Path: csiph.com!aioe.org!bofh.it!news.nic.it!robomod From: Felix Natter Newsgroups: linux.debian.maint.java Subject: Re: Help to detect java classes in drop-seq (covid-19 relevant) needed Date: Thu, 21 May 2020 21:40:01 +0200 Message-ID: References: X-Original-To: Andreas Tille X-Mailbox-Line: From debian-java-request@lists.debian.org Thu May 21 19:36:53 2020 Old-Return-Path: X-Amavis-Spam-Status: No, score=-7.8 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FOURLA=0.1, FREEMAIL_FROM=0.001, LDO_WHITELIST=-5, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H2=-0.001] autolearn=ham autolearn_force=no X-Policyd-Weight: using cached result; rate: -5.5 Old-Dkim-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=gmx.net; s=badeba3b8450; t=1590089795; bh=buAPbBvsR0JDj1fD6KgKnDyXyQo25BWun0eBC/1iBDc=; h=X-UI-Sender-Class:From:To:Cc:Subject:References:Date:In-Reply-To; b=VGeVIi31fWgfZQNIG3YxFcNbrfg77eBt9LQd3SYc1/E9dTT8+wkdu/wBsxZBOdeJ+ X4SryZVKGAQC/B1ECPvKu3AIQ5L9dUJGrq8YmYrSXt4l1f65Y5Km7beYl0rWH0V4UE 9d8PWRCpDzbb1ajDg+7Xe1EBgiPFqRFNBVZmLshk= X-Ui-Sender-Class: 01bb95c1-4bf8-414a-932a-4f6e2808ef9c User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Provags-ID: V03:K1:zZCHwLCYGADmExj7Pg7HG6/TvBDt8c835/xWf7Whoe+3G4RtLqu 3y1+1dCXeFcgVlctz/6GQVYS/GxUKSRJwhQVd8yKlXk2oG4a5g6msxTrdrraAc27rH0KrJR IH9viZzBGMesC+akOuMKsqvu+/ylgJeJMNGugYDsV5ooN7/1sedPWMevRDBtnzJcUqeL8R7 5zssHc+x+q/ZGdbZOBWSw== X-Ui-Out-Filterresults: notjunk:1;V03:K0:GJSBDyd5KGk=:qW3rQ0Xo6vQlw/Dd3K6W18 I8ERBfb2EvsbHzJUHjPJ421uP1RykfeaPz/EVDgzEmf9Q9NrGd3WdIkGiNXi863ge1gCjy1nL hJ+WpuufuTQ6P7SHxUwLdRyL+PknYpslJcQN1Y1uUYCO/+NUHpsLXdui2bF9XJCNm/8/k4WLb beWhH5Q4JR9Iyg/IpapDzYOoAaNcG3r/NtjULsbVt7KUeKpPRzHS0M7R0+KebiDwb3WdK8BMf 6UKQJp9iakh+LFXMMQcRIQIFlrMrPIQkVyOYKPHdw3bGR2vq3OjqdaoQJnWsYbEqmcXQ+fCGQ DewqMzx0tN/dKSucdsotEtBW5AtHLyI0Zg12/PGxf+JUvPalxJ3l/TqA8sMlSnMx46xYN4hpV wMUTJmjIJW36fbj5ZeRuy9D9FnrkImT+O/W8zWS/254EQjSD84SlvpwnbEp3ztqFDrwB3AO6l eqYImOIk/+LQvZG2tYn2BuPu47l4t9Tt8QZUvOuFG5N+koBN5DXZ9fQmdNQe0+WGNeMYoLzwT vbo1BTM4FjqCLNk5f1xLqdqy89atAXei/vnFFG5Xr/1gSHEkUWZA0MYarvEiWHq/DQBsM9Cih 0a65Gciuvi+48CnoX7eFsJyrxxcActMIMPCeUsEA7ZEIe9ddOIMU3FiUlD4Sza9FNnCh6TWWt aYRR7pElTL2+Nw/YeUnDJFhMwjmmk6cXMOQfa2uFmUbQZhQldGFtqlGf6VIOc9OidH5EF11o9 iOtLv0Y6EwGH6rjcsNplue1cGrBdVy70n5s6mxmWsaILnZxeG1T9c14AIF/2D1wOBcQYnORGQ 9O0cbjVaTZMSOvTDRpeqeY5qtdryWkE/y+029lPmXFdE8N4TX2zQr2PMgUJIdxbuWdnXqp6/l 3Oy4f47yfNr2KHgIPC51l3+WGJMxOVG9zv/zWvGa+3JY19+kZGTjdYgF/ksWh2MfJjFvsE7D4 c4nc9UbCnPrBHZ46n3JXIsYQtbzxgwnknsXaTFszDIl3i4pn6bD4GqgYh2NCx2Uq95yzBd5uK rpVqKKwbEORfXyMqcLyJnWiZUTBtLwopiN4mZxcL0POEB9kIyPwi7Kq6NQiDgg1TC6lYZyF8b rHJHeUTryrsJEOGQpFy71A3khFJDeqcTJxQuqoGl1rf6cTRRtStTw7e6ITIjtwpKT56FMJ8DQ 8hx72iA1RS07E0gKG6Lcn3kdEYMGQAIu7EGoTXiqb2gpNhhuTzqvT9suYBHOX6x3bI12ErjLG VFvEAvCjUxhiorbKj Content-Transfer-Encoding: quoted-printable X-Mailing-List: archive/latest/22208 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/87d06x13nh.fsf@gmx.net Approved: robomod@news.nic.it Lines: 83 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Debian Java List , Debian Med Packaging Team X-Original-Date: Thu, 21 May 2020 21:36:34 +0200 X-Original-Message-ID: <87d06x13nh.fsf@gmx.net> X-Original-References: <20200520112049.GK12054@an3as.eu> <87eereshyx.fsf@gmx.net> <20200520200748.GN12054@an3as.eu> <20200521124639.GU12054@an3as.eu> Xref: csiph.com linux.debian.maint.java:11630 Andreas Tille writes: > Hi, hello Andreas, > On Wed, May 20, 2020 at 10:07:48PM +0200, Andreas Tille wrote: >> >> Thanks. This was pretty helpful. Now I need to package the >> remaining JAR which is not yet packaged from >> >> http://la4j.org/ > > I made some progress and also uploaded libla4j-java[1] to new. With > this I tried to build drop-seq[2] and stumbled upon two issues: > > At first a lintian issue: > > W: drop-seq-tools: classpath-contains-relative-path usr/share/java/drops= eq-2.3.0.jar: lib/FastInfoset-1.2.12.jar, lib/FastInfoset.jar, lib/FastInf > N: > N: The classpath listed in the jar file refers to a potential missing= jar > N: file. This could be the remnants of a build-time classpath that ar= e not > N: relevant for a JAR bundled in a Debian package. > N: > N: Alternatively, the classpath may be correct, but the package is la= cking > N: a jar file or a symlink to it. > N: > N: Note, Lintian assumes that all (relative) classpaths pointing to > N: /usr/share/java/ (but not subdirs thereof) are satisfied by depend= encies > N: as long as there is at least one strong libX-java dependency. > N: > N: Severity: warning > N: > N: Check: languages/java > > I have no idea what this means. A `grep -Ri fastinfoset` inside the sou= rce > tree remains empty. > The (current) problem is this in the jar-executable target: This causes the classpath for the runnable jar to be prefixed with lib/, but /usr/share/java/lib/... (or lib/...) does not exist. Please try to cha= nge it to: > The other one is a runtime error of the wrapper script: > > $ drop-seq > Error: Could not find or load main class org.broadinstitute.dropseqrna.c= mdline.DropSeqMain > Caused by: java.lang.NoClassDefFoundError: > picard/cmdline/PicardCommandLine This is a likely consequence of the lintian above: the dropseq jar does not refer to the correct classpath entry for picard.jar. If it still does not work, please post the META-INF/MANIFEST.MF contents of the usr/share/java/dropseq-2.3.0.jar (you can rename it to .zip, then open it with an archiver). Cheers and Best Regards, =2D- Felix Natter debian/rules!