[outreachy] Re: Bug#909707: hyphy: autopkgtest

[Andreas Tille]

Hi Ioannis,

On Thu, Oct 18, 2018 at 02:46:14AM +0100, Ioannis Valasakis wrote:
> I am interested in getting assigned this bug

There is no technical way to assign a bug - but readers of the bug log
will know now that somebody is working on it.

> and getting to know the process of creating an autopkg test :) Regards ioannis

The general description of best practices is in Debian Wiki:

   https://wiki.debian.org/ContinuousIntegration/AutopkgtestBestPractices

In the packaging template I've created for Debian Med packages there is
also a boilerplate for an autopkgtest:

   
https://salsa.debian.org/med-team/community/package_template/tree/master/debian/tests

Please note: We usually install the run-unit-test script in the docs of
a package to enable users to run the test as an example on the local
machine.

In the Debian Med policy

   https://med-team.pages.debian.net/policy/

you get general hints about packaging inside the Debian Med team.
Writing an autopkgtest boils down to adding the debian/tests dir to
the packaging.

Hope this helps as first hints - keep on asking here if something
remains unclear

   Andreas.

-- 
http://fam-tille.de

Re: 2019 DebianMed Sprint in Vilnius: 2019-03-09 - 2019-03-11

[Olivier Sallou]

On 10/17/2018 03:10 PM, Michael Crusoe wrote:
> You are welcome Olivier,
>
> At this point all information is public, so others are welcome to
> advertise :-)
>
> Beyond individuals travel/accommodations expenses, the only expense we
> will have is group meals; which we can request once we have a better
> idea about the number of people. Unless I'm forgetting something else?
>
we need a DPL approval for individual travel/accomodations expenses for
DDs for the sprint. This is managed globally by sprint organisator
rather than sending invidual requests.
Usually, for sprint approval, organizator specifies a number of DD with
an expected cost for later reimbursment

See for example a Perl sprint details:

  https://wiki.debian.org/Sprints/2017/DebianPerlSprint: budget part
  mail for DPL approval
https://lists.debian.org/debian-sprints/2017/04/msg1.html

travel part is of course an expected average (will vary according to DD
location)

Olivier
 
>
>
> În mie., 17 oct. 2018 la 15:24, Olivier Sallou
> mailto:olivier.sal...@irisa.fr>> a scris:
>
> Cool! and thanks for organizing.
>
> Do not forget to advertize on debian events (eve...@debian.org
> ) and debian sprints
> (debian-spri...@lists.debian.org
> ) to  ask for DPL approval
> for DD expenses/reimbursement [0]
>
>
> [0] https://wiki.debian.org/Sprints/HowTo
>
>
> Olivier
>
>
> On 10/17/2018 10:00 AM, Michael Crusoe wrote:
>> By popular acclaim, the 2019 Debian Med Sprint will be in March
>> from Saturday, March 9th until Monday, March 11th, 2019 in
>> Vilnius, Lithuania:
>>
>> https://wiki.debian.org/Sprints/2019/DebianMed2019
>>
>> Thanks to NVO Avilys for donating a nice working space!
>>
>> -- 
>> Michael R. Crusoe
>> Co-founder & Lead, Common Workflow Language project
>> 
>> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
>> https://orcid.org/-0002-2961-9670
>> 
>> m...@commonwl.org 
>
> -- 
> Olivier Sallou
> Univ Rennes, Inria, CNRS, IRISA
> Irisa, Campus de Beaulieu
> F-35042 RENNES - FRANCE
> Tel: 02.99.84.71.95
>
> gpg key id: 4096R/326D8438  (keyring.debian.org 
> )
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
>
>
>
> -- 
> Michael R. Crusoe
> Co-founder & Lead, Common Workflow Language project
> 
> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
> https://orcid.org/-0002-2961-9670
> 
> m...@commonwl.org 
> +1 480 627 9108 / +370 653 11125

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: IGV

[Olivier Sallou]

On 10/17/2018 02:57 PM, Andreas Tille wrote:
> On Wed, Oct 17, 2018 at 02:09:10PM +0200, Olivier Sallou wrote:
 in progress (not uploaded) igv packaging *should* be ok, but needs testing
>>> That's a problem for Bio-Linux 9 / Ubuntu 18.04 LTS, because the default
>>> is now Java 10 and the only other Java in the standard repo's is Java 8.
>> well, in my package env for new igv, I use Java 10, so will nto be a pb
> I can confirm that the package now builds also on my side
>
> Unfortunately if I start the package I get the following output:
>
> $ 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].
> 2018-10-17 14:37:58 INFO  DirectoryManager:179 - IGV Directory: 
> /home/andreas/igv
> 2018-10-17 14:37:59 INFO  Main:155 - Startup  IGV Version user not_set
> 2018-10-17 14:37:59 INFO  Main:156 - Java 10.0.2
> 2018-10-17 14:37:59 INFO  DirectoryManager:84 - Fetching user directory...
> 2018-10-17 14:37:59 INFO  Main:157 - Default User Directory: /home/andreas
> 2018-10-17 14:38:00 INFO  Main:158 - OS: Linux
>
>
> 2018-10-17 14:38:00 INFO  Main:208 - Unknown version: user
> 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
> java.lang.VerifyError: class 
> org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method 
> htsjdk.samtools.seekablestream.SeekableStream.mark(I)V

could be an htsjdk version issue versus what expects igv.
or getting 2 different definitions of
htsjdk.samtools.seekablestream.SeekableStream in classpath

> at java.base/java.lang.ClassLoader.defineClass1(Native Method)
> at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1009)
> at 
> java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
> at 
> java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:801)
> at 
> java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:699)
> at 
> java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:622)
> at 
> java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:580)
> at 
> java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
> at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
> at org.broad.igv.ui.Main.open(Main.java:282)
> at org.broad.igv.ui.Main$1.run(Main.java:109)
> 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.access$600(EventQueue.java:97)
> 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:87)
> 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)
> 2018-10-17 14:38:01 INFO  ShutdownThread:46 - Shutting down
>
>
> I'm running an up to date testing system.  Here is what reportbug
> generates:
>
> -- System Information:
> Debian Release: buster/sid
>   APT prefers testing
>   APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'), 
> (5, 'experimental')
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
>
> Kernel: Linux 4.18.0-2-amd64 (SMP w/4 CPU cores)
> Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8), 
> LAN

Re: IGV

[Andreas Tille]

Hi Olivier,

On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
> 
> > Unfortunately if I start the package I get the following output:
> >
> > $ 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].
> > 2018-10-17 14:37:58 INFO  DirectoryManager:179 - IGV Directory: 
> > /home/andreas/igv
> > 2018-10-17 14:37:59 INFO  Main:155 - Startup  IGV Version user not_set
> > 2018-10-17 14:37:59 INFO  Main:156 - Java 10.0.2
> > 2018-10-17 14:37:59 INFO  DirectoryManager:84 - Fetching user directory...
> > 2018-10-17 14:37:59 INFO  Main:157 - Default User Directory: /home/andreas
> > 2018-10-17 14:38:00 INFO  Main:158 - OS: Linux
> >
> >
> > 2018-10-17 14:38:00 INFO  Main:208 - Unknown version: user
> > 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
> > java.lang.VerifyError: class 
> > org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method 
> > htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
> 
> could be an htsjdk version issue versus what expects igv.
> or getting 2 different definitions of
> htsjdk.samtools.seekablestream.SeekableStream in classpath

I admit I had the same idea.

... 
> > libhtsjdk-java - 2.16.1+dfsg-1

while igv includes

htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar

I just realised that the Files-Excluded rules do not even remove this.
I assumed this would be excluded - so what about using the internal
code copy?  (Unfortunately I have no idea what to change to let this
happen.)

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: IGV

[Olivier Sallou]

On 10/18/2018 11:42 AM, Andreas Tille wrote:
> Hi Olivier,
>
> On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
>>> Unfortunately if I start the package I get the following output:
>>>
>>> $ 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].
>>> 2018-10-17 14:37:58 INFO  DirectoryManager:179 - IGV Directory: 
>>> /home/andreas/igv
>>> 2018-10-17 14:37:59 INFO  Main:155 - Startup  IGV Version user not_set
>>> 2018-10-17 14:37:59 INFO  Main:156 - Java 10.0.2
>>> 2018-10-17 14:37:59 INFO  DirectoryManager:84 - Fetching user directory...
>>> 2018-10-17 14:37:59 INFO  Main:157 - Default User Directory: /home/andreas
>>> 2018-10-17 14:38:00 INFO  Main:158 - OS: Linux
>>>
>>>
>>> 2018-10-17 14:38:00 INFO  Main:208 - Unknown version: user
>>> 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
>>> java.lang.VerifyError: class 
>>> org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method 
>>> htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
>> could be an htsjdk version issue versus what expects igv.
>> or getting 2 different definitions of
>> htsjdk.samtools.seekablestream.SeekableStream in classpath
> I admit I had the same idea.
>
> ... 
>>> libhtsjdk-java - 2.16.1+dfsg-1
> while igv includes
>
> htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar

the problem is org.broad.igv.util.stream.IGVSeekableBufferedStream
extends a class from htsjdk but redefines a method declared as final,
this is forbidden.
Don't understand however why it compiles.
Recent htsjdk (as we have), includes those methods and cannot be
overriden. Version 2.12 did not have those methods.

Using internal has the issue we don't have the source code for it
(though should match a commit). To get it work, we should simply remove
htsjdk related "compile" directive in build gradle file (added via our
patch)

>
> I just realised that the Files-Excluded rules do not even remove this.
> I assumed this would be excluded - so what about using the internal
> code copy?  (Unfortunately I have no idea what to change to let this
> happen.)
>
> Kind regards
>
>   Andreas.
>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: IGV

[Olivier Sallou]

On 10/18/2018 12:03 PM, Olivier Sallou wrote:
>
> On 10/18/2018 11:42 AM, Andreas Tille wrote:
>> Hi Olivier,
>>
>> On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
 Unfortunately if I start the package I get the following output:

 $ 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].
 2018-10-17 14:37:58 INFO  DirectoryManager:179 - IGV Directory: 
 /home/andreas/igv
 2018-10-17 14:37:59 INFO  Main:155 - Startup  IGV Version user not_set
 2018-10-17 14:37:59 INFO  Main:156 - Java 10.0.2
 2018-10-17 14:37:59 INFO  DirectoryManager:84 - Fetching user directory...
 2018-10-17 14:37:59 INFO  Main:157 - Default User Directory: /home/andreas
 2018-10-17 14:38:00 INFO  Main:158 - OS: Linux


 2018-10-17 14:38:00 INFO  Main:208 - Unknown version: user
 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
 java.lang.VerifyError: class 
 org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method 
 htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
>>> could be an htsjdk version issue versus what expects igv.
>>> or getting 2 different definitions of
>>> htsjdk.samtools.seekablestream.SeekableStream in classpath
>> I admit I had the same idea.


I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
fails with other X11 errors

2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
java.lang.IllegalArgumentException: Window must not be zero
    at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
    at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
    ..

this is above my knowledge of gui system in java
>>
>> ... 
 libhtsjdk-java - 2.16.1+dfsg-1
>> while igv includes
>>
>> htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar
> the problem is org.broad.igv.util.stream.IGVSeekableBufferedStream
> extends a class from htsjdk but redefines a method declared as final,
> this is forbidden.
> Don't understand however why it compiles.
> Recent htsjdk (as we have), includes those methods and cannot be
> overriden. Version 2.12 did not have those methods.
>
> Using internal has the issue we don't have the source code for it
> (though should match a commit). To get it work, we should simply remove
> htsjdk related "compile" directive in build gradle file (added via our
> patch)
>
>> I just realised that the Files-Excluded rules do not even remove this.
>> I assumed this would be excluded - so what about using the internal
>> code copy?  (Unfortunately I have no idea what to change to let this
>> happen.)
>>
>> Kind regards
>>
>>   Andreas.
>>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: IGV

[Olivier Sallou]

On 10/18/2018 12:15 PM, Olivier Sallou wrote:
>
> On 10/18/2018 12:03 PM, Olivier Sallou wrote:
>> On 10/18/2018 11:42 AM, Andreas Tille wrote:
>>> Hi Olivier,
>>>
>>> On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
> Unfortunately if I start the package I get the following output:
>
> $ 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].
> 2018-10-17 14:37:58 INFO  DirectoryManager:179 - IGV Directory: 
> /home/andreas/igv
> 2018-10-17 14:37:59 INFO  Main:155 - Startup  IGV Version user not_set
> 2018-10-17 14:37:59 INFO  Main:156 - Java 10.0.2
> 2018-10-17 14:37:59 INFO  DirectoryManager:84 - Fetching user directory...
> 2018-10-17 14:37:59 INFO  Main:157 - Default User Directory: /home/andreas
> 2018-10-17 14:38:00 INFO  Main:158 - OS: Linux
>
>
> 2018-10-17 14:38:00 INFO  Main:208 - Unknown version: user
> 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
> java.lang.VerifyError: class 
> org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final 
> method htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
 could be an htsjdk version issue versus what expects igv.
 or getting 2 different definitions of
 htsjdk.samtools.seekablestream.SeekableStream in classpath
>>> I admit I had the same idea.
>
> I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
> fails with other X11 errors
>
> 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
> java.lang.IllegalArgumentException: Window must not be zero
>     at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
>     at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
>     ..
>
> this is above my knowledge of gui system in java

in fact it seems to work. X11 error occurs when having multiple screens
and seems to relate to an openjdk bug [0].
With a single screen I could open and manipulate the GUI

I have pushed the patch update to manage current hstjdk debian version


[0] https://bugs.openjdk.java.net/browse/JDK-8204646

Olivier
>>> ... 
> libhtsjdk-java - 2.16.1+dfsg-1
>>> while igv includes
>>>
>>> htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar
>> the problem is org.broad.igv.util.stream.IGVSeekableBufferedStream
>> extends a class from htsjdk but redefines a method declared as final,
>> this is forbidden.
>> Don't understand however why it compiles.
>> Recent htsjdk (as we have), includes those methods and cannot be
>> overriden. Version 2.12 did not have those methods.
>>
>> Using internal has the issue we don't have the source code for it
>> (though should match a commit). To get it work, we should simply remove
>> htsjdk related "compile" directive in build gradle file (added via our
>> patch)
>>
>>> I just realised that the Files-Excluded rules do not even remove this.
>>> I assumed this would be excluded - so what about using the internal
>>> code copy?  (Unfortunately I have no idea what to change to let this
>>> happen.)
>>>
>>> Kind regards
>>>
>>>   Andreas.
>>>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: Figtree on Ubuntu

[Graham Inggs]

Hi Fabian

On 2018/10/17 16:02, Fabian Klötzl wrote:
That's weird. Building works fine on my Ubuntu 18.04. Unfortunately, I 
am not a Java person so I have no clue what to do.


Apparently this was due to the recent switch to openjdk-11 for 18.10.

I've uploaded with a workaround, hopefully this can still make it into 
the release.


Regards
Graham

Re: IGV

[Andreas Tille]

Hi Olivier,

On Thu, Oct 18, 2018 at 01:05:12PM +0200, Olivier Sallou wrote:
> > I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
> > fails with other X11 errors
> >
> > 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
> > java.lang.IllegalArgumentException: Window must not be zero
> >     at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
> >     at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
> >     ..
> >
> > this is above my knowledge of gui system in java
> 
> in fact it seems to work. X11 error occurs when having multiple screens
> and seems to relate to an openjdk bug [0].
> With a single screen I could open and manipulate the GUI
> 
> I have pushed the patch update to manage current hstjdk debian version

Sounds good.  Unfortunately I made an unfortunate observation:  If I
apply the following patch:

diff --git a/debian/copyright b/debian/copyright
index defa779..5305639 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,31 +1,21 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Source: http://www.broadinstitute.org/igv/projects/downloads
 Files-Excluded:
-igv.jar
-batik-codec.jar
-igv.bat
-igv.command
-lib/Jama-*
 lib/batik*
 lib/commons*
-lib/concurrent*
 lib/guava*
-lib/jargs*
+*/htsjdk*.jar
 lib/jcommon*
 lib/jfreechart*
-lib/junit-*
+*/junit-*.jar
 lib/log4j-*
-lib/sam-*
+*/picard-*.jar
+*/snappy-java-*.jar
 lib/swing-layout-*
-lib/xml-apis-*
-lib/bcprov*
-lib/jgrapht*
 lib/jide-oss-*
-lib/cofoja*
-lib/mysql-connector*
 lib/gson*
-test/lib/ant.jar
-test/lib/fest-assert*.jar
+*/ant.jar
+*/fest-Assert*.jar
 test/lib/fest-util*.jar
 test/lib/fest-reflect*.jar
 Disclaimer: This package is not part of the Debian operating system.


which does not mention not existing jars but more importantly removes
those jars we **think** we don't need - specifically  */htsjdk*.jar -
recreate the tarball and try to build ... the build fails again. :-( Its
also some htsjdk related error and I think there are more issues in this
approach.  It seems for whatever reason the build is done against the
internal copy but the result tries somehow to take the Debian installed
version.  I'm hesitating to push my changes since than we have a broken
IGV again.

What do you suggest as next step?  I might create a branch to let others
have a look.

Kind regards

   Andreas.


-- 
http://fam-tille.de

Re: Figtree on Ubuntu

[Graham Inggs]

Hi Fabian

On 2018/10/18 13:26, Graham Inggs wrote:
I've uploaded with a workaround, hopefully this can still make it into 
the release.


It is in!

Would you be able to complete steps 3 and 4 of the SRU procedure [1]?
No need to subscribe 'ubuntu-sponsors' to the bug, I can sponsor an 
upload for you.


Regards
Graham


[1] https://wiki.ubuntu.com/StableReleaseUpdates#Procedure

Re: IGV

[Olivier Sallou]

On 10/18/2018 04:06 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Thu, Oct 18, 2018 at 01:05:12PM +0200, Olivier Sallou wrote:
>>> I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
>>> fails with other X11 errors
>>>
>>> 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
>>> java.lang.IllegalArgumentException: Window must not be zero
>>>     at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
>>>     at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
>>>     ..
>>>
>>> this is above my knowledge of gui system in java
>> in fact it seems to work. X11 error occurs when having multiple screens
>> and seems to relate to an openjdk bug [0].
>> With a single screen I could open and manipulate the GUI
>>
>> I have pushed the patch update to manage current hstjdk debian version
> Sounds good.  Unfortunately I made an unfortunate observation:  If I
> apply the following patch:
>
> diff --git a/debian/copyright b/debian/copyright
> index defa779..5305639 100644
> --- a/debian/copyright
> +++ b/debian/copyright
> @@ -1,31 +1,21 @@
>  Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
>  Source: http://www.broadinstitute.org/igv/projects/downloads
>  Files-Excluded:
> -igv.jar
> -batik-codec.jar
> -igv.bat
> -igv.command
> -lib/Jama-*
>  lib/batik*
>  lib/commons*
> -lib/concurrent*
>  lib/guava*
> -lib/jargs*
> +*/htsjdk*.jar

oohhh, I did not see that htsjdk was part of package, though it had been
removed. Explains a few things
I gonna take your updates and test

>  lib/jcommon*
>  lib/jfreechart*
> -lib/junit-*
> +*/junit-*.jar
>  lib/log4j-*
> -lib/sam-*
> +*/picard-*.jar
> +*/snappy-java-*.jar
>  lib/swing-layout-*
> -lib/xml-apis-*
> -lib/bcprov*
> -lib/jgrapht*
>  lib/jide-oss-*
> -lib/cofoja*
> -lib/mysql-connector*
>  lib/gson*
> -test/lib/ant.jar
> -test/lib/fest-assert*.jar
> +*/ant.jar
> +*/fest-Assert*.jar
>  test/lib/fest-util*.jar
>  test/lib/fest-reflect*.jar
>  Disclaimer: This package is not part of the Debian operating system.
>
>
> which does not mention not existing jars but more importantly removes
> those jars we **think** we don't need - specifically  */htsjdk*.jar -
> recreate the tarball and try to build ... the build fails again. :-( Its
> also some htsjdk related error and I think there are more issues in this
> approach.  It seems for whatever reason the build is done against the
> internal copy but the result tries somehow to take the Debian installed
> version.  I'm hesitating to push my changes since than we have a broken
> IGV again.
>
> What do you suggest as next step?  I might create a branch to let others
> have a look.
>
> Kind regards
>
>Andreas.
>
>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: IGV

[Olivier Sallou]

On 10/18/2018 04:06 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Thu, Oct 18, 2018 at 01:05:12PM +0200, Olivier Sallou wrote:
>>> I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
>>> fails with other X11 errors
>>>
>>> 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
>>> java.lang.IllegalArgumentException: Window must not be zero
>>>     at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
>>>     at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
>>>     ..
>>>
>>> this is above my knowledge of gui system in java
>> in fact it seems to work. X11 error occurs when having multiple screens
>> and seems to relate to an openjdk bug [0].
>> With a single screen I could open and manipulate the GUI
>>
>> I have pushed the patch update to manage current hstjdk debian version
> Sounds good.  Unfortunately I made an unfortunate observation:  If I
> apply the following patch:
>
> diff --git a/debian/copyright b/debian/copyright
> index defa779..5305639 100644
> --- a/debian/copyright
> +++ b/debian/copyright
> @@ -1,31 +1,21 @@
>  Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
>  Source: http://www.broadinstitute.org/igv/projects/downloads
>  Files-Excluded:
> -igv.jar
> -batik-codec.jar
> -igv.bat
> -igv.command
> -lib/Jama-*
>  lib/batik*
>  lib/commons*
> -lib/concurrent*
>  lib/guava*
> -lib/jargs*
> +*/htsjdk*.jar
>  lib/jcommon*
>  lib/jfreechart*
> -lib/junit-*
> +*/junit-*.jar
>  lib/log4j-*
> -lib/sam-*
> +*/picard-*.jar
> +*/snappy-java-*.jar
>  lib/swing-layout-*
> -lib/xml-apis-*
> -lib/bcprov*
> -lib/jgrapht*
>  lib/jide-oss-*
> -lib/cofoja*
> -lib/mysql-connector*
>  lib/gson*
> -test/lib/ant.jar
> -test/lib/fest-assert*.jar
> +*/ant.jar
> +*/fest-Assert*.jar
>  test/lib/fest-util*.jar
>  test/lib/fest-reflect*.jar
>  Disclaimer: This package is not part of the Debian operating system.

testing with your removals, you only need to add to build gradle file
the ref to htsjdk


diff --git a/debian/patches/fix_gradle.patch
b/debian/patches/fix_gradle.patch
index 421a147..b2a0ac4 100644
--- a/debian/patches/fix_gradle.patch
+++ b/debian/patches/fix_gradle.patch
@@ -34,7 +34,7 @@ Forwarded: no
  sourceSets {
  main {
  java {
-@@ -45,6 +54,27 @@
+@@ -45,6 +54,28 @@
  dependencies {
  // Use the newer JIDE lib for Java 9 builds
  compile fileTree(dir: 'lib', include: '*.jar', exclude:
'jide-oss-3.5.5.jar') + fileTree(dir: 'lib_java9', include: '*.jar')
@@ -59,10 +59,11 @@ Forwarded: no
 +    compile "org.apache.logging.log4j:log4j-1.2-api:debian"
 +    compile "org.apache.logging.log4j:log4j-core:debian"
 +    compile "org.swinglabs:swing-layout:debian"
++    compile "com.github.samtools:htsjdk:debian"
  testCompile fileTree(dir: 'test/lib', include: '*.jar')
  }
 
-@@ -93,12 +123,13 @@
+@@ -93,12 +124,13 @@
  } 
  compileJava {



I pushed the update on patch (but your copyright patch is not yet there)

With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar
removed from upstream source, it compiles fine for me.

Olivier
>
>
> which does not mention not existing jars but more importantly removes
> those jars we **think** we don't need - specifically  */htsjdk*.jar -
> recreate the tarball and try to build ... the build fails again. :-( Its
> also some htsjdk related error and I think there are more issues in this
> approach.  It seems for whatever reason the build is done against the
> internal copy but the result tries somehow to take the Debian installed
> version.  I'm hesitating to push my changes since than we have a broken
> IGV again.
>
> What do you suggest as next step?  I might create a branch to let others
> have a look.
>
> Kind regards
>
>Andreas.
>
>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Re: IGV

[Andreas Tille]

Hi Olivier,

On Thu, Oct 18, 2018 at 06:18:58PM +0200, Olivier Sallou wrote:
> 
> testing with your removals, you only need to add to build gradle file
> the ref to htsjdk

I've now pushed the freshly stripped upstream version since we
both agree that a competing htsjdk is not a good idea.
 
> I pushed the update on patch (but your copyright patch is not yet there)
> 
> With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar
> removed from upstream source, it compiles fine for me.

I confirm it compiles fine now.  However:


$ LC_ALL=C igv
Error: Unable to initialize main class org.broad.igv.ui.Main
Caused by: java.lang.NoClassDefFoundError: 
htsjdk/samtools/seekablestream/ISeekableStreamFactory


Sorry to admit that we seem to need another iteration to get igv out.
 
Thanks a lot for your effort

  Andreas.

-- 
http://fam-tille.de

Re: IGV

[Olivier Sallou]

On 10/18/2018 08:25 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Thu, Oct 18, 2018 at 06:18:58PM +0200, Olivier Sallou wrote:
>> testing with your removals, you only need to add to build gradle file
>> the ref to htsjdk
> I've now pushed the freshly stripped upstream version since we
> both agree that a competing htsjdk is not a good idea.
>  
>> I pushed the update on patch (but your copyright patch is not yet there)
>>
>> With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar
>> removed from upstream source, it compiles fine for me.
> I confirm it compiles fine now.  However:
>
>
> $ LC_ALL=C igv
> Error: Unable to initialize main class org.broad.igv.ui.Main
> Caused by: java.lang.NoClassDefFoundError: 
> htsjdk/samtools/seekablestream/ISeekableStreamFactory

I just pulled from git, rebuilt and tried with new deb, and got no
issue, GUI started as expected.
This kind of error suggest that it did not found in igv classpath the
htsjdk.jar (not installed or not in in command classpath).

>
>
> Sorry to admit that we seem to need another iteration to get igv out.
>  
> Thanks a lot for your effort
>
>   Andreas.
>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438