gcc-6.3.0: fatal error: stdlib.h: No such file or directory about fast5 HOT 1 OPEN

Hi
Just encountered the same problem. I found some information on that problem here

Essentially in your gcc it jumps from your defined include path to the next in the list which in my case was -I ../include . Obviously it did not find anything there (have a look at what the make command produces).

In the setup.py there is actually a fix included:

# don't indiscriminately add /usr/include to work around bug:
# https://lists.fedoraproject.org/archives/list/[email protected]/thread/Q5SWCUUMWQ4EMS7CU2CBOZHV3WZYOOTT/
for d in [hdf5_include_dir]:
    if d != '/usr/include':
        extra_compile_args += ['-isystem', d]
#extra_compile_args += ['-O0', '-g3', '-ggdb', '-fno-eliminate-unused-debug-types', '-v']

which did not work in our case as we had an unusual include path which was not /usr/include and therefore the patch did not do its job. Adapting it worked fine for us.

from fast5.