compilation troubles: unrecognized command line option "-Wno-long-double"
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Leonard Burtscher
Dec 8, 2009, 6:17:05 AM12/8/09
to PyMC
Hi,
I am new to this list. I am a Ph.D. student in astronomy and would
like to try PyMC for an MCMC model of interferometric visibilities.
After downloading the latest code via svn, I tried to compile it on my
MacBook. The machine is
$ uname -a
Darwin maclb.mpia-hd.mpg.de 10.2.0 Darwin Kernel Version 10.2.0: Tue
Nov 3 10:37:10 PST 2009; root:xnu-1486.2.11~1/RELEASE_I386 i386
The compilation exited with an error (full log: please see below),
apparently because of
cc1: error: unrecognized command line option "-Wno-long-double"
I am using
$ cc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5646) (dot
1)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There
is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
Should I be using a different compiler?
I also tried Daniel O'Donovan's recommendation for compiling the code
under Snow Leopard (http://groups.google.com/group/pymc/browse_thread/
thread/7726b9d4979e18c3) but that led to other problems (please see
further below). It says that
/sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
definition appears wrong for platform (bad gcc/glibc config?)."
(among other things)
Thanks for your help,
Leonard
--
maclb:pymc-read-only leo$ python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --
compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --
fcompiler options
running build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
f2py:> build/src.macosx-10.5-i386-2.5/pymc/flibmodule.c
creating build
creating build/src.macosx-10.5-i386-2.5
creating build/src.macosx-10.5-i386-2.5/pymc
IOError: [Errno 2] No such file or directory: 'skip:ppnd7'. Skipping
file "skip:ppnd7".
Reading fortran codes...
Reading file 'pymc/flib.f' (format:fix,strict)
updatevars:p: attempt to change 'dimension(k-1)' to 'dimension(k)'.
Ignoring.
Reading file 'pymc/histogram.f' (format:fix,strict)
rmbadname1: Replacing "index" with "index_bn".
Reading file 'pymc/flib_blas.f' (format:fix,strict)
Reading file 'pymc/math.f' (format:fix,strict)
Reading file 'pymc/gibbsit.f' (format:fix,strict)
updatevars: "character curterms(20)*24" is mapped to "character
curterms(20,24)"
updatevars: "character septerms(20)*24" is mapped to "character
septerms(20,24)"
updatevars: "character tokens(maxtok)*(*)" is mapped to "character
tokens(maxtok,(*))"
rmbadname1: Replacing "index" with "index_bn".
rmbadname1: Replacing "len" with "len_bn".
Line #1125 in pymc/gibbsit.f:" DOUBLE PRECISION INTENT
(CACHE,HIDE), DIMENSION(2*ITERACNT) :: WORK"
updatevars: attempt to change the type of "work" ("integer") to
"double precision". Ignoring.
Post-processing...
Block: flib
Block: symmetrize
Block: logsum
Block: logsum_cpx
Block: combinationln
Block: expand_triangular
Block: mod_to_circle
Block: standardize
Block: gammln
Block: mvgammln
Block: factrl
Block: factln
Block: rskewnorm
Block: uniform_like
Block: duniform_like
Block: exponweib
Block: exponweib_ppf
Block: constrain
Block: poisson
Block: trpoisson
Block: t
Block: multinomial
Block: weibull
Block: logistic
Block: normal
Block: hnormal
Block: lognormal
Block: arlognormal
Block: gev
Block: gev_ppf
Block: gamma
Block: igamma
Block: hyperg
Block: geometric
Block: dirichlet
Block: cauchy
Block: negbin
Block: negbin2
Block: binomial
Block: bernoulli
Block: beta_like
Block: betabin_like
Block: mvhyperg
Block: dirmultinom
Block: wishart
Block: trace
Block: gamfun
Block: gammds
Block: gser
Block: gcf
Block: gammq
Block: trans
Block: matmult
Block: dtrm
Block: elgs
Block: bico
Block: chol
Block: hermpoly
Block: uniform
Block: set_uniform
Block: categorical
Block: rcat
Block: logit
Block: invlogit
Block: stukel_logit
Block: stukel_invlogit
Block: vonmises
Block: fixed_binsize
sortvarnames: failed to compute dependencies because of cyclic
dependencies between x, nx
Block: weighted_fixed_binsize
sortvarnames: failed to compute dependencies because of cyclic
dependencies between w, x, nx
Block: fixed_binsize_nd
sortvarnames: failed to compute dependencies because of cyclic
dependencies between n, nx, bin0, delta, x, d
Block: qsorti
"object of type 'builtin_function_or_method' has no len()" in
evaluating 'len(ord)' (available names: [])
Block: checksymm
Block: chol_mvnorm
Block: cov_mvnorm
Block: prec_mvnorm
Block: blas_wishart
Block: blas_wishart_cov
Block: blas_inv_wishart
Block: dtrsm_wrap
Block: dtrmm_wrap
Block: dchdc_wrap
Block: dpotrs_wrap
Block: ppnd16
Block: calerf
Block: derf
Block: derfc
Block: derfcx
Block: gibbsit
Block: matinput
Block: vecinput
Block: oneparse
Block: gibbmain
Block: empquant
Block: dichot
Block: thin
Block: mctest
Block: indtest
Block: mcest
Block: ppnd7
Block: ssort
Post-processing (stage 2)...
Building modules...
Building module "flib"...
Constructing wrapper function "symmetrize"...
symmetrize(c,[cmin,cmax])
Constructing wrapper function "logsum"...
s = logsum(x)
Constructing wrapper function "logsum_cpx"...
s = logsum_cpx(x)
Creating wrapper for Fortran function
"combinationln"("combinationln")...
Constructing wrapper function "combinationln"...
combinationln = combinationln(n,k)
Constructing wrapper function "expand_triangular"...
t = expand_triangular(d,f)
Constructing wrapper function "mod_to_circle"...
mx = mod_to_circle(x,u,l)
Constructing wrapper function "standardize"...
z = standardize(x,loc,scale)
Creating wrapper for Fortran function "gammln"("gammln")...
Constructing wrapper function "gammln"...
gammln = gammln(xx)
Creating wrapper for Fortran function "mvgammln"("mvgammln")...
Constructing wrapper function "mvgammln"...
mvgammln = mvgammln(x,k)
Creating wrapper for Fortran function "factrl"("factrl")...
Constructing wrapper function "factrl"...
factrl = factrl(n)
Creating wrapper for Fortran function "factln"("factln")...
Constructing wrapper function "factln"...
factln = factln(n)
Constructing wrapper function "rskewnorm"...
x = rskewnorm(nx,mu,tau,alph,rn)
Constructing wrapper function "uniform_like"...
like = uniform_like(x,lower,upper)
Constructing wrapper function "duniform_like"...
like = duniform_like(x,lower,upper)
Constructing wrapper function "exponweib"...
like = exponweib(x,a,c,loc,scale)
Constructing wrapper function "exponweib_ppf"...
ppf = exponweib_ppf(q,a,c)
Constructing wrapper function "constrain"...
pass = constrain(x,a,b,allow_equal)
Constructing wrapper function "poisson"...
like = poisson(x,mu)
Constructing wrapper function "trpoisson"...
like = trpoisson(x,mu,k)
Constructing wrapper function "t"...
like = t(x,nu)
Constructing wrapper function "multinomial"...
like = multinomial(x,n,p)
Constructing wrapper function "weibull"...
like = weibull(x,alpha,beta)
Constructing wrapper function "logistic"...
like = logistic(x,mu,tau)
Constructing wrapper function "normal"...
like = normal(x,mu,tau)
Constructing wrapper function "hnormal"...
like = hnormal(x,tau)
Constructing wrapper function "lognormal"...
like = lognormal(x,mu,tau)
Constructing wrapper function "arlognormal"...
like = arlognormal(x,mu,sigma,rho,beta)
Constructing wrapper function "gev"...
like = gev(x,xi,mu,sigma)
Constructing wrapper function "gev_ppf"...
ppf = gev_ppf(q,xi)
Constructing wrapper function "gamma"...
like = gamma(x,alpha,beta)
Constructing wrapper function "igamma"...
like = igamma(x,alpha,beta)
Constructing wrapper function "hyperg"...
like = hyperg(x,draws,success,total)
Constructing wrapper function "geometric"...
like = geometric(x,p)
Constructing wrapper function "dirichlet"...
like = dirichlet(x,theta)
Constructing wrapper function "cauchy"...
like = cauchy(x,alpha,beta)
Constructing wrapper function "negbin"...
like = negbin(x,r,p)
Constructing wrapper function "negbin2"...
like = negbin2(x,mu,a)
Constructing wrapper function "binomial"...
like = binomial(x,n,p)
Constructing wrapper function "bernoulli"...
like = bernoulli(x,p)
Constructing wrapper function "beta_like"...
like = beta_like(x,alpha,beta)
Constructing wrapper function "betabin_like"...
like = betabin_like(x,alpha,beta,n)
Constructing wrapper function "mvhyperg"...
like = mvhyperg(x,color)
Constructing wrapper function "dirmultinom"...
like = dirmultinom(x,theta)
Constructing wrapper function "wishart"...
like = wishart(x,n,sigma)
Constructing wrapper function "trace"...
trace(mat,tr,[k])
Constructing wrapper function "gamfun"...
gx = gamfun(xx)
Creating wrapper for Fortran function "gammds"("gammds")...
Constructing wrapper function "gammds"...
gammds = gammds(y,p,ifault)
Constructing wrapper function "gser"...
gser(gamser,a,x,gln)
Constructing wrapper function "gcf"...
gcf(gammcf,a,x,gln)
Creating wrapper for Fortran function "gammq"("gammq")...
Constructing wrapper function "gammq"...
gammq = gammq(a,x)
Constructing wrapper function "trans"...
tmat = trans(mat)
Constructing wrapper function "matmult"...
prod = matmult(mat1,mat2)
Constructing wrapper function "dtrm"...
d = dtrm(a)
Constructing wrapper function "elgs"...
elgs(a,indx,[n])
Creating wrapper for Fortran function "bico"("bico")...
Constructing wrapper function "bico"...
bico = bico(n,k)
Constructing wrapper function "chol"...
c = chol(a,[n])
Constructing wrapper function "hermpoly"...
cx = hermpoly(n,x)
Creating wrapper for Fortran function "uniform"("uniform")...
Constructing wrapper function "uniform"...
uniform = uniform()
Constructing wrapper function "set_uniform"...
set_uniform(seed1,seed2)
Constructing wrapper function "categorical"...
like = categorical(x,p)
Constructing wrapper function "rcat"...
s = rcat(p,rands)
Constructing wrapper function "logit"...
ltheta = logit(theta)
Constructing wrapper function "invlogit"...
theta = invlogit(ltheta)
Constructing wrapper function "stukel_logit"...
ltheta = stukel_logit(theta,a1,a2,[overwrite_theta])
Constructing wrapper function "stukel_invlogit"...
theta = stukel_invlogit(ltheta,a1,a2,[overwrite_ltheta])
Constructing wrapper function "vonmises"...
like = vonmises(x,mu,kappa)
Constructing wrapper function "fixed_binsize"...
h = fixed_binsize(x,bin0,delta,n)
Constructing wrapper function "weighted_fixed_binsize"...
h = weighted_fixed_binsize(x,w,bin0,delta,n)
Constructing wrapper function "fixed_binsize_nd"...
count = fixed_binsize_nd(x,bin0,delta,n,nc)
Constructing wrapper function "qsorti"...
qsorti(ord,a,[n])
Constructing wrapper function "checksymm"...
cs = checksymm(x)
Constructing wrapper function "chol_mvnorm"...
like = chol_mvnorm(x,mu,sig,[overwrite_x,overwrite_mu])
Constructing wrapper function "cov_mvnorm"...
like = cov_mvnorm(x,mu,c,[overwrite_x,overwrite_mu,overwrite_c])
Constructing wrapper function "prec_mvnorm"...
like = prec_mvnorm(x,mu,tau,
[overwrite_x,overwrite_mu,overwrite_tau])
Constructing wrapper function "blas_wishart"...
like = blas_wishart(x,n,t,[overwrite_x,overwrite_t])
Constructing wrapper function "blas_wishart_cov"...
like = blas_wishart_cov(x,n,v,[overwrite_x,overwrite_v])
Constructing wrapper function "blas_inv_wishart"...
like = blas_inv_wishart(x,n,t,[overwrite_x,overwrite_t])
Constructing wrapper function "dtrsm_wrap"...
dtrsm_wrap(a,b,side,transa,uplo)
Constructing wrapper function "dtrmm_wrap"...
dtrmm_wrap(a,b,side,transa,uplo)
Constructing wrapper function "dchdc_wrap"...
piv,info = dchdc_wrap(a)
Constructing wrapper function "dpotrs_wrap"...
info = dpotrs_wrap(chol_fac,b,[uplo])
Creating wrapper for Fortran function "ppnd16"("ppnd16")...
Constructing wrapper function "ppnd16"...
ppnd16 = ppnd16(p,ifault)
Constructing wrapper function "calerf"...
calerf(arg,result,jint)
Creating wrapper for Fortran function "derf"("derf")...
Constructing wrapper function "derf"...
derf = derf(x)
Creating wrapper for Fortran function "derfc"("derfc")...
Constructing wrapper function "derfc"...
derfc = derfc(x)
Creating wrapper for Fortran function "derfcx"("derfcx")...
Constructing wrapper function "derfcx"...
derfcx = derfcx(x)
Constructing wrapper function "matinput"...
matinput(uid,matout,rowused,colused,r15,[rowmax,colmax])
Constructing wrapper function "vecinput"...
vecinput(uid,vecout,vecused,r15,[vecmax])
Constructing wrapper function "oneparse"...
getarrdims:warning: assumed shape array, using 0 instead of '(*)'
oneparse(instring,delimit,tokens,tokcnt,r15,[maxtok])
Constructing wrapper function "gibbmain"...
nmin,kthin,nburn,nprec,kmind = gibbmain(original,q,r,s,epsilon)
Creating wrapper for Fortran function "empquant"("empquant")...
Constructing wrapper function "empquant"...
getarrdims:warning: assumed shape array, using 0 instead of '*'
empquant = empquant(data,q,work,[iteracnt])
Constructing wrapper function "dichot"...
dichot(data,cutpt,zt,[iteracnt])
Constructing wrapper function "thin"...
thin(series,kthin,result,thincnt,[iteracnt])
Constructing wrapper function "mctest"...
mctest(data,g2,bic,[datacnt])
Constructing wrapper function "indtest"...
indtest(data,g2,bic,[datacnt])
Constructing wrapper function "mcest"...
mcest(data,alpha,beta,[datacnt])
Creating wrapper for Fortran function "ppnd7"("ppnd7")...
Constructing wrapper function "ppnd7"...
ppnd7 = ppnd7(p,ifault)
Constructing wrapper function "ssort"...
ssort(x,y,kflag,[n])
Constructing COMMON block support for "unif_seeds"...
s1,s2
Wrote C/API module "flib" to file "build/src.macosx-10.5-i386-2.5/
pymc/flibmodule.c"
Fortran 77 wrappers are saved to "build/src.macosx-10.5-i386-2.5/pymc/
flib-f2pywrappers.f"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
copying /sw/lib/python2.5/site-packages/numpy/f2py/src/fortranobject.c
-> build/src.macosx-10.5-i386-2.5
copying /sw/lib/python2.5/site-packages/numpy/f2py/src/fortranobject.h
-> build/src.macosx-10.5-i386-2.5
adding 'build/src.macosx-10.5-i386-2.5/pymc/flib-f2pywrappers.f' to
sources.
building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/linalg_utilsmodule.c
creating build/src.macosx-10.5-i386-2.5/pymc/gp
Reading fortran codes...
Reading file 'pymc/gp/linalg_utils.f' (format:fix,strict)
Post-processing...
Block: linalg_utils
Block: remove_duplicates
Block: check_repeats
Block: dcopy_wrap
Block: diag_call
Block: cov_fun
Block: basis_diag_call
Block: dtrmm_wrap
Block: dtrsm_wrap
Block: dpotrf_wrap
Block: gp_array_logp
Post-processing (stage 2)...
Building modules...
Constructing call-back function
"cb_cov_fun_in_diag_call__user__routines"
def cov_fun(xe): return q
Building module "linalg_utils"...
Constructing wrapper function "remove_duplicates"...
nr,rf,rt,nu,xu,ui = remove_duplicates(x)
Constructing wrapper function "check_repeats"...
f,new_indices,n_new_indices = check_repeats(x,x_sofar,f_sofar)
Constructing wrapper function "dcopy_wrap"...
dcopy_wrap(x,y)
Constructing wrapper function "diag_call"...
v = diag_call(x,cov_fun,[cov_fun_extra_args])
Constructing wrapper function "basis_diag_call"...
v = basis_diag_call(basis_x)
Constructing wrapper function "dtrmm_wrap"...
dtrmm_wrap(a,b,[uplo,transa])
Constructing wrapper function "dtrsm_wrap"...
dtrsm_wrap(a,b,[uplo,transa,alpha])
Constructing wrapper function "dpotrf_wrap"...
info = dpotrf_wrap(a)
Constructing wrapper function "gp_array_logp"...
like = gp_array_logp(x,mu,sig,[overwrite_x,overwrite_mu])
Wrote C/API module "linalg_utils" to file "build/src.macosx-10.5-
i386-2.5/pymc/gp/linalg_utilsmodule.c"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/incomplete_cholmodule.c
Reading fortran codes...
Reading file 'pymc/gp/incomplete_chol.f' (format:fix,strict)
Post-processing...
Block: incomplete_chol
Block: ichol_continue
Block: rowfun
Block: ichol
Block: rowfun
Block: ichol_basis
Block: ichol_full
Post-processing (stage 2)...
Building modules...
Constructing call-back function
"cb_rowfun_in_ichol_continue__user__routines"
def rowfun(itot,x,rowvec): return
Constructing call-back function "cb_rowfun_in_ichol__user__routines"
def rowfun(i,x,rowvec): return
Building module "incomplete_chol"...
Constructing wrapper function "ichol_continue"...
m,piv = ichol_continue(sig,diag,piv,reltol,x,rowfun,mold,
[overwrite_x,rowfun_extra_args])
Constructing wrapper function "ichol"...
sig,m,piv = ichol(diag,reltol,x,rowfun,rl,
[overwrite_x,rowfun_extra_args])
Constructing wrapper function "ichol_basis"...
sig,p,m = ichol_basis(basis,nug,reltol)
Constructing wrapper function "ichol_full"...
sig,m,p = ichol_full(c,reltol)
Wrote C/API module "incomplete_chol" to file "build/src.macosx-10.5-
i386-2.5/pymc/gp/incomplete_cholmodule.c"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
isotropic_cov_funsmodule.c
creating build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs
Reading fortran codes...
Reading file 'pymc/gp/cov_funs/
isotropic_cov_funs.f' (format:fix,strict)
Reading file 'blas/BLAS/dscal.f' (format:fix,strict)
Post-processing...
Block: isotropic_cov_funs
Block: imul
Block: symmetrize
Block: stein_spatiotemporal
Block: matern
Block: gaussian
Block: exponential
Block: brownian
Block: frac_brownian
Block: pow_exp
Block: sphere
Block: quadratic
Block: dgamma
Block: rkbesl
Block: dscal
Post-processing (stage 2)...
Building modules...
Building module "isotropic_cov_funs"...
Constructing wrapper function "imul"...
imul(c,a,[cmin,cmax,symm])
Constructing wrapper function "symmetrize"...
symmetrize(c,[cmin,cmax])
Constructing wrapper function "stein_spatiotemporal"...
stein_spatiotemporal(c,gt,origin_val,[cmin,cmax,symm])
Constructing wrapper function "matern"...
matern(c,diff_degree,[cmin,cmax,symm])
Constructing wrapper function "gaussian"...
gaussian(c,[cmin,cmax,symm])
Constructing wrapper function "exponential"...
exponential(c,[cmin,cmax,symm])
Constructing wrapper function "brownian"...
brownian(c,x,y,[cmin,cmax,symm])
Constructing wrapper function "frac_brownian"...
frac_brownian(c,x,y,h,[cmin,cmax,symm])
Constructing wrapper function "pow_exp"...
pow_exp(c,pow,[cmin,cmax,symm])
Constructing wrapper function "sphere"...
sphere(c,[cmin,cmax,symm])
Constructing wrapper function "quadratic"...
quadratic(c,phi,[cmin,cmax,symm])
Creating wrapper for Fortran function "dgamma"("dgamma")...
Constructing wrapper function "dgamma"...
dgamma = dgamma(x)
Constructing wrapper function "rkbesl"...
bk = rkbesl(x,alpha,nb,ize,ncalc)
Constructing wrapper function "dscal"...
getarrdims:warning: assumed shape array, using 0 instead of '*'
dscal(n,da,dx,incx)
Wrote C/API module "isotropic_cov_funs" to file "build/
src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/isotropic_cov_funsmodule.c"
Fortran 77 wrappers are saved to "build/src.macosx-10.5-i386-2.5/pymc/
gp/cov_funs/isotropic_cov_funs-f2pywrappers.f"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
isotropic_cov_funs-f2pywrappers.f' to sources.
building extension "pymc.gp.cov_funs.distances" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
distancesmodule.c
Reading fortran codes...
Reading file 'pymc/gp/cov_funs/distances.f' (format:fix,strict)
Post-processing...
Block: distances
Block: euclidean
Block: geographic
Block: paniso_geo_rad
Block: aniso_geo_rad
Post-processing (stage 2)...
Building modules...
Building module "distances"...
Constructing wrapper function "euclidean"...
euclidean(d,x,y,[cmin,cmax,symm])
Constructing wrapper function "geographic"...
geographic(d,x,y,[cmin,cmax,symm])
Constructing wrapper function "paniso_geo_rad"...
paniso_geo_rad(d,x,y,ctrs,scals,[cmin,cmax,symm])
Constructing wrapper function "aniso_geo_rad"...
aniso_geo_rad(d,x,y,inc,ecc,[cmin,cmax,symm])
Wrote C/API module "distances" to file "build/src.macosx-10.5-
i386-2.5/pymc/gp/cov_funs/distancesmodule.c"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
running build_py
creating build/lib.macosx-10.5-i386-2.5
creating build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/CircularStochastic.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/CommonDeterministics.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/Container.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.5-
i386-2.5/pymc
copying pymc/MCMC.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/Matplot.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/Model.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/Node.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/NormalApproximation.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/PyMCObjects.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/ScipyDistributions.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/StepMethods.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/__init__.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/decorators.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/diagnostics.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/distributions.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/graph.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/threadpool.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/utils.py -> build/lib.macosx-10.5-i386-2.5/pymc
creating build/lib.macosx-10.5-i386-2.5/pymc/database
copying pymc/database/__init__.py -> build/lib.macosx-10.5-i386-2.5/
pymc/database
copying pymc/database/base.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/hdf5.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/mysql.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/no_trace.py -> build/lib.macosx-10.5-i386-2.5/
pymc/database
copying pymc/database/pickle.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/ram.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/sqlite.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/txt.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
creating build/lib.macosx-10.5-i386-2.5/pymc/examples
copying pymc/examples/DisasterModel.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/__init__.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/custom_step.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/model_1.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_1_gof.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_1_missing.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/model_2.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_3.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_4.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/run_simple.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/run_simple_von_mises.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/simple.py -> build/lib.macosx-10.5-i386-2.5/pymc/
examples
copying pymc/examples/simple_von_mises.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/straightlinefit.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
creating build/lib.macosx-10.5-i386-2.5/pymc/tests
copying pymc/tests/__init__.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/objectmodel.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_AM.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_LazyFunction.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_container.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_convergence.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_cov.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/test_database.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_distributions.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_graph.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_interactive.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_mean.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_observation.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_realization.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_utils.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
creating build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp
copying pymc/gp/Covariance.py -> build/lib.macosx-10.5-i386-2.5/pymc/
gp
copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp
copying pymc/gp/GPutils.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/Mean.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp
copying pymc/gp/PyMC_objects.py -> build/lib.macosx-10.5-i386-2.5/pymc/
gp
copying pymc/gp/Realization.py -> build/lib.macosx-10.5-i386-2.5/pymc/
gp
copying pymc/gp/__init__.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/gpplots.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
creating build/lib.macosx-10.5-i386-2.5/pymc/gp/cov_funs
copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp/cov_funs
copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp/cov_funs
copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp/cov_funs
copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp/cov_funs
copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp/cov_funs
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Found executable /usr/bin/ifort
customize GnuFCompiler
Could not locate executable g77
customize Gnu95FCompiler
Found executable /sw/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pymc.flib' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -Wno-long-double -mno-fused-madd -
DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
creating build/temp.macosx-10.5-i386-2.5
creating build/temp.macosx-10.5-i386-2.5/cephes
creating build/temp.macosx-10.5-i386-2.5/build
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -
I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/
python2.5 -c'
extra options: '-msse3'
gcc: build/src.macosx-10.5-i386-2.5/fortranobject.c
cc1: error: unrecognized command line option "-Wno-long-double"
cc1: error: unrecognized command line option "-Wno-long-double"
error: Command "gcc -fno-strict-aliasing -Wno-long-double -mno-fused-
madd -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -
DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -I/sw/lib/python2.5/
site-packages/numpy/core/include -I/sw/include/python2.5 -c build/
src.macosx-10.5-i386-2.5/fortranobject.c -o build/temp.macosx-10.5-
i386-2.5/build/src.macosx-10.5-i386-2.5/fortranobject.o -msse3" failed
with exit status 1
--
maclb:pymc-read-only leo$ python setup.py clean
running clean
removing 'build/temp.macosx-10.5-i386-2.5' (and everything under it)
maclb:pymc-read-only leo$ LDFLAGS="-Wall -undefined dynamic_lookup -
bundle -arch i386 -arch x86_64" FFLAGS="-arch i386 -arch x86_64"
CFLAGS="-arch i386 -arch x86_64" python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --
compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --
fcompiler options
running build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/flib-f2pywrappers.f' to
sources.
building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
isotropic_cov_funs-f2pywrappers.f' to sources.
building extension "pymc.gp.cov_funs.distances" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Found executable /usr/bin/ifort
customize GnuFCompiler
Could not locate executable g77
customize Gnu95FCompiler
Found executable /sw/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pymc.flib' extension
compiling C sources
C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -
arch i386 -arch x86_64
creating build/temp.macosx-10.5-i386-2.5
creating build/temp.macosx-10.5-i386-2.5/cephes
creating build/temp.macosx-10.5-i386-2.5/build
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -
I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/
python2.5 -c'
extra options: '-msse3'
gcc: build/src.macosx-10.5-i386-2.5/fortranobject.c
In file included from /sw/include/python2.5/Python.h:57,
from build/src.macosx-10.5-i386-2.5/fortranobject.h:
7,
from build/src.macosx-10.5-i386-2.5/fortranobject.c:
2:
/sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
definition appears wrong for platform (bad gcc/glibc config?)."
lipo: can't figure out the architecture type of: /var/folders/YO/
YOADMSqSEl4jYv9pOLJSqk+++TI/-Tmp-//ccF8R4sr.out
In file included from /sw/include/python2.5/Python.h:57,
from build/src.macosx-10.5-i386-2.5/fortranobject.h:
7,
from build/src.macosx-10.5-i386-2.5/fortranobject.c:
2:
/sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
definition appears wrong for platform (bad gcc/glibc config?)."
lipo: can't figure out the architecture type of: /var/folders/YO/
YOADMSqSEl4jYv9pOLJSqk+++TI/-Tmp-//ccF8R4sr.out
error: Command "gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -
arch i386 -arch x86_64 -DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-
i386-2.5 -I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/
include/python2.5 -c build/src.macosx-10.5-i386-2.5/fortranobject.c -o
build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/
fortranobject.o -msse3" failed with exit status 1
I am new to this list. I am a Ph.D. student in astronomy and would
like to try PyMC for an MCMC model of interferometric visibilities.
After downloading the latest code via svn, I tried to compile it on my
MacBook. The machine is
$ uname -a
Darwin maclb.mpia-hd.mpg.de 10.2.0 Darwin Kernel Version 10.2.0: Tue
Nov 3 10:37:10 PST 2009; root:xnu-1486.2.11~1/RELEASE_I386 i386
The compilation exited with an error (full log: please see below),
apparently because of
cc1: error: unrecognized command line option "-Wno-long-double"
I am using
$ cc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5646) (dot
1)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There
is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
Should I be using a different compiler?
I also tried Daniel O'Donovan's recommendation for compiling the code
under Snow Leopard (http://groups.google.com/group/pymc/browse_thread/
thread/7726b9d4979e18c3) but that led to other problems (please see
further below). It says that
/sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
definition appears wrong for platform (bad gcc/glibc config?)."
(among other things)
Thanks for your help,
Leonard
--
maclb:pymc-read-only leo$ python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --
compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --
fcompiler options
running build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
f2py:> build/src.macosx-10.5-i386-2.5/pymc/flibmodule.c
creating build
creating build/src.macosx-10.5-i386-2.5
creating build/src.macosx-10.5-i386-2.5/pymc
IOError: [Errno 2] No such file or directory: 'skip:ppnd7'. Skipping
file "skip:ppnd7".
Reading fortran codes...
Reading file 'pymc/flib.f' (format:fix,strict)
updatevars:p: attempt to change 'dimension(k-1)' to 'dimension(k)'.
Ignoring.
Reading file 'pymc/histogram.f' (format:fix,strict)
rmbadname1: Replacing "index" with "index_bn".
Reading file 'pymc/flib_blas.f' (format:fix,strict)
Reading file 'pymc/math.f' (format:fix,strict)
Reading file 'pymc/gibbsit.f' (format:fix,strict)
updatevars: "character curterms(20)*24" is mapped to "character
curterms(20,24)"
updatevars: "character septerms(20)*24" is mapped to "character
septerms(20,24)"
updatevars: "character tokens(maxtok)*(*)" is mapped to "character
tokens(maxtok,(*))"
rmbadname1: Replacing "index" with "index_bn".
rmbadname1: Replacing "len" with "len_bn".
Line #1125 in pymc/gibbsit.f:" DOUBLE PRECISION INTENT
(CACHE,HIDE), DIMENSION(2*ITERACNT) :: WORK"
updatevars: attempt to change the type of "work" ("integer") to
"double precision". Ignoring.
Post-processing...
Block: flib
Block: symmetrize
Block: logsum
Block: logsum_cpx
Block: combinationln
Block: expand_triangular
Block: mod_to_circle
Block: standardize
Block: gammln
Block: mvgammln
Block: factrl
Block: factln
Block: rskewnorm
Block: uniform_like
Block: duniform_like
Block: exponweib
Block: exponweib_ppf
Block: constrain
Block: poisson
Block: trpoisson
Block: t
Block: multinomial
Block: weibull
Block: logistic
Block: normal
Block: hnormal
Block: lognormal
Block: arlognormal
Block: gev
Block: gev_ppf
Block: gamma
Block: igamma
Block: hyperg
Block: geometric
Block: dirichlet
Block: cauchy
Block: negbin
Block: negbin2
Block: binomial
Block: bernoulli
Block: beta_like
Block: betabin_like
Block: mvhyperg
Block: dirmultinom
Block: wishart
Block: trace
Block: gamfun
Block: gammds
Block: gser
Block: gcf
Block: gammq
Block: trans
Block: matmult
Block: dtrm
Block: elgs
Block: bico
Block: chol
Block: hermpoly
Block: uniform
Block: set_uniform
Block: categorical
Block: rcat
Block: logit
Block: invlogit
Block: stukel_logit
Block: stukel_invlogit
Block: vonmises
Block: fixed_binsize
sortvarnames: failed to compute dependencies because of cyclic
dependencies between x, nx
Block: weighted_fixed_binsize
sortvarnames: failed to compute dependencies because of cyclic
dependencies between w, x, nx
Block: fixed_binsize_nd
sortvarnames: failed to compute dependencies because of cyclic
dependencies between n, nx, bin0, delta, x, d
Block: qsorti
"object of type 'builtin_function_or_method' has no len()" in
evaluating 'len(ord)' (available names: [])
Block: checksymm
Block: chol_mvnorm
Block: cov_mvnorm
Block: prec_mvnorm
Block: blas_wishart
Block: blas_wishart_cov
Block: blas_inv_wishart
Block: dtrsm_wrap
Block: dtrmm_wrap
Block: dchdc_wrap
Block: dpotrs_wrap
Block: ppnd16
Block: calerf
Block: derf
Block: derfc
Block: derfcx
Block: gibbsit
Block: matinput
Block: vecinput
Block: oneparse
Block: gibbmain
Block: empquant
Block: dichot
Block: thin
Block: mctest
Block: indtest
Block: mcest
Block: ppnd7
Block: ssort
Post-processing (stage 2)...
Building modules...
Building module "flib"...
Constructing wrapper function "symmetrize"...
symmetrize(c,[cmin,cmax])
Constructing wrapper function "logsum"...
s = logsum(x)
Constructing wrapper function "logsum_cpx"...
s = logsum_cpx(x)
Creating wrapper for Fortran function
"combinationln"("combinationln")...
Constructing wrapper function "combinationln"...
combinationln = combinationln(n,k)
Constructing wrapper function "expand_triangular"...
t = expand_triangular(d,f)
Constructing wrapper function "mod_to_circle"...
mx = mod_to_circle(x,u,l)
Constructing wrapper function "standardize"...
z = standardize(x,loc,scale)
Creating wrapper for Fortran function "gammln"("gammln")...
Constructing wrapper function "gammln"...
gammln = gammln(xx)
Creating wrapper for Fortran function "mvgammln"("mvgammln")...
Constructing wrapper function "mvgammln"...
mvgammln = mvgammln(x,k)
Creating wrapper for Fortran function "factrl"("factrl")...
Constructing wrapper function "factrl"...
factrl = factrl(n)
Creating wrapper for Fortran function "factln"("factln")...
Constructing wrapper function "factln"...
factln = factln(n)
Constructing wrapper function "rskewnorm"...
x = rskewnorm(nx,mu,tau,alph,rn)
Constructing wrapper function "uniform_like"...
like = uniform_like(x,lower,upper)
Constructing wrapper function "duniform_like"...
like = duniform_like(x,lower,upper)
Constructing wrapper function "exponweib"...
like = exponweib(x,a,c,loc,scale)
Constructing wrapper function "exponweib_ppf"...
ppf = exponweib_ppf(q,a,c)
Constructing wrapper function "constrain"...
pass = constrain(x,a,b,allow_equal)
Constructing wrapper function "poisson"...
like = poisson(x,mu)
Constructing wrapper function "trpoisson"...
like = trpoisson(x,mu,k)
Constructing wrapper function "t"...
like = t(x,nu)
Constructing wrapper function "multinomial"...
like = multinomial(x,n,p)
Constructing wrapper function "weibull"...
like = weibull(x,alpha,beta)
Constructing wrapper function "logistic"...
like = logistic(x,mu,tau)
Constructing wrapper function "normal"...
like = normal(x,mu,tau)
Constructing wrapper function "hnormal"...
like = hnormal(x,tau)
Constructing wrapper function "lognormal"...
like = lognormal(x,mu,tau)
Constructing wrapper function "arlognormal"...
like = arlognormal(x,mu,sigma,rho,beta)
Constructing wrapper function "gev"...
like = gev(x,xi,mu,sigma)
Constructing wrapper function "gev_ppf"...
ppf = gev_ppf(q,xi)
Constructing wrapper function "gamma"...
like = gamma(x,alpha,beta)
Constructing wrapper function "igamma"...
like = igamma(x,alpha,beta)
Constructing wrapper function "hyperg"...
like = hyperg(x,draws,success,total)
Constructing wrapper function "geometric"...
like = geometric(x,p)
Constructing wrapper function "dirichlet"...
like = dirichlet(x,theta)
Constructing wrapper function "cauchy"...
like = cauchy(x,alpha,beta)
Constructing wrapper function "negbin"...
like = negbin(x,r,p)
Constructing wrapper function "negbin2"...
like = negbin2(x,mu,a)
Constructing wrapper function "binomial"...
like = binomial(x,n,p)
Constructing wrapper function "bernoulli"...
like = bernoulli(x,p)
Constructing wrapper function "beta_like"...
like = beta_like(x,alpha,beta)
Constructing wrapper function "betabin_like"...
like = betabin_like(x,alpha,beta,n)
Constructing wrapper function "mvhyperg"...
like = mvhyperg(x,color)
Constructing wrapper function "dirmultinom"...
like = dirmultinom(x,theta)
Constructing wrapper function "wishart"...
like = wishart(x,n,sigma)
Constructing wrapper function "trace"...
trace(mat,tr,[k])
Constructing wrapper function "gamfun"...
gx = gamfun(xx)
Creating wrapper for Fortran function "gammds"("gammds")...
Constructing wrapper function "gammds"...
gammds = gammds(y,p,ifault)
Constructing wrapper function "gser"...
gser(gamser,a,x,gln)
Constructing wrapper function "gcf"...
gcf(gammcf,a,x,gln)
Creating wrapper for Fortran function "gammq"("gammq")...
Constructing wrapper function "gammq"...
gammq = gammq(a,x)
Constructing wrapper function "trans"...
tmat = trans(mat)
Constructing wrapper function "matmult"...
prod = matmult(mat1,mat2)
Constructing wrapper function "dtrm"...
d = dtrm(a)
Constructing wrapper function "elgs"...
elgs(a,indx,[n])
Creating wrapper for Fortran function "bico"("bico")...
Constructing wrapper function "bico"...
bico = bico(n,k)
Constructing wrapper function "chol"...
c = chol(a,[n])
Constructing wrapper function "hermpoly"...
cx = hermpoly(n,x)
Creating wrapper for Fortran function "uniform"("uniform")...
Constructing wrapper function "uniform"...
uniform = uniform()
Constructing wrapper function "set_uniform"...
set_uniform(seed1,seed2)
Constructing wrapper function "categorical"...
like = categorical(x,p)
Constructing wrapper function "rcat"...
s = rcat(p,rands)
Constructing wrapper function "logit"...
ltheta = logit(theta)
Constructing wrapper function "invlogit"...
theta = invlogit(ltheta)
Constructing wrapper function "stukel_logit"...
ltheta = stukel_logit(theta,a1,a2,[overwrite_theta])
Constructing wrapper function "stukel_invlogit"...
theta = stukel_invlogit(ltheta,a1,a2,[overwrite_ltheta])
Constructing wrapper function "vonmises"...
like = vonmises(x,mu,kappa)
Constructing wrapper function "fixed_binsize"...
h = fixed_binsize(x,bin0,delta,n)
Constructing wrapper function "weighted_fixed_binsize"...
h = weighted_fixed_binsize(x,w,bin0,delta,n)
Constructing wrapper function "fixed_binsize_nd"...
count = fixed_binsize_nd(x,bin0,delta,n,nc)
Constructing wrapper function "qsorti"...
qsorti(ord,a,[n])
Constructing wrapper function "checksymm"...
cs = checksymm(x)
Constructing wrapper function "chol_mvnorm"...
like = chol_mvnorm(x,mu,sig,[overwrite_x,overwrite_mu])
Constructing wrapper function "cov_mvnorm"...
like = cov_mvnorm(x,mu,c,[overwrite_x,overwrite_mu,overwrite_c])
Constructing wrapper function "prec_mvnorm"...
like = prec_mvnorm(x,mu,tau,
[overwrite_x,overwrite_mu,overwrite_tau])
Constructing wrapper function "blas_wishart"...
like = blas_wishart(x,n,t,[overwrite_x,overwrite_t])
Constructing wrapper function "blas_wishart_cov"...
like = blas_wishart_cov(x,n,v,[overwrite_x,overwrite_v])
Constructing wrapper function "blas_inv_wishart"...
like = blas_inv_wishart(x,n,t,[overwrite_x,overwrite_t])
Constructing wrapper function "dtrsm_wrap"...
dtrsm_wrap(a,b,side,transa,uplo)
Constructing wrapper function "dtrmm_wrap"...
dtrmm_wrap(a,b,side,transa,uplo)
Constructing wrapper function "dchdc_wrap"...
piv,info = dchdc_wrap(a)
Constructing wrapper function "dpotrs_wrap"...
info = dpotrs_wrap(chol_fac,b,[uplo])
Creating wrapper for Fortran function "ppnd16"("ppnd16")...
Constructing wrapper function "ppnd16"...
ppnd16 = ppnd16(p,ifault)
Constructing wrapper function "calerf"...
calerf(arg,result,jint)
Creating wrapper for Fortran function "derf"("derf")...
Constructing wrapper function "derf"...
derf = derf(x)
Creating wrapper for Fortran function "derfc"("derfc")...
Constructing wrapper function "derfc"...
derfc = derfc(x)
Creating wrapper for Fortran function "derfcx"("derfcx")...
Constructing wrapper function "derfcx"...
derfcx = derfcx(x)
Constructing wrapper function "matinput"...
matinput(uid,matout,rowused,colused,r15,[rowmax,colmax])
Constructing wrapper function "vecinput"...
vecinput(uid,vecout,vecused,r15,[vecmax])
Constructing wrapper function "oneparse"...
getarrdims:warning: assumed shape array, using 0 instead of '(*)'
oneparse(instring,delimit,tokens,tokcnt,r15,[maxtok])
Constructing wrapper function "gibbmain"...
nmin,kthin,nburn,nprec,kmind = gibbmain(original,q,r,s,epsilon)
Creating wrapper for Fortran function "empquant"("empquant")...
Constructing wrapper function "empquant"...
getarrdims:warning: assumed shape array, using 0 instead of '*'
empquant = empquant(data,q,work,[iteracnt])
Constructing wrapper function "dichot"...
dichot(data,cutpt,zt,[iteracnt])
Constructing wrapper function "thin"...
thin(series,kthin,result,thincnt,[iteracnt])
Constructing wrapper function "mctest"...
mctest(data,g2,bic,[datacnt])
Constructing wrapper function "indtest"...
indtest(data,g2,bic,[datacnt])
Constructing wrapper function "mcest"...
mcest(data,alpha,beta,[datacnt])
Creating wrapper for Fortran function "ppnd7"("ppnd7")...
Constructing wrapper function "ppnd7"...
ppnd7 = ppnd7(p,ifault)
Constructing wrapper function "ssort"...
ssort(x,y,kflag,[n])
Constructing COMMON block support for "unif_seeds"...
s1,s2
Wrote C/API module "flib" to file "build/src.macosx-10.5-i386-2.5/
pymc/flibmodule.c"
Fortran 77 wrappers are saved to "build/src.macosx-10.5-i386-2.5/pymc/
flib-f2pywrappers.f"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
copying /sw/lib/python2.5/site-packages/numpy/f2py/src/fortranobject.c
-> build/src.macosx-10.5-i386-2.5
copying /sw/lib/python2.5/site-packages/numpy/f2py/src/fortranobject.h
-> build/src.macosx-10.5-i386-2.5
adding 'build/src.macosx-10.5-i386-2.5/pymc/flib-f2pywrappers.f' to
sources.
building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/linalg_utilsmodule.c
creating build/src.macosx-10.5-i386-2.5/pymc/gp
Reading fortran codes...
Reading file 'pymc/gp/linalg_utils.f' (format:fix,strict)
Post-processing...
Block: linalg_utils
Block: remove_duplicates
Block: check_repeats
Block: dcopy_wrap
Block: diag_call
Block: cov_fun
Block: basis_diag_call
Block: dtrmm_wrap
Block: dtrsm_wrap
Block: dpotrf_wrap
Block: gp_array_logp
Post-processing (stage 2)...
Building modules...
Constructing call-back function
"cb_cov_fun_in_diag_call__user__routines"
def cov_fun(xe): return q
Building module "linalg_utils"...
Constructing wrapper function "remove_duplicates"...
nr,rf,rt,nu,xu,ui = remove_duplicates(x)
Constructing wrapper function "check_repeats"...
f,new_indices,n_new_indices = check_repeats(x,x_sofar,f_sofar)
Constructing wrapper function "dcopy_wrap"...
dcopy_wrap(x,y)
Constructing wrapper function "diag_call"...
v = diag_call(x,cov_fun,[cov_fun_extra_args])
Constructing wrapper function "basis_diag_call"...
v = basis_diag_call(basis_x)
Constructing wrapper function "dtrmm_wrap"...
dtrmm_wrap(a,b,[uplo,transa])
Constructing wrapper function "dtrsm_wrap"...
dtrsm_wrap(a,b,[uplo,transa,alpha])
Constructing wrapper function "dpotrf_wrap"...
info = dpotrf_wrap(a)
Constructing wrapper function "gp_array_logp"...
like = gp_array_logp(x,mu,sig,[overwrite_x,overwrite_mu])
Wrote C/API module "linalg_utils" to file "build/src.macosx-10.5-
i386-2.5/pymc/gp/linalg_utilsmodule.c"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/incomplete_cholmodule.c
Reading fortran codes...
Reading file 'pymc/gp/incomplete_chol.f' (format:fix,strict)
Post-processing...
Block: incomplete_chol
Block: ichol_continue
Block: rowfun
Block: ichol
Block: rowfun
Block: ichol_basis
Block: ichol_full
Post-processing (stage 2)...
Building modules...
Constructing call-back function
"cb_rowfun_in_ichol_continue__user__routines"
def rowfun(itot,x,rowvec): return
Constructing call-back function "cb_rowfun_in_ichol__user__routines"
def rowfun(i,x,rowvec): return
Building module "incomplete_chol"...
Constructing wrapper function "ichol_continue"...
m,piv = ichol_continue(sig,diag,piv,reltol,x,rowfun,mold,
[overwrite_x,rowfun_extra_args])
Constructing wrapper function "ichol"...
sig,m,piv = ichol(diag,reltol,x,rowfun,rl,
[overwrite_x,rowfun_extra_args])
Constructing wrapper function "ichol_basis"...
sig,p,m = ichol_basis(basis,nug,reltol)
Constructing wrapper function "ichol_full"...
sig,m,p = ichol_full(c,reltol)
Wrote C/API module "incomplete_chol" to file "build/src.macosx-10.5-
i386-2.5/pymc/gp/incomplete_cholmodule.c"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
isotropic_cov_funsmodule.c
creating build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs
Reading fortran codes...
Reading file 'pymc/gp/cov_funs/
isotropic_cov_funs.f' (format:fix,strict)
Reading file 'blas/BLAS/dscal.f' (format:fix,strict)
Post-processing...
Block: isotropic_cov_funs
Block: imul
Block: symmetrize
Block: stein_spatiotemporal
Block: matern
Block: gaussian
Block: exponential
Block: brownian
Block: frac_brownian
Block: pow_exp
Block: sphere
Block: quadratic
Block: dgamma
Block: rkbesl
Block: dscal
Post-processing (stage 2)...
Building modules...
Building module "isotropic_cov_funs"...
Constructing wrapper function "imul"...
imul(c,a,[cmin,cmax,symm])
Constructing wrapper function "symmetrize"...
symmetrize(c,[cmin,cmax])
Constructing wrapper function "stein_spatiotemporal"...
stein_spatiotemporal(c,gt,origin_val,[cmin,cmax,symm])
Constructing wrapper function "matern"...
matern(c,diff_degree,[cmin,cmax,symm])
Constructing wrapper function "gaussian"...
gaussian(c,[cmin,cmax,symm])
Constructing wrapper function "exponential"...
exponential(c,[cmin,cmax,symm])
Constructing wrapper function "brownian"...
brownian(c,x,y,[cmin,cmax,symm])
Constructing wrapper function "frac_brownian"...
frac_brownian(c,x,y,h,[cmin,cmax,symm])
Constructing wrapper function "pow_exp"...
pow_exp(c,pow,[cmin,cmax,symm])
Constructing wrapper function "sphere"...
sphere(c,[cmin,cmax,symm])
Constructing wrapper function "quadratic"...
quadratic(c,phi,[cmin,cmax,symm])
Creating wrapper for Fortran function "dgamma"("dgamma")...
Constructing wrapper function "dgamma"...
dgamma = dgamma(x)
Constructing wrapper function "rkbesl"...
bk = rkbesl(x,alpha,nb,ize,ncalc)
Constructing wrapper function "dscal"...
getarrdims:warning: assumed shape array, using 0 instead of '*'
dscal(n,da,dx,incx)
Wrote C/API module "isotropic_cov_funs" to file "build/
src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/isotropic_cov_funsmodule.c"
Fortran 77 wrappers are saved to "build/src.macosx-10.5-i386-2.5/pymc/
gp/cov_funs/isotropic_cov_funs-f2pywrappers.f"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
isotropic_cov_funs-f2pywrappers.f' to sources.
building extension "pymc.gp.cov_funs.distances" sources
f2py options: []
f2py:> build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
distancesmodule.c
Reading fortran codes...
Reading file 'pymc/gp/cov_funs/distances.f' (format:fix,strict)
Post-processing...
Block: distances
Block: euclidean
Block: geographic
Block: paniso_geo_rad
Block: aniso_geo_rad
Post-processing (stage 2)...
Building modules...
Building module "distances"...
Constructing wrapper function "euclidean"...
euclidean(d,x,y,[cmin,cmax,symm])
Constructing wrapper function "geographic"...
geographic(d,x,y,[cmin,cmax,symm])
Constructing wrapper function "paniso_geo_rad"...
paniso_geo_rad(d,x,y,ctrs,scals,[cmin,cmax,symm])
Constructing wrapper function "aniso_geo_rad"...
aniso_geo_rad(d,x,y,inc,ecc,[cmin,cmax,symm])
Wrote C/API module "distances" to file "build/src.macosx-10.5-
i386-2.5/pymc/gp/cov_funs/distancesmodule.c"
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
running build_py
creating build/lib.macosx-10.5-i386-2.5
creating build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/CircularStochastic.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/CommonDeterministics.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/Container.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.5-
i386-2.5/pymc
copying pymc/MCMC.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/Matplot.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/Model.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/Node.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/NormalApproximation.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/PyMCObjects.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/ScipyDistributions.py -> build/lib.macosx-10.5-i386-2.5/
pymc
copying pymc/StepMethods.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/__init__.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/decorators.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/diagnostics.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/distributions.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/graph.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/threadpool.py -> build/lib.macosx-10.5-i386-2.5/pymc
copying pymc/utils.py -> build/lib.macosx-10.5-i386-2.5/pymc
creating build/lib.macosx-10.5-i386-2.5/pymc/database
copying pymc/database/__init__.py -> build/lib.macosx-10.5-i386-2.5/
pymc/database
copying pymc/database/base.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/hdf5.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/mysql.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/no_trace.py -> build/lib.macosx-10.5-i386-2.5/
pymc/database
copying pymc/database/pickle.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/ram.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/sqlite.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
copying pymc/database/txt.py -> build/lib.macosx-10.5-i386-2.5/pymc/
database
creating build/lib.macosx-10.5-i386-2.5/pymc/examples
copying pymc/examples/DisasterModel.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/__init__.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/custom_step.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/model_1.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_1_gof.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_1_missing.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/model_2.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_3.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/model_4.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/run_simple.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
copying pymc/examples/run_simple_von_mises.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/simple.py -> build/lib.macosx-10.5-i386-2.5/pymc/
examples
copying pymc/examples/simple_von_mises.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/straightlinefit.py -> build/lib.macosx-10.5-
i386-2.5/pymc/examples
copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.5-i386-2.5/
pymc/examples
creating build/lib.macosx-10.5-i386-2.5/pymc/tests
copying pymc/tests/__init__.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/objectmodel.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_AM.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_LazyFunction.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_container.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_convergence.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_cov.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/test_database.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_distributions.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_graph.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_interactive.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_mean.py -> build/lib.macosx-10.5-i386-2.5/pymc/
tests
copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_observation.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_realization.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.5-
i386-2.5/pymc/tests
copying pymc/tests/test_utils.py -> build/lib.macosx-10.5-i386-2.5/
pymc/tests
creating build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp
copying pymc/gp/Covariance.py -> build/lib.macosx-10.5-i386-2.5/pymc/
gp
copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp
copying pymc/gp/GPutils.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/Mean.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp
copying pymc/gp/PyMC_objects.py -> build/lib.macosx-10.5-i386-2.5/pymc/
gp
copying pymc/gp/Realization.py -> build/lib.macosx-10.5-i386-2.5/pymc/
gp
copying pymc/gp/__init__.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
copying pymc/gp/gpplots.py -> build/lib.macosx-10.5-i386-2.5/pymc/gp
creating build/lib.macosx-10.5-i386-2.5/pymc/gp/cov_funs
copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp/cov_funs
copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp/cov_funs
copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.5-i386-2.5/
pymc/gp/cov_funs
copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp/cov_funs
copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.5-
i386-2.5/pymc/gp/cov_funs
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Found executable /usr/bin/ifort
customize GnuFCompiler
Could not locate executable g77
customize Gnu95FCompiler
Found executable /sw/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pymc.flib' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -Wno-long-double -mno-fused-madd -
DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
creating build/temp.macosx-10.5-i386-2.5
creating build/temp.macosx-10.5-i386-2.5/cephes
creating build/temp.macosx-10.5-i386-2.5/build
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -
I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/
python2.5 -c'
extra options: '-msse3'
gcc: build/src.macosx-10.5-i386-2.5/fortranobject.c
cc1: error: unrecognized command line option "-Wno-long-double"
cc1: error: unrecognized command line option "-Wno-long-double"
error: Command "gcc -fno-strict-aliasing -Wno-long-double -mno-fused-
madd -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -
DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -I/sw/lib/python2.5/
site-packages/numpy/core/include -I/sw/include/python2.5 -c build/
src.macosx-10.5-i386-2.5/fortranobject.c -o build/temp.macosx-10.5-
i386-2.5/build/src.macosx-10.5-i386-2.5/fortranobject.o -msse3" failed
with exit status 1
--
maclb:pymc-read-only leo$ python setup.py clean
running clean
removing 'build/temp.macosx-10.5-i386-2.5' (and everything under it)
maclb:pymc-read-only leo$ LDFLAGS="-Wall -undefined dynamic_lookup -
bundle -arch i386 -arch x86_64" FFLAGS="-arch i386 -arch x86_64"
CFLAGS="-arch i386 -arch x86_64" python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --
compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --
fcompiler options
running build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/flib-f2pywrappers.f' to
sources.
building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/
isotropic_cov_funs-f2pywrappers.f' to sources.
building extension "pymc.gp.cov_funs.distances" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Found executable /usr/bin/ifort
customize GnuFCompiler
Could not locate executable g77
customize Gnu95FCompiler
Found executable /sw/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pymc.flib' extension
compiling C sources
C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -
arch i386 -arch x86_64
creating build/temp.macosx-10.5-i386-2.5
creating build/temp.macosx-10.5-i386-2.5/cephes
creating build/temp.macosx-10.5-i386-2.5/build
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-
i386-2.5/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -
I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/
python2.5 -c'
extra options: '-msse3'
gcc: build/src.macosx-10.5-i386-2.5/fortranobject.c
In file included from /sw/include/python2.5/Python.h:57,
from build/src.macosx-10.5-i386-2.5/fortranobject.h:
7,
from build/src.macosx-10.5-i386-2.5/fortranobject.c:
2:
/sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
definition appears wrong for platform (bad gcc/glibc config?)."
lipo: can't figure out the architecture type of: /var/folders/YO/
YOADMSqSEl4jYv9pOLJSqk+++TI/-Tmp-//ccF8R4sr.out
In file included from /sw/include/python2.5/Python.h:57,
from build/src.macosx-10.5-i386-2.5/fortranobject.h:
7,
from build/src.macosx-10.5-i386-2.5/fortranobject.c:
2:
/sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
definition appears wrong for platform (bad gcc/glibc config?)."
lipo: can't figure out the architecture type of: /var/folders/YO/
YOADMSqSEl4jYv9pOLJSqk+++TI/-Tmp-//ccF8R4sr.out
error: Command "gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -
arch i386 -arch x86_64 -DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-
i386-2.5 -I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/
include/python2.5 -c build/src.macosx-10.5-i386-2.5/fortranobject.c -o
build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/
fortranobject.o -msse3" failed with exit status 1
Dan O'Donovan
Dec 8, 2009, 6:29:13 AM12/8/09
to py...@googlegroups.com
> I also tried Daniel O'Donovan's recommendation for compiling the code
> under Snow Leopard (http://groups.google.com/group/pymc/browse_thread/
> thread/7726b9d4979e18c3) but that led to other problems (please see
> further below). It says that
>
> /sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
> definition appears wrong for platform (bad gcc/glibc config?).
>
This error:
/sw/include/python2.5/pyport.h:761:2: error: #error "LONG_BIT
definition appears wrong for platform (bad gcc/glibc config?)."
$ file /sw/bin/python2.5
)
and as your running snow leopard on a Core 2 Duo computer gcc wants to build 64 bit code. I would recommend (if you haven't already) re-installing fink to get a 64 bit version, or using the system Python (the one that comes with Snow Leopard). Alternatively, to build 32 bit code, you could try leaving out the -arch x84_64 bit and just keeping the -arch i386 parts.
Hope that helps!
Dan
Leonard Burtscher
Dec 8, 2009, 8:01:54 AM12/8/09
to py...@googlegroups.com
Hi Dan,
Thanks for your quick response.
Am 08.12.2009 um 12:29 schrieb Dan O'Donovan:
> makes me think that your python2.5 is 32 bit
Yes, that's right, I was running 32-bit python2.5.
> I would recommend (if you haven't already) re-installing fink to get a 64 bit version, or using the system Python (the one that comes with Snow Leopard).
I followed the instructions on the fink page to upgrade my 10.5 installation to a 32-bit fink installation for 10.6. Did I not understand you right in the previous, famous :-), post in that pyMC will not run 64-bit? So why should I upgrade to 64-bit?
I also tried using the system python (2.6.1) but then it didn't find a Fortran compiler anymore... :-/ (I have Developer Tools installed). Isn't a Fortran compiler part of GCC?
> Alternatively, to build 32 bit code, you could try leaving out the -arch x84_64 bit and just keeping the -arch i386 parts.
OK, I tried that but apparently the Fortran compiler doesn't like the -arch option:
f951: Fehler: nicht erkannte Kommandozeilenoption »-arch«
(For some reason this was now in German; means: "command line option not recognized '-arch'").
I googled around and found that other people have had similar problems (<http://trac.macports.org/ticket/20361> or <http://projects.scipy.org/scipy/ticket/915>). The recommendation seems to be to not use the -arch option with Fortran compilers. I wonder why this option works fine with you and Anan.
Thanks,
Leonard
--
$ LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386" FFLAGS="-arch i386" CFLAGS="-arch i386" python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
gcc: cephes/i0.c
gcc: cephes/c2f.c
cephes/c2f.c:9: warning: function declaration isn't a prototype
gcc: build/src.macosx-10.5-i386-2.5/pymc/flibmodule.c
compiling Fortran sources
Fortran f77 compiler: /sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -arch i386 -O3 -funroll-loops
Fortran f90 compiler: /sw/bin/gfortran -Wall -fno-second-underscore -arch i386 -O3 -funroll-loops
Fortran fix compiler: /sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -arch i386 -O3 -funroll-loops
creating build/temp.macosx-10.5-i386-2.5/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/python2.5 -c'
gfortran:f77: pymc/flib.f
f951: Fehler: nicht erkannte Kommandozeilenoption »-arch«
f951: Fehler: nicht erkannte Kommandozeilenoption »-arch«
error: Command "/sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -arch i386 -O3 -funroll-loops -DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/python2.5 -c -c pymc/flib.f -o build/temp.macosx-10.5-i386-2.5/pymc/flib.o" failed with exit status 1
Thanks for your quick response.
Am 08.12.2009 um 12:29 schrieb Dan O'Donovan:
> makes me think that your python2.5 is 32 bit
> I would recommend (if you haven't already) re-installing fink to get a 64 bit version, or using the system Python (the one that comes with Snow Leopard).
I also tried using the system python (2.6.1) but then it didn't find a Fortran compiler anymore... :-/ (I have Developer Tools installed). Isn't a Fortran compiler part of GCC?
> Alternatively, to build 32 bit code, you could try leaving out the -arch x84_64 bit and just keeping the -arch i386 parts.
f951: Fehler: nicht erkannte Kommandozeilenoption »-arch«
(For some reason this was now in German; means: "command line option not recognized '-arch'").
I googled around and found that other people have had similar problems (<http://trac.macports.org/ticket/20361> or <http://projects.scipy.org/scipy/ticket/915>). The recommendation seems to be to not use the -arch option with Fortran compilers. I wonder why this option works fine with you and Anan.
Thanks,
Leonard
--
$ LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386" FFLAGS="-arch i386" CFLAGS="-arch i386" python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/flib-f2pywrappers.f' to sources.
building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/gp/cov_funs/isotropic_cov_funs-f2pywrappers.f' to sources.
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
adding 'build/src.macosx-10.5-i386-2.5/pymc/flib-f2pywrappers.f' to sources.
building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-i386-2.5' to include_dirs.
creating build/temp.macosx-10.5-i386-2.5
creating build/temp.macosx-10.5-i386-2.5/cephes
creating build/temp.macosx-10.5-i386-2.5/build
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/python2.5 -c'
creating build/temp.macosx-10.5-i386-2.5/cephes
creating build/temp.macosx-10.5-i386-2.5/build
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5
creating build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/pymc
extra options: '-msse3'
gcc: build/src.macosx-10.5-i386-2.5/fortranobject.c
gcc: cephes/chbevl.c
gcc: build/src.macosx-10.5-i386-2.5/fortranobject.c
gcc: cephes/i0.c
gcc: cephes/c2f.c
cephes/c2f.c:9: warning: function declaration isn't a prototype
gcc: build/src.macosx-10.5-i386-2.5/pymc/flibmodule.c
compiling Fortran sources
Fortran f77 compiler: /sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -arch i386 -O3 -funroll-loops
Fortran f90 compiler: /sw/bin/gfortran -Wall -fno-second-underscore -arch i386 -O3 -funroll-loops
Fortran fix compiler: /sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -arch i386 -O3 -funroll-loops
creating build/temp.macosx-10.5-i386-2.5/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/python2.5 -c'
gfortran:f77: pymc/flib.f
f951: Fehler: nicht erkannte Kommandozeilenoption »-arch«
f951: Fehler: nicht erkannte Kommandozeilenoption »-arch«
error: Command "/sw/bin/gfortran -Wall -ffixed-form -fno-second-underscore -arch i386 -O3 -funroll-loops -DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-i386-2.5 -I/sw/lib/python2.5/site-packages/numpy/core/include -I/sw/include/python2.5 -c -c pymc/flib.f -o build/temp.macosx-10.5-i386-2.5/pymc/flib.o" failed with exit status 1
Anand Patil
Dec 8, 2009, 8:14:33 AM12/8/09
to py...@googlegroups.com
Hi Leonard,
On Tue, Dec 8, 2009 at 1:01 PM, Leonard Burtscher
<burt...@mpia-hd.mpg.de> wrote:
> I googled around and found that other people have had similar problems (<http://trac.macports.org/ticket/20361> or <http://projects.scipy.org/scipy/ticket/915>). The recommendation seems to be to not use the -arch option with Fortran compilers. I wonder why this option works fine with you and Anan.
I've been using the MacPorts python 2.6, and couldn't get things
working without the -arch flags. Haven't tried with Fink though. I did
try with the system Python, but it was a long time ago, and I
eventually gave up and started using MacPorts.
Anand
(spelled my own name wrong in my last email to you)
> --
>
> You received this message because you are subscribed to the Google Groups "PyMC" group.
> To post to this group, send email to py...@googlegroups.com.
> To unsubscribe from this group, send email to pymc+uns...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/pymc?hl=en.
>
>
>
On Tue, Dec 8, 2009 at 1:01 PM, Leonard Burtscher
<burt...@mpia-hd.mpg.de> wrote:
> I googled around and found that other people have had similar problems (<http://trac.macports.org/ticket/20361> or <http://projects.scipy.org/scipy/ticket/915>). The recommendation seems to be to not use the -arch option with Fortran compilers. I wonder why this option works fine with you and Anan.
working without the -arch flags. Haven't tried with Fink though. I did
try with the system Python, but it was a long time ago, and I
eventually gave up and started using MacPorts.
Anand
(spelled my own name wrong in my last email to you)
>
> You received this message because you are subscribed to the Google Groups "PyMC" group.
> To post to this group, send email to py...@googlegroups.com.
> To unsubscribe from this group, send email to pymc+uns...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/pymc?hl=en.
>
>
>
Chris Fonnesbeck
Dec 8, 2009, 5:39:48 PM12/8/09
to PyMC
On Dec 9, 2:14 am, Anand Patil <anand.prabhakar.pa...@gmail.com>
wrote:
Matplotlib, and PyMC for Snow Leopard together as one package. You can
grab it from macinscience.org, under the "SciPy Superpack" page; it
runs on 10.6's own 64-bit python.
cf
wrote:
> Hi Leonard,
>
> On Tue, Dec 8, 2009 at 1:01 PM, Leonard Burtscher
>
>
> On Tue, Dec 8, 2009 at 1:01 PM, Leonard Burtscher
>
> <burtsc...@mpia-hd.mpg.de> wrote:
> > I googled around and found that other people have had similar problems (<http://trac.macports.org/ticket/20361> or <http://projects.scipy.org/scipy/ticket/915>). The recommendation seems to be to not use the -arch option with Fortran compilers. I wonder why this option works fine with you and Anan.
>
> I've been using the MacPorts python 2.6, and couldn't get things
> working without the -arch flags. Haven't tried with Fink though. I did
> try with the system Python, but it was a long time ago, and I
> eventually gave up and started using MacPorts.
>
For those Mac users interested, I distribute builds of Numpy, Scipy,
> > I googled around and found that other people have had similar problems (<http://trac.macports.org/ticket/20361> or <http://projects.scipy.org/scipy/ticket/915>). The recommendation seems to be to not use the -arch option with Fortran compilers. I wonder why this option works fine with you and Anan.
>
> I've been using the MacPorts python 2.6, and couldn't get things
> working without the -arch flags. Haven't tried with Fink though. I did
> try with the system Python, but it was a long time ago, and I
> eventually gave up and started using MacPorts.
>
Matplotlib, and PyMC for Snow Leopard together as one package. You can
grab it from macinscience.org, under the "SciPy Superpack" page; it
runs on 10.6's own 64-bit python.
cf
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