From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 07 03:20:58 2018 Received: (at 31721) by debbugs.gnu.org; 7 Jun 2018 07:20:58 +0000 Received: from localhost ([127.0.0.1]:37376 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQpE9-0002vL-UM for submit@debbugs.gnu.org; Thu, 07 Jun 2018 03:20:58 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:37230) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQpE8-0002vC-5Z for 31721@debbugs.gnu.org; Thu, 07 Jun 2018 03:20:56 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 1632C1179B9B; Thu, 7 Jun 2018 09:20:55 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:user-agent:references :received:received:received:received; s=mdc; t=1528356049; x= 1530170450; bh=OaPac1sGa7qkYxWefMZ5gBL2ZYfmhT5LnwsPfCUNlEo=; b=H +dAR86FhotiN9bHetPL6GQ2k6DLmI2jpD0ME3JoVGgp9KHebbs7xpyagmC2s5hMc RgS8WVZT0RCycsQCSpg3iHe6iGojQK89FubBwZg/LTbR0sNCSyCHQs/lPQYi91ca rYSobzcfvp4wi+bxPvfOYVyLEePnYTbpYliP0B2Idw= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id OOxCMSIBe5Hs; Thu, 7 Jun 2018 09:20:49 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Thu, 7 Jun 2018 09:20:49 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) by HTCAONE.mdc-berlin.net (141.80.180.120) with Microsoft SMTP Server (TLS) id 14.3.399.0; Thu, 7 Jun 2018 09:20:48 +0200 Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Thu, 7 Jun 2018 09:20:47 +0200 References: <8736y11o2q.fsf@mdc-berlin.de> <20180607010620.31fbf16c@scratchpost.org> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Danny Milosavljevic Subject: Re: =?utf-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages In-Reply-To: <20180607010620.31fbf16c@scratchpost.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 7 Jun 2018 09:20:37 +0200 Message-ID: <877enbyse2.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.2.1013-23892.005 X-TM-AS-Result: No-5.814000-8.000000-10 X-TMASE-MatchedRID: O/y65JfDwwt73HU3OUveQfHkpkyUphL9M9g+YfdqJKHfUZT83lbkEDCs Ame4bhohs6xTkEgjiiSC2+nAZJSfpgH/zrweiLuzcxGQfOZHrIfvSp2iuuHtorUV4VfJ6SB0vsU 5jRUBF/oUSFM3d6sZGaaurWop/1N8AW5RnLqQx4cYteHAndhXo30tCKdnhB581kTfEkyaZdz6C0 ePs7A07SAJgyd9wrc8J4LDjIHJEcpK0o9X7v8PUdlPzWENHBupIT3gBanW/MHufPjdhb/qGw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.814000-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.2.1013-23892.005 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 31721 Cc: 31721@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Danny Milosavljevic writes: >> The errors are either about duplicates as in java-picard-2.10.3: >> >> duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class > > That's... bad. What if those files differed? Which one would be used at > runtime? I wonder where they come from. Is this from a dependency or are there actually two such classes? >> or about missing files as in dropseq-tools: >> >> java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-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? To satisfy the dropseq-tools build system the dependencies a symlinked to the build directory. I suspect that the error is something to do with that. > 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/MANIFEST.MF > before invoking "jar -i". > Then "jar -i" will index those - and all java packages can use regular inputs > instead of propagated inputs. I've tested that locally already - and it > works fine. Is it correct that this would ensure that in case of duplicate class names this would pick the class from the current package? -- Ricardo