Mailman 3 March 2005 - SciPy-User

stats newbie question
by r help 16 Mar '05

16 Mar '05

hi i am attempting to use the cdf of a lognormal distribution but i cant seem to locate the docs to do this correctly. ive been trying from scipy import * from scipy.stats import * then i try lognorm.cdf(1,1) stats.lognorm.cdf(1,1) which just give errors. can anyone shed some light on how to access the lognorm distribution. -gong __________________________________ Do you Yahoo!? Yahoo! Small Business - Try our new resources site! http://smallbusiness.yahoo.com/resources/

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Re: [Numpy-discussion] Re: [SciPy-user] Current thoughts on future directions
by Fernando Perez 15 Mar '05

15 Mar '05

Michiel Jan Laurens de Hoon wrote: > Perry Greenfield wrote: [weave & f2py in the core] >>That they are perfectly fine to go into the core. In fact, if they are >>used by any of the extra packages, they should be in the core to >>eliminate the extra step in the installation of those packages. >> > > -0. > 1) In der Beschraenkung zeigt sich der Meister. In other words, avoid > software bloat. > 2) f2py is a Fortran-Python interface generator, once the interface is > created there is no need for the generator. > 3) I'm sure f2py is useful, but I doubt that it has very general > usefulness. There are lots of other useful Python packages, but we're > not including them in scipy-core either. > 4) f2py and weave don't fit in well with the rest of scipy-core, which > is mainly standard numerical algorithms. I'd like to argue that these two tools are actually critically important in the core of a python for scientific computing toolkit, at its most basic layer. The reason is that python's dynamic runtime type checking makes it impossible to write efficient loop-based code, as we all know. And it is not always feasible to write all algorithms in terms of Numeric vector operations: sometimes you just need to write an indexed loop. At this point, the standard python answer is 'go write an extension module'. While writing extension modules by hand, from scratch, is not all that hard, it certainly presents a significant barrier for less experienced programmers. And yet both weave and f2py make it incredibly easy to get working compiled array code in no time at all. I say this from direct experience, having pointed colleagues to weave and f2py for this very problem. After handing them some notes I have to get started, they've come back saying "I can't believe it was that easy: in a few minutes I had sped up the loop I needed with a bit of C, and now I can continue working on the problem I'm interested in". I know for a fact that if I'd told them to write a full extension module by hand, the result would have been quite different. The reality is that, in scientific work, you are likely to run into this problem at a very early stage, much more so than for other kinds of python usage. For this reason, it is important that the basic toolset provides a clean solution from the start. At least that's been my experience. Regards, f

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Re: Partial Derivatives
by R. Padraic Springuel 15 Mar '05

15 Mar '05

I know its been a while since I last brought this up (Vol 19, Issue 1), but after some digging, I've discovered Scientific.Functions.Derivatives (it came with the Enthought Edition of python that I use). It defines a DerivVar type that works well for taking derivatives of functions, supporting partial derivatives (even cross partials) very well. I haven't fully tested the limits of its accuracy, but some basic tests show it to be at least as accurate as the top level derivative function in scipy. Perhaps instead of trying to modify derivative (and central_diff_weights) it'll be easier in future versions of scipy to include this type and raise it to the top level. -- R. Padraic Springuel

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Re: [SciPy-user] Re: optimize.leastsq -> fjac and the covariance redux
by Brendan Simons 15 Mar '05

15 Mar '05

OK, solved both problems. The r matrix obtained from fjac must be post multiplied by the permutation matrix, not its transpose. Line 254 in minpack.py should be changed from: R = dot(r, transpose(perm)) to: R = dot(r, perm) That gets the ordering of the Covariance to match my test. As for the second issue, (the fact that giving Dfun=J in leastsq leads to the wrong minimum) I did some googling and found this post from John Hunter a year ago: >John Hunter scipy-user(a)scipy.net >Mon, 21 Apr 2003 13:55:09 -0500 > >I am using leastsq to do a best fit to a simple >exponential function. >In my test script, I find that if I use col_deriv=0, I >get a different >answer than I get if I do a col_deriv=1 with the err >func returning >the transposed jacobian. When I compare the true >parameters with the >best fit parameters, the correct answer is with >col_deriv=1 but not >with col_deriv=0. Am I misusing this parameter or is >something amiss? --example snipped-- Sure enough, providing the transpose of J to Dfun, and setting col_deriv = True gives the right answer! This is obviously a bug in how leastsq handles col_deriv, and needs to be looked at. The good news is I now have a covariance matrix! Thanks Travis! -Brendan On March 15 I wrote: > >Here C has all the right outputs, but in the wrong >order. Evidently >we're applying the >ipvt permutation matrix wrong somehow. > >Here's something worse. If I include the jacobian in >the leastsq call >as follows >pMin, C, infodict, ier, mesg = leastsq(resid, p0, >args=(y_meas, x), >Dfun = J, full_output=True) >the resulting pMin is the same as p0, and C is way off >of C_true. What >gives? -Brendan ______________________________________________________________________ Post your free ad now! http://personals.yahoo.ca

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plotting with xplt
by Evelien Vanhollebeke 15 Mar '05

15 Mar '05

Hi everybody, I wondered if anyone has ever tried with xplt to plot multiple figures on one page. I know it is easy with pylab, but I would like to try it in xplt. One of the reasons is that in pylab I can't make a ps file consisting of different pages without doing a "psmerge" or something like that. If anyone has ever been successful on this, I hope I can get some ideas/examples on how to do it. I am still in the process of deciding which plotting package fulfills my needs. Thanks! Evelien

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Re: optimize.leastsq -> fjac and the covariance redux
by Brendan Simons 14 Mar '05

14 Mar '05

Aha! Great job. I do want to learn CVS at some point, but it's probably not worth the effort to get me developer access, especially as my implementation would probably not the most efficient. If you're willing to implement the Covariance output yourself, please send me a note when it's committed. Thanks again for your help. -Brendan --- Travis Oliphant <oliphant(a)ee.byu.edu> wrote: > Brendan Simons wrote: > > Thanks for the example script. > > I think I've got it worked out. > > The only problem with the script is that fjac is in > "column-order" i.e. > Fortran order. So, really what we have provided is > r.T > > Note that there are several q-r factorizations for a > given matrix, so > comparing r is not useful. > > If you change this line: > > r = mat(MLab.triu(fjac[:,:n])) > > to this: > > r = mat(MLab.triu(transpose(fjac)[:n,:])) > > the results match up !!! > > With the change, I get > > C > Matrix([[ 0.821428641610194, -0.589285827415852, > 0.089285739190248], > [-0.589285827415852, 0.726785855320911, > -0.133928600229779], > [ 0.089285739190248, -0.133928600229779, > 0.026785719996822]]) > > C_true > [[ 0.821428571428571 -0.589285714285714 > 0.089285714285714] > [-0.589285714285714 0.726785714285714 > -0.133928571428571] > [ 0.089285714285714 -0.133928571428571 > 0.026785714285714]] > > C_true2 > [[ 0.82142857142857 -0.589285714285713 > 0.089285714285714] > [-0.589285714285714 0.726785714285714 > -0.133928571428571] > [ 0.089285714285714 -0.133928571428571 > 0.026785714285714]] > > > This is great. I'll see if I can't put in a new > optional output for > leastsq that makes use of this. > > If you'd like to do it, then that would be great > too. It is easy to > commit to CVS once you have developer access. If > you are interested > then I could get you set up. > > You would need to check out a "logged-in" version of > the CVS tree and > then committing is as easy as > > cvs commit -m "Some comments" > > > Thanks for your help. > > -Travis > > ______________________________________________________________________ Post your free ad now! http://personals.yahoo.ca

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Re: [Numpy-discussion] Current thoughts on future directions
by Stephen Walton 14 Mar '05

14 Mar '05

Michiel Jan Laurens de Hoon wrote: > I agree that Netlib should be in SciPy. But why should Netlib be in > scipy_base? It should not, and I'm sorry if my original message made it sound like I was advocating for that. I was mainly advocating for f2py to be in scipy_base.

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Re: optimize.leastsq -> fjac and the covariance redux
by Brendan Simons 14 Mar '05

14 Mar '05

>Brendan, > >Thanks for your detailed comments. I would love to >see the covariance >matrix as a standard optional output. If you can help >us get there from >the code that would be great. > >As I look at the Fortran docstring, I think it's >pretty clear that the >leastsq Python docstring is wrong (sorry about that >since I probably >wrote it...) fjac is basically the R matrix (once you >apply some >permutations), thus, I'm pretty sure you can use the >upper triangular >part of the fjac matrix with the ipvt vector (also in >infodict) to >caculate the covariance matrix as you describe. > >So, I would construct a permutation matrix P (using >ipvt) like this: > >n = len(ipvt) >p = mat(take(eye(n),ipvt)) > >and then get R using some thing like > >r = mat(MLab.triu(fjac)) >R = r * p.T > >Then covariance matrix estimate is > >C = (R.T * R).I > > >This is totally untested, but I think you are on the >right track to use >fjac as the R matrix of the QR factorization. > >Thanks for your help, > >-Travis Travis, I too would like to see the covariance in the leastsq optional outputs. Using your suggestion, I whipped up the following script, which fits a simple quadratic (chosen because I can calculate the jacobian easily by hand): #---begin script-------- """script to test the fjac output matrix of scipy.optimize.leastsq Placed in public domain by Brendan Simons March 2005 """ from scipy import * import MLab from scipy.optimize import leastsq x = array([0., 1., 2., 3., 4., 5.], typecode='f') coeffs = [4., 3., 5.] yErrs = array([0.1, 0.2, -0.1, 0.05, 0, -.02], typecode='f') m = len(x) n = len(coeffs) def evalY(p, x): """a simple quadratic""" return p[2]*x**2 + p[1]*x + p[0] def J(p, x): """the jacobian of a quadratic""" result = zeros([m,n], typecode='f') result[:, 0] = ones(m, typecode='f') result[:, 1] = x result[:, 2] = x*x return result def resid(p, y, x): return y - evalY(p, x) y_true = y(coeffs, x) y_meas = y_true + yErrs p0 = [3., 2., 4.] pMin, infodict, ier, mesg = leastsq(resid, p0, args=(y_meas, x), full_output=True) fjac = infodict['fjac'] ipvt = infodict['ipvt'] #here's travis' suggestion perm = mat(take(eye(n),ipvt-1)) r = mat(MLab.triu(fjac[:,:n])) R = r * perm.T C = (R.T * R).I #check against know algorithms for computing C Q_true, R_true = linalg.qr(J(pMin, x)) C_true = linalg.inv(dot(transpose(J(pMin, x)), J(pMin, x))) C_true2 = linalg.inv(dot(transpose(R_true), R_true)) print 'pMin' print pMin print '\nfjac' print fjac print'\nipvt' print ipvt print '\nperm' print perm print '\nr' print r print '\nR' print R print '\nR_true' print R_true print '\nC' print C print '\nC_true' print C_true print '\nC_true2' print C_true2 #---end script-------- Note that I had to make the following modifications to your algorithm: a) The Fortran docstring says r is in the first nxn submatrix of fjac, so I truncated fjac with [:, :n] before applying MLab.triu b) the identity matrix columns returned by ipvt are 1-based, not 0-based (Fortran is 1-based I guess). So I subtracted 1 in which results in perm = mat(take(eye(n),ipvt-1)) The results from the script are as follows: #--- begin script output---- pMin [ 4.13714286 2.93428571 5.00714286] fjac [[-31.28897539 -0.03196014 -0.12784056 -0.28764125 -0.51136222 -0.79900346] [ -7.19103119 1.81357942 0.59589038 0.51365984 0.17797854 -0.41115309] [ -1.75780755 1.30104626 -1.10335453 0.03523648 -0.29732131 -0.95308465]] ipvt [3 2 1] perm Matrix([[ 0., 0., 1.], [ 0., 1., 0.], [ 1., 0., 0.]]) r Matrix([[-31.28897539, -0.03196014, -0.12784056], [ 0. , 1.81357942, 0.59589038], [ 0. , 0. , -1.10335453]]) R Matrix([[ -0.12784056, -0.03196014, -31.28897539], [ 0.59589038, 1.81357942, 0. ], [ -1.10335453, 0. , 0. ]]) R_true [[ -2.44948983 -6.12372446 -22.45365715] [ 0. 4.18329954 20.916502 ] [ 0. 0. 6.11010218] [ 0. 0. 0. ] [ 0. 0. 0. ] [ 0. 0. 0. ]] C Matrix([[ 8.21428627e-001, -2.69897976e-001, -3.08050728e-003], [-2.69897976e-001, 3.92718047e-001, 7.01607645e-004], [-3.08050728e-003, 7.01607645e-004, 1.03332016e-003]]) C_true [[ 0.8214277 -0.58928472 0.08928555] [-0.58928496 0.72678488 -0.13392843] [ 0.08928559 -0.13392843 0.02678569]] C_true2 [[ 0.82142925 -0.58928621 0.08928578] [-0.58928627 0.72678584 -0.13392855] [ 0.08928579 -0.13392855 0.0267857 ]] #--- end script output---- So you can see it doesn't work as expected. C does not equal C_true. More troublesome is that *no* columns of fjac resemble R_true, no matter what permutation matrix is applied. At this point I'm lost as to what is what. Any suggestions? -Brendan -- PS, If and when we figure out the answer, I'd like to submit the change to CVS. However, never having done such a thing, I will need some instruction. ______________________________________________________________________ Post your free ad now! http://personals.yahoo.ca

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advice on scipy installation
by Darren Dale 14 Mar '05

14 Mar '05

Hello scipy users, I am having some trouble with installing scipy-0.3.2, specifically linking to atlas. I asked a question about this a month or two ago, and didnt receive a response. Please, I would really appreciate some help, and I think I located a bug. First, I have read all the documentation about installing scipy: I am using site.cfg to reflect my setup. The output of system_info.py is included at the end of this email, all the atlas, lapack, and blas info was found and reported (with the exception of blas_src_info and lapack_src_info, which are not available on my machine). So up to this point, things look good. The trouble starts when I try to run python setup.py build. At this point I am getting NOT AVAILABLE messages, but for packages that system_info.py had just successfully queried. Why would system_info.py report the existence of packages when I run it manually, but fail to report the same packages during installation? I think I have a lead. site.cfg is not being read during the build, because the installer is looking for it at ./site.cfg instead of at ./scipy_core/scipy_distutils/site.cfg. I think the offending line is around line 287 in system_info.py: cf = os.path.join(os.path.split(os.path.abspath(__file__))[0], 'site.cfg') __file__ is ./setup.py during the build, and ./scipy_core/scipy_distutils/system_info.py when I call system_info.py. Could somebody recommend a fix? Do I copy site.cfg to ./? I dont think this is the right thing to do, but I dont know how to point cf to the right location (I still have a lot to learn about python). Thank you for your time. Darren Here is the output of: python setup_atlas_version.py build_ext --inplace --force ______________________________________________________________ atlas_threads_info: scipy_distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: scipy_distutils.system_info.atlas_info NOT AVAILABLE Traceback (most recent call last): File "setup_atlas_version.py", line 27, in ? setup(**configuration()) File "setup_atlas_version.py", line 17, in configuration raise AtlasNotFoundError,AtlasNotFoundError.__doc__ scipy_distutils.system_info.AtlasNotFoundError: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. output from system_info.py listed below: ______________________________________________________________ _pkg_config_info: NOT AVAILABLE agg2_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE atlas_blas_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/liblapack.so ) ( paths: /usr/lib/libblas.so ) ( paths: /usr/lib/libcblas.so ) ( paths: /usr/lib/libatlas.so ) system_info.atlas_blas_info ( include_dirs = /usr/include/atlas:/usr/local/include:/usr/include ) ( paths: /usr/include/atlas/atlas_cNCmm.h,/usr/include/atlas/atlas_smvN.h,/usr/include/atlas/atlas_smvS.h,/usr/include/atlas/atlas_smvT.h,/usr/include/atlas/atlas_dNCmm.h,/usr/include/atlas/atlas_type.h,/usr/include/atlas/atlas_zmvN.h,/usr/include/atlas/atlas_zmvS.h,/usr/include/atlas/atlas_zmvT.h,/usr/include/atlas/atlas_sNCmm.h,/usr/include/atlas/atlas_zNCmm.h,/usr/include/atlas/atlas_zsysinfo.h,/usr/include/atlas/atlas_ctrsmXover.h,/usr/include/atlas/atlas_ztrsmXover.h,/usr/include/atlas/atlas_csysinfo.h,/usr/include/atlas/atlas_dtrsmXover.h,/usr/include/atlas/atlas_ssysinfo.h,/usr/include/atlas/atlas_cr1.h,/usr/include/atlas/atlas_cmv.h,/usr/include/atlas/atlas_dr1.h,/usr/include/atlas/atlas_dmv.h,/usr/include/atlas/atlas_sr1.h,/usr/include/atlas/atlas_smv.h,/usr/include/atlas/atlas_zr1.h,/usr/include/atlas/atlas_zmv.h,/usr/include/atlas/atlas_strsmXover.h,/usr/include/atlas/atlas_dsysinfo.h,/usr/include/atlas/atlas_cacheedge.h,/usr/include/atlas/atlas_buildinfo.h,/usr/include/atlas/atlas_cmvN.h,/usr/include/atlas/atlas_cmvS.h,/usr/include/atlas/atlas_cmvT.h,/usr/include/atlas/atlas_dmvN.h,/usr/include/atlas/atlas_dmvS.h,/usr/include/atlas/atlas_dmvT.h ) ( paths: /usr/include/atlas ) ( paths: /usr/include/atlas/cblas.h,/usr/include/atlas/cblas.h ) FOUND: libraries = ['lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c include_dirs = ['/usr/include/atlas'] atlas_blas_threads_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/liblapack.so ) ( paths: /usr/lib/libblas.so ) ( paths: /usr/lib/libcblas.so ) ( paths: /usr/lib/libatlas.so ) system_info.atlas_blas_threads_info ( include_dirs = /usr/include/atlas:/usr/local/include:/usr/include ) ( paths: /usr/include/atlas/atlas_cNCmm.h,/usr/include/atlas/atlas_smvN.h,/usr/include/atlas/atlas_smvS.h,/usr/include/atlas/atlas_smvT.h,/usr/include/atlas/atlas_dNCmm.h,/usr/include/atlas/atlas_type.h,/usr/include/atlas/atlas_zmvN.h,/usr/include/atlas/atlas_zmvS.h,/usr/include/atlas/atlas_zmvT.h,/usr/include/atlas/atlas_sNCmm.h,/usr/include/atlas/atlas_zNCmm.h,/usr/include/atlas/atlas_zsysinfo.h,/usr/include/atlas/atlas_ctrsmXover.h,/usr/include/atlas/atlas_ztrsmXover.h,/usr/include/atlas/atlas_csysinfo.h,/usr/include/atlas/atlas_dtrsmXover.h,/usr/include/atlas/atlas_ssysinfo.h,/usr/include/atlas/atlas_cr1.h,/usr/include/atlas/atlas_cmv.h,/usr/include/atlas/atlas_dr1.h,/usr/include/atlas/atlas_dmv.h,/usr/include/atlas/atlas_sr1.h,/usr/include/atlas/atlas_smv.h,/usr/include/atlas/atlas_zr1.h,/usr/include/atlas/atlas_zmv.h,/usr/include/atlas/atlas_strsmXover.h,/usr/include/atlas/atlas_dsysinfo.h,/usr/include/atlas/atlas_cacheedge.h,/usr/include/atlas/atlas_buildinfo.h,/usr/include/atlas/atlas_cmvN.h,/usr/include/atlas/atlas_cmvS.h,/usr/include/atlas/atlas_cmvT.h,/usr/include/atlas/atlas_dmvN.h,/usr/include/atlas/atlas_dmvS.h,/usr/include/atlas/atlas_dmvT.h ) ( paths: /usr/include/atlas ) ( paths: /usr/include/atlas/cblas.h,/usr/include/atlas/cblas.h ) FOUND: libraries = ['lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c include_dirs = ['/usr/include/atlas'] atlas_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/liblapack.so ) ( paths: /usr/lib/libblas.so ) ( paths: /usr/lib/libcblas.so ) ( paths: /usr/lib/libatlas.so ) ( paths: /usr/lib/liblapack.so ) system_info.atlas_info ( include_dirs = /usr/include/atlas:/usr/local/include:/usr/include ) ( paths: /usr/include/atlas/atlas_cNCmm.h,/usr/include/atlas/atlas_smvN.h,/usr/include/atlas/atlas_smvS.h,/usr/include/atlas/atlas_smvT.h,/usr/include/atlas/atlas_dNCmm.h,/usr/include/atlas/atlas_type.h,/usr/include/atlas/atlas_zmvN.h,/usr/include/atlas/atlas_zmvS.h,/usr/include/atlas/atlas_zmvT.h,/usr/include/atlas/atlas_sNCmm.h,/usr/include/atlas/atlas_zNCmm.h,/usr/include/atlas/atlas_zsysinfo.h,/usr/include/atlas/atlas_ctrsmXover.h,/usr/include/atlas/atlas_ztrsmXover.h,/usr/include/atlas/atlas_csysinfo.h,/usr/include/atlas/atlas_dtrsmXover.h,/usr/include/atlas/atlas_ssysinfo.h,/usr/include/atlas/atlas_cr1.h,/usr/include/atlas/atlas_cmv.h,/usr/include/atlas/atlas_dr1.h,/usr/include/atlas/atlas_dmv.h,/usr/include/atlas/atlas_sr1.h,/usr/include/atlas/atlas_smv.h,/usr/include/atlas/atlas_zr1.h,/usr/include/atlas/atlas_zmv.h,/usr/include/atlas/atlas_strsmXover.h,/usr/include/atlas/atlas_dsysinfo.h,/usr/include/atlas/atlas_cacheedge.h,/usr/include/atlas/atlas_buildinfo.h,/usr/include/atlas/atlas_cmvN.h,/usr/include/atlas/atlas_cmvS.h,/usr/include/atlas/atlas_cmvT.h,/usr/include/atlas/atlas_dmvN.h,/usr/include/atlas/atlas_dmvS.h,/usr/include/atlas/atlas_dmvT.h ) ( paths: /usr/include/atlas ) ( paths: /usr/include/atlas/cblas.h,/usr/include/atlas/cblas.h ) FOUND: libraries = ['lapack', 'lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 include_dirs = ['/usr/include/atlas'] atlas_threads_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/liblapack.so ) ( paths: /usr/lib/libblas.so ) ( paths: /usr/lib/libcblas.so ) ( paths: /usr/lib/libatlas.so ) ( paths: /usr/lib/liblapack.so ) system_info.atlas_threads_info ( include_dirs = /usr/include/atlas:/usr/local/include:/usr/include ) ( paths: /usr/include/atlas/atlas_cNCmm.h,/usr/include/atlas/atlas_smvN.h,/usr/include/atlas/atlas_smvS.h,/usr/include/atlas/atlas_smvT.h,/usr/include/atlas/atlas_dNCmm.h,/usr/include/atlas/atlas_type.h,/usr/include/atlas/atlas_zmvN.h,/usr/include/atlas/atlas_zmvS.h,/usr/include/atlas/atlas_zmvT.h,/usr/include/atlas/atlas_sNCmm.h,/usr/include/atlas/atlas_zNCmm.h,/usr/include/atlas/atlas_zsysinfo.h,/usr/include/atlas/atlas_ctrsmXover.h,/usr/include/atlas/atlas_ztrsmXover.h,/usr/include/atlas/atlas_csysinfo.h,/usr/include/atlas/atlas_dtrsmXover.h,/usr/include/atlas/atlas_ssysinfo.h,/usr/include/atlas/atlas_cr1.h,/usr/include/atlas/atlas_cmv.h,/usr/include/atlas/atlas_dr1.h,/usr/include/atlas/atlas_dmv.h,/usr/include/atlas/atlas_sr1.h,/usr/include/atlas/atlas_smv.h,/usr/include/atlas/atlas_zr1.h,/usr/include/atlas/atlas_zmv.h,/usr/include/atlas/atlas_strsmXover.h,/usr/include/atlas/atlas_dsysinfo.h,/usr/include/atlas/atlas_cacheedge.h,/usr/include/atlas/atlas_buildinfo.h,/usr/include/atlas/atlas_cmvN.h,/usr/include/atlas/atlas_cmvS.h,/usr/include/atlas/atlas_cmvT.h,/usr/include/atlas/atlas_dmvN.h,/usr/include/atlas/atlas_dmvS.h,/usr/include/atlas/atlas_dmvT.h ) ( paths: /usr/include/atlas ) ( paths: /usr/include/atlas/cblas.h,/usr/include/atlas/cblas.h ) FOUND: libraries = ['lapack', 'lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 include_dirs = ['/usr/include/atlas'] blas_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/libblas.so ) FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 blas_opt_info: running build_src building extension "atlas_version" sources creating build/src adding 'build/src/atlas_version_0x53b6c39a.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'atlas_version' extension compiling C sources i686-pc-linux-gnu-gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -fPIC' creating build/temp.linux-i686-2.3 creating build/temp.linux-i686-2.3/build creating build/temp.linux-i686-2.3/build/src compile options: '-I/usr/include/atlas -I/usr/include/python2.3 -c' i686-pc-linux-gnu-gcc: build/src/atlas_version_0x53b6c39a.c i686-pc-linux-gnu-gcc -pthread -shared build/temp.linux-i686-2.3/build/src/atlas_version_0x53b6c39a.o -L/usr/lib -latlas -o build/temp.linux-i686-2.3/atlas_version.so FOUND: libraries = ['lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] include_dirs = ['/usr/include/atlas'] blas_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE boost_python_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE dfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE dfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE djbfft_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE fftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE fftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE freetype2_info: FOUND: libraries = ['freetype', 'z'] define_macros = [('FREETYPE2_INFO', '"\\"9.7.3\\""'), ('FREETYPE2_VERSION_9_7_3', None)] include_dirs = ['/usr/include/freetype2'] gdk_2_info: FOUND: libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_2_INFO', '"\\"2.6.2\\""'), ('GDK_VERSION_2_6_2', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_info: FOUND: libraries = ['gdk', 'Xi', 'Xext', 'X11', 'm', 'glib'] library_dirs = ['/usr/X11R6/lib'] define_macros = [('GDK_INFO', '"\\"1.2.10\\""'), ('GDK_VERSION_1_2_10', None)] include_dirs = ['/usr/include/gtk-1.2', '/usr/X11R6/include', '/usr/include/glib-1.2', '/usr/lib/glib/include'] gdk_pixbuf_2_info: FOUND: libraries = ['gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GDK_PIXBUF_2_INFO', '"\\"2.6.2\\""'), ('GDK_PIXBUF_VERSION_2_6_2', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_pixbuf_xlib_2_info: FOUND: libraries = ['gdk_pixbuf_xlib-2.0', 'gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_PIXBUF_XLIB_2_INFO', '"\\"2.6.2\\""'), ('GDK_PIXBUF_XLIB_VERSION_2_6_2', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_x11_2_info: FOUND: libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_X11_2_INFO', '"\\"2.6.2\\""'), ('GDK_X11_VERSION_2_6_2', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gtkp_2_info: FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GTKP_2_INFO', '"\\"2.6.2\\""'), ('GTK_VERSION_2_6_2', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gtkp_x11_2_info: FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GTKP_X11_2_INFO', '"\\"2.6.2\\""'), ('GTK_X11_VERSION_2_6_2', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] lapack_atlas_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/liblapack.so ) ( paths: /usr/lib/libblas.so ) ( paths: /usr/lib/libcblas.so ) ( paths: /usr/lib/libatlas.so ) ( paths: /usr/lib/liblapack.so ) system_info.lapack_atlas_info ( include_dirs = /usr/include/atlas:/usr/local/include:/usr/include ) ( paths: /usr/include/atlas/atlas_cNCmm.h,/usr/include/atlas/atlas_smvN.h,/usr/include/atlas/atlas_smvS.h,/usr/include/atlas/atlas_smvT.h,/usr/include/atlas/atlas_dNCmm.h,/usr/include/atlas/atlas_type.h,/usr/include/atlas/atlas_zmvN.h,/usr/include/atlas/atlas_zmvS.h,/usr/include/atlas/atlas_zmvT.h,/usr/include/atlas/atlas_sNCmm.h,/usr/include/atlas/atlas_zNCmm.h,/usr/include/atlas/atlas_zsysinfo.h,/usr/include/atlas/atlas_ctrsmXover.h,/usr/include/atlas/atlas_ztrsmXover.h,/usr/include/atlas/atlas_csysinfo.h,/usr/include/atlas/atlas_dtrsmXover.h,/usr/include/atlas/atlas_ssysinfo.h,/usr/include/atlas/atlas_cr1.h,/usr/include/atlas/atlas_cmv.h,/usr/include/atlas/atlas_dr1.h,/usr/include/atlas/atlas_dmv.h,/usr/include/atlas/atlas_sr1.h,/usr/include/atlas/atlas_smv.h,/usr/include/atlas/atlas_zr1.h,/usr/include/atlas/atlas_zmv.h,/usr/include/atlas/atlas_strsmXover.h,/usr/include/atlas/atlas_dsysinfo.h,/usr/include/atlas/atlas_cacheedge.h,/usr/include/atlas/atlas_buildinfo.h,/usr/include/atlas/atlas_cmvN.h,/usr/include/atlas/atlas_cmvS.h,/usr/include/atlas/atlas_cmvT.h,/usr/include/atlas/atlas_dmvN.h,/usr/include/atlas/atlas_dmvS.h,/usr/include/atlas/atlas_dmvT.h ) ( paths: /usr/include/atlas ) ( paths: /usr/include/atlas/cblas.h,/usr/include/atlas/cblas.h ) FOUND: libraries = ['lapack', 'lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 include_dirs = ['/usr/include/atlas'] lapack_atlas_threads_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/liblapack.so ) ( paths: /usr/lib/libblas.so ) ( paths: /usr/lib/libcblas.so ) ( paths: /usr/lib/libatlas.so ) ( paths: /usr/lib/liblapack.so ) system_info.lapack_atlas_threads_info ( include_dirs = /usr/include/atlas:/usr/local/include:/usr/include ) ( paths: /usr/include/atlas/atlas_cNCmm.h,/usr/include/atlas/atlas_smvN.h,/usr/include/atlas/atlas_smvS.h,/usr/include/atlas/atlas_smvT.h,/usr/include/atlas/atlas_dNCmm.h,/usr/include/atlas/atlas_type.h,/usr/include/atlas/atlas_zmvN.h,/usr/include/atlas/atlas_zmvS.h,/usr/include/atlas/atlas_zmvT.h,/usr/include/atlas/atlas_sNCmm.h,/usr/include/atlas/atlas_zNCmm.h,/usr/include/atlas/atlas_zsysinfo.h,/usr/include/atlas/atlas_ctrsmXover.h,/usr/include/atlas/atlas_ztrsmXover.h,/usr/include/atlas/atlas_csysinfo.h,/usr/include/atlas/atlas_dtrsmXover.h,/usr/include/atlas/atlas_ssysinfo.h,/usr/include/atlas/atlas_cr1.h,/usr/include/atlas/atlas_cmv.h,/usr/include/atlas/atlas_dr1.h,/usr/include/atlas/atlas_dmv.h,/usr/include/atlas/atlas_sr1.h,/usr/include/atlas/atlas_smv.h,/usr/include/atlas/atlas_zr1.h,/usr/include/atlas/atlas_zmv.h,/usr/include/atlas/atlas_strsmXover.h,/usr/include/atlas/atlas_dsysinfo.h,/usr/include/atlas/atlas_cacheedge.h,/usr/include/atlas/atlas_buildinfo.h,/usr/include/atlas/atlas_cmvN.h,/usr/include/atlas/atlas_cmvS.h,/usr/include/atlas/atlas_cmvT.h,/usr/include/atlas/atlas_dmvN.h,/usr/include/atlas/atlas_dmvS.h,/usr/include/atlas/atlas_dmvT.h ) ( paths: /usr/include/atlas ) ( paths: /usr/include/atlas/cblas.h,/usr/include/atlas/cblas.h ) FOUND: libraries = ['lapack', 'lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 include_dirs = ['/usr/include/atlas'] lapack_info: ( library_dirs = /usr/lib:/usr/local/lib ) ( paths: /usr/lib/liblapack.so ) FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 lapack_opt_info: /scratch/python/SciPy_complete-0.3.2/scipy_core/scipy_distutils/system_info.py:812: FutureWarning: hex()/oct() of negative int will return a signed string inPython 2.4 and up magic = hex(hash(`config`)) running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0xe146d5ff.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext Could not locate executable f77 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext FOUND: libraries = ['lapack', 'lapack', 'blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] include_dirs = ['/usr/include/atlas'] lapack_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE numarray_info: ( include_dirs = /usr/include/python2.3 ) ( paths: /usr/include/python2.3/numarray/arrayobject.h ) FOUND: define_macros = [('NUMARRAY_VERSION', '"\\"1.1.1\\""')] include_dirs = ['/usr/include/python2.3'] numpy_info: ( include_dirs = /usr/include/python2.3 ) ( paths: /usr/include/python2.3/Numeric/arrayobject.h ) FOUND: define_macros = [('NUMERIC_VERSION', '"\\"23.8\\""')] include_dirs = ['/usr/include/python2.3'] sfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE sfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE wx_info: FOUND: libraries = ['wx_gtk2-2.4'] extra_link_args = ['-pthread'] define_macros = [('WX_INFO', '"\\"2.4.2\\""'), ('WX_VERSION_2_4_2', None), ('WX_RELEASE_2_4', None), ('GTK_NO_CHECK_CASTS', None), ('__WXGTK__', None), ('_FILE_OFFSET_BITS', '64'), ('_LARGE_FILES', None)] include_dirs = ['/usr/lib/wx/include/gtk2-2.4'] x11_info: ( library_dirs = /usr/X11R6/lib:/usr/lib ) ( include_dirs = /usr/X11R6/include:/usr/include ) ( paths: /usr/X11R6/lib/libX11.so ) ( paths: /usr/X11R6/include/X11/X.h ) FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] xft_info: FOUND: libraries = ['Xft', 'X11', 'freetype', 'Xrender', 'fontconfig'] define_macros = [('XFT_INFO', '"\\"2.1.2.2\\""'), ('XFT_VERSION_2_1_2_2', None)] include_dirs = ['/usr/include/freetype2', '/usr/include/freetype2/config'] selected output from python setup.py build: ________________________________________________________ lapack_opt_info: atlas_threads_info: scipy_distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: scipy_distutils.system_info.atlas_info NOT AVAILABLE scipy_core/scipy_distutils/system_info.py:909: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 blas_info: FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 blas_opt_info: atlas_blas_threads_info: scipy_distutils.system_info.atlas_blas_threads_info NOT AVAILABLE atlas_blas_info: scipy_distutils.system_info.atlas_blas_info NOT AVAILABLE scipy_core/scipy_distutils/system_info.py:982: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77

3 4

CVS build + Livedocs
by Nikolai Hlubek 14 Mar '05

14 Mar '05

Hi everyone, I'm a bit lost when trying to use the livedocs with the latest cvs build. 1.) The building process seems to ignore my atlas packages and uses only lapack. This is the error I get: /scratch/hlubek/cvs/scipy/scipy_core/scipy_distutils/ system_info.py:653: UserWarning: ********************************************************************* Could not find lapack library within the ATLAS installation. ********************************************************************* warnings.warn(message) /scratch/hlubek/cvs/scipy/scipy_core/scipy_distutils/ system_info.py:865: FutureWarning: hex()/oct() of negative int will return a signed string in Python 2.4 and up magic = hex(hash(`config`)) I'm using debian sarge with the atlas2-sse2 packages but atlas3-sse2 is also installed due to some python-2.3 dependencies. The output of system_info.py can be found below. 2.) When using the livedocs I don't get all of the help files. I.e. scipy.xplt.histogram is displaying an empty help string in the livedocs, although running >> ??scipy.xplt.histogram from ipython clearly shows that it is available. scipy.xplt.legend isn't even available in the livedocs, as are many other methods and all of the source files. Could these two issues be related? Or has anyone another idea what I am doing wrong? Thanks for your help, Nikolai _pkg_config_info: NOT AVAILABLE agg2_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE atlas_blas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) ( paths: /usr/lib/sse2/libf77blas.so ) ( paths: /usr/lib/sse2/libcblas.so ) ( paths: /usr/lib/sse2/libatlas.so ) ( include_dirs = /usr/local/include:/usr/include ) ( paths: /usr/include/atlas_misc.h,/usr/include/atlas_enum.h,/usr/ include/atlas_aux.h,/usr/include/atlas_type.h ) ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/sse2'] language = c atlas_blas_threads_info: Setting PTATLAS=ATLAS ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) ( paths: /usr/lib/sse2/libatlas.so ) ( paths: /usr/lib/sse2/libatlas.a ) NOT AVAILABLE atlas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) ( paths: /usr/lib/sse2/libf77blas.so ) ( paths: /usr/lib/sse2/libcblas.so ) ( paths: /usr/lib/sse2/libatlas.so ) ( paths: /usr/lib/sse2/liblapack_atlas.so ) system_info.atlas_info ( include_dirs = /usr/local/include:/usr/include ) ( paths: /usr/include/atlas_misc.h,/usr/include/atlas_enum.h,/usr/ include/atlas_aux.h,/usr/include/atlas_type.h ) ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/sse2'] language = c define_macros = [('ATLAS_WITHOUT_LAPACK', None)] atlas_threads_info: Setting PTATLAS=ATLAS ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) ( paths: /usr/lib/sse2/libatlas.so ) ( paths: /usr/lib/sse2/libatlas.a ) ( paths: /usr/lib/sse2/liblapack_atlas.so ) system_info.atlas_threads_info NOT AVAILABLE blas_info: ( library_dirs = /usr/local/lib:/usr/lib ) NOT AVAILABLE blas_opt_info: running build_src building extension "atlas_version" sources creating build creating build/src adding 'build/src/atlas_version_0xaa8955e5.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'atlas_version' extension compiling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC' creating build/temp.linux-i686-2.3 creating build/temp.linux-i686-2.3/build creating build/temp.linux-i686-2.3/build/src compile options: '-I/usr/include/python2.3 -c' gcc: build/src/atlas_version_0xaa8955e5.c gcc -pthread -shared build/temp.linux-i686-2.3/build/src/ atlas_version_0xaa8955e5.o -L/usr/lib/sse2 -lf77blas -lcblas -latlas -o build/temp.linux-i686-2.3/atlas_version.so Command: /usr/bin/python -c "import imp;imp.load_dynamic (\"atlas_version\",\"atlas_version.so\")" Status: 1 Output: Traceback (most recent call last): File "<string>", line 1, in ? ImportError: /usr/lib/sse2/libf77blas.so.2: undefined symbol: e_wsfe ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/sse2'] language = c define_macros = [('NO_ATLAS_INFO', 2)] blas_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE boost_python_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE dfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE dfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE djbfft_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE fftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) ( paths: /usr/lib/librfftw.so ) ( paths: /usr/lib/libfftw.so ) ( paths: /usr/include/fftw.h,/usr/include/rfftw.h ) ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['rfftw', 'fftw'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW_H', None)] include_dirs = ['/usr/include'] fftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) ( paths: /usr/lib/librfftw_threads.so ) ( paths: /usr/lib/libfftw_threads.so ) ( paths: /usr/include/fftw_threads.h,/usr/include/rfftw_threads.h ) ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['rfftw_threads', 'fftw_threads'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW_THREADS_H', None)] include_dirs = ['/usr/include'] freetype2_info: NOT AVAILABLE gdk_2_info: NOT AVAILABLE gdk_info: NOT AVAILABLE gdk_pixbuf_2_info: NOT AVAILABLE gdk_pixbuf_xlib_2_info: NOT AVAILABLE gdk_x11_2_info: NOT AVAILABLE gtkp_2_info: NOT AVAILABLE gtkp_x11_2_info: NOT AVAILABLE lapack_atlas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) ( paths: /usr/lib/sse2/liblapack_atlas.so ) ( paths: /usr/lib/sse2/libf77blas.so ) ( paths: /usr/lib/sse2/libcblas.so ) ( paths: /usr/lib/sse2/libatlas.so ) ( paths: /usr/lib/sse2/liblapack_atlas.so ) system_info.lapack_atlas_info ( include_dirs = /usr/local/include:/usr/include ) ( paths: /usr/include/atlas_misc.h,/usr/include/atlas_enum.h,/usr/ include/atlas_aux.h,/usr/include/atlas_type.h ) ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) FOUND: libraries = ['lapack_atlas', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/sse2'] language = c define_macros = [('ATLAS_WITH_LAPACK_ATLAS', None)] lapack_atlas_threads_info: Setting PTATLAS=ATLAS ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/atlas,/usr/lib/sse2 ) ( paths: /usr/lib/sse2/liblapack_atlas.so ) ( paths: /usr/lib/sse2/libatlas.so ) ( paths: /usr/lib/sse2/liblapack_atlas.a ) ( paths: /usr/lib/sse2/libatlas.a ) ( paths: /usr/lib/sse2/liblapack_atlas.so ) system_info.lapack_atlas_threads_info NOT AVAILABLE lapack_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/lib/liblapack.a ) ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 lapack_opt_info: running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0x31b82f3b.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext Command: /usr/bin/python -c "import imp;imp.load_dynamic (\"atlas_version\",\"atlas_version.so\")" Status: 1 Output: Traceback (most recent call last): File "<string>", line 1, in ? ImportError: /usr/lib/sse2/libf77blas.so.2: undefined symbol: e_wsfe ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['f77blas', 'cblas', 'atlas', 'lapack'] library_dirs = ['/usr/lib/sse2', '/usr/lib'] define_macros = [('ATLAS_WITHOUT_LAPACK', None), ('NO_ATLAS_INFO', 2)] language = f77 lapack_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE numarray_info: ( include_dirs = /usr/include/python2.3 ) ( paths: /usr/include/python2.3/numarray/arrayobject.h ) ( library_dirs = ) FOUND: define_macros = [('NUMARRAY_VERSION', '"\\"1.1.1\\""')] include_dirs = ['/usr/include/python2.3'] numpy_info: ( include_dirs = /usr/include/python2.3 ) ( paths: /usr/include/python2.3/Numeric/arrayobject.h ) ( library_dirs = ) FOUND: define_macros = [('NUMERIC_VERSION', '"\\"23.7\\""')] include_dirs = ['/usr/include/python2.3'] sfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE sfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE wx_info: Could not locate executable wx-config File not found: wx-config. Cannot determine wx info. NOT AVAILABLE x11_info: ( library_dirs = /usr/X11R6/lib:/usr/lib ) ( include_dirs = /usr/X11R6/include:/usr/include ) ( paths: /usr/X11R6/lib/libX11.so ) ( paths: /usr/X11R6/include/X11/X.h ) ( library_dirs = /usr/X11R6/lib:/usr/lib ) FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] xft_info: NOT AVAILABLE

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