This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Having trouble building VG in Ubuntu

Hello,

I am trying to build vg on Ubuntu in WSL. After installing the dependencies and executing the make command, I receive the following output to the terminal:

In file included from /usr/include/pybind11/cast.h:16,
                 from /usr/include/pybind11/attr.h:13,
                 from /usr/include/pybind11/pybind11.h:13,
                 from /home/ayush/vg/deps/vcflib/src/pythonffi.cpp:9:
/usr/include/pybind11/detail/type_caster_base.h: In function ‘std::string pybind11::detail::error_string()’:
/usr/include/pybind11/detail/type_caster_base.h:482:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
  482 |             frame = frame->f_back;
      |                          ^~
In file included from /home/ayush/anaconda3/include/python3.11/Python.h:42,
                 from /usr/include/pybind11/detail/common.h:215,
                 from /usr/include/pybind11/pytypes.h:12,
                 from /usr/include/pybind11/cast.h:13,
                 from /usr/include/pybind11/attr.h:13,
                 from /usr/include/pybind11/pybind11.h:13,
                 from /home/ayush/vg/deps/vcflib/src/pythonffi.cpp:9:
/home/ayush/anaconda3/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
   22 | typedef struct _frame PyFrameObject;
      |                ^~~~~~
gmake[3]: Leaving directory '/home/ayush/vg/deps/vcflib/build'
[100%] Built target vcfglbound
gmake[3]: Leaving directory '/home/ayush/vg/deps/vcflib/build'
[100%] Built target vcfinfosummarize
gmake[3]: Leaving directory '/home/ayush/vg/deps/vcflib/build'
[100%] Built target vcfcreatemulti
gmake[3]: *** [CMakeFiles/pyvcflib.dir/build.make:79: CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o] Error 1
gmake[3]: Leaving directory '/home/ayush/vg/deps/vcflib/build'
gmake[2]: *** [CMakeFiles/Makefile2:2519: CMakeFiles/pyvcflib.dir/all] Error 2
gmake[2]: Leaving directory '/home/ayush/vg/deps/vcflib/build'
gmake[1]: *** [Makefile:149: all] Error 2
gmake[1]: Leaving directory '/home/ayush/vg/deps/vcflib/build'
make: *** [Makefile:694: lib/libvcflib.a] Error 2
vg
• 1,929 views • link
updated by Ram Ram • written by ayushm64 • ayushm64

ayushm64 why did you delete this post?

• 0 views • link
written by Ram Ram

I didn't think anyone else would find it useful.

• 0 views • link
written by ayushm64 • ayushm64

That's not your call to make. No one can possibly know whether or not someone would find your post helpful - a post is definitely unhelpful only in a few niche cases, and yours is not one of them.

• 0 views • link
written by Ram Ram

1 answer

Building for a specific reason? There is a static binary available for unix that should work for Ubuntu: https://github.com/vgteam/vg/releases/tag/v1.56.0

• 0 views • link
written by GenoMax GenoMax

This is exactly what I needed, thank you so much!!!!!

• 0 views • link
written by ayushm64 • ayushm64

Log in to answer this question.

More posts like this