From mboxrd@z Thu Jan 1 00:00:00 1970 From: Danny Milosavljevic Subject: Re: =?utf-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages Date: Thu, 7 Jun 2018 01:06:20 +0200 Message-ID: <20180607010620.31fbf16c@scratchpost.org> References: <8736y11o2q.fsf@mdc-berlin.de> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; boundary="Sig_/XxSnllG_Qtx0B.o77yRboP5"; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:56410) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fQhVi-0003ZH-2E for guix-devel@gnu.org; Wed, 06 Jun 2018 19:06:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fQhVe-0004ME-SS for guix-devel@gnu.org; Wed, 06 Jun 2018 19:06:34 -0400 Received: from dd26836.kasserver.com ([85.13.145.193]:45502) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fQhVe-0004Lh-KQ for guix-devel@gnu.org; Wed, 06 Jun 2018 19:06:30 -0400 In-Reply-To: <8736y11o2q.fsf@mdc-berlin.de> 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" To: Ricardo Wurmus Cc: guix-devel@gnu.org --Sig_/XxSnllG_Qtx0B.o77yRboP5 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Ricardo, did you get a bug# for this? I can't see it on https://debbugs.gnu.org/cgi= /pkgreport.cgi?pkg=3Dguix ... > The errors are either about duplicates as in java-picard-2.10.3: >=20 > duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class That's... bad. What if those files differed? Which one would be used at runtime? > or about missing files as in dropseq-tools: >=20 > java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s= 14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar That's also bad. How does it run at all if its dependencies are missing? > I have removed the phase in these packages, but that=E2=80=99s not ideal. I think that's suboptimal in the above cases since those error messages rep= ort real problems, or in the first case at least pointing to a potential proble= m. > Can we make this phase more robust? Right now, it just invokes jar -i with the finished jar file. That's as simple as it gets - and I specifical= ly did only that minimal implementation for this cycle in order to only fix ou= r GC problem with java packages. The only thing I can think of that would improve things long term: The phase can add relative paths to all the dependencies to META-INF/MANIFE= ST.MF before invoking "jar -i". Then "jar -i" will index those - and all java packages can use regular inpu= ts instead of propagated inputs. I've tested that locally already - and it works fine. --Sig_/XxSnllG_Qtx0B.o77yRboP5 Content-Type: application/pgp-signature Content-Description: OpenPGP digital signature -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEds7GsXJ0tGXALbPZ5xo1VCwwuqUFAlsYaOwACgkQ5xo1VCww uqWqIAf9G/6omIr4RxntIiO/pUZjE9yEYrHbhQOtYO934lNTk3DRbbyfeAvrUiAt c9bm5Tmwv7IpLqbM4djD/iiwJYGoFHPzlhXTo0JZanW5td/VL2IgaWtrvLgeqUNr THpBCoXHOnhN7yBRagH7ffPEuFwus2Z503sBSZWnfrZcFl8SNQEVKm7IFYADTYWk 7A7H8EDO/Ov1XoCFO2dheGNQvVkFvyDQF4JR7obSHPMzYUuXPc+VjoiWs6G1BLeW IbWOsDrQ0zCb3telQ9q68QkuuG3s965/PtGuGXrTqiX/fn8RHFoBU2g/e5mx6+7N zn4Ptzw63AOrQeyXm0KK05hc3v68TQ== =2HU5 -----END PGP SIGNATURE----- --Sig_/XxSnllG_Qtx0B.o77yRboP5--