In [1]:
from IPython.display import Image
Image('quantopian.png')
Out[1]:
In [2]:
from IPython.display import Image
import prettyplotlib as ppl
from prettyplotlib import plt
import numpy as np
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica'], 'size': 22})
rc('xtick', labelsize=14)
rc('ytick', labelsize=14)
## for Palatino and other serif fonts use:
#rc('font',**{'family':'serif','serif':['Palatino']})
rc('text', usetex=True)
%matplotlib inline
In [3]:
Image('backbox_ml.png')
Out[3]:
In [4]:
Image('openbox_pp.png')
Out[4]:
Moreover...
In [5]:
from scipy import stats
# set every possibility to be equally possible
x_coin = np.linspace(0, 1, 101)
In [6]:
import prettyplotlib as ppl
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, xlabel=r'Hypothesis for chance of heads',
ylabel=r'Probability of hypothesis',
title=r'Prior probability distribution after no coin tosses')
ppl.plot(ax, x_coin, stats.beta(2, 2).pdf(x_coin), linewidth=3.)
ax.set_xticklabels([r'0\%', r'20\%', r'40\%', r'60\%', r'80\%', r'100\%']);
fig.savefig('coin1.png')
In [7]:
Image('coin1.png')
Out[7]:
In [8]:
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, xlabel='Hypothesis for chance of heads',
ylabel='Probability of hypothesis',
title='Posterior probability distribution after first heads')
ppl.plot(ax, x_coin, stats.beta(3, 2).pdf(x_coin), linewidth=3.)
ax.set_xticklabels([r'0\%', r'20\%', r'40\%', r'60\%', r'80\%', r'100\%']);
plt.savefig('coin2.png')
In [9]:
Image('coin2.png')
Out[9]:
In [10]:
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, xlabel='Hypothesis for chance of heads',
ylabel='Probability of hypothesis',
title='Posterior probability distribution after 1 head, 1 tail')
ppl.plot(ax, x_coin, stats.beta(3, 3).pdf(x_coin), linewidth=3.)
ax.set_xticklabels(['0\%', '20\%', '40\%', '60\%', '80\%', '100\%']);
fig.savefig('coin3.png')
In [11]:
Image('coin3.png')
Out[11]:
In [12]:
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, xlabel='Hypothesis for chance of heads',
ylabel='Probability of hypothesis',
title='Posterior probability distribution after 20 heads and 20 tails')
ppl.plot(ax, x_coin, stats.beta(22, 22).pdf(x_coin), linewidth=3.)
ax.set_xticklabels(['0\%', '20\%', '40\%', '60\%', '80\%', '100\%']);
fig.savefig('coin4.png')
In [13]:
Image('coin4.png')
Out[13]:
$\theta$: Parameters of model (chance of getting heads)).
In [15]:
from scipy import stats
fig = ppl.plt.figure(figsize=(14, 6))
ax1 = fig.add_subplot(121, title='What we want', ylim=(0, .5), xlabel=r'$\theta$', ylabel=r'$P(\theta)$')
ppl.plot(ax1, np.linspace(-4, 4, 100), stats.norm.pdf(np.linspace(-3, 3, 100)), linewidth=4.)
ax2 = fig.add_subplot(122, title='What we get', xlim=(-4, 4), ylim=(0, 1800), xlabel=r'$\theta$', ylabel='\# of samples')
ppl.hist(ax2, np.random.randn(10000), bins=20);
fig.savefig('wantget.png')
In [ ]:
Image('wantget.png')
In [16]:
size = 200
true_intercept = 1
true_slope = 2
x = np.linspace(0, 1, size)
# y = a + b*x
true_regression_line = true_intercept + true_slope * x
# add noise
y = true_regression_line + np.random.normal(scale=.5, size=size)
data = dict(x=x, y=y)
In [19]:
fig = plt.figure(figsize=(7, 7))
ax = fig.add_subplot(111, xlabel='Value of gold', ylabel='Value of gold miners', title='Synthetic data and underlying model')
ppl.scatter(ax, x, y, label='sampled data')
ppl.plot(ax, x, true_regression_line, label='true regression line', linewidth=4.)
ax.legend(loc=2);
fig.savefig('synth_data.png')
In [20]:
Image('synth_data.png')
Out[20]:
with $$ \epsilon \sim \mathcal{N}(0, \sigma^2) $$
In [23]:
!conda install pymc
Conda package not available for pymc, attempting to install via pip
Downloading/unpacking pymc
Downloading pymc-2.3.tar.gz (13.1MB): 13.1MB downloaded
Running setup.py egg_info for package pymc
build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
f2py:> build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c
IOError: [Errno 2] No such file or directory: 'skip:ppnd7'. Skipping file "skip:ppnd7".
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(na)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(nb)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (nmu)' to 'dimension(nmu)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (na)' to 'dimension(na)'. Ignoring.
rmbadname1: Replacing "index" with "index_bn".
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".
sortvarnames: failed to compute dependencies because of cyclic dependencies between x, nx
sortvarnames: failed to compute dependencies because of cyclic dependencies between w, x, nx
sortvarnames: failed to compute dependencies because of cyclic dependencies between n, nx, bin0, delta, x, d
"object of type 'builtin_function_or_method' has no len()" in evaluating 'len(ord)' (available names: [])
Reading fortran codes...
Reading file 'pymc/flib.f' (format:fix,strict)
Reading file 'pymc/histogram.f' (format:fix,strict)
Reading file 'pymc/flib_blas.f' (format:fix,strict)
Reading file 'pymc/blas_wrap.f' (format:fix,strict)
Reading file 'pymc/math.f' (format:fix,strict)
Reading file 'pymc/gibbsit.f' (format:fix,strict)
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
{'attrspec': ['intent(hide)']}
In: :flib:pymc/flib.f:expand_triangular
vars2fortran: No typespec for argument "nf".
{'attrspec': ['intent(hide)']}
In: :flib:pymc/flib.f:expand_triangular
vars2fortran: No typespec for argument "n".
Block: expand_triangular
Block: mod_to_circle
Block: standardize
Block: gammln
Block: mvgammln
Block: factrl
Block: factln
Block: normcdf
Block: sn_like
Block: rskewnorm
Block: uniform_like
Block: uniform_grad_x
Block: uniform_grad_l
Block: uniform_grad_u
Block: duniform_like
Block: exponweib
Block: exponweib_gx
Block: exponweib_gl
Block: exponweib_gk
Block: exponweib_ga
Block: exponweib_gs
Block: exponweib_ppf
Block: constrain
Block: poisson
Block: poisson_gmu
Block: trpoisson
Block: trpoisson_gmu
Block: t
Block: t_grad_x
Block: t_grad_nu
Block: chi2_grad_nu
Block: nct
Block: multinomial
Block: weibull
Block: weibull_gx
Block: weibull_ga
Block: weibull_gb
Block: logistic
Block: normal
Block: normal_grad_tau
Block: normal_grad_x
Block: normal_grad_mu
Block: hnormal
Block: hnormal_gradx
Block: hnormal_gradtau
Block: lognormal
Block: lognormal_gradx
Block: lognormal_gradmu
Block: lognormal_gradtau
Block: arlognormal
Block: gev
Block: gev_ppf
Block: gamma
Block: gamma_grad_x
Block: gamma_grad_alpha
Block: gamma_grad_beta
Block: igamma
Block: igamma_grad_x
Block: igamma_grad_alpha
Block: igamma_grad_beta
Block: hyperg
Block: geometric
Block: geometric_gp
Block: dirichlet
Block: cauchy
Block: cauchy_grad_x
Block: cauchy_grad_a
Block: cauchy_grad_b
Block: negbin
Block: negbin2
Block: negbin2_gmu
Block: negbin2_ga
Block: binomial
Block: binomial_gp
Block: bernoulli
Block: bern_grad_p
Block: beta_like
Block: beta_grad_x
Block: beta_grad_a
Block: beta_grad_b
Block: betabin_like
Block: betabin_ga
Block: betabin_gb
Block: mvhyperg
Block: dirmultinom
Block: wishart
Block: trace
Block: gamfun
Block: gammds
Block: psi
Block: gser
Block: gcf
Block: gammq
Block: trans
Block: matmult
Block: dtrm
Block: elgs
Block: bico
Block: chol
Block: hermpoly
Block: set_uniform
Block: categorical
Block: rcat
Block: logit
Block: invlogit
Block: stukel_logit
Block: stukel_invlogit
Block: vonmises
Block: pareto
Block: truncated_pareto
Block: fixed_binsize
Block: weighted_fixed_binsize
Block: fixed_binsize_nd
{'attrspec': ['dimension(n)']}
In: :flib:pymc/histogram.f:qsorti
vars2fortran: No typespec for argument "ord".
Block: qsorti
Block: checksymm
Block: chol_mvnorm
Block: cov_mvnorm
Block: prec_mvnorm
Block: blas_wishart
Block: blas_wishart_cov
{'attrspec': ['intent(hide)']}
In: :flib:pymc/blas_wrap.f:dcopy_wrap
vars2fortran: No typespec for argument "nx".
Block: dcopy_wrap
Block: dtrmm_wrap
Block: dtrsm_wrap
Block: dpotrf_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 "normcdf"...
normcdf(x)
Constructing wrapper function "sn_like"...
like = sn_like(x,mu,tau,alph)
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 "uniform_grad_x"...
gradxlike = uniform_grad_x(x,lower,upper)
Constructing wrapper function "uniform_grad_l"...
gradllike = uniform_grad_l(x,lower,upper)
Constructing wrapper function "uniform_grad_u"...
gradulike = uniform_grad_u(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_gx"...
gradlike = exponweib_gx(x,alpha,k,loc,scale)
Constructing wrapper function "exponweib_gl"...
gradlike = exponweib_gl(x,alpha,k,loc,scale)
Constructing wrapper function "exponweib_gk"...
gradlike = exponweib_gk(x,alpha,k,loc,scale)
Constructing wrapper function "exponweib_ga"...
gradlike = exponweib_ga(x,alpha,k,loc,scale,[nk])
Constructing wrapper function "exponweib_gs"...
gradlike = exponweib_gs(x,alpha,k,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 "poisson_gmu"...
gradlike = poisson_gmu(x,mu)
Constructing wrapper function "trpoisson"...
like = trpoisson(x,mu,k)
Constructing wrapper function "trpoisson_gmu"...
gradlike = trpoisson_gmu(x,mu,k)
Constructing wrapper function "t"...
like = t(x,nu)
Constructing wrapper function "t_grad_x"...
gradlikex = t_grad_x(x,nu)
Constructing wrapper function "t_grad_nu"...
gradlikenu = t_grad_nu(x,nu)
Constructing wrapper function "chi2_grad_nu"...
gradlikenu = chi2_grad_nu(x,nu)
Constructing wrapper function "nct"...
like = nct(x,mu,lam,nu)
Constructing wrapper function "multinomial"...
like = multinomial(x,n,p)
Constructing wrapper function "weibull"...
like = weibull(x,alpha,beta)
Constructing wrapper function "weibull_gx"...
gradlike = weibull_gx(x,alpha,beta)
Constructing wrapper function "weibull_ga"...
gradlike = weibull_ga(x,alpha,beta)
Constructing wrapper function "weibull_gb"...
gradlike = weibull_gb(x,alpha,beta)
Constructing wrapper function "logistic"...
like = logistic(x,mu,tau)
Constructing wrapper function "normal"...
like = normal(x,mu,tau)
Constructing wrapper function "normal_grad_tau"...
grad_tau_like = normal_grad_tau(x,mu,tau)
Constructing wrapper function "normal_grad_x"...
grad_x_like = normal_grad_x(x,mu,tau)
Constructing wrapper function "normal_grad_mu"...
gradmulike = normal_grad_mu(x,mu,tau)
Constructing wrapper function "hnormal"...
like = hnormal(x,tau)
Constructing wrapper function "hnormal_gradx"...
gradlike = hnormal_gradx(x,tau)
Constructing wrapper function "hnormal_gradtau"...
gradlike = hnormal_gradtau(x,tau)
Constructing wrapper function "lognormal"...
like = lognormal(x,mu,tau)
Constructing wrapper function "lognormal_gradx"...
gradlike = lognormal_gradx(x,mu,tau)
Constructing wrapper function "lognormal_gradmu"...
gradlike = lognormal_gradmu(x,mu,tau)
Constructing wrapper function "lognormal_gradtau"...
gradlike = lognormal_gradtau(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 "gamma_grad_x"...
gradxlike = gamma_grad_x(x,alpha,beta)
Constructing wrapper function "gamma_grad_alpha"...
gradalphalike = gamma_grad_alpha(x,alpha,beta)
Constructing wrapper function "gamma_grad_beta"...
gradbetalike = gamma_grad_beta(x,alpha,beta)
Constructing wrapper function "igamma"...
like = igamma(x,alpha,beta)
Constructing wrapper function "igamma_grad_x"...
gradxlike = igamma_grad_x(x,alpha,beta)
Constructing wrapper function "igamma_grad_alpha"...
gradalphalike = igamma_grad_alpha(x,alpha,beta)
Constructing wrapper function "igamma_grad_beta"...
gradbetalike = igamma_grad_beta(x,alpha,beta)
Constructing wrapper function "hyperg"...
like = hyperg(x,draws,success,total)
Constructing wrapper function "geometric"...
like = geometric(x,p)
Constructing wrapper function "geometric_gp"...
gradlike = geometric_gp(x,p)
Constructing wrapper function "dirichlet"...
like = dirichlet(x,theta)
Constructing wrapper function "cauchy"...
like = cauchy(x,alpha,beta)
Constructing wrapper function "cauchy_grad_x"...
gradlike = cauchy_grad_x(x,alpha,beta)
Constructing wrapper function "cauchy_grad_a"...
gradlike = cauchy_grad_a(x,alpha,beta)
Constructing wrapper function "cauchy_grad_b"...
gradlike = cauchy_grad_b(x,alpha,beta)
Constructing wrapper function "negbin"...
like = negbin(x,r,p)
Constructing wrapper function "negbin2"...
like = negbin2(x,mu,a)
Constructing wrapper function "negbin2_gmu"...
gradlike = negbin2_gmu(x,mu,alpha)
Constructing wrapper function "negbin2_ga"...
gradlike = negbin2_ga(x,mu,alpha)
Constructing wrapper function "binomial"...
like = binomial(x,n,p)
Constructing wrapper function "binomial_gp"...
gradlike = binomial_gp(x,n,p)
Constructing wrapper function "bernoulli"...
like = bernoulli(x,p)
Constructing wrapper function "bern_grad_p"...
grad_like = bern_grad_p(x,p)
Constructing wrapper function "beta_like"...
like = beta_like(x,alpha,beta)
Constructing wrapper function "beta_grad_x"...
gradlikex = beta_grad_x(x,alpha,beta)
Constructing wrapper function "beta_grad_a"...
gradlikea = beta_grad_a(x,alpha,beta)
Constructing wrapper function "beta_grad_b"...
gradlikeb = beta_grad_b(x,alpha,beta)
Constructing wrapper function "betabin_like"...
like = betabin_like(x,alpha,beta,n)
Constructing wrapper function "betabin_ga"...
gradlike = betabin_ga(x,alpha,beta,n)
Constructing wrapper function "betabin_gb"...
gradlike = betabin_gb(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)
Creating wrapper for Fortran function "psi"("psi")...
Constructing wrapper function "psi"...
psi = psi(x)
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)
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 "pareto"...
like = pareto(x,alpha,m)
Constructing wrapper function "truncated_pareto"...
like = truncated_pareto(x,alpha,m,b)
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 "dcopy_wrap"...
dcopy_wrap(x,y)
Constructing wrapper function "dtrmm_wrap"...
dtrmm_wrap(a,b,side,transa,uplo,alpha)
Constructing wrapper function "dtrsm_wrap"...
dtrsm_wrap(a,b,side,transa,uplo,alpha)
Constructing wrapper function "dpotrf_wrap"...
info = dpotrf_wrap(a)
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-x86_64-2.7/pymc/flibmodule.c"
Fortran 77 wrappers are saved to "build/src.macosx-10.5-x86_64-2.7/pymc/flib-f2pywrappers.f"
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
adding 'build/src.macosx-10.5-x86_64-2.7/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-x86_64-2.7/pymc/gp/linalg_utilsmodule.c
Reading fortran codes...
Reading file 'pymc/gp/linalg_utils.f' (format:fix,strict)
Reading file 'pymc/blas_wrap.f' (format:fix,strict)
Post-processing...
Block: linalg_utils
Block: remove_duplicates
Block: check_repeats
Block: diag_call
Block: cov_fun
{'attrspec': ['intent(hide)']}
In: :linalg_utils:pymc/gp/linalg_utils.f:basis_diag_call
vars2fortran: No typespec for argument "nbas".
Block: basis_diag_call
Block: gp_array_logp
Block: asqs
{'attrspec': ['intent(hide)']}
In: :linalg_utils:pymc/blas_wrap.f:dcopy_wrap
vars2fortran: No typespec for argument "nx".
Block: dcopy_wrap
Block: dtrmm_wrap
Block: dtrsm_wrap
Block: dpotrf_wrap
Block: dchdc_wrap
Block: dpotrs_wrap
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 "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 "gp_array_logp"...
like = gp_array_logp(x,mu,sig,[overwrite_x,overwrite_mu])
Constructing wrapper function "asqs"...
asqs(c,s,[cmin,cmax])
Constructing wrapper function "dcopy_wrap"...
dcopy_wrap(x,y)
Constructing wrapper function "dtrmm_wrap"...
dtrmm_wrap(a,b,side,transa,uplo,alpha)
Constructing wrapper function "dtrsm_wrap"...
dtrsm_wrap(a,b,side,transa,uplo,alpha)
Constructing wrapper function "dpotrf_wrap"...
info = dpotrf_wrap(a)
Constructing wrapper function "dchdc_wrap"...
piv,info = dchdc_wrap(a)
Constructing wrapper function "dpotrs_wrap"...
info = dpotrs_wrap(chol_fac,b,[uplo])
Wrote C/API module "linalg_utils" to file "build/src.macosx-10.5-x86_64-2.7/pymc/gp/linalg_utilsmodule.c"
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
f2py:> build/src.macosx-10.5-x86_64-2.7/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
{'attrspec': ['intent(hide)']}
In: :incomplete_chol:pymc/gp/incomplete_chol.f:ichol_basis
vars2fortran: No typespec for argument "n_nug".
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-x86_64-2.7/pymc/gp/incomplete_cholmodule.c"
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
f2py:> build/src.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs/isotropic_cov_funsmodule.c
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: matern
Block: nsmatrn
Block: stein_spatiotemporal
Block: nsst
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 "matern"...
matern(c,diff_degree,[cmin,cmax,symm])
Constructing wrapper function "nsmatrn"...
nsmatrn(c,ddx,ddy,hx,hy,nmax,[cmin,cmax,symm])
Constructing wrapper function "stein_spatiotemporal"...
stein_spatiotemporal(c,gt,origin_val,[cmin,cmax,symm])
Constructing wrapper function "nsst"...
nsst(c,gt,origin_val,hx,hy,[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-x86_64-2.7/pymc/gp/cov_funs/isotropic_cov_funsmodule.c"
Fortran 77 wrappers are saved to "build/src.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs/isotropic_cov_funs-f2pywrappers.f"
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
adding 'build/src.macosx-10.5-x86_64-2.7/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-x86_64-2.7/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-x86_64-2.7/pymc/gp/cov_funs/distancesmodule.c"
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
build_src: building npy-pkg config files
warning: no files found matching 'README.txt'
warning: no files found matching 'INSTALL.txt'
warning: no files found matching 'docs/UserGuide.pdf'
Installing collected packages: pymc
Running setup.py install for pymc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
adding 'build/src.macosx-10.5-x86_64-2.7/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-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
adding 'build/src.macosx-10.5-x86_64-2.7/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-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
build_src: building npy-pkg config files
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/local/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pymc.flib' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -I//anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/opt/zlib/include
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-x86_64-2.7 -I//anaconda/lib/python2.7/site-packages/numpy/core/include -I//anaconda/include/python2.7 -c'
extra options: '-msse3'
gcc: cephes/i0.c
gcc: cephes/c2f.c
gcc: build/src.macosx-10.5-x86_64-2.7/fortranobject.c
In file included from build/src.macosx-10.5-x86_64-2.7/fortranobject.c:2:
In file included from build/src.macosx-10.5-x86_64-2.7/fortranobject.h:13:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:
//anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
^
build/src.macosx-10.5-x86_64-2.7/fortranobject.c:338:30: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((fp->defs[i].func==NULL)) {
~~~~~~~~~~~~~~~~^~~~~~
build/src.macosx-10.5-x86_64-2.7/fortranobject.c:338:30: note: remove extraneous parentheses around the comparison to silence this warning
if ((fp->defs[i].func==NULL)) {
~ ^ ~
build/src.macosx-10.5-x86_64-2.7/fortranobject.c:338:30: note: use '=' to turn this equality comparison into an assignment
if ((fp->defs[i].func==NULL)) {
^~
=
2 warnings generated.
gcc: build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c
In file included from build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:18:
In file included from build/src.macosx-10.5-x86_64-2.7/fortranobject.h:13:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:
//anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
^
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:16934:7: warning: array index 2 is past the end of the array (which contains 2 elements) [-Warray-bounds]
d = shape(x,2);
^ ~
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:86:24: note: expanded from macro 'shape'
#define shape(var,dim) var ## _Dims[dim]
^
<scratch space>:394:1: note: expanded from here
x_Dims
^
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:16835:3: note: array 'x_Dims' declared here
npy_intp x_Dims[2] = {-1, -1};
^
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:181:12: warning: unused function 'f2py_size' [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^
3 warnings generated.
gcc: cephes/chbevl.c
compiling Fortran sources
Fortran f77 compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -m64 -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -fno-second-underscore -m64 -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -m64 -fPIC -O3 -funroll-loops
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-x86_64-2.7 -I//anaconda/lib/python2.7/site-packages/numpy/core/include -I//anaconda/include/python2.7 -c'
gfortran:f77: pymc/flib.f
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Warning: Nonconforming tab character in column 1 of line 4626
Warning: Nonconforming tab character in column 1 of line 4628
Warning: Nonconforming tab character in column 1 of line 4630
Warning: Nonconforming tab character in column 1 of line 4632
Warning: Nonconforming tab character in column 1 of line 4633
Warning: Nonconforming tab character in column 1 of line 4634
Warning: Nonconforming tab character in column 1 of line 4635
Warning: Nonconforming tab character in column 1 of line 4637
Warning: Nonconforming tab character in column 1 of line 4638
Warning: Nonconforming tab character in column 1 of line 4639
Warning: Nonconforming tab character in column 1 of line 4640
Warning: Nonconforming tab character in column 1 of line 4642
Warning: Nonconforming tab character in column 1 of line 4643
Warning: Nonconforming tab character in column 1 of line 4644
Warning: Nonconforming tab character in column 1 of line 4645
Warning: Nonconforming tab character in column 1 of line 4646
pymc/flib.f:316.55:
DOUBLE PRECISION mu_now, tau_now, alph_now, d_now, like
1
Warning: Unused variable 'd_now' declared at (1)
pymc/flib.f:314.42:
INTEGER i, nx, nalph, nmu, ntau, tnx
1
Warning: Unused variable 'tnx' declared at (1)
pymc/flib.f:442.71:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'gradxlike' at (1)
pymc/flib.f:461.40:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'high' declared at (1)
pymc/flib.f:458.36:
INTEGER n, nlower, nupper, i
1
Warning: Unused variable 'i' declared at (1)
pymc/flib.f:461.29:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'like' declared at (1)
pymc/flib.f:461.34:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'low' declared at (1)
pymc/flib.f:442.39:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'lower' at (1)
pymc/flib.f:442.45:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'upper' at (1)
pymc/flib.f:442.33:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'x' at (1)
pymc/flib.f:692.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:760.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:834.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:906.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:976.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:1186.29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:1185.51:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumfact' declared at (1)
pymc/flib.f:1185.27:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumx' declared at (1)
pymc/flib.f:1300.55:
DOUBLE PRECISION mu(nmu), gradlike(nmu),grad, cdf
1
Warning: Unused variable 'cdf' declared at (1)
pymc/flib.f:1302.29:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:1302.36:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'gammq' declared at (1)
pymc/flib.f:1301.59:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumcdf' declared at (1)
pymc/flib.f:1301.51:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumfact' declared at (1)
pymc/flib.f:1301.27:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumx' declared at (1)
pymc/flib.f:1402.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2154.40:
DOUBLE PRECISION gradlike(n), grad
1
Warning: Unused variable 'grad' declared at (1)
pymc/flib.f:2665.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2728.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2793.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2903.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2959.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3021.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3396.58:
DOUBLE PRECISION gradlike(nx), atmp, btmp, PI, glike
1
Warning: Unused variable 'glike' declared at (1)
pymc/flib.f:3646.37:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:3646.29:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3706.37:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:3706.29:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3836.29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:4039.26:
DOUBLE PRECISION psi
1
Warning: Unused variable 'psi' declared at (1)
pymc/flib.f:4266.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:4332.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:5184.35:
DOUBLE PRECISION like, factln, infinity, sump
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:5186.23:
INTEGER i,j,n_tmp
1
Warning: Unused variable 'n_tmp' declared at (1)
pymc/flib.f:5434.26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f:5488.25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1)
pymc/flib.f:5481.26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f:5535.25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1)
pymc/flib.f:5528.26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f: In function 'elgs':
pymc/flib.f:4882:0: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pymc/flib.f: In function 'exponweib_gl':
pymc/flib.f:778:0: warning: 'nc' may be used uninitialized in this function [-Wuninitialized]
pymc/flib.f: In function 'exponweib_gs':
pymc/flib.f:994:0: warning: 'nc' may be used uninitialized in this function [-Wuninitialized]
gfortran:f77: pymc/histogram.f
gfortran:f77: pymc/flib_blas.f
pymc/flib_blas.f:202.25:
DOUBLE PRECISION PI
1
Warning: Unused variable 'pi' declared at (1)
gfortran:f77: pymc/blas_wrap.f
gfortran:f77: pymc/math.f
pymc/math.f:396.6:
DOUBLE PRECISION FUNCTION DERF(X)
1
Warning: 'derf' declared at (1) is also the name of an intrinsic. It can only be called via an explicit interface or if declared EXTERNAL.
pymc/math.f:417.6:
DOUBLE PRECISION FUNCTION DERFC(X)
1
Warning: 'derfc' declared at (1) is also the name of an intrinsic. It can only be called via an explicit interface or if declared EXTERNAL.
gfortran:f77: pymc/gibbsit.f
pymc/gibbsit.f:2160.5:
215 IF (R .GT. .5898437) GO TO 220
1
Warning: Label 215 at (1) defined but not used
pymc/gibbsit.f:2077.5:
115 IF (R .GT. .5898437) GO TO 120
1
Warning: Label 115 at (1) defined but not used
pymc/gibbsit.f:2064.5:
15 IF (KFLAG.GE.1) GO TO 30
1
Warning: Label 15 at (1) defined but not used
pymc/gibbsit.f:1204.48:
cutpt = empquant(original,iteracnt,qhat,work)
1
Warning: Type mismatch in argument 'work' at (1); passed INTEGER(4) to REAL(8)
gfortran:f77: build/src.macosx-10.5-x86_64-2.7/pymc/flib-f2pywrappers.f
/usr/local/bin/gfortran -Wall -L/usr/local/opt/zlib/lib build/temp.macosx-10.5-x86_64-2.7/cephes/i0.o build/temp.macosx-10.5-x86_64-2.7/cephes/c2f.o build/temp.macosx-10.5-x86_64-2.7/cephes/chbevl.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/fortranobject.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib.o build/temp.macosx-10.5-x86_64-2.7/pymc/histogram.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib_blas.o build/temp.macosx-10.5-x86_64-2.7/pymc/blas_wrap.o build/temp.macosx-10.5-x86_64-2.7/pymc/math.o build/temp.macosx-10.5-x86_64-2.7/pymc/gibbsit.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gfortran/4.7.2/gfortran/lib/gcc/x86_64-apple-darwin12.2.0/4.7.2 -lgfortran -o build/lib.macosx-10.5-x86_64-2.7/pymc/flib.so -Wl,-framework -Wl,Accelerate
Undefined symbols for architecture x86_64:
"_PyArg_ParseTupleAndKeywords", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
"_PyCObject_AsVoidPtr", referenced from:
_initflib in flibmodule.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyCObject_FromVoidPtr", referenced from:
_fortran_getattr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
"_PyCObject_Type", referenced from:
_initflib in flibmodule.o
_F2PyCapsule_Check in fortranobject.o
"_PyComplex_FromDoubles", referenced from:
_f2py_rout_flib_logsum_cpx in flibmodule.o
"_PyComplex_Type", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
"_PyDict_DelItemString", referenced from:
_fortran_setattr in fortranobject.o
"_PyDict_GetItemString", referenced from:
_initflib in flibmodule.o
_fortran_getattr in fortranobject.o
"_PyDict_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyDict_SetItemString", referenced from:
_initflib in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
_PyFortranObject_New in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyErr_Clear", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
_fortran_repr in fortranobject.o
"_PyErr_Format", referenced from:
_initflib in flibmodule.o
_fortran_call in fortranobject.o
"_PyErr_NewException", referenced from:
_initflib in flibmodule.o
"_PyErr_Occurred", referenced from:
_initflib in flibmodule.o
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
...
"_PyErr_Print", referenced from:
_initflib in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_SetString", referenced from:
_initflib in flibmodule.o
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
"_PyEval_RestoreThread", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
_f2py_rout_flib_sn_like in flibmodule.o
_f2py_rout_flib_rskewnorm in flibmodule.o
...
"_PyEval_SaveThread", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
_f2py_rout_flib_sn_like in flibmodule.o
_f2py_rout_flib_rskewnorm in flibmodule.o
...
"_PyExc_AttributeError", referenced from:
_initflib in flibmodule.o
_fortran_setattr in fortranobject.o
"_PyExc_ImportError", referenced from:
_initflib in flibmodule.o
"_PyExc_MemoryError", referenced from:
_string_from_pyobj in flibmodule.o
"_PyExc_RuntimeError", referenced from:
_initflib in flibmodule.o
_fortran_call in fortranobject.o
"_PyExc_TypeError", referenced from:
_fortran_call in fortranobject.o
_array_from_pyobj in fortranobject.o
"_PyExc_ValueError", referenced from:
_string_from_pyobj in flibmodule.o
_array_from_pyobj in fortranobject.o
"_PyFloat_Type", referenced from:
_double_from_pyobj in flibmodule.o
"_PyImport_ImportModule", referenced from:
_initflib in flibmodule.o
"_PyMem_Free", referenced from:
_fortran_dealloc in fortranobject.o
"_PyModule_GetDict", referenced from:
_initflib in flibmodule.o
"_PyNumber_Float", referenced from:
_double_from_pyobj in flibmodule.o
"_PyNumber_Int", referenced from:
_int_from_pyobj in flibmodule.o
"_PyObject_GetAttrString", referenced from:
_initflib in flibmodule.o
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
_fortran_repr in fortranobject.o
"_PyObject_IsTrue", referenced from:
_f2py_rout_flib_constrain in flibmodule.o
"_PyObject_SetAttrString", referenced from:
_initflib in flibmodule.o
"_PyObject_Str", referenced from:
_string_from_pyobj in flibmodule.o
_array_from_pyobj in fortranobject.o
"_PyObject_Type", referenced from:
_array_from_pyobj in fortranobject.o
"_PySequence_Check", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
"_PySequence_GetItem", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
"_PyString_AsString", referenced from:
_fortran_repr in fortranobject.o
_array_from_pyobj in fortranobject.o
"_PyString_ConcatAndDel", referenced from:
_fortran_getattr in fortranobject.o
"_PyString_FromFormat", referenced from:
_fortran_repr in fortranobject.o
"_PyString_FromString", referenced from:
_initflib in flibmodule.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
"_PyType_IsSubtype", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
_string_from_pyobj in flibmodule.o
_array_from_pyobj in fortranobject.o
"_PyType_Type", referenced from:
_initflib in flibmodule.o
"_Py_BuildValue", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
"_Py_FindMethod", referenced from:
_fortran_getattr in fortranobject.o
"_Py_InitModule4_64", referenced from:
_initflib in flibmodule.o
"__PyObject_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
"__Py_NoneStruct", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
Undefined symbols for architecture x86_64:
"_PyArg_ParseTupleAndKeywords", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
"_PyCObject_AsVoidPtr", referenced from:
_initflib in flibmodule.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyCObject_FromVoidPtr", referenced from:
_fortran_getattr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
"_PyCObject_Type", referenced from:
_initflib in flibmodule.o
_F2PyCapsule_Check in fortranobject.o
"_PyComplex_FromDoubles", referenced from:
_f2py_rout_flib_logsum_cpx in flibmodule.o
"_PyComplex_Type", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
"_PyDict_DelItemString", referenced from:
_fortran_setattr in fortranobject.o
"_PyDict_GetItemString", referenced from:
_initflib in flibmodule.o
_fortran_getattr in fortranobject.o
"_PyDict_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyDict_SetItemString", referenced from:
_initflib in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
_PyFortranObject_New in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyErr_Clear", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
_fortran_repr in fortranobject.o
"_PyErr_Format", referenced from:
_initflib in flibmodule.o
_fortran_call in fortranobject.o
"_PyErr_NewException", referenced from:
_initflib in flibmodule.o
"_PyErr_Occurred", referenced from:
_initflib in flibmodule.o
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
...
"_PyErr_Print", referenced from:
_initflib in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
"_PyErr_SetString", referenced from:
_initflib in flibmodule.o
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
"_PyEval_RestoreThread", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
_f2py_rout_flib_sn_like in flibmodule.o
_f2py_rout_flib_rskewnorm in flibmodule.o
...
"_PyEval_SaveThread", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
_f2py_rout_flib_sn_like in flibmodule.o
_f2py_rout_flib_rskewnorm in flibmodule.o
...
"_PyExc_AttributeError", referenced from:
_initflib in flibmodule.o
_fortran_setattr in fortranobject.o
"_PyExc_ImportError", referenced from:
_initflib in flibmodule.o
"_PyExc_MemoryError", referenced from:
_string_from_pyobj in flibmodule.o
"_PyExc_RuntimeError", referenced from:
_initflib in flibmodule.o
_fortran_call in fortranobject.o
"_PyExc_TypeError", referenced from:
_fortran_call in fortranobject.o
_array_from_pyobj in fortranobject.o
"_PyExc_ValueError", referenced from:
_string_from_pyobj in flibmodule.o
_array_from_pyobj in fortranobject.o
"_PyFloat_Type", referenced from:
_double_from_pyobj in flibmodule.o
"_PyImport_ImportModule", referenced from:
_initflib in flibmodule.o
"_PyMem_Free", referenced from:
_fortran_dealloc in fortranobject.o
"_PyModule_GetDict", referenced from:
_initflib in flibmodule.o
"_PyNumber_Float", referenced from:
_double_from_pyobj in flibmodule.o
"_PyNumber_Int", referenced from:
_int_from_pyobj in flibmodule.o
"_PyObject_GetAttrString", referenced from:
_initflib in flibmodule.o
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
_fortran_repr in fortranobject.o
"_PyObject_IsTrue", referenced from:
_f2py_rout_flib_constrain in flibmodule.o
"_PyObject_SetAttrString", referenced from:
_initflib in flibmodule.o
"_PyObject_Str", referenced from:
_string_from_pyobj in flibmodule.o
_array_from_pyobj in fortranobject.o
"_PyObject_Type", referenced from:
_array_from_pyobj in fortranobject.o
"_PySequence_Check", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
"_PySequence_GetItem", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
"_PyString_AsString", referenced from:
_fortran_repr in fortranobject.o
_array_from_pyobj in fortranobject.o
"_PyString_ConcatAndDel", referenced from:
_fortran_getattr in fortranobject.o
"_PyString_FromFormat", referenced from:
_fortran_repr in fortranobject.o
"_PyString_FromString", referenced from:
_initflib in flibmodule.o
_fortran_getattr in fortranobject.o
_fortran_repr in fortranobject.o
"_PyType_IsSubtype", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
_string_from_pyobj in flibmodule.o
_array_from_pyobj in fortranobject.o
"_PyType_Type", referenced from:
_initflib in flibmodule.o
"_Py_BuildValue", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
"_Py_FindMethod", referenced from:
_fortran_getattr in fortranobject.o
"_Py_InitModule4_64", referenced from:
_initflib in flibmodule.o
"__PyObject_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
"__Py_NoneStruct", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -L/usr/local/opt/zlib/lib build/temp.macosx-10.5-x86_64-2.7/cephes/i0.o build/temp.macosx-10.5-x86_64-2.7/cephes/c2f.o build/temp.macosx-10.5-x86_64-2.7/cephes/chbevl.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/fortranobject.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib.o build/temp.macosx-10.5-x86_64-2.7/pymc/histogram.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib_blas.o build/temp.macosx-10.5-x86_64-2.7/pymc/blas_wrap.o build/temp.macosx-10.5-x86_64-2.7/pymc/math.o build/temp.macosx-10.5-x86_64-2.7/pymc/gibbsit.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gfortran/4.7.2/gfortran/lib/gcc/x86_64-apple-darwin12.2.0/4.7.2 -lgfortran -o build/lib.macosx-10.5-x86_64-2.7/pymc/flib.so -Wl,-framework -Wl,Accelerate" failed with exit status 1
Complete output from command //anaconda/bin/python -c "import setuptools;__file__='/private/var/folders/6l/83vj6nxn6g1b6l2c9ycym4hc0000gn/T/pip_build_olga/pymc/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/6l/83vj6nxn6g1b6l2c9ycym4hc0000gn/T/pip-PlF1xm-record/install-record.txt --single-version-externally-managed:
running install
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
build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
adding 'build/src.macosx-10.5-x86_64-2.7/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-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
adding 'build/src.macosx-10.5-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
adding 'build/src.macosx-10.5-x86_64-2.7/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-x86_64-2.7/fortranobject.c' to sources.
adding 'build/src.macosx-10.5-x86_64-2.7' to include_dirs.
build_src: building npy-pkg config files
running build_py
creating build/lib.macosx-10.5-x86_64-2.7
creating build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/calc_utils.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/CircularStochastic.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/CommonDeterministics.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/Container.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/datatypes.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/decorators.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/diagnostics.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/distributions.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/graph.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/Matplot.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/MCMC.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/Model.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/Node.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/NormalApproximation.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/NumpyDeterministics.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/progressbar.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/PyMCObjects.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/ScipyDistributions.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/six.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/StepMethods.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/threadpool.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
copying pymc/utils.py -> build/lib.macosx-10.5-x86_64-2.7/pymc
creating build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/base.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/hdf5.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/hdf5ea.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/no_trace.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/pickle.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/ram.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/sqlite.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
copying pymc/database/txt.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/database
creating build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/custom_step.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/disaster_model.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/disaster_model_gof.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/disaster_model_linear.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/disaster_model_missing.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/disaster_model_null.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/melanoma.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/melanoma_data.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
copying pymc/examples/zip.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples
creating build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/basiscov.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/cov.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/covparams.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/MCMC.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/mean.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/mesh_choice.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/observation.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/PyMCmodel.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
copying pymc/examples/gp/realizations.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/examples/gp
creating build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/objectmodel.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_AM.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_container.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_convergence.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_cov.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_database.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_distributions.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_gradients.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_graph.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_interactive.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_mean.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_missing.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_observation.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_realization.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
copying pymc/tests/test_utils.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/tests
creating build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/Covariance.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/gp_submodel.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/gpplots.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/GPutils.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/Mean.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/Realization.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
copying pymc/gp/step_methods.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp
creating build/lib.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/nsmatern.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.5-x86_64-2.7/pymc/gp/cov_funs
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/local/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pymc.flib' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -I//anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/opt/zlib/include
creating build/temp.macosx-10.5-x86_64-2.7
creating build/temp.macosx-10.5-x86_64-2.7/cephes
creating build/temp.macosx-10.5-x86_64-2.7/build
creating build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7
creating build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-x86_64-2.7 -I//anaconda/lib/python2.7/site-packages/numpy/core/include -I//anaconda/include/python2.7 -c'
extra options: '-msse3'
gcc: cephes/i0.c
gcc: cephes/c2f.c
gcc: build/src.macosx-10.5-x86_64-2.7/fortranobject.c
In file included from build/src.macosx-10.5-x86_64-2.7/fortranobject.c:2:
In file included from build/src.macosx-10.5-x86_64-2.7/fortranobject.h:13:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:
//anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
^
build/src.macosx-10.5-x86_64-2.7/fortranobject.c:338:30: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((fp->defs[i].func==NULL)) {
~~~~~~~~~~~~~~~~^~~~~~
build/src.macosx-10.5-x86_64-2.7/fortranobject.c:338:30: note: remove extraneous parentheses around the comparison to silence this warning
if ((fp->defs[i].func==NULL)) {
~ ^ ~
build/src.macosx-10.5-x86_64-2.7/fortranobject.c:338:30: note: use '=' to turn this equality comparison into an assignment
if ((fp->defs[i].func==NULL)) {
^~
=
2 warnings generated.
gcc: build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c
In file included from build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:18:
In file included from build/src.macosx-10.5-x86_64-2.7/fortranobject.h:13:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from //anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:
//anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
^
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:16934:7: warning: array index 2 is past the end of the array (which contains 2 elements) [-Warray-bounds]
d = shape(x,2);
^ ~
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:86:24: note: expanded from macro 'shape'
#define shape(var,dim) var ## _Dims[dim]
^
<scratch space>:394:1: note: expanded from here
x_Dims
^
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:16835:3: note: array 'x_Dims' declared here
npy_intp x_Dims[2] = {-1, -1};
^
build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.c:181:12: warning: unused function 'f2py_size' [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^
3 warnings generated.
gcc: cephes/chbevl.c
compiling Fortran sources
Fortran f77 compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -m64 -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -fno-second-underscore -m64 -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -m64 -fPIC -O3 -funroll-loops
creating build/temp.macosx-10.5-x86_64-2.7/pymc
compile options: '-DNO_ATLAS_INFO=3 -Ibuild/src.macosx-10.5-x86_64-2.7 -I//anaconda/lib/python2.7/site-packages/numpy/core/include -I//anaconda/include/python2.7 -c'
gfortran:f77: pymc/flib.f
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pymc/flib.f:316.55:
1
Warning: Unused variable 'd_now' declared at (1)
pymc/flib.f:314.42:
INTEGER i, nx, nalph, nmu, ntau, tnx
1
Warning: Unused variable 'tnx' declared at (1)
pymc/flib.f:442.71:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'gradxlike' at (1)
pymc/flib.f:461.40:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'high' declared at (1)
pymc/flib.f:458.36:
INTEGER n, nlower, nupper, i
1
Warning: Unused variable 'i' declared at (1)
pymc/flib.f:461.29:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'like' declared at (1)
pymc/flib.f:461.34:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'low' declared at (1)
pymc/flib.f:442.39:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'lower' at (1)
pymc/flib.f:442.45:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'upper' at (1)
pymc/flib.f:442.33:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'x' at (1)
pymc/flib.f:692.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:760.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:834.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:906.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:976.41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:1186.29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:1185.51:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumfact' declared at (1)
pymc/flib.f:1185.27:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumx' declared at (1)
pymc/flib.f:1300.55:
DOUBLE PRECISION mu(nmu), gradlike(nmu),grad, cdf
1
Warning: Unused variable 'cdf' declared at (1)
pymc/flib.f:1302.29:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:1302.36:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'gammq' declared at (1)
pymc/flib.f:1301.59:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumcdf' declared at (1)
pymc/flib.f:1301.51:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumfact' declared at (1)
pymc/flib.f:1301.27:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumx' declared at (1)
pymc/flib.f:1402.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2154.40:
DOUBLE PRECISION gradlike(n), grad
1
Warning: Unused variable 'grad' declared at (1)
pymc/flib.f:2665.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2728.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2793.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2903.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2959.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3021.29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3396.58:
DOUBLE PRECISION gradlike(nx), atmp, btmp, PI, glike
1
Warning: Unused variable 'glike' declared at (1)
pymc/flib.f:3646.37:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:3646.29:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3706.37:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:3706.29:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3836.29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:4039.26:
DOUBLE PRECISION psi
1
Warning: Unused variable 'psi' declared at (1)
pymc/flib.f:4266.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:4332.29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:5184.35:
DOUBLE PRECISION like, factln, infinity, sump
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:5186.23:
INTEGER i,j,n_tmp
1
Warning: Unused variable 'n_tmp' declared at (1)
pymc/flib.f:5434.26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f:5488.25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1)
pymc/flib.f:5481.26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f:5535.25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1)
pymc/flib.f:5528.26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f: In function 'elgs':
pymc/flib.f:4882:0: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pymc/flib.f: In function 'exponweib_gl':
pymc/flib.f:778:0: warning: 'nc' may be used uninitialized in this function [-Wuninitialized]
pymc/flib.f: In function 'exponweib_gs':
pymc/flib.f:994:0: warning: 'nc' may be used uninitialized in this function [-Wuninitialized]
gfortran:f77: pymc/histogram.f
gfortran:f77: pymc/flib_blas.f
pymc/flib_blas.f:202.25:
DOUBLE PRECISION PI
1
Warning: Unused variable 'pi' declared at (1)
gfortran:f77: pymc/blas_wrap.f
gfortran:f77: pymc/math.f
pymc/math.f:396.6:
DOUBLE PRECISION FUNCTION DERF(X)
1
Warning: 'derf' declared at (1) is also the name of an intrinsic. It can only be called via an explicit interface or if declared EXTERNAL.
pymc/math.f:417.6:
DOUBLE PRECISION FUNCTION DERFC(X)
1
Warning: 'derfc' declared at (1) is also the name of an intrinsic. It can only be called via an explicit interface or if declared EXTERNAL.
gfortran:f77: pymc/gibbsit.f
pymc/gibbsit.f:2160.5:
215 IF (R .GT. .5898437) GO TO 220
1
Warning: Label 215 at (1) defined but not used
pymc/gibbsit.f:2077.5:
1
Warning: Label 115 at (1) defined but not used
pymc/gibbsit.f:2064.5:
15 IF (KFLAG.GE.1) GO TO 30
1
Warning: Label 15 at (1) defined but not used
pymc/gibbsit.f:1204.48:
cutpt = empquant(original,iteracnt,qhat,work)
1
Warning: Type mismatch in argument 'work' at (1); passed INTEGER(4) to REAL(8)
gfortran:f77: build/src.macosx-10.5-x86_64-2.7/pymc/flib-f2pywrappers.f
/usr/local/bin/gfortran -Wall -L/usr/local/opt/zlib/lib build/temp.macosx-10.5-x86_64-2.7/cephes/i0.o build/temp.macosx-10.5-x86_64-2.7/cephes/c2f.o build/temp.macosx-10.5-x86_64-2.7/cephes/chbevl.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/fortranobject.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib.o build/temp.macosx-10.5-x86_64-2.7/pymc/histogram.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib_blas.o build/temp.macosx-10.5-x86_64-2.7/pymc/blas_wrap.o build/temp.macosx-10.5-x86_64-2.7/pymc/math.o build/temp.macosx-10.5-x86_64-2.7/pymc/gibbsit.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gfortran/4.7.2/gfortran/lib/gcc/x86_64-apple-darwin12.2.0/4.7.2 -lgfortran -o build/lib.macosx-10.5-x86_64-2.7/pymc/flib.so -Wl,-framework -Wl,Accelerate
Undefined symbols for architecture x86_64:
"_PyArg_ParseTupleAndKeywords", referenced from:
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
_f2py_rout_flib_standardize in flibmodule.o
...
"_PyCObject_AsVoidPtr", referenced from:
_initflib in flibmodule.o
_F2PyCapsule_AsVoidPtr in fortranobject.o
"_PyCObject_FromVoidPtr", referenced from:
_fortran_getattr in fortranobject.o
_F2PyCapsule_FromVoidPtr in fortranobject.o
"_PyCObject_Type", referenced from:
_initflib in flibmodule.o
_F2PyCapsule_Check in fortranobject.o
"_PyComplex_FromDoubles", referenced from:
_f2py_rout_flib_logsum_cpx in flibmodule.o
"_PyComplex_Type", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
"_PyDict_DelItemString", referenced from:
_fortran_setattr in fortranobject.o
"_PyDict_GetItemString", referenced from:
_initflib in flibmodule.o
_fortran_getattr in fortranobject.o
"_PyDict_New", referenced from:
_PyFortranObject_New in fortranobject.o
_PyFortranObject_NewAsAttr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyDict_SetItemString", referenced from:
_initflib in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
_PyFortranObject_New in fortranobject.o
_fortran_getattr in fortranobject.o
_fortran_setattr in fortranobject.o
"_PyErr_Clear", referenced from:
_int_from_pyobj in flibmodule.o
_double_from_pyobj in flibmodule.o
_F2PyDict_SetItemString in fortranobject.o
_fortran_repr in fortranobject.o
"_PyErr_Format", referenced from:
_initflib in flibmodule.o
_fortran_call in fortranobject.o
"_PyErr_NewException", referenced from:
_initflib in flibmodule.o
"_PyErr_Occurred", referenced from:
_initflib in flibmodule.o
_f2py_rout_flib_symmetrize in flibmodule.o
_f2py_rout_flib_logsum in flibmodule.o
_f2py_rout_flib_logsum_cpx in flibmodule.o
_f2py_rout_flib_combinationln in flibmodule.o
_f2py_rout_flib_expand_triangular in flibmodule.o
_f2py_rout_flib_mod_to_circle in flibmodule.o
...
"_PyErr_Print", referenced from:
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ld: symbol(s) not found for architecture x86_64
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ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -L/usr/local/opt/zlib/lib build/temp.macosx-10.5-x86_64-2.7/cephes/i0.o build/temp.macosx-10.5-x86_64-2.7/cephes/c2f.o build/temp.macosx-10.5-x86_64-2.7/cephes/chbevl.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flibmodule.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/fortranobject.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib.o build/temp.macosx-10.5-x86_64-2.7/pymc/histogram.o build/temp.macosx-10.5-x86_64-2.7/pymc/flib_blas.o build/temp.macosx-10.5-x86_64-2.7/pymc/blas_wrap.o build/temp.macosx-10.5-x86_64-2.7/pymc/math.o build/temp.macosx-10.5-x86_64-2.7/pymc/gibbsit.o build/temp.macosx-10.5-x86_64-2.7/build/src.macosx-10.5-x86_64-2.7/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gfortran/4.7.2/gfortran/lib/gcc/x86_64-apple-darwin12.2.0/4.7.2 -lgfortran -o build/lib.macosx-10.5-x86_64-2.7/pymc/flib.so -Wl,-framework -Wl,Accelerate" failed with exit status 1
----------------------------------------
Cleaning up...
Command //anaconda/bin/python -c "import setuptools;__file__='/private/var/folders/6l/83vj6nxn6g1b6l2c9ycym4hc0000gn/T/pip_build_olga/pymc/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/6l/83vj6nxn6g1b6l2c9ycym4hc0000gn/T/pip-PlF1xm-record/install-record.txt --single-version-externally-managed failed with error code 1 in /private/var/folders/6l/83vj6nxn6g1b6l2c9ycym4hc0000gn/T/pip_build_olga/pymc
Storing complete log in /Users/olga/.pip/pip.log
Could not install 'pymc' using pip
In [24]:
import pymc as pm
with pm.Model() as model: # model specifications in PyMC3 are wrapped in a with-statement
# Define priors
alpha = pm.Normal('alpha', mu=0, sd=20)
beta = pm.Normal('beta', mu=0, sd=20)
sigma = pm.Uniform('sigma', lower=0, upper=20)
# Define linear regression
y_est = alpha + beta * x
# Define likelihood
likelihood = pm.Normal('y', mu=y_est, sd=sigma, observed=y)
# Inference!
start = pm.find_MAP() # Find starting value by optimization
step = pm.NUTS(state=start) # Instantiate MCMC sampling algorithm
trace = pm.sample(2000, step, start=start, progressbar=False) # draw 2000 posterior samples using NUTS sampling
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-24-262be0b52243> in <module>()
----> 1 import pymc as pm
2
3 with pm.Model() as model: # model specifications in PyMC3 are wrapped in a with-statement
4 # Define priors
5 alpha = pm.Normal('alpha', mu=0, sd=20)
ImportError: No module named pymc
In [ ]:
with pm.Model() as model:
# specify glm and pass in data. The resulting linear model, its likelihood and
# and all its parameters are automatically added to our model.
pm.glm.glm('y ~ x', data)
step = pm.NUTS() # Instantiate MCMC sampling algorithm
trace = pm.sample(2000, step, progressbar=False) # draw 2000 posterior samples using NUTS sampling
In [ ]:
fig = pm.traceplot(trace, lines={'alpha': 1, 'beta': 2, 'sigma': .5});
In [ ]:
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, xlabel='Value of gold', ylabel='Value of gold miners', title='Posterior predictive regression lines')
ppl.scatter(ax, x, y, label='data')
glm.plot_posterior_predictive(trace, samples=100,
label='posterior predictive regression lines')
ppl.plot(ax, x, true_regression_line, label='true regression line', linewidth=5.)
ax.legend(loc=0);
fig.savefig('ppc1.png')
In [ ]:
Image('ppc1.png')
In [ ]:
# Add outliers
x_out = np.append(x, [.1, .15, .2, .25, .25])
y_out = np.append(y, [8, 6, 9, 7, 9])
data_out = dict(x=x_out, y=y_out)
fig = plt.figure(figsize=(7, 7))
ax = fig.add_subplot(111, xlabel='Value of gold', ylabel='Value of gold miners', title='Posterior predictive regression lines')
ppl.scatter(ax, x_out, y_out, label='data')
In [ ]:
with Model() as model:
glm.glm('y ~ x', data_out)
trace = sample(2000, NUTS(), progressbar=False)
In [ ]:
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, xlabel='Value of gold', ylabel='Value of gold miners', title='Posterior predictive regression lines')
ppl.scatter(ax, x_out, y_out, label='data')
glm.plot_posterior_predictive(trace, samples=100,
label='posterior predictive regression lines')
ppl.plot(ax, x, true_regression_line,
label='true regression line', linewidth=5.)
plt.legend(loc=0);
fig.savefig('ppc2.png')
In [ ]:
Image('ppc2.png')
In [ ]:
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111)
normal_dist = Normal.dist(mu=0, sd=1)
t_dist = T.dist(mu=0, lam=1, nu=1)
x_eval = np.linspace(-8, 8, 300)
ppl.plot(ax, x_eval, theano.tensor.exp(normal_dist.logp(x_eval)).eval(), label='Normal', linewidth=2.)
ppl.plot(ax, x_eval, theano.tensor.exp(t_dist.logp(x_eval)).eval(), label='Student T', linewidth=2.)
plt.xlabel('x')
plt.ylabel('Probability density')
plt.legend();
fig.savefig('t-dist.png')
In [ ]:
Image('t-dist.png')
In [ ]:
with pm.Model() as model_robust:
family = pm.glm.families.T()
pm.glm.glm('y ~ x', data_out, family=family)
trace_robust = pm.sample(2000, pm.NUTS(), progressbar=False)
In [ ]:
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, xlabel='Value of gold', ylabel='Value of gold miners', title='Posterior predictive regression lines')
ppl.scatter(ax, x_out, y_out)
glm.plot_posterior_predictive(trace_robust, samples=100,
label='posterior predictive regression lines')
ppl.plot(ax, x, true_regression_line,
label='true regression line', linewidth=5.)
plt.legend();
fig.savefig('ppc3.png')
In [ ]:
Image('ppc3.png')
In [ ]:
import zipline
import pytz
from datetime import datetime
fig = plt.figure(figsize=(8, 4))
prices = zipline.data.load_from_yahoo(stocks=['GLD', 'GDX'],
end=datetime(2013, 8, 1, 0, 0, 0, 0, pytz.utc)).dropna()[:1000]
prices.plot();
In [ ]:
fig = plt.figure(figsize=(9, 6))
ax = fig.add_subplot(111, xlabel='Price GDX in \$', ylabel='Price GLD in \$')
colors = np.linspace(0.1, 1, len(prices))
mymap = plt.get_cmap("winter")
sc = ax.scatter(prices.GDX, prices.GLD, c=colors, cmap=mymap, lw=0)
cb = plt.colorbar(sc)
cb.ax.set_yticklabels([str(p.date()) for p in prices[::len(prices)//10].index]);
fig.savefig('price_corr.png')
In [ ]:
Image('price_corr.png')
In [ ]:
with pm.Model() as model_reg:
family = pm.glm.families.Normal()
pm.glm.glm('GLD ~ GDX', prices, family=family)
trace_reg = pm.sample(2000, pm.NUTS(), progressbar=False)
In [ ]:
fig = plt.figure(figsize=(9, 6))
ax = fig.add_subplot(111, xlabel='Price GDX in $', ylabel='Price GLD in $',
title='Posterior predictive regression lines')
sc = ax.scatter(prices.GDX, prices.GLD, c=colors, cmap=mymap, lw=0)
glm.plot_posterior_predictive(trace_reg, samples=100,
label='posterior predictive regression lines',
lm=lambda x, sample: sample['Intercept'] + sample['GDX'] * x,
eval=np.linspace(prices.GDX.min(), prices.GDX.max(), 100))
cb = plt.colorbar(sc)
cb.ax.set_yticklabels([str(p.date()) for p in prices[::len(prices)//10].index]);
ax.legend(loc=0);
fig.savefig('ppc4.png')
In [ ]:
Image('ppc4.png')
In [ ]:
from pymc.distributions.timeseries import *
from theano.tensor import repeat
In [ ]:
model_randomwalk = pm.Model()
with model_randomwalk:
# std of random walk, best sampled in log space.
sigma_alpha, log_sigma_alpha = model_randomwalk.TransformedVar(
'sigma_alpha',
pm.Exponential.dist(1./.02, testval = .1),
pm.logtransform
)
sigma_beta, log_sigma_beta = model_randomwalk.TransformedVar(
'sigma_beta',
pm.Exponential.dist(1./.02, testval = .1),
pm.logtransform
)
In [ ]:
# To make the model simpler, we will apply the same coefficient for 50 data points at a time
subsample_alpha = 50
subsample_beta = 50
with model_randomwalk:
alpha = pm.GaussianRandomWalk('alpha', sigma_alpha**-2,
shape=len(prices) / subsample_alpha)
beta = pm.GaussianRandomWalk('beta', sigma_beta**-2,
shape=len(prices) / subsample_beta)
# Make coefficients have the same length as prices
alpha_r = repeat(alpha, subsample_alpha)
beta_r = repeat(beta, subsample_beta)
In [ ]:
with model_randomwalk:
# Define regression
regression = alpha_r + beta_r * prices.GDX.values
# Assume prices are Normally distributed, the mean comes from the regression.
sd = pm.Uniform('sd', 0, 20)
likelihood = pm.Normal('y',
mu=regression,
sd=sd,
observed=prices.GLD.values)
In [ ]:
from scipy import optimize
with model_randomwalk:
# First optimize random walk
start = pm.find_MAP(vars=[alpha, beta], fmin=optimize.fmin_l_bfgs_b)
# Sample
step = pm.NUTS(scaling=start)
trace_rw = pm.sample(2000, step, start=start, progressbar=False)
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fig = plt.figure(figsize=(8, 6))
ax = plt.subplot(111, xlabel='time', ylabel='alpha', title='Change of alpha over time.')
ppl.plot(ax, trace_rw[-1000:][alpha].T, 'r', alpha=.05);
ax.set_xticklabels([str(p.date()) for p in prices[::len(prices)//5].index]);
fig.savefig('rwalk_alpha.png')
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Image('rwalk_alpha.png')
In [ ]:
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, xlabel='time', ylabel='beta', title='Change of beta over time')
ppl.plot(ax, trace_rw[-1000:][beta].T, 'b', alpha=.05);
ax.set_xticklabels([str(p.date()) for p in prices[::len(prices)//5].index]);
fig.savefig('rwalk_beta.png')
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Image('rwalk_beta.png')
In [ ]:
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, xlabel='Price GDX in \$', ylabel='Price GLD in \$',
title='Posterior predictive regression lines')
colors = np.linspace(0.1, 1, len(prices))
colors_sc = np.linspace(0.1, 1, len(trace_rw[-500::10]['alpha'].T))
mymap = plt.get_cmap('winter')
mymap_sc = plt.get_cmap('winter')
xi = np.linspace(prices.GDX.min(), prices.GDX.max(), 50)
for i, (alpha, beta) in enumerate(zip(trace_rw[-500::10]['alpha'].T, trace_rw[-500::10]['beta'].T)):
for a, b in zip(alpha, beta):
ax.plot(xi, a + b*xi, alpha=.05, lw=1, c=mymap_sc(colors_sc[i]))
sc = ax.scatter(prices.GDX, prices.GLD, label='data', cmap=mymap, c=colors)
cb = plt.colorbar(sc)
cb.ax.set_yticklabels([str(p.date()) for p in prices[::len(prices)//10].index]);
fig.savefig('ppc5.png')
In [ ]:
Image('ppc5.png')
Scalability
Usability
Content source: olgabot/prettyplotlib
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