Problem installing cosmolopy in Snow Leopard

[Rodrigo Nemmen]

Dear All,

First of all, I find Cosmolopy very useful! Have been using it for
doing cosmological calculations involving quasars.

I am now trying to install it on Mac OS X. Tried using easy_install,
pip and even compiling from source. None suceeded yet. Below is a
description of the error I find.

OS/Python Specifications
=====================
CosmoloPy 0.1.100
OS: Mac OS X, Snow Leopard, v. 10.6.6
Python specs: 2.7 (r27:82500, Oct 22 2010, 11:32:40), installed via
Fink including scipy, numpy, matplotlib, etc

easy-install error
=============
When trying
$ sudo easy_install-2.7 Cosmolopy
I get the following error:

Searching for Cosmolopy
Reading http://pypi.python.org/simple/Cosmolopy/
Reading http://roban.github.com/CosmoloPy/
Best match: CosmoloPy 0.1.100
Downloading http://pypi.python.org/packages/source/C/CosmoloPy/CosmoloPy-0.1.100.tar.gz#md5=681de1c0898159cce6f8af17e1557d1a
Processing CosmoloPy-0.1.100.tar.gz
Running CosmoloPy-0.1.100/setup.py -q bdist_egg --dist-dir /tmp/
easy_install-EKIgWR/CosmoloPy-0.1.100/egg-dist-tmp-c4qvqk
ld: warning: in /sw/lib/python2.7/config/libpython2.7.dylib, file was
built for i386 which is not the architecture being linked (x86_64)
Undefined symbols:
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_Swig_var_tf_cbnu_get in power_wrap.o
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
"__Py_NotImplementedStruct", referenced from:
_SwigPyObject_richcompare in power_wrap.o
"_PyArg_ParseTuple", referenced from:
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__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyObject_IsTrue", referenced from:
_SwigPyObject_own in power_wrap.o
"_PyCObject_FromVoidPtr", referenced from:
_init_power in power_wrap.o
"_PyModule_AddObject", referenced from:
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"_PyObject_CallFunctionObjArgs", referenced from:
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"_PyString_FromFormat", referenced from:
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_SwigPyPacked_repr in power_wrap.o
_SwigPyPacked_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
_SwigPyObject_print in power_wrap.o
"_PyLong_AsDouble", referenced from:
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"_PyDict_SetItem", referenced from:
_init_power in power_wrap.o
_init_power in power_wrap.o
"_PyLong_FromVoidPtr", referenced from:
_SwigPyObject_format in power_wrap.o
_SwigPyObject_long in power_wrap.o
"_PyExc_OverflowError", referenced from:
_Swig_var_tf_cbnu_set in power_wrap.o
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyTuple_SetItem", referenced from:
_SwigPyObject_format in power_wrap.o
"_PyExc_NameError", referenced from:
_swig_varlink_setattr in power_wrap.o
_swig_varlink_getattr in power_wrap.o
"_PyFloat_Type", referenced from:
_SWIG_AsVal_double in power_wrap.o
"_PyString_Format", referenced from:
_SwigPyObject_format in power_wrap.o
"_PyBool_FromLong", referenced from:
_SwigPyObject_own in power_wrap.o
"_PyArg_UnpackTuple", referenced from:
_SwigPyObject_own in power_wrap.o
"_PyExc_ZeroDivisionError", referenced from:
_Swig_var_tf_cbnu_set in power_wrap.o
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyInt_AsLong", referenced from:
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__wrap_TFmdm_set_cosm in power_wrap.o
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"_PyObject_Init", referenced from:
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"_PyExc_AttributeError", referenced from:
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__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyCObject_Import", referenced from:
_init_power in power_wrap.o
"_PyErr_SetString", referenced from:
_swig_varlink_setattr in power_wrap.o
_swig_varlink_getattr in power_wrap.o
_Swig_var_tf_cbnu_set in power_wrap.o
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyString_FromString", referenced from:
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_SwigPyObject_str in power_wrap.o
_SwigPyObject_format in power_wrap.o
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_swig_varlink_str in power_wrap.o
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_swig_varlink_str in power_wrap.o
_SWIG_Python_DestroyModule in power_wrap.o
_SwigPyPacked_str in power_wrap.o
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"_PyString_AsString", referenced from:
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_SwigPyObject_print in power_wrap.o
"_PyExc_SyntaxError", referenced from:
_Swig_var_tf_cbnu_set in power_wrap.o
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyExc_IOError", referenced from:
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__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyErr_Clear", referenced from:
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_init_power in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_Py_InitModule4_64", referenced from:
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_init_power in power_wrap.o
"_PyObject_Malloc", referenced from:
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_init_power in power_wrap.o
_init_power in power_wrap.o
_init_power in power_wrap.o
_SwigPyObject_dealloc in power_wrap.o
"_PyExc_ValueError", referenced from:
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__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"__Py_TrueStruct", referenced from:
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__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyType_Type", referenced from:
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_SwigPyObject_dealloc in power_wrap.o
"_PyExc_RuntimeError", referenced from:
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__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyObject_Free", referenced from:
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"_PyExc_MemoryError", referenced from:
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__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
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"_PyInt_FromLong", referenced from:
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__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"__PyObject_GetDictPtr", referenced from:
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__wrap_TFmdm_set_cosm in power_wrap.o
"_PyFloat_AsDouble", referenced from:
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_SwigPyObject_repr in power_wrap.o
_SwigPyObject_repr in power_wrap.o
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"_PyExc_TypeError", referenced from:
_Swig_var_tf_cbnu_set in power_wrap.o
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyType_IsSubtype", referenced from:
_SWIG_AsVal_double in power_wrap.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
error: Setup script exited with error: command 'gcc' failed with exit
status 1

Compiling from source
===================
Then I tried compiling from the source:
$ python2.7 setup.py build
and again got an error:

running build
running build_py
running build_ext
building 'cosmolopy.EH._power' extension
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-
prototypes -I/sw/include/python2.7 -c ./cosmolopy/EH/power_wrap.c -o
build/temp.macosx-10.6-i386-2.7/./cosmolopy/EH/power_wrap.o
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-
prototypes -I/sw/include/python2.7 -c ./cosmolopy/EH/power.c -o build/
temp.macosx-10.6-i386-2.7/./cosmolopy/EH/power.o
gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 build/
temp.macosx-10.6-i386-2.7/./cosmolopy/EH/power_wrap.o build/
temp.macosx-10.6-i386-2.7/./cosmolopy/EH/power.o -o build/
lib.macosx-10.6-i386-2.7/cosmolopy/EH/_power.so
ld: warning: in /sw/lib/python2.7/config/libpython2.7.dylib, file was
built for i386 which is not the architecture being linked (x86_64)
Undefined symbols:
"_PyFloat_FromDouble", referenced from:
_Swig_var_tf_cbnu_get in power_wrap.o
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
"__Py_NotImplementedStruct", referenced from:
_SwigPyObject_richcompare in power_wrap.o
"_PyArg_ParseTuple", referenced from:
__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyObject_IsTrue", referenced from:
_SwigPyObject_own in power_wrap.o
"_PyCObject_FromVoidPtr", referenced from:
_init_power in power_wrap.o
"_PyModule_AddObject", referenced from:
_init_power in power_wrap.o
"_PyObject_CallFunctionObjArgs", referenced from:
_SwigPyObject_dealloc in power_wrap.o
"_PyString_FromFormat", referenced from:
_SwigPyPacked_str in power_wrap.o
_SwigPyPacked_repr in power_wrap.o
_SwigPyPacked_repr in power_wrap.o
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"_PyLong_AsDouble", referenced from:
_SWIG_AsVal_double in power_wrap.o
"_PyDict_SetItem", referenced from:
_init_power in power_wrap.o
_init_power in power_wrap.o
"_PyLong_FromVoidPtr", referenced from:
_SwigPyObject_format in power_wrap.o
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"_PyExc_OverflowError", referenced from:
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"_PyTuple_SetItem", referenced from:
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"_PyExc_NameError", referenced from:
_swig_varlink_setattr in power_wrap.o
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"_PyFloat_Type", referenced from:
_SWIG_AsVal_double in power_wrap.o
"_PyString_Format", referenced from:
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"_PyBool_FromLong", referenced from:
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"_PyInt_AsLong", referenced from:
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__wrap_TFmdm_set_cosm in power_wrap.o
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_init_power in power_wrap.o
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_init_power in power_wrap.o
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"_PyExc_AttributeError", referenced from:
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__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyCObject_Import", referenced from:
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"_PyString_AsString", referenced from:
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__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyExc_IOError", referenced from:
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__wrap_TFmdm_onek_hmpc in power_wrap.o
__wrap_TFmdm_onek_mpc in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyErr_Clear", referenced from:
_SWIG_AsVal_double in power_wrap.o
_init_power in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_Py_InitModule4_64", referenced from:
_init_power in power_wrap.o
_init_power in power_wrap.o
"_PyObject_Malloc", referenced from:
_init_power in power_wrap.o
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"__Py_TrueStruct", referenced from:
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"_PyExc_IndexError", referenced from:
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__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
__wrap_TFmdm_set_cosm in power_wrap.o
"_PyType_Type", referenced from:
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"_PyObject_Free", referenced from:
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"_PyModule_GetDict", referenced from:
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"_PyExc_MemoryError", referenced from:
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"_PyInt_FromLong", referenced from:
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"_PyExc_SystemError", referenced from:
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"_PyType_IsSubtype", referenced from:
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ld: symbol(s) not found
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

Any idea of what's going on? Any help much appreciated!

Best,

Rodrigo

--
http://www.if.ufrgs.br/~rns

[Roban]

Hi,

I'm sorry, I'm not using OS X right now, so I can't check this out
myself. It looks like the problem with building from source is not
with cosmolopy, but something to do with having python libraries
installed for the wrong architecture or maybe mixed 32 and 64 bit
libraries.

If you don't need the perturbation theory routines, then it should be
simple to install without needing to compile anything, so I can try to
rig up an alternate setup.py for that purpose...

-Roban

On Feb 18, 9:24 pm, Rodrigo Nemmen <rsnem...@gmail.com> wrote:
> Dear All,
>
> First of all, I find Cosmolopy very useful! Have been using it for
> doing cosmological calculations involving quasars.
>
> I am now trying to install it on Mac OS X. Tried using easy_install,
> pip and even compiling from source. None suceeded yet. Below is a
> description of the error I find.
>
> OS/Python Specifications
> =====================
> CosmoloPy 0.1.100
> OS: Mac OS X, Snow Leopard, v. 10.6.6
> Python specs: 2.7 (r27:82500, Oct 22 2010, 11:32:40), installed via
> Fink including scipy, numpy, matplotlib, etc
>
> easy-install error
> =============
> When trying
> $ sudo easy_install-2.7 Cosmolopy
> I get the following error:
>
> Searching for Cosmolopy
> Readinghttp://pypi.python.org/simple/Cosmolopy/

> Readinghttp://roban.github.com/CosmoloPy/
> Best match: CosmoloPy 0.1.100
> Downloadinghttp://pypi.python.org/packages/source/C/CosmoloPy/CosmoloPy-0.1.100....

[Rodrigo Nemmen]

Dear Roban,

Thanks for your reply.

Could you prepare the alternate setup.py that does not compile the
perturbation routines (or give me directions about how to do that
myself)?

Best,

Rodrigo

[Roban Hultman Kramer]

Hello Rodrigo,

I think this should do it. Try downloading one of these links:

(as a zip file:) http://github.com/roban/CosmoloPy/zipball/0.1.101
(or as a tarball:) http://github.com/roban/CosmoloPy/tarball/0.1.101

Then unpack and run:

sudo python setup_alt.py install

And please do let me know how that works out for you.

Thanks very much for the feedback! I'm sure it will help other users, as well.

-Roban

[Rodrigo Nemmen]

Hi Roban,

There is no setup_alt.py in the package that you supplied.

I tried running
$ sudo python setup.py install
and got the same problem as before.

Best,

Rodrigo

--
http://www.if.ufrgs.br/~rns/

[Roban Hultman Kramer]

Hi,

Sorry! Somehow I tagged the wrong version. Here are links that should
definitely contain the new setup_alt.py

http://github.com/roban/CosmoloPy/tarball/master
http://github.com/roban/CosmoloPy/zipball/master

Really sorry about that. Let me know how it goes.

-Roban

[Roban Hultman Kramer]

Hi Rodrigo,

I just realized that you weren't CCed on the last email I sent, and
you may not be on the mailing list. Hope the message below helps.
Please let me know how it works out for you.

-Roban

On Tue, Feb 22, 2011 at 9:57 PM, Roban Hultman Kramer

[Rodrigo Nemmen]

Hi Roban,

It worked this time! Thanks!!

When importing cosmolopy I get the following warning:

"Error importing EH.power. See EH/installation.txt.
Some functions (transfer_function_EH, etc.) will not work."

I guess that refers to the routines that were not compiled, right?

Best,

Rodrigo



On Feb 28, 10:20 am, Roban Hultman Kramer <roban.kra...@phys.ethz.ch>
wrote:

> Hi Rodrigo,
>
> I just realized that you weren't CCed on the last email I sent, and
> you may not be on the mailing list. Hope the message below helps.
> Please let me know how it works out for you.
>
> -Roban
>
> On Tue, Feb 22, 2011 at 9:57 PM, Roban Hultman Kramer
>
>
>
> <roban.kra...@phys.ethz.ch> wrote:
> > Hi,
>
> > Sorry! Somehow I tagged the wrong version. Here are links that should
> > definitely contain the new setup_alt.py
>
> >http://github.com/roban/CosmoloPy/tarball/master
> >http://github.com/roban/CosmoloPy/zipball/master
>
> > Really sorry about that. Let me know how it goes.
>
> > -Roban
>

> > On Tue, Feb 22, 2011 at 9:18 PM, Rodrigo Nemmen <rsnem...@gmail.com> wrote:
> >> Hi Roban,
>
> >> There is no setup_alt.py in the package that you supplied.
>
> >> I tried running
> >> $ sudo python setup.py install
> >> and got the same problem as before.
>
> >> Best,
>
> >> Rodrigo
>
> >> --
> >>http://www.if.ufrgs.br/~rns/
>
> >> On Tue, Feb 22, 2011 at 9:57 AM, Roban Hultman Kramer
> >> <roban.kra...@phys.ethz.ch> wrote:
> >>> Hello Rodrigo,
>
> >>> I think this should do it. Try downloading one of these links:
>

> >>> (as a zip file:)http://github.com/roban/CosmoloPy/zipball/0.1.101
> >>> (or as a tarball:)http://github.com/roban/CosmoloPy/tarball/0.1.101

>
> >>> Then unpack and run:
>
> >>>  sudo python setup_alt.py install
>
> >>> And please do let me know how that works out for you.
>
> >>> Thanks very much for the feedback! I'm sure it will help other users, as well.
>
> >>> -Roban
>

> ...
>
> read more »

[Roban Hultman Kramer]

Yes, that's correct. Perhaps I'll remove the warning since many people
may want to install without compiling the power spectrum stuff.

[Roban]

In case the import warning is annoying you, I've removed it in the new
version of CosmoloPy (0.1.102), available from pypi (http://
pypi.python.org/pypi/CosmoloPy/) or github (http://roban.github.com/
CosmoloPy/).

Now you get ImportError if you try to use a function that calls the
matter transfer function code in cosmolopy.perturbation, but otherwise
there should be no error or warning.

-Roban

> ...
>
> read more »