[Biopython-dev] Updating C extensions to Python 3

[Peter]

On Sat, Dec 25, 2010 at 11:24 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> However, it looks like Python 2.4 and 2.5 have broken
> (on both Linux and Windows, probably on Mac too but
> that build slave is off at the minute):
> http://events.open-bio.org:8010/tgrid
>
> If you can fix Python 2.5 but not Python 2.4, don't
> worry - we've said Biopython 1.57 won't officially
> support Python 2.4 anyway.

It looks like the first commit "some code cleanup" broke Python 2.5,
https://github.com/biopython/biopython/commit/afa764f9d86951fdf43613e974e9baad9b26056c

$ python2.5 setup.py build
running build
running build_py
running build_ext
building 'Bio.Cluster.cluster' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC
-I/home/peterjc/lib/python2.5/site-packages/numpy/core/include
-I/home/peterjc/include/python2.5 -c Bio/Cluster/clustermodule.c -o
build/temp.linux-i686-2.5/Bio/Cluster/clustermodule.o
Bio/Cluster/clustermodule.c:1032: warning: implicit declaration of
function ‘PyVarObject_HEAD_INIT’
Bio/Cluster/clustermodule.c:1033: error: initializer element is not constant
Bio/Cluster/clustermodule.c:1033: error: (near initialization for
‘PyNodeType.ob_refcnt’)
Bio/Cluster/clustermodule.c:1033: error: expected ‘}’ before string constant
Bio/Cluster/clustermodule.c: In function ‘PyTree_dealloc’:
Bio/Cluster/clustermodule.c:1079: warning: implicit declaration of
function ‘Py_TYPE’
Bio/Cluster/clustermodule.c:1079: error: invalid type argument of ‘->’
(have ‘int’)
Bio/Cluster/clustermodule.c: At top level:
Bio/Cluster/clustermodule.c:1335: error: initializer element is not constant
Bio/Cluster/clustermodule.c:1335: error: (near initialization for
‘PyTreeType.ob_refcnt’)
Bio/Cluster/clustermodule.c:1335: error: expected ‘}’ before string constant
Bio/Cluster/clustermodule.c: In function ‘initcluster’:
Bio/Cluster/clustermodule.c:2855: warning: implicit declaration of
function ‘GETSTATE’
Bio/Cluster/clustermodule.c:2855: warning: initialization makes
pointer from integer without a cast
error: command 'gcc' failed with exit status 1

Peter