From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add vcflib. Date: Wed, 23 Mar 2016 14:49:07 +0100 Message-ID: References: <878u1aa62m.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:46274) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aijA3-0001gZ-CM for guix-devel@gnu.org; Wed, 23 Mar 2016 09:49:27 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aij9z-0007ir-3N for guix-devel@gnu.org; Wed, 23 Mar 2016 09:49:23 -0400 In-Reply-To: <878u1aa62m.fsf@gnu.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Roel Janssen Cc: guix-devel@gnu.org Roel Janssen 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 .o, but > instead add the right directives to the linker. I see what you mean. This is ugly, but there isn=E2=80=99t much you can = do about this. I=E2=80=99ve encountered many packages that do the same (som= e of which also involve tabix), and in the case of =E2=80=9Clibvcflib.a=E2=80=9D= it really does seem very hard to untangle dependencies further. =E2=80=9Cfilevercmp=E2=80=9D and =E2=80=9Cfsom=E2=80=9D don=E2=80=99t ins= tall 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=E2=80=99t yet looked at your patche= s, but the justification you give is valid; I looked at the Makefiles of vcflib and included projects and I think this is okay. ~~ Ricardo