Path: csiph.com!news.mixmin.net!weretis.net!feeder1.news.weretis.net!newsfeed.CARNet.hr!news.spin.it!bofh.it!news.nic.it!robomod From: Vincent Danjean Newsgroups: linux.debian.maint.java Subject: Asking help for the picard-tools package Date: Tue, 08 Sep 2015 02:10:02 +0200 Message-ID: X-Original-To: debian-java@lists.debian.org X-Mailbox-Line: From debian-java-request@lists.debian.org Tue Sep 8 00:03:00 2015 Old-Return-Path: X-Amavis-Spam-Status: No, score=-4.499 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, FREEMAIL_FORGED_FROMDOMAIN=0.198, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=0.001, LDO_WHITELIST=-5, MEDS2=2, RCVD_IN_DNSWL_LOW=-0.7, RP_MATCHES_RCVD=0.001, WORD_WITHOUT_VOWELS=1] autolearn=no autolearn_force=no X-Policyd-Weight: using cached result; rate: -6.1 X-Enigmail-Draft-Status: N1110 User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.8.1.22) Gecko/20091109 Lightning/0.8 Thunderbird/2.0.0.22 Mnenhy/0.7.5.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Mailing-List: archive/latest/18647 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/55EE259E.30809@free.fr Approved: robomod@news.nic.it Lines: 38 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: debian-med-packaging@lists.alioth.debian.org X-Original-Date: Tue, 8 Sep 2015 02:02:38 +0200 X-Original-Message-ID: <55EE259E.30809@free.fr> Xref: csiph.com linux.debian.maint.java:8333 Hi, After the htsjdk package, I tried to update the picard-tools package itself. Sources can be obtained with git clone git://anonscm.debian.org/debian-med/picard-tools.git Of course, to compile it, you need the previous libhtsjdk-java package. You can find a compiled version in my own repo (see my signature for the APT repo or manually download it from https://people.debian.org/~vdanjean/debian/pool/main/libh/libhtsjdk-java/ ) I'm annoyed with the current package: the tests fail when the sources are in a directory containing a '+'. And, due to the repack and the +dfsg suffix, my sbuilder put the source into a «BUILDDIR»/picard-tools-1.138+dfsg.1 directory. I manually reproduce the problem: "dpkg-buildpackage -us -uc" works perfectly when invoked from a 'picard-tools' directory, but fails during the tests if I rename the directory into 'picard-tools-1.138+dfsg.1'. In the log, we can found: [testng] WARNING 2015-09-07 23:25:58 ClassFinder could not read entriesjava.io.FileNotFoundException: /home/vdanjean/«BUILDDIR»/picard-tools-1.138 dfsg.1/classes/picard (No such file or directory) The '+' as been replaced by a ' ' Is this a known issue with java tools? Is there a workaround? Google did not show me anything relevant. Regards, Vincent -- Vincent Danjean GPG key ID 0xD17897FA vdanjean@debian.org GPG key fingerprint: 621E 3509 654D D77C 43F5 CA4A F6AE F2AF D178 97FA Unofficial pkgs: http://moais.imag.fr/membres/vincent.danjean/deb.html APT repo: deb http://people.debian.org/~vdanjean/debian unstable main