Build fails Jellyfish 2.3.0 with Python bindings

[Parsoa]

I get the following output when building Jellyfish 2.3.0 tarball on Ubuntu 18.0.2 LTS with python bindings enabled. Configure runs ok but make seems not to find some needed sources. Builds fine if I configure without python bindings and make.

make  all-am
make[1]: Entering directory '/root/jellyfish-2.3.0'
  CXX      lib/rectangular_binary_matrix.lo
  CXX      lib/mer_dna.lo
  CXX      lib/storage.lo
  CXX      lib/allocators_mmap.lo
  CXX      lib/misc.lo
  CXX      lib/int128.lo
  CXX      lib/thread_exec.lo
  CXX      lib/jsoncpp.lo
  CXX      lib/time.lo
  CXX      lib/generator_manager.lo
  CXXLD    libjellyfish-2.0.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CXX      swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo
  CXXLD    swig/python/_dna_jellyfish.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CXX      sub_commands/jellyfish.o
  CXX      sub_commands/count_main.o
  CXX      sub_commands/info_main.o
  CXX      sub_commands/dump_main.o
  CXX      sub_commands/histo_main.o
  CXX      sub_commands/stats_main.o
  CXX      sub_commands/merge_main.o
  CXX      sub_commands/bc_main.o
  CXX      sub_commands/query_main.o
  CXX      sub_commands/cite_main.o
  CXX      sub_commands/mem_main.o
  CXX      jellyfish/merge_files.o
  CXXLD    bin/jellyfish
  PYTHONC  swig/python/__init__.pyc
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python2.7/py_compile.py", line 106, in compile
    with open(file, 'U') as f:
IOError: [Errno 2] No such file or directory: 'swig/python/dna_jellyfish.py'
Makefile:2849: recipe for target 'swig/python/__init__.pyc' failed
make[1]: *** [swig/python/__init__.pyc] Error 1
make[1]: Leaving directory '/root/jellyfish-2.3.0'
Makefile:977: recipe for target 'all' failed
make: *** [all] Error 2
make  install-am
make[1]: Entering directory '/root/jellyfish-2.3.0'
  PYTHONC  swig/python/__init__.pyc
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python2.7/py_compile.py", line 106, in compile
    with open(file, 'U') as f:
IOError: [Errno 2] No such file or directory: 'swig/python/dna_jellyfish.py'
Makefile:2849: recipe for target 'swig/python/__init__.pyc' failed
make[1]: *** [swig/python/__init__.pyc] Error 1
make[1]: Leaving directory '/root/jellyfish-2.3.0'
Makefile:2643: recipe for target 'install' failed
make: *** [install] Error 2

[fplazaonate]

I have the same problem. The file setup.py is missing in the swig/python directory

[rafaeldelucena]

@fplaza can you provide a PR which fixes it?

[fplazaonate]

I am afraid I can't. I guess the entire package has to be rebuilt with autoreconf Meanwhile, you can use older versions of jellyfish

[gmarcais]

The distribution tarball was regenerated. Not sure why these files were missing in the first place. It should compile fine now.