Le mer. 19 juil. 2023, 06:58, Andreas Tille a écrit :
> Hi Olivier,
>
> Am Mon, Jul 17, 2023 at 12:13:30PM +0200 schrieb olivier sallou:
> > logol is not maintained anymore for quite some time now
> >
> > effort to keep in line with swi-prolog updates (need to recompi
seems biojava now ships several jar files (core, biosql, ...) and not a
bundle anymore, used by logol,
see list of jar files available:
https://packages.debian.org/sid/all/libbiojava1.9-java/filelist
would need to patch logol to import/load expected jar files (and find which
ones are needed...) i
logol is not maintained anymore for quite some time now
effort to keep in line with swi-prolog updates (need to recompile on each
ABI break of swi-prolog) AND biojava requires frequent work for an old
software with low usage.
I would let it be removed
--
gpg key id: 4096R/326D8438 (keyrin
On Wed, 2022-12-21 at 19:39 +0530, Nilesh Patra wrote:
> On Wed, 21 Dec 2022 12:32:25 +0100 olivier sallou
> wrote:
> > On Wed, 2022-12-21 at 11:02 +0100, olivier sallou wrote:
> > > looks like a python3 issue (though was already adapter to py3...)
> > >
> &
upstream, in develop branch has disabled mason2 testing for gcc > 10 ,
don't know why, but let's do the same as it is the one failing now with
indeed superior gcc
I am adapting the patch and testing again.
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 520
I pushed a patch d/patches/fix_python3_tests whic fixes almost all test
issues(python3 related)
BUT remains a failing test with mason2 which is not related to py3
issue (no bytes-like error)
after build, can be reproduced with
in a temp dir:
python3 /<>/apps/mason2/tests/run_tests.py
/opt/d
On Wed, 2022-12-21 at 11:02 +0100, olivier sallou wrote:
> looks like a python3 issue (though was already adapter to py3...)
>
> will have a look and reproduce
I could reproduce and found an issue with demo_checker.py handling with
python3
I have a patch. will test it and upload
>
looks like a python3 issue (though was already adapter to py3...)
will have a look and reproduce
Olivier
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
after investigation, logol does not find anymore libswipl.so.8, need
version providing .so.9
compiled program link to .so.x versions, forcing package recompilation
Le mar. 13 déc. 2022 à 22:03, Paul Gevers a écrit :
> Source: swi-prolog, logol
> Control: found -1 swi-prolog/9.0.2+dfsg-1
> Contr
Tests need to be run as root, or use a specific config file and use non
root writable directories.
Will try to change tests to do so.
Regarding issue itself, programs compiled by swi prolog usually require
recompilation on swi prolog updates.
Will try to rebuild and check
Le mar. 13 déc. 2022,
Le dim. 23 oct. 2022, 19:21, Lev Lamberov a écrit :
> Hi Paul,
>
> Вс 23 окт 2022 @ 10:10 Paul Gevers :
>
> > Hi Lev,
> >
> > On 23-10-2022 09:40, Lev Lamberov wrote:
> >> I'm not sure it is the solution, it needs testing. The change in
> >> swi-prolog concerns pre-compiled prolog source code, wh
Le ven. 30 sept. 2022 à 07:20, Andreas Tille a écrit :
> Am Fri, Sep 30, 2022 at 02:20:26AM +0200 schrieb olivier sallou:
> > Will try to have a look, but i have no perl knowledge and software is
> quite
> > old now...
>
I have a patch. With this patch, tests are ok, but
Will try to have a look, but i have no perl knowledge and software is quite
old now...
Le jeu. 29 sept. 2022, 19:44, Andreas Tille a écrit :
> Control: tags -1 help
>
> Hi Aaron and Olivier,
>
> do you have some idea how to fix this bug?
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-til
Nati
> > veMethodAccessorImpl.java:62)
> > at
> > java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(
> > DelegatingMethodAccessorImpl.java:43)
> > at
> > org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
> > at
> > org.gradle.api.internal.project.taskfa
Le jeu. 3 mars 2022, 20:51, Paul Gevers a écrit :
> Hi Lev,
>
> On 03-03-2022 08:46, dogs...@riseup.net wrote:
> > swi-prolog package (namely, swi-prolog-core) provides an easy way to
> > require some particular ABI since 8.2.0+dfsg-2 uploaded on Jun 9, 2020.
> > Specifically, in this case logol
Le lun. 28 févr. 2022 à 06:37, a écrit :
> Dear Olivier,
>
> sorry for the delay with my message and thanks for your input.
>
> olivier sallou писал 2022-02-25 12:12:
> > ok,
> > after a quick look, issue is Logol is compiled against swi-prolog, and
> > there
ok,
after a quick look, issue is Logol is compiled against swi-prolog, and
there is an ABI issue I think, getting error:
incompatible version (file: 67, Prolog: 68)]
Recompiling logol in sid against swi-prolog 8.4.2+dfsg-2 results in correct
execution/tests.
So, 2 things:
* As swi-prolog is onl
Hi,
Logol is not maintained for quite a long time now, i will try to have a
look, but i am ok to get logol removed from testing to avoid blocking swi
prolog
Olivier
Le jeu. 24 févr. 2022, 19:36, Paul Gevers a écrit :
> Source: swi-prolog, logol
> Control: found -1 swi-prolog/8.4.2+dfsg-2
> Cont
Seems that a dependency (tenacity) has been changed with broken api
Need to change code to use new tenacity version
Le dim. 13 févr. 2022, 08:21, Lucas Nussbaum a écrit :
> Source: biomaj3-download
> Version: 3.2.4-1
> Severity: serious
> Justification: FTBFS
> Tags: bookworm sid ftbfs
> User:
d like to forward this to Debian Java list for comments.
>
> Kind regards
>
> Andreas.
>
> On Mon, May 17, 2021 at 01:50:01PM +0200, olivier sallou wrote:
> > Issue seems to be related to xml-apis.jar not being symlinked itself
> >
> > /usr/share/java# ls *x
Issue seems to be related to xml-apis.jar not being symlinked itself
/usr/share/java# ls *xml-api*
xml-apis-1.4.01.jar xml-apis-ext-1.4.01.jar xml-apis-ext.jar
Usually, java libs have a versioned file and an unversionned file which is
a symlink to versioned one (see above).
xml-apis here is not
need to check, but I suppose referenced lib changed its path or name in
dependencies...
Le lun. 17 mai 2021 à 13:33, Andreas Beckmann a écrit :
> Package: logol
> Version: 1.7.9-2
> Severity: serious
> User: debian...@lists.debian.org
> Usertags: piuparts
>
> Hi,
>
> during a test with piuparts
e to delete file:
> targets/unit-test-
> wd/ch.systemsx.cisd.base.unix.UnixTests/someDanglingLink]
> Exception in thread "main" org.apache.commons.io.IOExceptionList: 1
> exceptions: [java.io.IOException: Unable to delete file:
> targets/unit-test-
> wd/ch.systemsx.cisd.b
are/java/j2ssh-core.jar: Permission denied
> > > > make[2]: *** [Makefile:48: uk/ac/sanger/artemis/Action.class]
> > Error 126
> > >
> > > The full build log is available from:
> > >
> > http://qa-logs.debian.net/2020/06/20/artemis_17.0.1+dfsg-2
Le mar. 9 juin 2020 à 16:47, Aaron M. Ucko a écrit :
> Andreas Tille writes:
>
> > On Tue, Jun 09, 2020 at 02:25:58PM +0200, Étienne Mollier wrote:
> >> My current impression is that makeblastdb is unable to work
> >> properly on most 32 bits machines, because the amount of memory
> >> needing t
Le jeu. 28 mai 2020 à 13:00, Andreas Tille a écrit :
> Hi Olivier and Vincent
>
> On Thu, May 28, 2020 at 09:47:37AM +0300, Adrian Bunk wrote:
> >
> > picard-tools build depends on libguava-java-doc,
> > which is no longer built by src:guava-libraries.
>
Hi andreas,
looking at issue, where did y
Le jeu. 28 mai 2020 à 13:00, Andreas Tille a écrit :
> Hi Olivier and Vincent
>
> On Thu, May 28, 2020 at 09:47:37AM +0300, Adrian Bunk wrote:
> >
> > picard-tools build depends on libguava-java-doc,
> > which is no longer built by src:guava-libraries.
>
> I've tried to simply leave out libguava-
Le mer. 4 mars 2020 à 16:38, eamanu a écrit :
> Hi olivier,
>
> On 04/03/2020 12:13, olivier sallou wrote:
> > Hi,
> > I saw you started some work on python-ftputil to fix #952208.
> >
> > I just pushed to git repo a fix for that.
>
> I am a little conf
Hi,
I saw you started some work on python-ftputil to fix #952208.
I just pushed to git repo a fix for that.
Will you push new patch release soon? Or should I do?
I wonder however why you pushed a gbp.conf (not really expected usually)
setting branch as debian/master , which does not exists and d
I pushed to git a patch that seems to fix the undefined ref to InitGoogle...
Still need to test full build (very long...)
Olivier
pbcommand in debian (latest from github) provide a different API, but
pbcommand doc and README all show previous API example and show usage
of get_pbparser function, but this method is not present anymore.
It is not possible to *guess* what should be used instead.
--
gpg key id: 4096R/326D843
Tried to look at python3 port.
However it depends on pbcommand, and pbcommand api is different from
expected by kinetictools (means py2 version is broken).
Trying to see how to use current pbcommand api, but looks quite different.
Olivier
py3 fix sent and uploaded, by introduces new py3 packages, so in NEW queue
for the moment
rent.fa: No such file or
> directory
> *** Test: FAILURE on diff .fa
> autopkgtest [08:02:15]: test run-unit-test: -------]
>
>
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@alioth-lists.debian.net
&g
On 10/4/19 3:07 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Fri, Oct 04, 2019 at 02:14:02PM +0200, olivier sallou wrote:
>>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>>> reference.
>> I really do not see what error could be. Maybe a
> at ./snapfun_dir/prof.f:876
> #5 0x55a7ca3b0967 in prof
> at ./snapfun_dir/prof.f:108
> #6 0x55a7ca39f25e in main
> at ./snapfun_dir/prof.f:179
> Segmentation fault (core dumped)
>
> On Thu, Oct 3, 2019 at 12:35 PM olivier sallou wrote:
>
>>
>>
>> Le je
Le jeu. 3 oct. 2019 à 12:08, Michael Crusoe a
écrit :
> On Sat, 9 Mar 2019 17:44:02 +0100 olivier sallou
> wrote:
> > Looking at core generated file and using gdb we see that it fails in
> > fortran lib.
> >
> > Either program tries something wrong in a fortran u
ave non :-(
was expecting something from debian mentors which was in cc...
>
> 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
Le mer. 21 août 2019 à 15:21, Andreas Tille a écrit :
> Control: tags -1 help
>
> Hi,
>
> I removed Python2 support from this package in Git[1]. Unfortunately the
> autopkgtest failure is for Python3. Graham, I understood your
> mail that you've found a solution - but I do not understand what
>
not
supported and clean step is ran before patches
So feel free to use this patch, but I do not really like it :-(
From 4b07d43ce328690fac4965aafc4d3252c72b95ec Mon Sep 17 00:00:00 2001
From: Olivier Sallou
Date: Wed, 21 Aug 2019 12:03:31 +
Subject: [PATCH] remove sphinx related doc
kage.php?p=obitools
>
> Cheers,
>
> Ivo
>
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
--
Olivier Sallou
Un
const { return
line_string() ; }
do the job and test pass
but I would prefer a c++ friend to acknowledge this It works but I
do not if there are side effects
Olivier
>
> Thanks for your analysis anyway
>
> Andreas.
>
> On Tue, Aug 20, 2019 at 03:36:48PM +0200,
> _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&)
> [with _CharT = char; _Traits = std::char_traits; _Alloc =
> std::allocator]'
> 732 | operator=(basic_string&& __str)
> | ^~~~
> make[3]: *** [Makef
archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
>
> ___
> Debian-med-packaging mailing list
>
- Andreas Tille a écrit :
> Hi Debian Java team,
>
> On Tue, Mar 05, 2019 at 12:19:40AM +, Santiago Vila wrote:
> > jh_build -J hac.jar src
> > find src -name *.java -and -type f -print0 | xargs -s 512000 -0
> > /usr/lib/jvm/default-java/bin/javac -g -cp :debian/_jh_build.hac -d
> > deb
- Mail original -
> De: "Matthias Klose"
> À: "submit"
> Envoyé: Lundi 4 Mars 2019 17:40:08
> Objet: [Debian-med-packaging] Bug#923731: igv depends on packages which were
> removed in picard-tools
> Package: src:igv,src:picard-tools
> Severity: serious
> Tags: sid buster
>
> Another
Hi,
I am aware of the issue. I discovered issue yesterday while trying to
update package with latest version.
I was about to add info in changelog this morning...
I created an issue in swi-prolog. This dependency update seems to introduce
the error, failing to load a library.
Related issue is #9
On 12/19/18 11:46 AM, Andreas Tille wrote:
> Hi,
>
> On Wed, Dec 19, 2018 at 10:39:55AM +0100, Olivier Sallou wrote:
>>> The missing class is in libjaxb-api-java. Just make sure it's on the
>>> CLASSPATH.
>> yeap, an other issue at java migration to openj
On 12/19/18 11:46 AM, Andreas Tille wrote:
> Hi,
>
> On Wed, Dec 19, 2018 at 10:39:55AM +0100, Olivier Sallou wrote:
>>> The missing class is in libjaxb-api-java. Just make sure it's on the
>>> CLASSPATH.
>> yeap, an other issue at java migration to openj
jdk 10/11
Adding this lib to deps should fix the pb
> Regards,
>
> Markus
>
>
>
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/li
1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/exe/Distributor.java:23:
>> warning: [deprecation] Observable in java.util has been deprecated
>> [javac] import java.util.Observable;
>> [javac] ^
> Any more hints?
>
> 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
m.nih.gov/viewvc/v1?view=revision&revision=79929
>
> Olivier, will you have time to integrate these changes, or should I?
no time for the moment, if you can do it, I would appreciate
thanks
Olivier
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RE
issue is not related to an internet access.
it tries to get local host name or address
: java.net.InetAddress.getLocalHost(..)
and result in java.net.UnknownHostException: profitbricks-build15-amd64:
profitbricks-build15-amd64: Temporary failure in name resolution
According to Java:
This is achiev
additional remark:
igv will in this case need to depend on java >= 11 as this modification for
build and runtime will work only for jdk11 and above
this jdk module/deprecation transition is quite a pain and make it difficult to
get packages work for different jdk versions
- Mail origin
the problem is those packages are deprecated and cannot be used with jdk 11.
Forcing use of a previous jdk will work will this jdk is available in
debian.
the problemis to get something working both for "old" jdk and "new"
jdks I think upstream focused on older versions (installed in more
- Mail original -
> De: "andreas"
> À: 912...@bugs.debian.org, "Debian Java List"
> Envoyé: Mercredi 31 Octobre 2018 07:07:36
> Objet: Re: Bug#912385: rdp-classifier FTBFS with OpenJDK 11
> Control: tags -1 help
>
> Hi,
>
> I'm afraid I need help for this bug from the Debian Java te
- Mail original -
> De: "andreas"
> À: 912...@bugs.debian.org
> Envoyé: Mercredi 31 Octobre 2018 07:10:01
> Objet: [Debian-med-packaging] Bug#912386: rdp-readseq FTBFS with OpenJDK 11
> Control: tags -1 help
>
> Hi,
>
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 ups
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
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:
>>>>> Un
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
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
s.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
> at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110)
> at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter
dOperationExecutor.java:110)
> at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110)
> at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExec
On 09/18/2018 10:02 AM, Olivier Sallou wrote:
>
> On 09/17/2018 04:36 PM, Andreas Tille wrote:
>> Control: tags -1 pending
>>
>> This issue should be fixed in
>>
>> https://salsa.debian.org/med-team/picard-tools/commit/4da851972983cee93a3cce27bfbb40f9648d
; at
> java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at
> build_e2g2wljk0xfne1q452c0qhi2d.ensureBuildPrerequisites(/build/picard-tools-2.18.14+dfsg/build.gradle:53)
> at
> build_e2g2wljk0xfne1q452c0qhi2
Cool, thanks
Le mar. 28 août 2018 à 18:46, Alexandre Viau a écrit :
> On Sat, 25 Aug 2018 19:44:12 +0200 olivier sallou
> wrote:
> > Hi,
> > My packages have been removed from testing due to this bug.
> > Can we remove failing test and lower bug severity waiting for up
Hi,
My packages have been removed from testing due to this bug.
Can we remove failing test and lower bug severity waiting for upstream fix?
Else i will need to patch my packages to remove influx support, removing
features.
Bug impact looks quite low.
Thanks
Olivier
ltest-2.1.10+dfsg'
>> make: *** [debian/rules:11: build-indep] Error 2
>> dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit
>> status 2
>>
>>
>> Th
Le dim. 19 août 2018 à 16:17, Bernd Rinn a écrit :
> On 08/19/2018 04:02 PM, olivier sallou wrote:
> >
> >
> > Le dim. 19 août 2018 à 15:23, Bernd Rinn > <mailto:br...@ethz.ch>> a écrit :
> >
> > Hi Andreas,
> >
> > I have no
Bernd,
> >
> > could you give some hints about the missing classes?
> >
> > On Tue, Aug 14, 2018 at 12:23:22PM +0200, olivier sallou wrote:
> >> Le mar. 14 août 2018 à 11:32, Andreas Tille a écrit
> :
> >>
> >>> A problem occurred evaluating root pr
Le mar. 14 août 2018 à 11:32, Andreas Tille a écrit :
> Hi,
>
> upstream of libsis-jhdf5-java[1] has switched to gradle in its new
> version that is compatible with HDF5 1.10. I tried to adapt debian/rules
> from previous manual build to buildsystem=gradle but got:
>
> ...
> Parallel execution i
Hi,
Any chance to close this bug before removal? I have some packages depending
on it.
Thanks
Olivier
Le lun. 23 juil. 2018 à 17:38, Alexandre Viau a écrit :
> On 2018-07-23 11:23 AM, olivier sallou wrote:
> > Maybe a bug should be filled upstream
>
> Hello,
>
> Thank you for caring and putting time into this.
>
> The bug is in influxdb-python due to a breaking cha
I created an issue on upstream repo [0]
A temporary workaround could be to skip this test waiting for an upstream
resolution or explanation.
Indeed, problem may have no real incidence on usage but only on tests.
Bug could remain opened but lowered as it does not prevent its usage or
build.
[0] h
Installing numpy 1.13.3 (from pypi) which is used version in tox.ini makes
tests OK.
Fails with numpy 1.14.5 (debian default)
Maybe a bug should be filled upstream
I made a quick test and could reproduce the error using nose for testing.
However, using tox, all tests are ok (which is the tool described in readme
of repo)
On 06/01/2018 11:12 AM, Graham Inggs wrote:
> On 01/06/2018 07:23, olivier sallou wrote:
>> Ncurses dep must be set by swi prolog compiler, when creating a
>> binary from
>> logol prolog files. Logol itself does nothing related to this lib.
>>
>> If compiler ad
Ncurses dep must be set by swi prolog compiler, when creating a binary from
logol prolog files. Logol itself does nothing related to this lib.
If compiler adds some unused deps, can't really fix that.
Why setting this to serious?
Olivier
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, Bas Couwenberg wrote:
>>> On 2018-04-16 08:18, Andreas Tille wrote:
>>>> it seems something has ch
edium.com/@afinlay/whats-new-in-java-fx-java-9-updates-a90dd3d4dbba
>
> If the package works without JavaFX you should consider disabling that
> for the time being.
>
> You can also explicitly build with OpenJDK 8, but that will just get
> you a different RC bug because openjdk-8
This bug introduce reverse dependency package issues that will lead to
their removal.
For some packages in debianmed, i could patch to remove python influxdb use
(which makes use of pandas). This would remove some features but would keep
packages in the meanwhile
But this may not be so simple for
/python-thriftpy.git
/packages is missing in both URLs
>
> Can you please push?
>
> 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 (keyrin
git/source
Thanks anyway
>
> 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
do you want to open a Request Of Removal bug
>>> to get this settled?
>>>
>>> I'd also think that the bug is only closes in the case that package
>>> python3-biomaj3 "Provides: biomaj" to provide a clean upgrade path.
>>>
>>> Kind
htsjdk and picard-tools test issues are gradle related.
After some deeper tests and discussions with debian-java team, it
appears the errors faced in testing (after the patches I proposed on
testng) are related to the gradle version on debian.
Someone in java team should upgrade to an upper release
On 10/31/2017 03:05 PM, Olivier Sallou wrote:
> testng maven definition needs to be modified in build.graddle to match
> testng debian pom.
>
> Following patch fix the compilation for tests:
>
> --- a/build.gradle
> +++ b/build.gradle
> @@ -32,7
adle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>> at
>> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:45)
>> at
>> org.gradle.api.internal.tasks.execu
Hi,
I have added a patch (and updated one) to use base testing instead of using
scalatest library, as it is not available in debian.
I also disabled scala related tests (as scalatest not available).
With this, the package builds fine. I do not checked how it *works*...
Compilation is fine but is s
- Mail original -
> De: "Andreas Tille"
> À: 877...@bugs.debian.org, "Charles Plessy" , "Olivier
> Sallou" , "Vincent
> Danjean"
> Cc: "Debian Bug Tracking System"
> Envoyé: Mercredi 11 Octobre 2017 11:22:18
>
Will try to look, but error is completly unknown and strange to me
Olivier
Le mer. 11 oct. 2017 11:23, Andreas Tille a écrit :
> Hi folks,
>
> it seems no-one of the Java-competent uploaders cared for this in the
> first place and so I gave the new version a shot in Git. It seems
> to be a
there is a patch in d/patches that removes drmaa support from upstream code.
This was at time of sge/drmaa removal from Debian.
So drmaa is not used at all, only the symlink remained (certainly an error
forgetting to clean the link file).
Gonna update to remove link from package, and see if drmaa
Sure, will do.
Logol optionally depends on drmaa
Can work without functionally, but need jar as dependency.
Have always been the case, so i wobder if at some time there was some changes
in libdrmaa-java. Anyway, will look soon.
- Andreas Tille a écrit :
> Hi Olivier,
>
> could you please
This issue is only related to upgrades if previous jdk was Java 7. It needs
Java 8.
User only needs to execute it with Java8.
As this package version is deprecated in favor of biomaj3 (in NEW queue at
this time), this is not really needed to fix.
94f8277946f52c78dd6227c55969957e97d78bed
Author: Olivier Sallou
Date: Wed Sep 6 06:55:06 2017 +
fix licensing
diff --git a/debian/changelog b/debian/changelog
index 2cacb32..c2add21 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,8 @@
-python-py-zipkin (0.9.0-2) UNRELEASED
Le mar. 5 sept. 2017 à 21:00, Ben Plotnick a écrit :
> Hi Chris,
>
> On Tue, 29 Aug 2017 20:24:55 +0100 Chris Lamb wrote:
> > Source: python-py-zipkin
> > Version: 0.9.0-1
> > Severity: serious
> > Justication: Policy 12.5
> > X-Debbugs-CC: Olivier Sall
confirmation: biomaj-watcher has been compiled with jdk8
on upgrades, if jdk7 is installed, it will fail to execute/install
in case of upgrade, we switch from jdk7 to jdk8, but install is first
made against jdk7.
jdk must be upgraded first, then biomaj-watcher can be installed.
Solution would
(only apt-get dist-upgrade) works fine.
>
> There is probably an insufficiently versioned Depends (or Breaks) ...
> but I have no idea which package could be meant with
> Unsupported major.minor version 52.0
>
>
> cheers,
>
> Andreas
>
>
> _________
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