[Biopython] Fwd: question on installation of BioPython on Mac OS 10.7

[Iddo Friedberg]

---------- Forwarded message ----------
From: Daria Fedyukina <fedyukina at gmail.com>
Date: Mon, Feb 27, 2012 at 5:15 PM
Subject: Re: [Biopython] question on installation of BioPython on Mac OS
10.7
To: Iddo Friedberg <idoerg at gmail.com>


Hi Iddo,

I have installed NumPy. Thank you very much for finding the right version
for me. I cannot understand how I missed it.

I thought I installed NumPy correctly: I double clicked on it, I agreed on
terms and conditions, I saw "installation is successful"
After that I did not see any new folder or package in my Applications
folder except previous numpy-1.6.1-py2.7-python.org-macosx10.3.dmg file.
I drag and dropped numpy-1.6.1-py2.7.mpkg file in Applications just in case.

I do not know what to do with this .mpkg file because if I double click on
it, it gives me hte same installation wizard as before, all steps are the
same, nothing chages.

I went to my X11 -> went inside biopython-1.58 older -> typed "python
setup.py build" -> it again asked me if I want to proceed without NumPy. It
did not see that I installed NumPy. It means I did not install it right.

I looked online, the instructions talk about some kind of binary here
http://docs.scipy.org/doc/numpy/user/install.html for Mac OS X, but it does
not look any different from what I have already done.

Would you be so kind as to provide some insight on what they want?
THank you again.

-Daria


P.S. I got Mac 3 months ago, I always thought that it is more convenient
for programming in general. Well..... It was easier to install biopython on
windows. This is a very interesting case.



On Feb 27, 2012, at 3:27 PM, Iddo Friedberg wrote:

Daria,

Seems like there is a NumPy for Python 2.7 on Mac:

http://sourceforge.net/projects/numpy/files/NumPy/1.6.1/

In any case, you should not skip the NumPy installation. Even if for teh
combination of your OS and Python version there is only NumPy for Python
2.6, you should install that. There is very little difference between
Python 2.6 and 2.7, and NumPy should not break (and, in any case, seems
like your desired version is in the link above).

HTH,

Iddo

On Mon, Feb 27, 2012 at 4:00 PM, Daria Fedyukina <fedyukina at gmail.com>wrote:

> Hello,
>
> I am trying to install BioPython 1.58. My BioPython and python are both in
> the Applications folder.
> My configuration is:
> OS: Mac OS 10.7.3
> Python: 2.7.2
> Apple Xcode is installed.
> NumPy is not installed (could not install for 2.7, only available for 2.6;
> decided to skip)
>
> When I try to install it, I go to X11 -> go inside biopython-1.58 older ->
> type "python setup.py build" -> choose to proceed without NumPy -> get an
> error.
>
> Here how it looks:
> bash-3.2$ cd biopython-1.58
> bash-3.2$ ls
> Bio             DEPRECATED      MANIFEST.in     README          build
> BioSQL          Doc             NEWS            Scripts         do2to3.py
> CONTRIB         LICENSE         PKG-INFO        Tests           setup.py
> bash-3.2$ python setup.py build
> running build
> running build_py
>
> Numerical Python (NumPy) is not installed.
>
> This package is required for many Biopython features.  Please install
> it before you install Biopython. You can install Biopython anyway, but
> anything dependent on NumPy will not work. If you do this, and later
> install NumPy, you should then re-install Biopython.
>
> You can find NumPy at http://numpy.scipy.org
>
> Do you want to continue this installation? (y/N):
> y
> running build_ext
> building 'Bio.cpairwise2' extension
> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot
> /Developer/SDKs/MaSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3
> -IBio -I/Library/Fraworks/Python.framework/Versions/2.7/include/python2.7
> -c Bio/cpairwise2module.-o
> build/temp.macosx-10.6-intel-2.7/Bio/cpairwise2module.o
> In file included from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/unicodeobject.h:4,
>                 from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/Python.h:85,
>                 from Bio/cpairwise2module.c:12:
> /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h:
> No ch file or directory
> In file included from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/unicodeobject.h:4,
>                 from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/Python.h:85,
>                 from Bio/cpairwise2module.c:12:
> /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h:
> No ch file or directory
> lipo: can't figure out the architecture type of:
> /var/folders/nt/1ppm7j953zv2qylmtwydqm0000gn/T//ccODIZmY.out
> error: command 'gcc-4.2' failed with exit status 1
> bash-3.2$
>
> I googled this error, it turned out that gcc-4.2 needs to be installed. I
> did. Then, the situation is exactly the same when I repeat biopython
> installation.
>
> Does anyone know what could've happened? My only suspicion now is that
> Lion is messing stuff up. Looks like Snow Leopard works better.
>
> Thank you very much for any help or advice!
> -Daria
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.