ail original -
> De: "Markus Koschany"
> À: 895...@bugs.debian.org
> Envoyé: Vendredi 9 Novembre 2018 16:33:33
> Objet: [Debian-med-packaging] Bug#895765: IGV FTBFS with Java 11
> Hi,
>
> igv also FTBFS with Java 11 now. However the fix is trivial. The package
>
Hi,
igv also FTBFS with Java 11 now. However the fix is trivial. The package
must build-depend on libjaxb-api-java because those classes were removed
from the JDK. Then you need to remove the
--add-modules', 'java.xml.bind'
line in fix_gradle.patch.
Please find attached a patch that makes the n
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 agr
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 pu
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
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
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.IllegalArgumentEx
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 o
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
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
>>>
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
> >
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 o
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.
>
On 04/16/2018 04:38 PM, Andreas Tille wrote:
> Hi Olivier,
>
> could you provide a patch assumed we'll stick to Java 9 and higher?
I tried to add module, but javafx module is not found on system.
In debian package, I found only openjfx8, no port available for java9 ?
There is a bug [0] requestin
Hi Olivier,
could you provide a patch assumed we'll stick to Java 9 and higher?
(Could you also have a look into artemis, htsjdk and picard-tools
if your time permits?)
Kind regards
Andreas.
On Mon, Apr 16, 2018 at 10:17:57AM +0200, Olivier Sallou wrote:
>
>
> On 04/16/2018 09:32 AM, B
On 04/16/2018 09:32 AM, Bas Couwenberg wrote:
> On 2018-04-16 08:18, Andreas Tille wrote:
>> it seems something has changed with openfx since the errors below are
>> all mentioning something like "import javafx. ...". Do you have any
>> hint how this can be fixed?
>
> There is no OpenJFX for Ope
On 2018-04-16 08:18, Andreas Tille wrote:
it seems something has changed with openfx since the errors below are
all mentioning something like "import javafx. ...". Do you have any
hint how this can be fixed?
There is no OpenJFX for OpenJDK 9, see:
https://lists.debian.org/debian-java/2018/04
Hi,
it seems something has changed with openfx since the errors below are
all mentioning something like "import javafx. ...". Do you have any
hint how this can be fixed?
Kind regards
Andreas.
On Sun, Apr 15, 2018 at 08:55:57PM +0200, Andreas Beckmann wrote:
> Source: igv
> Version: 2.4
Source: igv
Version: 2.4.6+dfsg-1
Severity: serious
Justification: fails to build from source
Hi,
igv FTBFS with openjdk-9 as the default jdk:
debian/rules build
dh build --with javahelper
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
jh_linkjars
dh_auto_build
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