pangenome/smoothxg

Cmake error

Closed this issue · 4 comments

egoltsman commented

Hi,
I got interested in the solution you suggested to a vg user in
vgteam/vg#2957 as I have a similar case and I'm struggling to make sense of the complex graphs I'm getting from MSA-based graph constructors (tried cactus, msga, seqwish). When trying to install smoothxg I get an error from Cmake suggesting that I'm missing some dependencies. Could you please advise on what this is about?

-- Looking for pthread.h
[ 45%] Building CXX object CMakeFiles/argstest-multiple-inclusion.dir/test/multiple_inclusion_2.cxx.o
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Performing Test HAS_FLTO - Success
-- LTO enabled
bash: scripts/generate_git_version.sh: No such file or directory
CMake Error at CMakeLists.txt:558 (install):
  install TARGETS given no ARCHIVE DESTINATION for static library target
  "odgi_pybind11".
Nheyer commented

Did you include --recursive when you cloned the repository ?

egoltsman commented

I did. I've now gotten past this error after using a newer cmake. Now its croaking when building odgi, which is the same error I get when building odgi standalone. Is there a python env I need to have set?

[ 99%] Built target libodgi_shared
Scanning dependencies of target odgi_pybind11
[100%] Building CXX object CMakeFiles/odgi_pybind11.dir/src/pythonmodule.cpp.o
In file included from /global/homes/e/eugeneg/utils/vgteam/smoothxg/deps/odgi/deps/pybind11/include/pybind11/pytypes.h:12,
                 from /global/homes/e/eugeneg/utils/vgteam/smoothxg/deps/odgi/deps/pybind11/include/pybind11/cast.h:13,
                 from /global/homes/e/eugeneg/utils/vgteam/smoothxg/deps/odgi/deps/pybind11/include/pybind11/attr.h:13,
                 from /global/homes/e/eugeneg/utils/vgteam/smoothxg/deps/odgi/deps/pybind11/include/pybind11/pybind11.h:44,
                 from /global/homes/e/eugeneg/utils/vgteam/smoothxg/deps/odgi/src/pythonmodule.cpp:6:
/global/homes/e/eugeneg/utils/vgteam/smoothxg/deps/odgi/deps/pybind11/include/pybind11/detail/common.h:126:10: fatal error: Python.h: No such file or directory
 #include <Python.h>
          ^~~~~~~~~~
compilation terminated.
gmake[5]: *** [CMakeFiles/odgi_pybind11.dir/build.make:63: CMakeFiles/odgi_pybind11.dir/src/pythonmodule.cpp.o] Error 1
gmake[4]: *** [CMakeFiles/Makefile2:95: CMakeFiles/odgi_pybind11.dir/all] Error 2
gmake[4]: *** Waiting for unfinished jobs....
[100%] Built target odgi
gmake[3]: *** [Makefile:130: all] Error 2
gmake[2]: *** [CMakeFiles/odgi.dir/build.make:112: odgi-prefix/src/odgi-stamp/odgi-build] Error 2
gmake[1]: *** [CMakeFiles/Makefile2:269: CMakeFiles/odgi.dir/all] Error 2
Nheyer commented

it looks like you are missing the python developer headers, if you have sudo access you can run apt install python3-dev or the equivalent, if not you will have to manually install the headers

egoltsman commented

Ah, I didn't have the right python loaded. That fixed it. Thanks!