numpy compile problems in newest HDDM

Christopher Chatham

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Jun 25, 2014, 11:31:52 AM6/25/14

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Thanks everybody for this amazing tool! But I'm having trouble getting the examples to work in ipython due to a numpy compile problem (I think).

I used a fresh install of anaconda and then followed instructions for installing HDDM; upon navigating to the examples directory and trying to run the example script I got a numpy compile problem, which could be alleviated by updating numpy, only for another numpy error to emerge a few steps later in the process.

I've attached all my commands and output below.

(fresh install of most recent anaconda)

(output of "which ipython" is //anaconda/bin/ipython)

Christophers-MacBook-Pro-3:/ christopherchatham$ conda install -c pymc pymc

Fetching package metadata: ...

Solving package specifications: .

Package plan for installation in environment //anaconda:

The following packages will be downloaded:

package | build

---------------------------|-----------------

pymc-2.3.2 | np18py27_0 757 KB

python-2.7.7 | 2 10.0 MB

pytz-2014.4 | py27_0 172 KB

six-1.7.2 | py27_0 15 KB

------------------------------------------------------------

Total: 10.9 MB

The following packages will be UN-linked:

package | build

---------------------------|-----------------

python-2.7.7 | 0

pytz-2014.3 | py27_0

six-1.6.1 | py27_0

The following packages will be linked:

package | build

---------------------------|-----------------

pymc-2.3.2 | np18py27_0 hard-link

python-2.7.7 | 2 hard-link

pytz-2014.4 | py27_0 hard-link

six-1.7.2 | py27_0 hard-link

Proceed ([y]/n)? y

Fetching packages ...

pymc-2.3.2-np1 100% |################################################################| Time: 0:00:01 481.47 kB/s

python-2.7.7-2 100% |################################################################| Time: 0:00:18 570.99 kB/s

pytz-2014.4-py 100% |################################################################| Time: 0:00:00 452.23 kB/s

six-1.7.2-py27 100% |################################################################| Time: 0:00:00 70.55 kB/s

Extracting packages ...

[ COMPLETE ] |##################################################################################| 100%

Unlinking packages ...

[ COMPLETE ] |##################################################################################| 100%

Linking packages ...

[ COMPLETE ] |##################################################################################| 100%

Christophers-MacBook-Pro-3:/ christopherchatham$ conda install -c twiecki hddm

Fetching package metadata: ...

Solving package specifications: ...............

Package plan for installation in environment //anaconda:

The following packages will be downloaded:

package | build

---------------------------|-----------------

hddm-0.5.2 | np17py27_0 21.9 MB

kabuki-0.5.2 | np17py27_0 34.8 MB

matplotlib-1.3.1 | np17py27_0 34.1 MB

numpy-1.7.1 | py27_2 2.8 MB

pandas-0.13.0 | np17py27_0 4.0 MB

patsy-0.2.1 | np17py27_0 220 KB

pydot-1.0.28 | py27_0 35 KB

pymc-2.3 | np17py27_0 762 KB

pyparsing-1.5.6 | py27_0 61 KB

scipy-0.13.2 | np17py27_1 11.7 MB

------------------------------------------------------------

Total: 110.4 MB

The following packages will be UN-linked:

package | build

---------------------------|-----------------

matplotlib-1.3.1 | np18py27_1

numpy-1.8.1 | py27_0

pandas-0.14.0 | np18py27_0

patsy-0.2.1 | np18py27_0

pymc-2.3.2 | np18py27_0

pyparsing-2.0.1 | py27_0

scipy-0.14.0 | np18py27_0

The following packages will be linked:

package | build

---------------------------|-----------------

hddm-0.5.2 | np17py27_0 hard-link

kabuki-0.5.2 | np17py27_0 hard-link

matplotlib-1.3.1 | np17py27_0 hard-link

numpy-1.7.1 | py27_2 hard-link

pandas-0.13.0 | np17py27_0 hard-link

patsy-0.2.1 | np17py27_0 hard-link

pydot-1.0.28 | py27_0 hard-link

pymc-2.3 | np17py27_0 hard-link

pyparsing-1.5.6 | py27_0 hard-link

scipy-0.13.2 | np17py27_1 hard-link

Proceed ([y]/n)? y

Fetching packages ...

hddm-0.5.2-np1 100% |################################################################| Time: 0:00:43 528.73 kB/s

kabuki-0.5.2-n 100% |################################################################| Time: 0:00:58 621.60 kB/s

matplotlib-1.3 100% |################################################################| Time: 0:01:05 550.33 kB/s

numpy-1.7.1-py 100% |################################################################| Time: 0:00:06 436.64 kB/s

pandas-0.13.0- 100% |################################################################| Time: 0:00:07 555.95 kB/s

patsy-0.2.1-np 100% |################################################################| Time: 0:00:01 131.72 kB/s

pydot-1.0.28-p 100% |################################################################| Time: 0:00:01 26.81 kB/s

pymc-2.3-np17p 100% |################################################################| Time: 0:00:01 469.70 kB/s

pyparsing-1.5. 100% |################################################################| Time: 0:00:00 471.71 kB/s

scipy-0.13.2-n 100% |################################################################| Time: 0:00:22 556.85 kB/s

Extracting packages ...

[ COMPLETE ] |##################################################################################| 100%

Unlinking packages ...

[ COMPLETE ] |##################################################################################| 100%

Linking packages ...

[ COMPLETE ] |##################################################################################| 100%

Christophers-MacBook-Pro-3:/ christopherchatham$ cd /anaconda/pkgs/hddm-0.5.2-np17py27_0/lib/python2.7/site-packages/hddm/examples/

Christophers-MacBook-Pro-3:examples christopherchatham$ ls

__init__.py simple_difficulty.csv

__init__.pyc simple_model.py

cavanagh_theta_nn.csv simple_model.pyc

plot_posterior_quantiles.py simple_subjs_difficulty.csv

plot_posterior_quantiles.pyc simple_subjs_difficulty_single.csv

simple_difficulty.conf

Christophers-MacBook-Pro-3:examples christopherchatham$ ipython

Python 2.7.7 |Anaconda 2.0.1 (x86_64)| (default, Jun 19 2014, 13:38:03)

Type "copyright", "credits" or "license" for more information.

IPython 2.1.0 -- An enhanced Interactive Python.

Anaconda is brought to you by Continuum Analytics.

Please check out: http://continuum.io/thanks and https://binstar.org

? -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help -> Python's own help system.

object? -> Details about 'object', use 'object??' for extra details.

In [1]: import hddm

---------------------------------------------------------------------------

ValueError Traceback (most recent call last)

<ipython-input-1-17365318b31c> in <module>()

----> 1 import hddm

//anaconda/lib/python2.7/site-packages/hddm/__init__.py in <module>()

5 __version__ = '0.5.2'

6

----> 7 import likelihoods

8 import generate

9 import utils

//anaconda/lib/python2.7/site-packages/hddm/likelihoods.py in <module>()

1 from __future__ import division

----> 2 import pymc as pm

3 import numpy as np

4 from scipy import stats

5

//anaconda/lib/python2.7/site-packages/pymc/__init__.pyc in <module>()

30 from .NumpyDeterministics import *

31 from .distributions import *

---> 32 from .Model import *

33 from .StepMethods import *

34 from .MCMC import *

//anaconda/lib/python2.7/site-packages/pymc/Model.py in <module>()

15 from numpy import zeros, floor

16 from numpy.random import randint

---> 17 from . import database

18 from .PyMCObjects import Stochastic, Deterministic, Node, Variable, Potential

19 from .Container import Container, ObjectContainer

//anaconda/lib/python2.7/site-packages/pymc/database/__init__.py in <module>()

54

55 try:

---> 56 from . import hdf5

57 except ImportError:

58 pass

//anaconda/lib/python2.7/site-packages/pymc/database/hdf5.py in <module>()

23 from pymc.database import base, pickle

24 from copy import copy

---> 25 import tables

26 import os

27 import warnings

//anaconda/lib/python2.7/site-packages/tables/__init__.py in <module>()

80

81 # Necessary imports to get versions stored on the cython extension

---> 82 from tables.utilsextension import (

83 get_pytables_version, get_hdf5_version, blosc_compressor_list,

84 blosc_compcode_to_compname_ as blosc_compcode_to_compname,

/anaconda/pkgs/hddm-0.5.2-np17py27_0/lib/python2.7/site-packages/hddm/examples/numpy.pxd in init tables.utilsextension (tables/utilsextension.c:15447)()

ValueError: numpy.ufunc has the wrong size, try recompiling

In [2]: exit

Christophers-MacBook-Pro-3:examples christopherchatham$ conda update numpy

Fetching package metadata: ..

Solving package specifications: .

Package plan for installation in environment //anaconda:

The following packages will be UN-linked:

package | build

---------------------------|-----------------

numpy-1.7.1 | py27_2

The following packages will be linked:

package | build

---------------------------|-----------------

numpy-1.8.1 | py27_0 hard-link

Proceed ([y]/n)? y

Unlinking packages ...

[ COMPLETE ] |##################################################################################| 100%

Linking packages ...

[ COMPLETE ] |##################################################################################| 100%

Christophers-MacBook-Pro-3:examples christopherchatham$ ipython

Python 2.7.7 |Anaconda 2.0.1 (x86_64)| (default, Jun 19 2014, 13:38:03)

Type "copyright", "credits" or "license" for more information.

IPython 2.1.0 -- An enhanced Interactive Python.

Anaconda is brought to you by Continuum Analytics.

Please check out: http://continuum.io/thanks and https://binstar.org

? -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help -> Python's own help system.

object? -> Details about 'object', use 'object??' for extra details.

In [1]: import hddm

In [2]: data = hddm.load_csv('simple_difficulty.csv')

In [3]: model = hddm.HDDM(data, depends_on={'v':'difficulty'})

---------------------------------------------------------------------------

TypeError Traceback (most recent call last)

<ipython-input-3-442fbac9eed4> in <module>()

----> 1 model = hddm.HDDM(data, depends_on={'v':'difficulty'})

//anaconda/lib/python2.7/site-packages/hddm/models/hddm_info.pyc in __init__(self, *args, **kwargs)

111 self.is_informative = kwargs.pop('informative', True)

112

--> 113 super(HDDM, self).__init__(*args, **kwargs)

114

115 def _create_stochastic_knodes(self, include):

//anaconda/lib/python2.7/site-packages/hddm/models/base.pyc in __init__(self, data, bias, include, wiener_params, p_outlier, **kwargs)

687 self.wfpt_class = hddm.likelihoods.generate_wfpt_stochastic_class(wp, cdf_range=self.cdf_range)

688

--> 689 super(HDDMBase, self).__init__(data, **kwargs)

690

691 def __getstate__(self):

//anaconda/lib/python2.7/site-packages/hddm/models/base.pyc in __init__(self, data, **kwargs)

38 self.std_depends = kwargs.pop('std_depends', False)

39

---> 40 super(AccumulatorModel, self).__init__(data, **kwargs)

41

42

//anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in __init__(self, data, is_group_model, depends_on, trace_subjs, plot_subjs, plot_var, group_only_nodes)

345 self.db = None

346

--> 347 self._setup_model()

348

349 def _setup_model(self):

//anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in _setup_model(self)

356

357 # constructs pymc nodes etc and connects them appropriately

--> 358 self.create_model()

359

360 def __getstate__(self):

//anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in create_model(self, max_retries)

426 for tries in range(max_retries):

427 try:

--> 428 _create()

429 except (pm.ZeroProbability, ValueError):

430 continue

//anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in _create()

422 def _create():

423 for knode in self.knodes:

--> 424 knode.create()

425

426 for tries in range(max_retries):

//anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in create(self)

165 kwargs['doc'] = node_name

166

--> 167 node = self.create_node(node_name, kwargs, grouped_data)

168

169 if node is not None:

//anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in create_node(self, node_name, kwargs, data)

173 def create_node(self, node_name, kwargs, data):

174 #actually create the node

--> 175 return self.pymc_node(name=node_name, **kwargs)

176

177 def create_tag_and_subj_idx(self, cols, uniq_elem):

//anaconda/lib/python2.7/site-packages/pymc/distributions.pyc in __init__(self, *args, **kwds)

269 random = debug_wrapper(random)

270 else:

--> 271 Stochastic.__init__(self, logp=logp, random=random, logp_partial_gradients = logp_partial_gradients, dtype=dtype,**arg_dict_out)

272

273 new_class.__name__ = name

//anaconda/lib/python2.7/site-packages/pymc/PyMCObjects.pyc in __init__(self, logp, doc, name, parents, random, trace, value, dtype, rseed, observed, cache_depth, plot, verbose, isdata, check_logp, logp_partial_gradients)

746 dtype=dtype,

747 plot=plot,

--> 748 verbose=verbose)

749

750 # self._logp.force_compute()

//anaconda/lib/python2.7/site-packages/pymc/Node.pyc in __init__(self, doc, name, parents, cache_depth, trace, dtype, plot, verbose)

214 self.extended_children = set()

215

--> 216 Node.__init__(self, doc, name, parents, cache_depth, verbose=verbose)

217

218 if self.dtype is None:

//anaconda/lib/python2.7/site-packages/pymc/Node.pyc in __init__(self, doc, name, parents, cache_depth, verbose)

125

126 # Initialize

--> 127 self.parents = parents

128

129 def _get_parents(self):

//anaconda/lib/python2.7/site-packages/pymc/Node.pyc in _set_parents(self, new_parents)

148

149 # Get new lazy function

--> 150 self.gen_lazy_function()

151

152 parents = property(

//anaconda/lib/python2.7/site-packages/pymc/PyMCObjects.pyc in gen_lazy_function(self)

795 [self]),

796 cache_depth=self._cache_depth)

--> 797 self._logp.force_compute()

798

799 self._logp_partial_gradients = {}

//anaconda/lib/python2.7/site-packages/pymc/LazyFunction.so in pymc.LazyFunction.LazyFunction.force_compute (pymc/LazyFunction.c:2409)()

//anaconda/lib/python2.7/site-packages/pymc/distributions.pyc in wrapper(**kwds)

2766 def wrapper(**kwds):

2767 value = kwds.pop('value')

-> 2768 return f(value, **kwds)

2769

2770 if arguments is None:

//anaconda/lib/python2.7/site-packages/hddm/likelihoods.pyc in wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier)

50 #create likelihood function

51 def wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier=0):

---> 52 return hddm.wfpt.wiener_like(x['rt'], v, sv, a, z, sz, t, st, p_outlier=p_outlier, **wp)

53

54

TypeError: Argument 'x' has incorrect type (expected numpy.ndarray, got Series)

In [4]: exit

conda update conda

Fetching package metadata: ..

# All requested packages already installed.

# packages in environment at //anaconda:

#

conda 3.5.5 py27_0

Thomas Wiecki

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Jul 1, 2014, 7:03:52 AM7/1/14

to hddm-...@googlegroups.com

Hi Chris,

Yes, unfortunately the pymc conda packages (and hddm as well I reckon) are out of date. I openend up a pymc issue here about it: https://github.com/pymc-devs/pymc/issues/556

In the mean time you could try to:

pip install pymc

pip install kabuki
pip install hddm

and let me know if there are problems with this approach.

Thomas

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Thomas Wiecki

PhD candidate, Brown University

Quantitative Researcher, Quantopian Inc, Boston

Christopher Chatham

unread,

Jul 1, 2014, 11:54:06 AM7/1/14

to hddm-...@googlegroups.com

Thanks, Thomas.

I can certainly wait until the conda packages are rebuilt (which sounds like it will be very soon), but as you requested to be informed about problems with the approach you suggested, I feel compelled to followup. Here are the results (and sorry in advance if I've done something bone-headed here):

sh-3.2# pip install pymc

Downloading/unpacking pymc

Downloading pymc-2.3.2.tar.gz (385kB): 385kB downloaded

Running setup.py (path:/private/tmp/pip_build_root/pymc/setup.py) egg_info for package pymc

build_src

building extension "pymc.flib" sources

f2py options: ['skip:ppnd7']

f2py:> build/src.macosx-10.9-intel-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 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-10.9-intel-2.7/pymc/flibmodule.c"

Fortran 77 wrappers are saved to "build/src.macosx-10.9-intel-2.7/pymc/flib-f2pywrappers.f"

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

adding 'build/src.macosx-10.9-intel-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-10.9-intel-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-10.9-intel-2.7/pymc/gp/linalg_utilsmodule.c"

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

building extension "pymc.gp.incomplete_chol" sources

f2py options: []

f2py:> build/src.macosx-10.9-intel-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-10.9-intel-2.7/pymc/gp/incomplete_cholmodule.c"

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources

f2py options: []

f2py:> build/src.macosx-10.9-intel-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-10.9-intel-2.7/pymc/gp/cov_funs/isotropic_cov_funsmodule.c"

Fortran 77 wrappers are saved to "build/src.macosx-10.9-intel-2.7/pymc/gp/cov_funs/isotropic_cov_funs-f2pywrappers.f"

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

adding 'build/src.macosx-10.9-intel-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-10.9-intel-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-10.9-intel-2.7/pymc/gp/cov_funs/distancesmodule.c"

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

build_src: building npy-pkg config files

warning: no files found matching 'docs/UserGuide.pdf'

warning: no files found matching '*.txt' under directory 'pymc'

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-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

adding 'build/src.macosx-10.9-intel-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-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

building extension "pymc.gp.incomplete_chol" sources

f2py options: []

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources

f2py options: []

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

adding 'build/src.macosx-10.9-intel-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-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

build_src: building npy-pkg config files

customize UnixCCompiler

customize UnixCCompiler using build_ext

customize Gnu95FCompiler

Could not locate executable gfortran

Could not locate executable f95

customize NAGFCompiler

customize AbsoftFCompiler

Could not locate executable f90

Could not locate executable f77

customize IBMFCompiler

Could not locate executable xlf90

Could not locate executable xlf

customize IntelFCompiler

Could not locate executable ifort

Could not locate executable ifc

customize GnuFCompiler

Could not locate executable g77

customize G95FCompiler

Could not locate executable g95

customize PGroupFCompiler

Could not locate executable pgfortran

don't know how to compile Fortran code on platform 'posix'

warning: build_ext: f77_compiler=None is not available.

building 'pymc.flib' extension

error: extension 'pymc.flib' has Fortran sources but no Fortran compiler found

Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/pymc/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-C1rl9h-record/install-record.txt --single-version-externally-managed --compile:

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-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

adding 'build/src.macosx-10.9-intel-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-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

building extension "pymc.gp.incomplete_chol" sources

f2py options: []

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources

f2py options: []

adding 'build/src.macosx-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

adding 'build/src.macosx-10.9-intel-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-10.9-intel-2.7/fortranobject.c' to sources.

adding 'build/src.macosx-10.9-intel-2.7' to include_dirs.

build_src: building npy-pkg config files

running build_py

creating build/lib.macosx-10.9-intel-2.7

creating build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/__init__.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/calc_utils.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/CircularStochastic.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/CommonDeterministics.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/Container.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/datatypes.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/decorators.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/diagnostics.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/distributions.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/graph.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/Matplot.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/MCMC.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/Model.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/Node.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/NormalApproximation.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/NumpyDeterministics.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/progressbar.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/PyMCObjects.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/ScipyDistributions.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/six.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/StepMethods.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/threadpool.py -> build/lib.macosx-10.9-intel-2.7/pymc

copying pymc/utils.py -> build/lib.macosx-10.9-intel-2.7/pymc

creating build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/__init__.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/base.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/hdf5.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/hdf5ea.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/no_trace.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/pickle.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/ram.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/sqlite.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

copying pymc/database/txt.py -> build/lib.macosx-10.9-intel-2.7/pymc/database

creating build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/__init__.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/custom_step.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/disaster_model.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/disaster_model_gof.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/disaster_model_linear.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/disaster_model_missing.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/disaster_model_null.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/melanoma.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/melanoma_data.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

copying pymc/examples/zip.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples

creating build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/__init__.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/basiscov.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/cov.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/covparams.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/MCMC.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/mean.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/mesh_choice.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/observation.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/PyMCmodel.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

copying pymc/examples/gp/realizations.py -> build/lib.macosx-10.9-intel-2.7/pymc/examples/gp

creating build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/objectmodel.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_AM.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_container.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_convergence.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_cov.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_database.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_distributions.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_gradients.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_graph.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_interactive.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_mean.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_missing.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_observation.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_realization.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

copying pymc/tests/test_utils.py -> build/lib.macosx-10.9-intel-2.7/pymc/tests

creating build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/__init__.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/Covariance.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/gp_submodel.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/gpplots.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/GPutils.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/Mean.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/Realization.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

copying pymc/gp/step_methods.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp

creating build/lib.macosx-10.9-intel-2.7/pymc/gp/cov_funs

copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp/cov_funs

copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp/cov_funs

copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp/cov_funs

copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp/cov_funs

copying pymc/gp/cov_funs/nsmatern.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp/cov_funs

copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.9-intel-2.7/pymc/gp/cov_funs

running build_ext

customize UnixCCompiler

customize UnixCCompiler using build_ext

customize Gnu95FCompiler

Could not locate executable gfortran

Could not locate executable f95

customize NAGFCompiler

customize AbsoftFCompiler

Could not locate executable f90

Could not locate executable f77

customize IBMFCompiler

Could not locate executable xlf90

Could not locate executable xlf

customize IntelFCompiler

Could not locate executable ifort

Could not locate executable ifc

customize GnuFCompiler

Could not locate executable g77

customize G95FCompiler

Could not locate executable g95

customize PGroupFCompiler

Could not locate executable pgfortran

don't know how to compile Fortran code on platform 'posix'

warning: build_ext: f77_compiler=None is not available.

building 'pymc.flib' extension

error: extension 'pymc.flib' has Fortran sources but no Fortran compiler found

----------------------------------------

Cleaning up...

Command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/pymc/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-C1rl9h-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/pymc

Storing debug log for failure in /var/root/Library/Logs/pip.log

sh-3.2# pip install kabuki

Downloading/unpacking kabuki

Downloading kabuki-0.5.4.tar.gz (44kB): 44kB downloaded

Running setup.py (path:/private/tmp/pip_build_root/kabuki/setup.py) egg_info for package kabuki

Traceback (most recent call last):

File "<string>", line 17, in <module>

File "/private/tmp/pip_build_root/kabuki/setup.py", line 12, in <module>

setup_requires=['NumPy >= 1.6.0', 'pymc == 2.3.2', 'pandas >= 0.12.0', 'matplotlib >= 1.0.0']

File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 112, in setup

_setup_distribution = dist = klass(attrs)

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 260, in __init__

self.fetch_build_eggs(attrs.pop('setup_requires'))

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 284, in fetch_build_eggs

parse_requirements(requires), installer=self.fetch_build_egg

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 569, in resolve

raise VersionConflict(dist,req) # XXX put more info here

pkg_resources.VersionConflict: (pandas 0.9.0.dev-1e68fd9-20120920 (/Library/Python/2.7/site-packages/pandas-0.9.0.dev_1e68fd9_20120920-py2.7-macosx-10.8-intel.egg), Requirement.parse('pandas>=0.12.0'))

Complete output from command python setup.py egg_info:

Traceback (most recent call last):

File "<string>", line 17, in <module>

File "/private/tmp/pip_build_root/kabuki/setup.py", line 12, in <module>

setup_requires=['NumPy >= 1.6.0', 'pymc == 2.3.2', 'pandas >= 0.12.0', 'matplotlib >= 1.0.0']

File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 112, in setup

_setup_distribution = dist = klass(attrs)

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 260, in __init__

self.fetch_build_eggs(attrs.pop('setup_requires'))

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 284, in fetch_build_eggs

parse_requirements(requires), installer=self.fetch_build_egg

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 569, in resolve

raise VersionConflict(dist,req) # XXX put more info here

pkg_resources.VersionConflict: (pandas 0.9.0.dev-1e68fd9-20120920 (/Library/Python/2.7/site-packages/pandas-0.9.0.dev_1e68fd9_20120920-py2.7-macosx-10.8-intel.egg), Requirement.parse('pandas>=0.12.0'))

----------------------------------------

Cleaning up...

Command python setup.py egg_info failed with error code 1 in /private/tmp/pip_build_root/kabuki

Storing debug log for failure in /var/root/Library/Logs/pip.log

sh-3.2# pip install hddm

Downloading/unpacking hddm

Downloading HDDM-0.5.3.tar.gz (993kB): 993kB downloaded

Running setup.py (path:/private/tmp/pip_build_root/hddm/setup.py) egg_info for package hddm

Traceback (most recent call last):

File "<string>", line 17, in <module>

File "/private/tmp/pip_build_root/hddm/setup.py", line 41, in <module>

ext_modules = ext_modules

File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 112, in setup

_setup_distribution = dist = klass(attrs)

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 260, in __init__

self.fetch_build_eggs(attrs.pop('setup_requires'))

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 284, in fetch_build_eggs

parse_requirements(requires), installer=self.fetch_build_egg

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 569, in resolve

raise VersionConflict(dist,req) # XXX put more info here

pkg_resources.VersionConflict: (pandas 0.9.0.dev-1e68fd9-20120920 (/Library/Python/2.7/site-packages/pandas-0.9.0.dev_1e68fd9_20120920-py2.7-macosx-10.8-intel.egg), Requirement.parse('pandas>=0.12.0'))

Complete output from command python setup.py egg_info:

Traceback (most recent call last):

File "<string>", line 17, in <module>

File "/private/tmp/pip_build_root/hddm/setup.py", line 41, in <module>

ext_modules = ext_modules

File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 112, in setup

_setup_distribution = dist = klass(attrs)

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 260, in __init__

self.fetch_build_eggs(attrs.pop('setup_requires'))

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/dist.py", line 284, in fetch_build_eggs

parse_requirements(requires), installer=self.fetch_build_egg

File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 569, in resolve

raise VersionConflict(dist,req) # XXX put more info here

pkg_resources.VersionConflict: (pandas 0.9.0.dev-1e68fd9-20120920 (/Library/Python/2.7/site-packages/pandas-0.9.0.dev_1e68fd9_20120920-py2.7-macosx-10.8-intel.egg), Requirement.parse('pandas>=0.12.0'))

----------------------------------------

Cleaning up...

Command python setup.py egg_info failed with error code 1 in /private/tmp/pip_build_root/hddm

Storing debug log for failure in /var/root/Library/Logs/pip.log

Thomas Wiecki

unread,

Jul 2, 2014, 3:57:40 AM7/2/14

to hddm-...@googlegroups.com

Hi Chris,

Can you try:

conda install -c pymc pymc

again. We released pymc 2.3.3 and just rebuilt it.

If that works, can you try:
pip install -U kabuki
pip install -U hddm

Which should pull in hddm 0.5.4 and let me know if that works.

Thomas

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Christopher Chatham

unread,

Jul 2, 2014, 8:28:47 AM7/2/14

to hddm-...@googlegroups.com

Thanks Thomas! Unfortunately it's ultimately not finding a Fortran compiler, though it appears to start having trouble at the Kabuki step.

Output below....

--------------------

Last login: Tue Jul 1 10:57:44 on ttys003

Christophers-MacBook-Pro-3:nfft-3.2.3 christopherchatham$ sudo su

Password:

sh-3.2# conda install -c pymc pymc

Fetching package metadata: ...

Solving package specifications: .

Package plan for installation in environment //anaconda:

The following packages will be downloaded:

package | build

---------------------------|-----------------

pymc-2.3.3 | np18py27_0 709 KB

The following packages will be UN-linked:

package | build

---------------------------|-----------------

matplotlib-1.3.1 | np17py27_0

pymc-2.3 | np17py27_0

pyparsing-1.5.6 | py27_0

scipy-0.13.2 | np17py27_1

The following packages will be linked:

package | build

---------------------------|-----------------

matplotlib-1.3.1 | np18py27_1 hard-link

pymc-2.3.3 | np18py27_0 hard-link

pyparsing-2.0.1 | py27_0 hard-link

scipy-0.14.0 | np18py27_0 hard-link

Proceed ([y]/n)? y

Fetching packages ...

pymc-2.3.3-np1 100% |##########################################################################################################| Time: 0:00:01 597.99 kB/s

Extracting packages ...

[ COMPLETE ] |############################################################################################################################| 100%

Unlinking packages ...

[ COMPLETE ] |############################################################################################################################| 100%

Linking packages ...

[ COMPLETE ] |############################################################################################################################| 100%

sh-3.2# pip install -U kabuki

Downloading/unpacking kabuki from https://pypi.python.org/packages/source/k/kabuki/kabuki-0.5.4.tar.gz#md5=31e044218c83de6bbb46628e0dbcdcfc

Downloading kabuki-0.5.4.tar.gz (44kB): 44kB downloaded

Running setup.py (path:/private/tmp/pip_build_root/kabuki/setup.py) egg_info for package kabuki

IOError: [Errno 2] No such file or directory: 'skip:ppnd7'. Skipping file "skip:ppnd7".

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"

Wrote C/API module "linalg_utils" to file "build/src.macosx-10.5-x86_64-2.7/pymc/gp/linalg_utilsmodule.c"

Wrote C/API module "incomplete_chol" to file "build/src.macosx-10.5-x86_64-2.7/pymc/gp/incomplete_cholmodule.c"

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"

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"

warning: no files found matching 'docs/UserGuide.pdf'

warning: no files found matching '*.txt' under directory 'pymc'

Could not locate executable gfortran

Could not locate executable f95

Could not locate executable f90

Could not locate executable f77

Could not locate executable xlf90

Could not locate executable xlf

Could not locate executable ifort

Could not locate executable ifc

Could not locate executable g77

Could not locate executable g95

Could not locate executable pgfortran

don't know how to compile Fortran code on platform 'posix'

warning: build_ext: f77_compiler=None is not available.

Traceback (most recent call last):

File "<string>", line 17, in <module>

File "/private/tmp/pip_build_root/kabuki/setup.py", line 12, in <module>

setup_requires=['NumPy >= 1.6.0', 'pymc == 2.3.2', 'pandas >= 0.12.0', 'matplotlib >= 1.0.0']

File "//anaconda/lib/python2.7/distutils/core.py", line 111, in setup

_setup_distribution = dist = klass(attrs)

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/dist.py", line 260, in __init__

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/dist.py", line 285, in fetch_build_eggs

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py", line 631, in resolve

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py", line 871, in best_match

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py", line 883, in obtain

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/dist.py", line 335, in fetch_build_egg

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/command/easy_install.py", line 595, in easy_install

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/command/easy_install.py", line 625, in install_item

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/command/easy_install.py", line 822, in install_eggs

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/command/easy_install.py", line 1028, in build_and_install

File "//anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/setuptools/command/easy_install.py", line 1016, in run_setup

distutils.errors.DistutilsError: Setup script exited with error: extension 'pymc.flib' has Fortran sources but no Fortran compiler found