Problem with Linux - Pynauty

[yonatanbitton]

Hello, I've switched to Linux after I couldn't run it with windows.

Now when I execute make pynauty I get the following error:

`build/temp.linux-x86_64-3.7/src/nautywrap.o -O4 -fPIC
In file included from src/nautywrap.c:16:0:
nauty/nauty.h:43:0: warning: "_FILE_OFFSET_BITS" redefined [enabled by default]
 #define _FILE_OFFSET_BITS 0
 ^
In file included from /home/yehonata/miniconda3/include/python3.7m/Python.h:8:0,
                 from src/nautywrap.c:15:
/home/yehonata/miniconda3/include/python3.7m/pyconfig.h:1494:0: note: this is the location of the previous definition
 #define _FILE_OFFSET_BITS 64
 ^
gcc -pthread -shared -B /home/yehonata/miniconda3/compiler_compat -L/home/yehonata/miniconda3/lib -Wl,-rpath=/home/yehonata/miniconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/src/nautywrap.o nauty/nauty.o nauty/nautil.o nauty/naugraph.o nauty/schreier.o nauty/naurng.o -o build/lib.linux-x86_64-3.7/pynauty/nautywrap.cpython-37m-x86_64-linux-gnu.so
/home/yehonata/miniconda3/compiler_compat/ld: nauty/naugraph.o: relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/home/yehonata/miniconda3/compiler_compat/ld: final link failed: nonrepresentable section on output
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
make: *** [pynauty] Error 1
`

What is wrong here?

[tvayer]

I think you have to recompile properly the pynauty library, since the version here is compiled for Mac and Python3.5. I am not a linux expert but maybe the python version you used is not the same as I used (I used python3.5) so maybe this is the reason..

I don't really have the time to maintain this repository for most of the plateforms and I can not reproduce your error but maybe you could check at https://github.com/sammorley-short/pynauty and https://web.cs.dal.ca/~peter/software/pynauty/html/install.html where there could be more hints