[Biopython] can't compile version from github

[Michael Thon]

On Dec 3, 2009, at 11:19 AM, Peter wrote:

> On Thu, Dec 3, 2009 at 5:20 AM, Michael Thon <mike.thon at gmail.com> wrote:
>> Don't know if this belongs on the dev mailing list or here...
> 
> Tricky - I might have picked the dev list, but this is fine.
> 
>> I just checked out a copy of biopython from the github repo and I
>> tried to install it in an non-root directory to try out a new feature.
>> 
>> here is the command I ran on the command line:
>> python setup.py install --prefix=/Users/mike/biopython_dev
>> 
>> Here is the offending part of the compile:
>> 
>> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
>> In file included from Bio/triemodule.c:3:
>> Bio/trie.h:12: warning: function declaration isn’t a prototype
>> 
>> The installer did not find the numpy that I installed using easy_install
>> so I continued without it and without Reportlab.  (Mac OS 10.6)
>> 
>> Mike
> 
> Ah - Snow Leopard. Are you using the Apple provided Python with Mac OS 10.6?
> Apple have as usual done odd things with Python, but people have
> reported getting
> it to work.

 
Yup, I'm using the Apple-provided python.  Below is the full output of the build phase.  

...so, as usual, I am off on a tangent instead of working on the stuff that actually needs to get done.  I don't really need to get this installed.  I just wanted to try the SeqFeature.extract method that you mentioned in a previous thread.  I realized that I probably don't need to compile all the C extensions to get that to work so I opened up SeqFeature.py to see what this method looks like.  I couldn't find it so I suppose this method has not made its way into the main git repo on github.  In the end, I wrote one myself but it would still be good to compare its output to what you have in biopython.

...but I still have this biopython from github that won't compile and it probably should.  So, if you have any ideas what might be wrong and how to fix it I can try it and report back.
-Mike

python setup.py build
running build
running build_py
*** Numerical Python *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Numerical Python at http://numpy.sourceforge.net/.

Do you want to continue this installation? (Y/n)  Y
*** Reportlab *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Reportlab at http://www.reportlab.org/downloads.html.

Do you want to continue this installation? (Y/n)  Y
running build_ext
building 'Bio.trie' extension
creating build/temp.macosx-10.6-universal-2.6
creating build/temp.macosx-10.6-universal-2.6/Bio
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c Bio/triemodule.c -o build/temp.macosx-10.6-universal-2.6/Bio/triemodule.o
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn’t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ‘_write_value_to_handle’:
Bio/triemodule.c:480: error: too few arguments to function ‘PyMarshal_WriteObjectToString’
Bio/triemodule.c:482: warning: passing argument 3 of ‘PyString_AsStringAndSize’ from incompatible pointer type
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn’t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ‘_write_value_to_handle’:
Bio/triemodule.c:480: error: too few arguments to function ‘PyMarshal_WriteObjectToString’
Bio/triemodule.c:482: warning: passing argument 3 of ‘PyString_AsStringAndSize’ from incompatible pointer type
In file included from Bio/triemodule.c:3:
Bio/trie.h:12: warning: function declaration isn’t a prototype
Bio/triemodule.c:389: warning: initialization from incompatible pointer type
Bio/triemodule.c: In function ‘_write_value_to_handle’:
Bio/triemodule.c:480: error: too few arguments to function ‘PyMarshal_WriteObjectToString’
Bio/triemodule.c:482: warning: passing argument 3 of ‘PyString_AsStringAndSize’ from incompatible pointer type
lipo: can't open input file: /var/folders/wI/wIckOkhJHe0hxBDeAEI1VE+++TI/-Tmp-//ccemhRHR.out (No such file or directory)
error: command 'gcc-4.2' failed with exit status 1