Hello,
I fixed bug #1058683, which showed up in igv after an important upgrade
of htsjdk.
Great idea to improve one's Advent bug squashing metrics: upgrade
software, break things, fill bugs, fix them.
Best,
--
Pierre
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x-parallel could help build pass on your system.
Should you want to, maybe you could try, so we could make igv build more
fool-proof
Nilesh
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Am Wed, Nov 10, 2021 at 04:57:56PM +0100 schrieb Pierre Gruet:
> > Sent via private mail to not bloat the list archive with binary files.
>
> Thanks! I saw the test failing on your side is a thread safety test. DO you
> have any idea why it fails on your machine? Are you enabling some
> multithrea
eventually got this fixed, but I truly hope it will be far easier with igv.
Smells like excluding the test is a sensible thing. On the other hand
if Salsa-CI and autobuilders would be OK I'd be fine if you do a source
only upload.
I should say I am hesitating to remove the test about thread s
d log please.
Sent via private mail to not bloat the list archive with binary files.
> I still have in mind some failures in libsis-jhdf5-java, which were caused
> by a tricky garbage collector problem showing up on some machines only. We
> eventually got this fixed, but I truly hope it
remember we need to stick for the current version for
the moment ;-) ).
Thanks for this fix.
Unfortunately I was running in a build failure in my pbuilder chroot
432 tests completed, 1 failed, 103 skipped
Finished generating test XML results (0.04 secs) into:
/build/igv-2.6.3+dfsg2
completed, 1 failed, 103 skipped
Finished generating test XML results (0.04 secs) into:
/build/igv-2.6.3+dfsg2/build_java11/test-results/test
Generating HTML test report...
Finished generating test html results (0.109 secs) into:
/build/igv-2.6.3+dfsg2/build_java11/reports/tests/test
:test FAILED
HI Andreas,
Le 28/09/2021 à 07:11, Andreas Tille a écrit :
Hi Pierre,
On Mon, Sep 27, 2021 at 08:38:34PM +0200, Pierre Gruet wrote:
Actually the situation is a bit complicated with igv:
- I am waiting for libgoby-java to exit NEW so that I can upload the version
currently packaged to main
Hi Pierre,
On Mon, Sep 27, 2021 at 08:38:34PM +0200, Pierre Gruet wrote:
>
> Actually the situation is a bit complicated with igv:
> - I am waiting for libgoby-java to exit NEW so that I can upload the version
> currently packaged to main instead of non-free;
> - Any newer upstrea
Hi Andreas,
Le 27/09/2021 à 17:26, Andreas Tille a écrit :
Hi Pierre,
I was running routine-update on igv and as usually some patches did not
applied. There is no urgent pressure to upgrade the package but its
raising a signal that the watch file is not working (due to changes on
github
Hi Pierre,
I was running routine-update on igv and as usually some patches did not
applied. There is no urgent pressure to upgrade the package but its
raising a signal that the watch file is not working (due to changes on
github). The status in Git has a fixed watch file and it would help to
Hi everyone,
I have fixed the RC bug in igv. Would you mind either reviewing [0] or
giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow igv
Thanks a lot,
Pierre
[0] https://salsa.debian.org/med-team/igv
Hi Pierre,
On Wed, Sep 02, 2020 at 12:34:05PM +0200, Pierre Gruet wrote:
> Would you mind pushing the changes and tags to Salsa so that I can get them?
Hups, done now. ;-)
> > Feel free to ping me in CC - I'm perfectly willing to sponsor packages
> > also in other teams. I'll check the list ri
Hi Andreas,
Le 02/09/2020 à 09:09, Andreas Tille a écrit :
> Hi Pierre,
>
> On Tue, Sep 01, 2020 at 10:54:52PM +0200, Pierre Gruet wrote:
>> I have worked on the packaging of igv 2.6.3+dfsg, which is in
>>
>> https://salsa.debian.org/med-team/igv
>>
>>
Hi Pierre,
On Tue, Sep 01, 2020 at 10:54:52PM +0200, Pierre Gruet wrote:
> I have worked on the packaging of igv 2.6.3+dfsg, which is in
>
> https://salsa.debian.org/med-team/igv
>
> This igv packaging still relies on its embedded jars. I have solved
> build issues related
Hi,
I have worked on the packaging of igv 2.6.3+dfsg, which is in
https://salsa.debian.org/med-team/igv
This igv packaging still relies on its embedded jars. I have solved
build issues related to gradle, another one linked to the current
version of htsjdk (solves Grave bug on igv), and had to
Hi Pierre,
On Wed, Aug 26, 2020 at 04:40:09PM +0200, Pierre Gruet wrote:
>
> I haven't asked, since I instead got informed about what blocks Scala
> packaging in an open bug asking for packaging Scala 2.12, of which thread
>
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=845113
Which ends
Hi Andreas,
Le 26/08/2020 à 07:13, Andreas Tille a écrit :
>>
>> BTW, snpeff depends on akka-actor, a (Scala+Java) library which still
>> has to be packaged, and I am afraid it will be blocked by the version of
>> Scala in Debian, itself being stuck to 2.11 as Scala build tool (SBT)
>> requires wo
On Tue, Aug 25, 2020 at 04:37:37PM +0200, Pierre Gruet wrote:
> >> I get this right, then also nextflow qualifies, which because of
> >> "capsule" seems kind of stuck.
>
> Thanks, I will populate the tab. I already have access to the file.
Nice.
> > Thanks to Pierre we are close to snpeff. Cyt
On 25.08.20 16:37, Pierre Gruet wrote:
> Le 25/08/2020 à 06:35, Andreas Tille a écrit :
>> On Tue, Aug 25, 2020 at 12:12:04AM +0200, Steffen Möller wrote:
>>> I created a "Java" tab on our spreadsheet. Would of course be great if
>>> that sees some momentum. Took the freedom to also add Cytoscape
Hi Steffen and Andreas,
Le 25/08/2020 à 06:35, Andreas Tille a écrit :
> On Tue, Aug 25, 2020 at 12:12:04AM +0200, Steffen Möller wrote:
>> I created a "Java" tab on our spreadsheet. Would of course be great if
>> that sees some momentum. Took the freedom to also add Cytoscape. And if
>> I get thi
On Tue, Aug 25, 2020 at 12:12:04AM +0200, Steffen Möller wrote:
> I created a "Java" tab on our spreadsheet. Would of course be great if
> that sees some momentum. Took the freedom to also add Cytoscape. And if
> I get this right, then also nextflow qualifies, which because of
> "capsule" seems kin
, Pierre Gruet wrote:
> Hi Andreas,
>
> Le 24/08/2020 à 12:39, Andreas Tille a écrit :
>> Hi Pierre,
>>
>> On Mon, Aug 24, 2020 at 12:08:28PM +0200, Pierre Gruet wrote:
>>> Contrarily to what I wrote a few days ago, I do not think we are ready
>>> to remove al
Hi Andreas,
Le 24/08/2020 à 12:39, Andreas Tille a écrit :
> Hi Pierre,
>
> On Mon, Aug 24, 2020 at 12:08:28PM +0200, Pierre Gruet wrote:
>> Contrarily to what I wrote a few days ago, I do not think we are ready
>> to remove all included jars in igv.
>> For instan
Hi Pierre,
On Mon, Aug 24, 2020 at 12:08:28PM +0200, Pierre Gruet wrote:
> 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 effor
o 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
Am 14.11.19 um 14:28 schrieb Olivier Sallou:
[...]
>> Try to disable the build-dependency and analyze how much code is
>> depending on it. Maybe it is not necessary to get a functional IGV
>> package, otherwise someone ™ must package it.
>
>
> the pb is to know w
On 11/14/19 2:10 PM, Markus Koschany wrote:
> Hi,
>
> Am 14.11.19 um 09:44 schrieb Andreas Tille:
>> Hi,
>>
>> I'd be very happy if Debian Java team could comment on the analysis
>> of libs done by Olivier to enable us upgrading IGV.
>>
>> On Thu
Hi,
Am 14.11.19 um 09:44 schrieb Andreas Tille:
> Hi,
>
> I'd be very happy if Debian Java team could comment on the analysis
> of libs done by Olivier to enable us upgrading IGV.
>
> On Thu, Nov 14, 2019 at 09:34:51AM +0100, Olivier Sallou wrote:
>>
>> I had
Hi,
I'd be very happy if Debian Java team could comment on the analysis
of libs done by Olivier to enable us upgrading IGV.
On Thu, Nov 14, 2019 at 09:34:51AM +0100, Olivier Sallou wrote:
>
> I had a quick look at latest version. It seems to be have been rewritten
> a lot, a lots
On 11/13/19 1:42 PM, Steffen Möller wrote:
> Hello,
>
> One of the packages that Debian should really shine with is IGV - it is
> used throughout the world to inspect RNAseq data. And the ones running
> IGV are not the ones who ran the analysis, so there should be tons of
> fol
On 11/13/19 1:42 PM, Steffen Möller wrote:
> Hello,
>
> One of the packages that Debian should really shine with is IGV - it is
> used throughout the world to inspect RNAseq data. And the ones running
> IGV are not the ones who ran the analysis, so there should be tons of
> fol
Hi Steffen,
I guess there is no need to advertise igv here on this list. We should
rather work on moving it to main - and I mean really **work** on this
since license wise it is free software but we are always have to fight
with binary JARs. In the same category of "free, but binaries inc
Hello,
One of the packages that Debian should really shine with is IGV - it is
used throughout the world to inspect RNAseq data. And the ones running
IGV are not the ones who ran the analysis, so there should be tons of
folks out there using it who are not already installing conda in
routine
Hi,
any comment from Debian Java team?
Kind regards
Andreas.
On Mon, Sep 16, 2019 at 09:57:58AM +0200, Olivier Sallou wrote:
>
> On 9/13/19 3:43 PM, Andreas Tille wrote:
> > Hi,
> >
> > I upgraded the igv packaging Git[1] to the latest upstream version. I
> &
On 9/13/19 3:43 PM, Andreas Tille wrote:
> Hi,
>
> I upgraded the igv packaging Git[1] to the latest upstream version. I
> never experienced a smooth upgrade to any igv version - but I always
> experienced help from a Java expert here on the list. May be it is time
> agai
Hi,
I upgraded the igv packaging Git[1] to the latest upstream version. I
never experienced a smooth upgrade to any igv version - but I always
experienced help from a Java expert here on the list. May be it is time
again to fix:
All input files are considered out-of-date for incremental task
On Mon, Dec 17, 2018 at 05:29:28PM +0100, Olivier Sallou wrote:
> > Thanks a lot. Could you please also have a look at igv in Git?
>
> What is the issue? I only see bug to switch to mariadb in debian tracker
https://lists.debian.org/debian-med/2018/12/msg00026.html
As always
Hi Emmanuel,
On Thu, Dec 06, 2018 at 10:10:57AM +0100, Emmanuel Bourg wrote:
> Le 06/12/2018 à 09:54, Andreas Tille a écrit :
>
> > I remember the advise to seek on codesearch.d.n for the import statement
> > to find out what Build-Depends might be needed but this search failed.
> > Any other hin
Le 06/12/2018 à 09:54, Andreas Tille a écrit :
> I remember the advise to seek on codesearch.d.n for the import statement
> to find out what Build-Depends might be needed but this search failed.
> Any other hint?
It's there though:
https://sources.debian.org/src/ant/1.10.5-2/src/main/org/apache/
Hi,
I've injected the new upstream version of IGV into Git[1] but it
fails to build:
...
Compiling with JDK Java compiler API.
/build/igv-2.4.16+dfsg/src/main/java/org/broad/igv/track/TribbleFeatureSource.java:29:
error: package org.apache.tools.ant.taskdefs.condition does not exist
i
Hi,
I updated igv to fix openjdk 11 build issue.
Compil is ok with jdk 11 and exec looks ok.
I have not uploaded it in case some issues were still pending
Olivier
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Hi Olivier,
On Wed, Oct 24, 2018 at 01:45:25PM +0200, Olivier Sallou wrote:
>
> On 10/24/18 1:12 PM, Andreas Tille wrote:
> > H, anyway - I'd love if we could find a (hopefully clean) way to
> > update discosnp and minia to the latest upstream versions. Its probably
> > not good to lag heavi
On 10/24/18 1:12 PM, Andreas Tille wrote:
> On Wed, Oct 24, 2018 at 01:03:50PM +0200, Olivier Sallou wrote:
>> On 10/24/18 11:49 AM, Andreas Tille wrote:
>>> On Wed, Oct 24, 2018 at 11:37:34AM +0200, Olivier Sallou wrote:
> so gatb core may need to add in its -dev includes those thridparty co
On Wed, Oct 24, 2018 at 01:03:50PM +0200, Olivier Sallou wrote:
>
> On 10/24/18 11:49 AM, Andreas Tille wrote:
> > On Wed, Oct 24, 2018 at 11:37:34AM +0200, Olivier Sallou wrote:
> >>> so gatb core may need to add in its -dev includes those thridparty code
> >>> headers too.
> >> even with loc
On 10/24/18 11:49 AM, Andreas Tille wrote:
> On Wed, Oct 24, 2018 at 11:37:34AM +0200, Olivier Sallou wrote:
>>> so gatb core may need to add in its -dev includes those thridparty code
>>> headers too.
>> even with local patching to use missing gatdb thridparty includes, code
>> fails to comp
On Wed, Oct 24, 2018 at 11:37:34AM +0200, Olivier Sallou wrote:
>
> > so gatb core may need to add in its -dev includes those thridparty code
> > headers too.
>
> even with local patching to use missing gatdb thridparty includes, code
> fails to compile, I think it expects a specific version
On 10/24/18 11:08 AM, Olivier Sallou wrote:
> On 10/24/18 10:56 AM, Olivier Sallou wrote:
>> On 10/24/18 9:51 AM, Andreas Tille wrote:
>>> On Wed, Oct 24, 2018 at 09:13:51AM +0200, Olivier Sallou wrote:
> PS: Do you have some free resources to check the cmake issue with
> gatb-core?
On 10/24/18 10:56 AM, Olivier Sallou wrote:
> On 10/24/18 9:51 AM, Andreas Tille wrote:
>> On Wed, Oct 24, 2018 at 09:13:51AM +0200, Olivier Sallou wrote:
PS: Do you have some free resources to check the cmake issue with
gatb-core?
>>> which issue ? Have not seen related mail.
>> https
On 10/24/18 9:51 AM, Andreas Tille wrote:
> On Wed, Oct 24, 2018 at 09:13:51AM +0200, Olivier Sallou wrote:
>>> PS: Do you have some free resources to check the cmake issue with gatb-core?
>> which issue ? Have not seen related mail.
> https://lists.debian.org/debian-med/2018/10/msg00073.html
> s
On Wed, Oct 24, 2018 at 09:13:51AM +0200, Olivier Sallou wrote:
> > PS: Do you have some free resources to check the cmake issue with gatb-core?
>
> which issue ? Have not seen related mail.
https://lists.debian.org/debian-med/2018/10/msg00073.html
says:
since a long time there are new versions
On 10/23/18 2:59 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Tue, Oct 23, 2018 at 10:40:29AM +0200, Olivier Sallou wrote:
>> I have added d/igv.manifest, and jar MANIFEST gets updated as well as
>> java:Depends.
>>
>> but file needs to be updates with package if new deps are added (did
>> n
Hi Olivier,
On Tue, Oct 23, 2018 at 10:40:29AM +0200, Olivier Sallou wrote:
>
> I have added d/igv.manifest, and jar MANIFEST gets updated as well as
> java:Depends.
>
> but file needs to be updates with package if new deps are added (did
> not check that all deps are ok)
I've added a TODO
deps are added (did
not check that all deps are ok)
Olivier
> When looking inside
>
> igv-2.4.6.jar: META-INF/MANIFEST.MF
> Manifest-Version: 1.0
> Permissions: all-permissions
> Application-Name: IGV
> Main-Class: org.broad.igv.ui.Main
>
>
> igv-2.4.14+dfsg.ja
the jars installed in the package.
> Could you check the manifest of the jar generated?
When looking inside
igv-2.4.6.jar: META-INF/MANIFEST.MF
Manifest-Version: 1.0
Permissions: all-permissions
Application-Name: IGV
Main-Class: org.broad.igv.ui.Main
igv-2.4.14+dfsg.jar: META-INF/MANIFEST.
Le 19/10/2018 à 13:20, Andreas Tille a écrit :
> Any comment from the Debian Java team?
If I remember well ${java:Depends} is inferred from the Class-Path
attribute in the MANIFEST.MF file of the jars installed in the package.
Could you check the manifest of the jar generated?
Emmanuel Bourg
On Fri, Oct 19, 2018 at 08:53:22AM +0200, Olivier Sallou wrote:
>
> 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 no
eam 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
od 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
Er
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
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
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:
fortunately if I start the package I get the following output:
>>>>>
>>>>> $ igv
>>>>>
>>>>>
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 t
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 out
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:
>
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 defau
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
On 10/17/2018 11:59 AM, Tony Travis wrote:
> On 17/10/2018 10:19, Olivier Sallou wrote:
>> [...]
>> new IGV needs Java 9 or above.
>> The problem is Java 8 to 9 introduced some breaking changes with modules
>> support.
> Hi, Olivier.
>
> The default un
On 17/10/2018 10:59, Tony Travis wrote:
> [...]
> 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.
Hi, Olivier.
Sorry, I missed this:
> Package java9-sdk is a virtual package provided by:
> openj
On 17/10/2018 10:19, Olivier Sallou wrote:
> [...]
> new IGV needs Java 9 or above.
> The problem is Java 8 to 9 introduced some breaking changes with modules
> support.
Hi, Olivier.
The default under Ubuntu-MATE 18.04 LTS is Java 10:
> /usr/lib/jvm/java-11-openjdk-amd64/bi
have an idea how to
>>> build igv?
>> Hi,
>> after lots of fixes, I could get igv build (and had to make a few
>> updates to d/bin/igv too)
>>
>> however, I removed the Java 9 module support for igv itself.. Could not
>> make it build to provide igv as a
On 10/16/2018 02:51 PM, Andreas Tille wrote:
> Hi Olivier,
>
> thanks a lot for looking into this.
>
> On Tue, Oct 16, 2018 at 10:45:08AM +0200, Olivier Sallou wrote:
>>
>>> sorry for the private ping, but may be you have an idea how to
>>> build igv?
>
On 10/16/2018 08:36 AM, Andreas Tille wrote:
> Hi Tony
>
> On Tue, Oct 16, 2018 at 12:27:26AM +0100, Tony Travis wrote:
>> Hi,
>>
>> The "igv" package imported from Debian-Med does not work correctly under
>> Ubuntu-MATE 18.04 LTS:
>>
>>
Hi Olivier,
thanks a lot for looking into this.
On Tue, Oct 16, 2018 at 10:45:08AM +0200, Olivier Sallou wrote:
>
>
> > sorry for the private ping, but may be you have an idea how to
> > build igv?
> Hi,
> after lots of fixes, I could get igv build (and had to make a fe
Hi Tony
On Tue, Oct 16, 2018 at 12:27:26AM +0100, Tony Travis wrote:
> Hi,
>
> The "igv" package imported from Debian-Med does not work correctly under
> Ubuntu-MATE 18.04 LTS:
>
> > lsb_release -d
> > Description:Ubuntu 18.04.1 LTS
> > ap
Hi,
The "igv" package imported from Debian-Med does not work correctly under
Ubuntu-MATE 18.04 LTS:
> lsb_release -d
> Description: Ubuntu 18.04.1 LTS
> apt-cache policy igv
> igv:
> Installed: 2.4.6+dfsg-1
> Candidate: 2.4.6+dfsg-1
> Version table:
>
On Thu, Jan 28, 2016 at 12:09 PM Andreas Tille wrote:
> Hi Michael,
>
> On Wed, Jan 27, 2016 at 10:06:49PM +0200, Michael Crusoe wrote:
> > and libhmsbeagle-java is missing a dependency on libhmsbeagle1v5 which is
> > also causing a problem. Looks like this was fixed in git but unreleased.
>
> I
Hi Michael,
On Wed, Jan 27, 2016 at 10:06:49PM +0200, Michael Crusoe wrote:
> and libhmsbeagle-java is missing a dependency on libhmsbeagle1v5 which is
> also causing a problem. Looks like this was fixed in git but unreleased.
I just uploaded the state from Git (+ upstream Git commits). I had de
On Wed, Jan 27, 2016 at 09:28:20PM +0200, Michael Crusoe wrote:
> You need to change the invocation in /usr/bin/tracer to be
>
> java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -classpath
> /usr/share/java/itext1.jar:$BEAST_LIB/tracer.jar
> dr.app.tracer.application.TracerApp
Works nicely
and libhmsbeagle-java is missing a dependency on libhmsbeagle1v5 which is
also causing a problem. Looks like this was fixed in git but unreleased.
On Wed, Jan 27, 2016 at 9:28 PM, Michael Crusoe
wrote:
> You need to change the invocation in /usr/bin/tracer to be
>
> java -Xms64m -Xmx1024m -Djava
You need to change the invocation in /usr/bin/tracer to be
java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -classpath
/usr/share/java/itext1.jar:$BEAST_LIB/tracer.jar
dr.app.tracer.application.TracerApp
On Wed, Jan 27, 2016 at 7:50 PM, Andreas Tille wrote:
> On Wed, Jan 27, 2016 at 04:2
On Wed, Jan 27, 2016 at 04:22:43PM +0100, Olivier Sallou wrote:
>
> override_dh_auto_build:
> .
> ant build
> # Build dist/tracer.jar
> ant -buildfile build_tracer.xml dist
>
>
> After build, classes appear in build directory
> (build/dr/app/tracer/) and included in dist/tracer
On 01/27/2016 02:36 PM, Andreas Tille wrote:
> On Wed, Jan 27, 2016 at 01:30:02PM +, olivier sallou wrote:
>> Le mer. 27 janv. 2016 14:17, Andreas Tille a écrit :
>>
>>> Hi Olivier,
>>>
>>> On Wed, Jan 27, 2016 at 11:42:41AM +, olivier sallou wrote:
Hi Andreas,
I had no answer
On Wed, Jan 27, 2016 at 01:30:02PM +, olivier sallou wrote:
> Le mer. 27 janv. 2016 14:17, Andreas Tille a écrit :
>
> > Hi Olivier,
> >
> > On Wed, Jan 27, 2016 at 11:42:41AM +, olivier sallou wrote:
> > > Hi Andreas,
> > > I had no answer to my mail, is my answer clear enough ?
> >
> >
r file. I will have a look at it
>
> Kind regards
>
> Andreas.
>
> > Le lun. 18 janv. 2016 à 10:57, olivier sallou
> a
> > écrit :
> >
> > >
> > >
> > > -- Forwarded message -
> > > From: Andreas Tille
> >
janv. 2016 à 10:40
> > Subject: Re: Bug#810842: [a...@debian.org: Bug#810842: igv: libsam-java
> > is gone]
> > To: olivier sallou
> >
> >
> > On Mon, Jan 18, 2016 at 09:17:54AM +, olivier sallou wrote:
> > > Le lun. 18 janv. 2016 à 10:07, Andreas Tille a
an.org: Bug#810842: igv: libsam-java
> is gone]
> To: olivier sallou
>
>
> On Mon, Jan 18, 2016 at 09:17:54AM +, olivier sallou wrote:
> > Le lun. 18 janv. 2016 à 10:07, Andreas Tille a écrit
> :
> >
> > > Hi Olivier,
> > >
&g
Hi Olivier,
On Mon, Jan 18, 2016 at 09:57:21AM +, olivier sallou wrote:
> > > > I made a try and beast tracer jar seems to build correcly.
> > >
> > > Could you commit the change for this?
> > >
> > I made no modification. Reactivating test in d/rules was fine for me
>
> > But there is no acc
-- Forwarded message -
From: Andreas Tille
Date: lun. 18 janv. 2016 à 10:40
Subject: Re: Bug#810842: [a...@debian.org: Bug#810842: igv: libsam-java is
gone]
To: olivier sallou
On Mon, Jan 18, 2016 at 09:17:54AM +, olivier sallou wrote:
> Le lun. 18 janv. 2016 à 10
- Mail original -
> De: "Olivier Sallou"
> À: "Andreas Tille"
> Cc: "Debian Med Project List"
> Envoyé: Dimanche 17 Août 2014 14:11:58
> Objet: Re: [Help] Latest version of IGV fails to build
>
>
>
> - Mail original -
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List"
> Envoyé: Vendredi 15 Août 2014 13:29:27
> Objet: [Help] Latest version of IGV fails to build
>
> Hi,
>
> I commited the packaging for last IGV to Git but it fails to bu
Le Fri, Aug 15, 2014 at 01:29:27PM +0200, Andreas Tille a écrit :
>
> I commited the packaging for last IGV to Git but it fails to build:
Hi Andreas,
it seems that you have forgotten to push the tag ‘upstream/2.3.34+dfsg’; can
you do it ?
Have a nice week-end,
--
Charles
--
To UNSUB
Hi,
I commited the packaging for last IGV to Git but it fails to build:
compile:
[javac] /tmp/buildd/igv-2.3.34+dfsg/build.xml:175: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to
false for repeatable builds
[javac] Compiling 864 sourc
The source was moved to guthub but nobody noticed. And
to say the truth I know who is responsible for this: You are since
you failed in firing up
reportbug igv
"new version available"
;-)
Tony, please, if you notice in the future that your favourite
distribution is lagging behi
the software we are working for to /usr/local.
Hi, Andreas.
The stand-alone version I'm using is 2.3.20 but the version in the
Ubuntu multiverse repo used by Bio-Linux is 2.3.14:
> root@wildcat:~# apt-cache policy igv
> igv:
> Installed: (none)
> Candidate: 2.3.14+dfsg-2
Hi Tony,
On Thu, Aug 14, 2014 at 03:18:12PM +0100, Tony Travis wrote:
>
> I'm running a (manually installed) stand-alone IGV using OpenJDK
>
> > root@wildcat:/usr/local/IGV# java -version
> > java version "1.7.0_55"
> > OpenJDK Runtime Enviro
On 14/08/14 14:52, Olivier Sallou wrote:
>
> On 08/14/2014 09:48 AM, Andreas Tille wrote:
>> Hi,
>>
>> according to
>>
>>https://qa.debian.org/excuses.php?package=igv
>>
>> igv depends from netbeans. I can not see netbeans mentioned explicitly
On 08/14/2014 09:48 AM, Andreas Tille wrote:
> Hi,
>
> according to
>
>https://qa.debian.org/excuses.php?package=igv
>
> igv depends from netbeans. I can not see netbeans mentioned explicitly
> in the list of dependencies nor was it added by ${java:Depends} when
>
Hi,
according to
https://qa.debian.org/excuses.php?package=igv
igv depends from netbeans. I can not see netbeans mentioned explicitly
in the list of dependencies nor was it added by ${java:Depends} when
looking at
apt-cache show igv
Has anybody a clue what's happening here?
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