Your message dated Fri, 19 Apr 2013 13:47:51 +0000 with message-id <[email protected]> and subject line Bug#705686: fixed in picard-tools 1.82-2 has caused the Debian Bug report #705686, regarding picard-tools BuildBamIndex fails to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 705686: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=705686 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: picard-tools Version: 1.82-1 "picard-tools BuildBamIndex ..." fails with Caused by: java.lang.ClassNotFoundException: net.sf.picard.util.BuildBamIndex ... In /usr/bin/picard-tools, changing BuildBamIndex) main=net.sf.picard.util.BuildBamIndex;; to BuildBamIndex) main=net.sf.picard.sam.BuildBamIndex;; fixes the problem. Probably all picard commands has to be checked. Regards, Ognyan Kulev
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--- Begin Message ---Source: picard-tools Source-Version: 1.82-2 We believe that the bug you reported is fixed in the latest version of picard-tools, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Olivier Sallou <[email protected]> (supplier of updated picard-tools package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 19 Apr 2013 14:26:23 +0200 Source: picard-tools Binary: libsam-java picard-tools Architecture: source all Version: 1.82-2 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Olivier Sallou <[email protected]> Description: libsam-java - Java library to manipulate SAM and BAM files picard-tools - Command line tools to manipulate SAM and BAM files Closes: 705686 Changes: picard-tools (1.82-2) unstable; urgency=low . * Fix classpath for BuildBamIndex (Closes: #705686). Checksums-Sha1: 1e7ca268e69d284b6ded451e065be7b25c68a158 2164 picard-tools_1.82-2.dsc 20a6e07a92002d1b8bd1caeec4a52a90408d2383 7888 picard-tools_1.82-2.debian.tar.gz 6449663d3913873157615cbbdd2ede9ceddc8997 208648 libsam-java_1.82-2_all.deb 30156b680e4bd488fb9506d59388e1e0bccc99fc 486988 picard-tools_1.82-2_all.deb Checksums-Sha256: 17af73ffcc0544eb31225ba1c2c2681d37aa55263d0419f2378a67e4eaa1d8c1 2164 picard-tools_1.82-2.dsc c78a1e939d958beebcdb6c4c918152a909665e0b1a09cf28099a80aac8484cc3 7888 picard-tools_1.82-2.debian.tar.gz 0df42b4d34c37933898d3f69b7085b293b6812515afff34581156400ea5060ca 208648 libsam-java_1.82-2_all.deb 39fdf8b7ebd798b82d956d59f21448f4368602db01485709b191e1de883c2446 486988 picard-tools_1.82-2_all.deb Files: fdd765613b9091b72cb8c99a57fa0671 2164 science optional picard-tools_1.82-2.dsc cc212fbf9a7805c1f3415a96beda20e3 7888 science optional picard-tools_1.82-2.debian.tar.gz 4bc6e2d955af74acf83456f8a1eca3c7 208648 java optional libsam-java_1.82-2_all.deb 9dc433836ecce916bf380b67eb48fc47 486988 science optional picard-tools_1.82-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBCAAGBQJRcUf/AAoJEHjcaNsybYQ42lYQAJ73A4y4IxpTmjyvLo88pMX3 ahujpPxIRS5/8sBg/QHzsy3tYUirny7oITF16jgHXpTnpwuW61hpKX1Jr49l8AuH TejgpmrgOm4NPqrvMDIL46c7ATXIuM8bKuj2nCGUXkVv93KmExYz638v1to0FlTl ouqMSq7zs94Ku/udPVajzyP+FqYnwMwDXBVH/GO7+zyI3E5TrqBwwNiKxxjukCeG C08sOFQSjzdvCWZReZoIOKH1qhuc1c+F/pbrmoYUkZh2vx9QJJ0W0KI91ExY23fm fIn/wOnXzLUy7A6ZjlQtuqZ0PiL4j/mCaN9SkaF1GAg4XxTYu2EUyOGtoTKInvYD fJhX7O+8mGFrRjGhqo7xLGhozdDrcroGzr1elurKDEtdPUtf8Q7ePcUsmUx87Y7O U8rlVdqZYV82poOnuRPcAC2cS77OnfTXhrIMj10a+PoZyuBcCYayIYlB29xyENns LHFHY6RHnMmrNg9v7VdOAnXYKHfB7YfgdArZ6Hdiru0XubV3nLFUepHyCKwYO/VV H1Y6u1l73CZTsuo1w8cSR8rj6w0xjAbQs0xtvnRzpYCb9woZw5kV//F6V0oTqDNO qLAP7Cfq5jPWIeaaDZolh8L55oJyz8RzDqNwB9AvLsIvWZ82im0n9hB3BU4euyce TRI28qxQGtTP1BVaQpmg =snVA -----END PGP SIGNATURE-----
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