[Biopython-dev] Biopython 1.70 release

Peter Cock p.j.a.cock at googlemail.com
Tue Jul 11 10:36:15 UTC 2017

Hmm. I'm not sure if there is any mechanism in setuptools for
us to specify we need Python's C headers present. This is kind
of assumed if compiling anything against the Python C API.

I don't think this causes any problems for the Biopython 1.70
release, but would be worth looking at in terms of reviewing
our installation documentation:


Thanks again,


On Tue, Jul 11, 2017 at 11:11 AM, Mateusz Korycinski
<mkorycinski at protonmail.ch> wrote:
> On Linux (Ubuntu 16.04.02) I was getting following error:
>     creating build/temp.linux-x86_64-3.5
>     creating build/temp.linux-x86_64-3.5/Bio
>     x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -g -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> -I/usr/include/python3.5m
> -I/root/virt_env/test_biopython3/include/python3.5m -c
> Bio/cpairwise2module.c -o build/temp.linux-x86_64-3.5/Bio/cpairwise2module.o
>     unable to execute 'x86_64-linux-gnu-gcc': No such file or directory
>     error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
>     ----------------------------------------
> Command "/root/virt_env/test_biopython3/bin/python3 -u -c "import
> setuptools,
> tokenize;__file__='/tmp/pip-eokznl75-build/setup.py';f=getattr(tokenize,
> 'open', open)(__file__);code=f.read().replace('\r\n',
> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
> /tmp/pip-avijolek-record/install-record.txt
> --single-version-externally-managed --compile --install-headers
> /root/virt_env/test_biopython3/include/site/python3.5/biopython" failed with
> error code 1 in /tmp/pip-eokznl75-build/
> Which was of course solved by installing python3-dev. Shouldn't that also go
> to the setup script?
> Then install and tests (Python 3.5.2): https://pastebin.com/Vz2yFRZF
> Everything seems to be fine here.
> Best regards,
> Mateusz Korycinski

More information about the Biopython-dev mailing list