From unknown Thu Jun 12 08:42:47 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#31721 <31721@debbugs.gnu.org> To: bug#31721 <31721@debbugs.gnu.org> Subject: Status: =?UTF-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages Reply-To: bug#31721 <31721@debbugs.gnu.org> Date: Thu, 12 Jun 2025 15:42:47 +0000 retitle 31721 =E2=80=9Cgenerate-jar-indices=E2=80=9D phase fails on many pa= ckages reassign 31721 guix submitter 31721 Ricardo Wurmus severity 31721 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Jun 05 07:16:14 2018 Received: (at submit) by debbugs.gnu.org; 5 Jun 2018 11:16:14 +0000 Received: from localhost ([127.0.0.1]:34393 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQ9wj-0000Y8-8p for submit@debbugs.gnu.org; Tue, 05 Jun 2018 07:16:13 -0400 Received: from eggs.gnu.org ([208.118.235.92]:34014) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQ9wh-0000Qs-3h for submit@debbugs.gnu.org; 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Tue, 5 Jun 2018 13:15:52 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) by HTCAONE.mdc-berlin.net (141.80.180.120) with Microsoft SMTP Server (TLS) id 14.3.399.0; Tue, 5 Jun 2018 13:15:51 +0200 Received: from localhost (141.80.113.51) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server id 14.3.399.0; Tue, 5 Jun 2018 13:15:51 +0200 User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Subject: =?utf-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages 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: Tue, 5 Jun 2018 13:15:41 +0200 Message-ID: <8736y11o2q.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.2.1013-23888.006 X-TM-AS-Result: No-0.756800-8.000000-10 X-TMASE-MatchedRID: LW0QVZJomtRj5V+yyEyArR+WEMjoO9WWff89g2Kh2O3JZP0jINAqUKPF jJEFr+olA6QGdvwfwZYCU1PRf9o2s90H8LFZNFG7MGpgBNI6BaMjVRx/JCfx9KwZErMOY9ks5NH J0XU4gZMR3Id0oDNiDQ5gkmiQlfc6cZ5A0WVBBDphc56VNA6OHuQqQRcy9fLuMsaAV4D1XEIkJe S/ERgZIGRaod0r0qzYq8qcP/NDW67uL6tuaI7WBwU3rb+f2fzbftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.756800-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.2.1013-23888.006 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit Cc: Danny Milosavljevic 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: -6.0 (------) The =E2=80=9Cgenerate-jar-indices=E2=80=9D phase fails on a couple of packa= ges, such as java-picard (all variants) dropseq-tools java-cisd-jhdf5 The errors are either about duplicates as in java-picard-2.10.3: duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class or about missing files as in dropseq-tools: java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14= f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar I have removed the phase in these packages, but that=E2=80=99s not ideal. Can we make this phase more robust? --=20 Ricardo 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 From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 07 04:27:51 2018 Received: (at 31721) by debbugs.gnu.org; 7 Jun 2018 08:27:51 +0000 Received: from localhost ([127.0.0.1]:37399 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQqGt-0004T8-Fi for submit@debbugs.gnu.org; Thu, 07 Jun 2018 04:27:51 -0400 Received: from mail-io0-f178.google.com ([209.85.223.178]:44064) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQqGs-0004Sv-DD for 31721@debbugs.gnu.org; Thu, 07 Jun 2018 04:27:50 -0400 Received: by mail-io0-f178.google.com with SMTP id g7-v6so10836097ioh.11 for <31721@debbugs.gnu.org>; Thu, 07 Jun 2018 01:27:50 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :cc; bh=UtNN+xt1WrKUr4b2NMmBK3mMdUfKCWIiUSFOv4SGCOg=; b=XWp4vqnQk2tLjjz8qILNmP6SYIX+4imDNjQpbXF5VBxOTMnAOrBosdkE7/WjMeR8dd TJjLo3j5IoQtmIWWV/xEIZGlYOL1QXQ8LOhZj3uLkKJEnymHSu2ChBCckRgvo4zZJDrA p7FHksxgDQd2+FGjIJFxq9SdNUY7iVAwXIX8JHwDmnva1jBUjVb80PXfA75NFJAX81s/ KMvEOxIfqcS8tx1YKq/TxsWLtlW0HWcDD/mIFPDthsVu0gtr/JMKqtwYCuGnHH7VLUgM yaNeAxn7rDSfE3Y6G8jWcu+fUw/QxUkEg+5dIUsoEop5dfGLie8TxJcKud1qFgFWTLEa YpCQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to:cc; bh=UtNN+xt1WrKUr4b2NMmBK3mMdUfKCWIiUSFOv4SGCOg=; b=qkTYqPRCSlyUVx0lE/V9HLl3P1apJr6TP3OlqoBGX7k7nNapaolFtz09/0CxXQDWhE kYB9wVgwK3a2twZ34ZgzY2CmCJyyF5fCy9hop1Uc/56pyEQnqGpRMZlS/DlFDF9YiiK0 z9afkPlt4imMs0/RLID7S6kFjlcfwyV9ClkdKjlzgs1/opV75It2HGzZVLT9cOr6gA+j KgQT8Xu+HWRG7mmEmL+g0xslY221TOvYo9QEs1lsr+5IqBJaQA6ossy0RLgql97b2zbo N1RGvR1m5q9UiL6U1uaoDGDcuUdszyWS3zeLojzqG3/czYx9Q/hUEwwZL7wr+cHA187p 7NmQ== X-Gm-Message-State: APt69E1vX1TFOzDSIFpgWrIxvWOlZwOgHlAanopC9Q7R/uE6ajjnzkoq WagWraHQEXLZWiJuPzFprSzgBOEvatpAQvusHw== X-Google-Smtp-Source: ADUXVKLYVc4eVq83MKNrUJ7KUGBof+WXzbb/jKDT5/EEu8nVU3usGOS79dB0XA6tGlDSX/5IaE+oKL3LHxyRYy18ke4= X-Received: by 2002:a6b:94c9:: with SMTP id w192-v6mr637544iod.89.1528360064218; Thu, 07 Jun 2018 01:27:44 -0700 (PDT) MIME-Version: 1.0 Received: by 2002:a4f:a84d:0:0:0:0:0 with HTTP; Thu, 7 Jun 2018 01:27:43 -0700 (PDT) In-Reply-To: <877enbyse2.fsf@elephly.net> References: <8736y11o2q.fsf@mdc-berlin.de> <20180607010620.31fbf16c@scratchpost.org> <877enbyse2.fsf@elephly.net> From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Date: Thu, 7 Jun 2018 10:27:43 +0200 Message-ID: Subject: =?UTF-8?Q?Re=3A_bug=2331721=3A_=E2=80=9Cgenerate=2Djar=2Dindices=E2=80=9D_phase_fail?= =?UTF-8?Q?s_on_many_packages?= To: Ricardo Wurmus Content-Type: multipart/alternative; boundary="000000000000b77d38056e090ec9" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 31721 Cc: Danny Milosavljevic , 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 (-) --000000000000b77d38056e090ec9 Content-Type: text/plain; charset="UTF-8" 2018-06-07 9:20 GMT+02:00 Ricardo Wurmus : > > 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? > > Is it possible that these come from a package, where a renamed dependency is used in the original build system, thus avoiding the name duplication? I will have a look at this package source... Will report back if I can confirm this assumption. > >> 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 > > > > --000000000000b77d38056e090ec9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
2018= -06-07 9:20 GMT+02:00 Ricardo Wurmus <ricardo.wurmus@mdc-berlin= .de>:

Danny Milosavljevic <dannym@sc= ratchpost.org> writes:

>> The errors are either about duplicates as in java-picard-2.10.3: >>
>>=C2=A0 =C2=A0 =C2=A0duplicate entry: htsjdk/samtools/AbstractB= AMFileIndex$1.class
>
> That's... bad.=C2=A0 What if those files differed?=C2=A0 Wh= ich one would be used at
> runtime?

I wonder where they come from.=C2=A0 Is this from a dependency or are there=
actually two such classes?


Is it possible= that these come from a package, where a renamed dependency is
us= ed in the original build system, thus avoiding the name duplication? I will= have a
look at this package source... Will report back if I can = confirm this assumption.

=C2=A0
>> or about missing files as in dropseq-tools:
>>
>>=C2=A0 =C2=A0 =C2=A0java.io.FileNotFoundException: /gnu/store/= q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/java/li= b/biojava-alignment.jar
>
> That's also bad.=C2=A0 How does it run at all if its depend= encies are missing?

To satisfy the dropseq-tools build system the dependencies a symlinked
to the build directory.=C2=A0 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/M= ANIFEST.MF
> before invoking "jar -i".
> Then "jar -i" will index those - and all java packages can u= se regular inputs
> instead of propagated inputs.=C2=A0 I've tested that locally alrea= dy - 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




--000000000000b77d38056e090ec9-- From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 07 04:46:50 2018 Received: (at 31721) by debbugs.gnu.org; 7 Jun 2018 08:46:50 +0000 Received: from localhost ([127.0.0.1]:37413 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQqZF-0004wk-NU for submit@debbugs.gnu.org; Thu, 07 Jun 2018 04:46:50 -0400 Received: from mail-it0-f49.google.com ([209.85.214.49]:53394) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fQqZD-0004wV-Ej for 31721@debbugs.gnu.org; Thu, 07 Jun 2018 04:46:48 -0400 Received: by mail-it0-f49.google.com with SMTP id a195-v6so11823682itd.3 for <31721@debbugs.gnu.org>; Thu, 07 Jun 2018 01:46:47 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :cc; bh=HHkWraoGN7HRGN7lizcEaC7i4KDI9v16dAFYpNNT25g=; b=dR26Tn+Gcr8fyAeWlY6wBVaPpvIfvNUKjC2gYRNtdFBeQ/fOoQ/nEBvbPKIYE2M2oQ jNL4Pr6TsUowBmB8IrvSoV5KAdEBctsYlkAOA33xqM/9WcfqP5R7yijgRJrYqzS8y1fU m1ycI2fPNNTjVNpxgXK3n8p0c/0/JBWUs5chwcW4qFFhrbqxJ/cMDZa03y6AFsCqRInv RknNHjP7b8zS7pU2qmmFvu+dSpyQujhT5J/imbKsGexR64KPqEAtcavHFFiGty2gpnPf FEof4aiB1yRGd3JCieW4tDUqnS/n12tB3nehTcD0ZKShbshuDq6Lg5TB2Y9nBVz5aIPp vCBA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to:cc; bh=HHkWraoGN7HRGN7lizcEaC7i4KDI9v16dAFYpNNT25g=; b=oBzhRr6DFf9WuOsy41sFrI0PmehGaDsdfEPdA/xk4AYOv9vhPbykmAAFZSoXaX2CM5 MvkLV/A6ACqhyqQMfR3FLIQ8f6BJPsZ8ShoVWE8OdpqibXuskCtNwKNjyX00gWvdYPcR ibTGAuw5ozsj80Vlzzv99BocdIcP8we7hXDuGRHq7ppYALDZmtPH5UOWN++/ykh2/X0+ /DQX4ZbwcNu79Pa5Ht3veyEOD2PYme5mzo16vIg72Y8bnPx7AouIxGSLLFg0qlIu8p6d vX66obccBPjRSjR12E/kZI1XB2WXD9mc/xq+sjcv0GRFV+WafYVS7igJvNBy3uI0eZeL xr/w== X-Gm-Message-State: APt69E1bcGt1g7PbLJHaFA+LXuhBDZyHHHHdcLFLQo5OtLXFGhHw4pfv 0Yvxjdf/eja+jHOTemYRfseVKRO8kM73uNrPJg== X-Google-Smtp-Source: ADUXVKLFHPfV60Mzsi5HBTYmijBQoKVaT3LbiGtXvHTSDrrP9THwJf8lFak+X9TwkEU3uNoSfLuJeoq8st/ftAkKhLM= X-Received: by 2002:a24:be85:: with SMTP id i127-v6mr1011206itf.131.1528361201820; Thu, 07 Jun 2018 01:46:41 -0700 (PDT) MIME-Version: 1.0 Received: by 2002:a4f:a84d:0:0:0:0:0 with HTTP; Thu, 7 Jun 2018 01:46:41 -0700 (PDT) In-Reply-To: References: <8736y11o2q.fsf@mdc-berlin.de> <20180607010620.31fbf16c@scratchpost.org> <877enbyse2.fsf@elephly.net> From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Date: Thu, 7 Jun 2018 10:46:41 +0200 Message-ID: Subject: =?UTF-8?Q?Re=3A_bug=2331721=3A_=E2=80=9Cgenerate=2Djar=2Dindices=E2=80=9D_phase_fail?= =?UTF-8?Q?s_on_many_packages?= To: Ricardo Wurmus Content-Type: multipart/alternative; boundary="00000000000085e845056e09527d" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 31721 Cc: Danny Milosavljevic , 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 (-) --00000000000085e845056e09527d Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 2018-06-07 10:27 GMT+02:00 G=C3=A1bor Boskovits : > 2018-06-07 9:20 GMT+02:00 Ricardo Wurmus : > >> >> 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? >> >> > Is it possible that these come from a package, where a renamed dependency > is > used in the original build system, thus avoiding the name duplication? I > will have a > look at this package source... Will report back if I can confirm this > assumption. > > This is what is in build.gradle: dependencies { compile('com.intel.gkl:gkl:0.8.5') { exclude module: 'htsjdk' } So we should exclude htsjdk module from gkl when building java-picard. Do we have a method to do that easily? > >> >> or about missing files as in dropseq-tools: >> >> >> >> java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn2 >> 6kbw4h3s14f33-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 >> >> >> >> > --00000000000085e845056e09527d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
2018= -06-07 10:27 GMT+02:00 G=C3=A1bor Boskovits <boskovits@gmail.com&g= t;:
2018-06-07 9:20 G= MT+02:00 Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>:

Danny Milosavljevic <dannym@scratchpost.org> writes:

>> The errors are either about duplicates as in java-picard-2.10.3: >>
>>=C2=A0 =C2=A0 =C2=A0duplicate entry: htsjdk/samtools/AbstractBAMFil= eIndex$1.class
>
> That's... bad.=C2=A0 What if those files differed?=C2=A0 Wh= ich one would be used at
> runtime?

I wonder where they come from.=C2=A0 Is this from a dependency or are there=
actually two such classes?


Is it possible tha= t these come from a package, where a renamed dependency is
used i= n the original build system, thus avoiding the name duplication? I will hav= e a
look at this package source... Will report back if I can conf= irm this assumption.

This is what is in build.gradle:
dependencies { compile(= 9;com.intel.gkl:gkl:0.8.5') { exclude modul= e: 'htsjdk' }
=C2=A0So we should exclude htsjdk = module from gkl when building java-picard.
Do we have a method to= do that easily?

=C2=A0
>> or about missing files as in dropseq-tools:
>>
>>=C2=A0 =C2=A0 =C2=A0java.io.Fil= eNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-dropse= q-tools-1.13/share/java/lib/biojava-alignment.jar
>
> That's also bad.=C2=A0 How does it run at all if its depend= encies are missing?

To satisfy the dropseq-tools build system the dependencies a symlinked
to the build directory.=C2=A0 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/M= ANIFEST.MF
> before invoking "jar -i".
> Then "jar -i" will index those - and all java packages can u= se regular inputs
> instead of propagated inputs.=C2=A0 I've tested that locally alrea= dy - 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





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