This is a reply to my-self, it might help others:
I noticed that with autotools the build is automatically // (-j option),
and that is why I had the issue with the missing fortran modules.
To avoid having errors it is mandatory to ask for the fortran modules to be built first,
and that happens in the file ‘Makefile.am’, in my case I had:
atomes_fortran = $(atomes_fortran_modules) $(atomes_fortran_files)
And I needed to add the following line:
atomes_fortran = $(atomes_fortran_modules) $(atomes_fortran_files)
$(patsubst %.F90,%.o,$(atomes_fortran_files)): $(patsubst %.F90,%.o,$(atomes_fortran_modules))
And that allows the ‘autotools’ build system to work as expected.
After the build I managed to run my app using:
flatpak run --socket=session-bus --nosocket=fallback-x11 --socket=x11 org.flatpak.atomes
The ‘–socket=session-bus’ correct the DBus error, while ‘x11’ related options correct a GTK display error, so now the flatpak seems to run fine, not sure that this way of doing is appropriate,
any advise would be appreciated.
S.