (dims[i] == 0) continue; (gdb) bt #0 PyArray_NewFromDescr (subtype=0x2aaaabf1dee0, descr=0x2aaaabf20140, nd=1, dims=0x2, strides=0x0, data=0x0, flags=0, obj=0x0) at arrayobject.c:5318 #1 0x00002aaaae12aea2 in NA_NewArray (buffer=0xa499e0, type=<value optimized out>, ndim=1, shape=0x2) at nd_image.h:212 #2 0x00002aaaae12bf7c in Py_FilterFunc (buffer=<value optimized out>, filter_size=<value optimized out>, output=0x7fffff88b9d8, data=<value optimized out>) at nd_image.c:351 #3 0x00002aaaae1320a9 in NI_GenericFilter (input=0xc68290, function=0x2aaaae12bf40 <Py_FilterFunc>, data=0x7fffff88ba80, footprint=<value optimized out>, output=0x95a070, mode=<value optimized out>, cvalue=0, origins=0xa88eb0) at ni_filters.c:858 #4 0x00002aaaae12c263 in Py_GenericFilter (obj=<value optimized out>, args=<value optimized out>) at nd_image.c:411 Cheers, Nils
On Thu, Mar 29, 2007 at 01:16:13PM +0200, Nils Wagner wrote:
Stefan van der Walt wrote:
On Thu, Mar 29, 2007 at 09:08:25AM +0200, Nils Wagner wrote:
I cannot build/install scipy from svn. Here is the output of
python setup.py install
Sorry, Nils, I'm just moving around parts of ndimage. I'll be done soon.
Now python setup.py install works fine for me, but I get a segfault running scipy.test(1) on a 64-bit machine using
scipy.__version__ '0.5.3.dev2888'
Like I said, I'm working on it. Already fixed the memory error in r2889. Cheers Stéfan
Stefan van der Walt wrote:
On Thu, Mar 29, 2007 at 01:16:13PM +0200, Nils Wagner wrote:
Stefan van der Walt wrote:
On Thu, Mar 29, 2007 at 09:08:25AM +0200, Nils Wagner wrote:
I cannot build/install scipy from svn. Here is the output of
python setup.py install
Sorry, Nils, I'm just moving around parts of ndimage. I'll be done soon.
Now python setup.py install works fine for me, but I get a segfault running scipy.test(1) on a 64-bit machine using
scipy.__version__
'0.5.3.dev2888'
Like I said, I'm working on it. Already fixed the memory error in r2889.
Cheers Stéfan
_______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
Thank you very much ! Cheers, Nils With python2.4 I get ====================================================================== FAIL: test_explicit (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.4/site-packages/scipy/odr/tests/test_odr.py", line 49, in test_explicit np.array([ 1.2646548050648876e+03, -5.4018409956678255e+01, File "/usr/lib64/python2.4/site-packages/numpy/testing/utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib64/python2.4/site-packages/numpy/testing/utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 1.26462971e+03, -5.42545890e+01, -8.64250389e-02]) y: array([ 1.26465481e+03, -5.40184100e+01, -8.78497122e-02]) ====================================================================== FAIL: test_multi (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.4/site-packages/scipy/odr/tests/test_odr.py", line 190, in test_multi np.array([ 4.3799880305938963, 2.4333057577497703, 8.0028845899503978, File "/usr/lib64/python2.4/site-packages/numpy/testing/utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib64/python2.4/site-packages/numpy/testing/utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 4.31272063, 2.44289312, 7.76215871, 0.55995622, 0.46423343]) y: array([ 4.37998803, 2.43330576, 8.00288459, 0.51011472, 0.51739023]) ---------------------------------------------------------------------- Ran 1629 tests in 3.383s FAILED (failures=2) With python2.5 I get ====================================================================== ERROR: test_explicit (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 46, in test_explicit out = explicit_odr.run() File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 1049, in run self.output = Output(apply(odr, args, kwds)) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 576, in __init__ self.stopreason = report_error(self.info) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 143, in report_error 'Iteration limit reached')[info % 10] IndexError: tuple index out of range ====================================================================== ERROR: test_lorentz (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 291, in test_lorentz out = l_odr.run() File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 1049, in run self.output = Output(apply(odr, args, kwds)) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 576, in __init__ self.stopreason = report_error(self.info) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 143, in report_error 'Iteration limit reached')[info % 10] IndexError: tuple index out of range ====================================================================== ERROR: test_multi (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 187, in test_multi out = multi_odr.run() File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 1049, in run self.output = Output(apply(odr, args, kwds)) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 576, in __init__ self.stopreason = report_error(self.info) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 143, in report_error 'Iteration limit reached')[info % 10] IndexError: tuple index out of range ====================================================================== ERROR: test_pearson (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 235, in test_pearson out = p_odr.run() File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 1049, in run self.output = Output(apply(odr, args, kwds)) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 576, in __init__ self.stopreason = report_error(self.info) File "/usr/local/lib64/python2.5/site-packages/scipy/odr/odrpack.py", line 143, in report_error 'Iteration limit reached')[info % 10] IndexError: tuple index out of range
Hello, I would like to know if there is somme kind of roadmap for the developpement of SciPy/Numpy, I can't find it on the web site, neither on this mailing list. For example, I would like to know: - When will be the next stable version of SciPy/Numpy? - What will be the new features in the next version of SciPy - When is SciPy 1.0 planned? I am ready to begin a roadmap page on scipy.org wiki (as long as these informations are available). Thanks a lot for your answers and for this great piece of software! -- Gilles
participants (3)
-
Gilles G. -
Nils Wagner -
Stefan van der Walt