Mailman 3 September 2002 - SciPy-Dev

test error on Solaris using Sun's compilers
by Skip Montanaro Sept. 11, 2002

Sept. 11, 2002

I installed SciPy on a Solaris machine using Sun's C and Fortran compilers (hint for the unwary: this was *not* a straightforward exercise). During the test run I got a single failure (this is reproducible, not an anomaly due to different random inputs): FAIL: check_basic (test_morestats.test_shapiro) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/skip/local/SunOS/lib/python2.2/site-packages/scipy/stats/tests/test_morestats.py", line 30, in check_basic assert_almost_equal(w,0.90047299861907959,8) File "/home/skip/local/SunOS/lib/python2.2/site-packages/scipy_base/testing.py", line 283, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: DESIRED: 0.900472998619 ACTUAL: 0.900472760201 After a little bit of debugging, I concluded the problem is most likely in the Fortran code. Using the first input list in the test: x1 = [0.11,7.87,4.61,10.14,7.95,3.14,0.46, 4.43,0.21,4.75,0.71,1.52,3.24, 0.93,0.42,4.97,9.53,4.55,0.47,6.66] I manually executed the code in scipy.stats.morestats.shapiro, and got different results from the statlib.swilk call. On the Sun I got: >>> scipy.stats.statlib.swilk(y,a[:N/2],init) (array([ 0.47337097, 0.32174039, 0.25566325, 0.20829722, 0.16863985, 0.13358422, 0.10147439, 0.07128929, 0.04232321, 0.01403512],'f'), 0.90047276020050049, 0.042089268565177917, 0) On Linux I got: >>> scipy.stats.statlib.swilk(y,a[:N/2],init) (array([ 0.47337109, 0.32174024, 0.25566328, 0.20829724, 0.16863985, 0.13358422, 0.1014744 , 0.0712893 , 0.04232322, 0.01403512],'f'), 0.90047299861907959, 0.042089745402336121, 0) I can try compiling the underlying Fortran file with different flags (no optimization for instance). What else could/should I try? Thanks, -- Skip Montanaro skip(a)pobox.com consulting: http://manatee.mojam.com/~skip/resume.html

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please kindly get back to me
by LAURENT MPETI KABILA Sept. 7, 2002

Sept. 7, 2002

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Emissionsreport
by Mailserver Sept. 7, 2002

Sept. 7, 2002

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cluster/src/vq_wrap.cpp not being compiled with C++
by Skip Montanaro Sept. 4, 2002

Sept. 4, 2002

I'm trying to build SciPy on a Solaris system (sunos 5.8) using Sun's C, C++ and Fortran compilers. I've fiddled and faddled 'til it got down to compiling .../scipy/cluster. It goes to compile the vq_wrap.cpp file and tries compiling it with 'cc' instead of 'CC'. Distutils generates this command: cc -DNDEBUG -O -I/home/skip/local/SunOS/include/python2.2 -c cluster/src/vq_wrap.cpp -o build/temp.solaris-2.8-sun4u-2.2/vq_wrap.o which generates this message: cc: No input file specified, no output generated If I simply change 'cc' to 'CC' it compiles fine. I would have thought distutils would recognize the need to use 'CC' if the file extension was '.cpp'. If I try running python setup.py build_ext --compiler=CC distutils raises a PlatformError: don't know how to compile C/C++ code on platform 'posix' with 'CC' compiler I don't see anything like a command/build_cpplib.py file which might tell how to build C++ extensions. Where should I be looking for clues? Thx, -- Skip Montanaro skip(a)pobox.com

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special.cdflib questions
by Christopher Fonnesbeck Sept. 3, 2002

Sept. 3, 2002

I am curious about the cdflib fortran modules in the special subdirectory of scipy: Why are there so many arguments for each distribution? For example, if I want to call cdfbin to calculate a parameter of a binomial distribution, I should not need to supply BOTH p and q=1-p ... also, the status and bound arguments seem like something you would have returned to you, rather than passed to the function. How would I know the status of the calculation before its calculated? Finally, none of the cdf's seem to return any values, despite what the inline comments say. I am obviously way confused about this code, so I am hoping someone out there can set me straight. Thanks, cjf -- Christopher J. Fonnesbeck Georgia Cooperative Fish & Wildlife Research Unit University of Georgia Athens, GA 30602 cjf {at} fonnesbeck.net Absent, adj.: Exposed to the attacks of friends and acquaintances; defamed; slandered.

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(no subject)
by wu jing Sept. 2, 2002

Sept. 2, 2002

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implicit typename warnings in weave
by Christopher Fonnesbeck Sept. 1, 2002

Sept. 1, 2002

I am now having problems with weave (0.2.3). Though the install of the package goes smoothly, the tests fail miserably, with the error messages punctuated with "implicit typename is deprecated" warnings. I am using gcc 3.2 nowadays, so I wonder if this could be related? A typical selection of errors looks as follows: /usr/include/c++/3.2/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <sstream> instead of the deprecated header <strstream.h>. To disable this warning use -Wno-deprecated. In file included from /tmp/test_files/sc_058975d6fda30b79a63e0e6ecfeb90e60.cpp:5: /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1143: no class template named `random_access_iterator' in `std' /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1279: no class template named `random_access_iterator' in `std' /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1409: warning: `typename Py::SeqBase<T>::iterator' is implicitly a typename /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1409: warning: implicit typename is deprecated, please see the documentation for details /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1409: warning: `typename Py::SeqBase<T>::iterator' is implicitly a typename /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1409: warning: implicit typename is deprecated, please see the documentation for details /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1410: warning: `typename Py::SeqBase<T>::iterator' is implicitly a typename /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1410: warning: implicit typename is deprecated, please see the documentation for details /usr/share/downloads/weave-0.2.3/weave/CXX/Objects.hxx:1410: warning: `typename Py::SeqBase<T>::iterator' is implicitly a typename etc. Anyone had similar problems? cjf -- Christopher J. Fonnesbeck Georgia Cooperative Fish & Wildlife Research Unit University of Georgia Athens, GA 30602 cjf {at} fonnesbeck.net Absent, adj.: Exposed to the attacks of friends and acquaintances; defamed; slandered.

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undefined symbol: clapack_sgesv
by Christopher Fonnesbeck Sept. 1, 2002

Sept. 1, 2002

I saw some postings back in april related to getting a message similar to the following: >>> import scipy exceptions.ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv This, despite the fact that clapack_sgesv is defined. Has there been any progress solving this bug? I compiles scipy (including ATLAS) on a RH machine using gcc3.2. cjf -- Christopher J. Fonnesbeck Georgia Cooperative Fish & Wildlife Research Unit University of Georgia Athens, GA 30602 cjf {at} fonnesbeck.net Absent, adj.: Exposed to the attacks of friends and acquaintances; defamed; slandered.

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ADV: Harvest lots of E-mail addresses quickly !
by james2000＠etang.com Sept. 1, 2002

Sept. 1, 2002

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