Re: [PATCH] Add vcflib.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

Roel Janssen <roel@gnu.org> writes:

> Dear Guix,
>
> In an effort to package freebayes, I would first like to add vcflib and
> its dependencies.  Therefore, I have attached eight patches.
>
> I've attempted to decouple the dependencies from vcflib, which worked
> for intervaltree and htslib.  The following dependencies are actually
> tightly coupled in the build process:
> - tabixpp
> - smithwaterman
> - multichoose
> - fsom
> - filevercmp
> - fastahack

Thank you for your efforts!

> To decouple these, we would need to include header files in the package
> output that aren't part of the public interface.  In addition to that,
> we would need to patch the build system to not look for <object>.o, but
> instead add the right directives to the linker.

I see what you mean.  This is ugly, but there isn’t much you can do
about this.  I’ve encountered many packages that do the same (some of
which also involve tabix), and in the case of “libvcflib.a” it really
does seem very hard to untangle dependencies further.

“filevercmp” and “fsom” don’t install libraries at all and apparently
are supposed to be included in other code.

> I don't think that is the desirable approach, because that would cause
> these packages to provide header files that should only be used
> internally.  Therefore, I use the source of these packages in vcflib,
> and unpack them in the vcflib project root, to avoid confusion on
> interfaces and fiddling with the build system.

This seems acceptable to me.  I haven’t yet looked at your patches, but
the justification you give is valid; I looked at the Makefiles of vcflib
and included projects and I think this is okay.

~~ Ricardo