Your message dated Wed, 02 Sep 2020 07:03:39 +0000
with message-id <e1kdmnz-0000we...@fasolo.debian.org>
and subject line Bug#968739: fixed in igv 2.6.3+dfsg-1
has caused the Debian Bug report #968739,
regarding igv will not run
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.
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--
968739: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=968739
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: igv
Version: 2.4.17+dfsg-1
Severity: grave
Justification: renders package unusable
Dear Maintainer,
The IGV package seems not to work. It throws a NoSuchMethodError exception
on startup with the following trace:
$ igv
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [org.broad.igv] additivity to [true].
log4j: Level value for org.broad.igv is [INFO].
log4j: org.broad.igv level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{yyyy-MM-dd HH:mm:ss} %-5p
%c{1}:%L - %m%n].
log4j: Adding appender named [console] to category [org.broad.igv].
2020-08-20 13:59:59 INFO DirectoryManager:179 - IGV Directory:
/home/bredelings/igv
2020-08-20 13:59:59 INFO Main:155 - Startup IGV Version user not_set
2020-08-20 13:59:59 INFO Main:156 - Java 11.0.8
2020-08-20 13:59:59 INFO DirectoryManager:84 - Fetching user directory...
2020-08-20 13:59:59 INFO Main:157 - Default User Directory: /home/bredelings
2020-08-20 13:59:59 INFO Main:158 - OS: Linux
2020-08-20 13:59:59 INFO Main:208 - Unknown version: user
2020-08-20 14:00:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
java.lang.NoSuchMethodError: 'void
htsjdk.tribble.util.ParsingUtils.registerHelperClass(java.lang.Class)'
at org.broad.igv.util.HttpUtils.<init>(HttpUtils.java:104)
at org.broad.igv.util.HttpUtils.getInstance(HttpUtils.java:97)
at org.broad.igv.ui.Main.open(Main.java:279)
at org.broad.igv.ui.Main$1.run(Main.java:110)
at
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
2020-08-20 14:00:01 INFO ShutdownThread:46 - Shutting down
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (2000, 'unstable'), (1999, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.7.0-2-amd64 (SMP w/12 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages igv depends on:
ii default-jre 2:1.11-72
ii junit4 4.12-8
ii libbatik-java 1.12-1.1
ii libbcprov-java 1.65-1
ii libcofoja-java 1.3-4
ii libcommons-io-java 2.6-2
ii libcommons-logging-java 1.2-2
ii libcommons-math-java 2.2-7
ii libcommons-net-java 3.6-1
ii libgoogle-gson-java 2.8.6-1
ii libguava-java 29.0-5
ii libhtsjdk-java 2.22.0+dfsg-1
ii libhttpclient-java 4.5.11-1
ii libhttpcore-java 4.4.13-1
ii libjama-java 1.0.3-1
ii libjargs-java 1.0.0-5
ii libjaxb-api-java 2.3.1-1
ii libjaxp1.3-java 1.3.05-5
ii libjcommon-java 1.0.23-1
ii libjfreechart-java 1.0.19-2
ii libjgrapht0.8-java 0.8.3-5
ii libjhdf5-java 2.11.0+dfsg-4
ii libjide-oss-java 3.7.6+dfsg-1
ii liblog4j1.2-java 1.2.17-9
ii liblog4j2-java 2.11.2-1
ii libpicard-java 2.22.8+dfsg-1
ii libswing-layout-java 1.0.4-4
ii libxml-commons-external-java 1.4.01-5
Versions of packages igv recommends:
ii libmariadb-java 2.5.3-1
igv suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: igv
Source-Version: 2.6.3+dfsg-1
Done: Pierre Gruet <pgtdeb...@free.fr>
We believe that the bug you reported is fixed in the latest version of
igv, 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 968...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <pgtdeb...@free.fr> (supplier of updated igv 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 01 Sep 2020 22:14:41 +0200
Source: igv
Binary: igv
Architecture: source all
Version: 2.6.3+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Pierre Gruet <pgtdeb...@free.fr>
Description:
igv - Integrative Genomics Viewer
Closes: 940606 968739
Changes:
igv (2.6.3+dfsg-1) unstable; urgency=medium
.
[ Andreas Tille ]
* Standards-Version: 4.5.0 (Rules-Requires-Root field added)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Use secure URI in Homepage field.
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
.
[ Pierre Gruet ]
* New upstream version
Closes: #940606
* Updating build directory to Java 11
* Add runtime dependency to batik
* Adapting paths for gradle as we use Debian libs
* Adapting the code, written for an old htsjdk version
Closes: #968739
* Skipping build-time tests that require an access to network
Checksums-Sha1:
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a074429832967304678d925f3b5e012ce64a76d1 111944404 igv_2.6.3+dfsg.orig.tar.xz
0a644083f46d865977236547d3d7229842e5c265 13800 igv_2.6.3+dfsg-1.debian.tar.xz
75b95c88c788afb9fc695fb9b507b8431145900a 3382200 igv_2.6.3+dfsg-1_all.deb
6faa4b921ccd4ed1d9231a8db6a84220d310e18f 19432 igv_2.6.3+dfsg-1_amd64.buildinfo
Checksums-Sha256:
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igv_2.6.3+dfsg-1.dsc
507b4b1331d258630a9719366a6585f3f7b7762c2825e10818888129a60d1709 111944404
igv_2.6.3+dfsg.orig.tar.xz
7ff65040b4d8aac38715a64276721ed9250e5dd35b81a983f66ce98eff2e549e 13800
igv_2.6.3+dfsg-1.debian.tar.xz
ad1802d5f04c6f400186f023de5c5a97f20b8ee4db7ba3d823544c78eaaa573b 3382200
igv_2.6.3+dfsg-1_all.deb
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igv_2.6.3+dfsg-1_amd64.buildinfo
Files:
ce0b8096939a6da87c3b5f57b5281630 2637 non-free/science optional
igv_2.6.3+dfsg-1.dsc
c310bbca9f02601545aeda609b2d90c4 111944404 non-free/science optional
igv_2.6.3+dfsg.orig.tar.xz
f3ab2eb693305f7732d83701d0ff8fe6 13800 non-free/science optional
igv_2.6.3+dfsg-1.debian.tar.xz
3f5a78efd3374f1538a5508b2524a363 3382200 non-free/science optional
igv_2.6.3+dfsg-1_all.deb
488eb6cbc9738ace9d6b49fe78a698b3 19432 non-free/science optional
igv_2.6.3+dfsg-1_amd64.buildinfo
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