Hello,
I am trying to install the Biopython module to sage's python installation. I am
running sage 5.0, which seems to be the latest version with a OSX 10.4 binary.
I am attempting to build biopython as follows:
sage --python setup.py build
but apparently there are some issues with gcc and sage. This is the output I
get after running that command.
running build
running build_py
running build_ext
building 'Bio.cpairwise2' extension
gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -IBio -I/Applications/sage/local/include/python2.7 -c
Bio/cpairwise2module.c -o build/temp.macosx-10.4-i386-2.7/Bio/cpairwise2module.o
In file included from
/Applications/sage/local/lib/gcc/i386-apple-darwin8.11.1/4.6.3/include-fixed/syslimits.h:7:0,
from
/Applications/sage/local/lib/gcc/i386-apple-darwin8.11.1/4.6.3/include-fixed/limits.h:34,
from /Applications/sage/local/include/python2.7/Python.h:19,
from Bio/cpairwise2module.c:12:
/Applications/sage/local/lib/gcc/i386-apple-darwin8.11.1/4.6.3/include-fixed/limits.h:169:61:
fatal error: limits.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1
>From this output it seems to me that the problem is that gcc can't find the
>file limits.h. I looked for this file inside the sage directory and it seems
>to be in the correct place
>(/Applications/sage/local/lib/gcc/i386-apple-darwin8.11.1/4.6.3/include-fixed/limits.h).
How can I resolve this issue? Any ideas on what might be going wrong?
Thank you for your help.
--
You received this message because you are subscribed to the Google Groups
"sage-support" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at http://groups.google.com/group/sage-support?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
