Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]
Hi, Le 21/08/2020 à 12:44, Andreas Tille a écrit : > Hi Pierre, > > On Fri, Aug 21, 2020 at 11:32:47AM +0200, Pierre Gruet wrote: >>> I injected the latest upstream version into Git. It does not include so >>> many binary jar's any more but I think its trying to download these >>> instead. I gave up for the moment since I have no idea about gradle. >>> >> Thanks! Many of those jars are in Debian packages, so there is hope to >> get rid of many, maybe all... I'm looking at it. >> Contrarily to what I wrote a few days ago, I do not think we are ready to remove all included jars in igv. For instance we would have to package libgoby-java, I have just made some packaging effort on its new upstream version [0] after Andreas began but, as Olivier noticed before on a previous upstream version [1], there are still many jars missing in Debian. We would also need to have the huge Amazon AWS SDK packaged... I will thus work on #968739 and on the new upstream version but I am afraid we will have to keep igv in non-free for the moment :-( > > Thanks a lot. That would be another mile stone! > > Kind regards > > Andreas. > All the best, Pierre [0] https://salsa.debian.org/med-team/libgoby-java/ [1] https://lists.debian.org/debian-med/2013/02/msg00152.html
Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]
Hi Pierre, On Fri, Aug 21, 2020 at 11:32:47AM +0200, Pierre Gruet wrote: > > I injected the latest upstream version into Git. It does not include so > > many binary jar's any more but I think its trying to download these > > instead. I gave up for the moment since I have no idea about gradle. > > > Thanks! Many of those jars are in Debian packages, so there is hope to > get rid of many, maybe all... I'm looking at it. Thanks a lot. That would be another mile stone! Kind regards Andreas. -- http://fam-tille.de
Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]
Hi Andreas, Le 21/08/2020 à 11:05, Andreas Tille a écrit : > Hi again, > > I injected the latest upstream version into Git. It does not include so > many binary jar's any more but I think its trying to download these > instead. I gave up for the moment since I have no idea about gradle. > Thanks! Many of those jars are in Debian packages, so there is hope to get rid of many, maybe all... I'm looking at it. > > Kind regards > > Andreas. > Best regards, Pierre
Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]
Hi again,
I injected the latest upstream version into Git. It does not include so
many binary jar's any more but I think its trying to download these
instead. I gave up for the moment since I have no idea about gradle.
Kind regards
Andreas.
On Fri, Aug 21, 2020 at 07:38:21AM +0200, Andreas Tille wrote:
> Hi Pierre,
>
> do you have some spare cycles for this issue?
>
> BTW, I do not think that we should stick to that now outdated
> version but while fixing the issue package latest upstream.
>
> On a more general note: Igv is another Java package that is in
> non-free only due to the included binary JARs. If we could that
> sorted out it probably could go into main which would be a real
> advantage.
>
> Kind regards
>
> Andreas.
>
>
> - Forwarded message from Benjamin Redelings
> -
>
> Date: Thu, 20 Aug 2020 14:01:13 -0400
> From: Benjamin Redelings
> To: Debian Bug Tracking System
> Subject: Bug#968739: igv will not run
> X-Debian-PR-Message: report 968739
> X-Debian-PR-Package: igv
> X-Debian-PR-Keywords:
> X-Debian-PR-Source: igv
>
> 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{-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.(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:
Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]
Hi Andreas,
Le 21/08/2020 à 07:38, Andreas Tille a écrit :
> Hi Pierre,
>
> do you have some spare cycles for this issue?
>
> BTW, I do not think that we should stick to that now outdated
> version but while fixing the issue package latest upstream.
>
> On a more general note: Igv is another Java package that is in
> non-free only due to the included binary JARs. If we could that
> sorted out it probably could go into main which would be a real
> advantage.
>
> Kind regards
>
> Andreas.
I will have a look at it!
Having this package leave non-free would indeed be great.
Best,
Pierre
>
>
> - Forwarded message from Benjamin Redelings
> -
>
> Date: Thu, 20 Aug 2020 14:01:13 -0400
> From: Benjamin Redelings
> To: Debian Bug Tracking System
> Subject: Bug#968739: igv will not run
> X-Debian-PR-Message: report 968739
> X-Debian-PR-Package: igv
> X-Debian-PR-Keywords:
> X-Debian-PR-Source: igv
>
> 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{-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.(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 junit44.12-8
&g
Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]
Hi Pierre,
do you have some spare cycles for this issue?
BTW, I do not think that we should stick to that now outdated
version but while fixing the issue package latest upstream.
On a more general note: Igv is another Java package that is in
non-free only due to the included binary JARs. If we could that
sorted out it probably could go into main which would be a real
advantage.
Kind regards
Andreas.
- Forwarded message from Benjamin Redelings
-
Date: Thu, 20 Aug 2020 14:01:13 -0400
From: Benjamin Redelings
To: Debian Bug Tracking System
Subject: Bug#968739: igv will not run
X-Debian-PR-Message: report 968739
X-Debian-PR-Package: igv
X-Debian-PR-Keywords:
X-Debian-PR-Source: igv
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{-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.(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 junit44.12-8
ii libbatik-java 1.12-1.1
ii libbcprov-java1.65-1
ii libcofoja-java1.3-4
ii libcommons-io-java2.6-2
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-java2.22.0+dfsg-1
ii libhttpclient-java4.5.11-1
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
Bug#968739: igv will not run
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{-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.(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 junit44.12-8
ii libbatik-java 1.12-1.1
ii libbcprov-java1.65-1
ii libcofoja-java1.3-4
ii libcommons-io-java2.6-2
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-java2.22.0+dfsg-1
ii libhttpclient-java4.5.11-1
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-java1.0.19-2
ii libjgrapht0.8-java0.8.3-5
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-java2.11.2-1
ii libpicard-java2.22.8+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
