Bug#944943: python-freecontact: needs an explicit build dependency on dh-python

2019-11-17 Thread Andreas Tille
Control: tags -1 moreinfo Hi Matthias, On Sun, Nov 17, 2019 at 07:07:32PM +, Matthias Klose wrote: > Package: src:python-freecontact > Version: 1.1-5 > Severity: serious > Tags: sid bullseye > > python3-all and python3-dev now dropped the dependency on > dh-python: > > [ Piotr Ożarowski ]

Bug#937657: Issue with numpy under Python 3.8

2019-11-17 Thread Andreas Tille
Hi Graham, On Sun, Nov 17, 2019 at 02:16:29PM +0200, Graham Inggs wrote: > If you look on the numpy tracker page [1], you'll see there is a note: > > "This package is part of the ongoing testing transition known as > python3.8. Please avoid uploads unrelated to this transition, they > would

Bug#937657: Issue with numpy under Python 3.8

2019-11-16 Thread Andreas Tille
Hi Rebecca, On Sat, Nov 16, 2019 at 09:16:17AM +, Rebecca N. Palmer wrote: > I think that just means "numpy hasn't yet been rebuilt for Python 3.8". (In > Python modules that include a C extension, the .py files are shared but the > C part is compiled separately for each Python version.) > >

Bug#937657: Issue with numpy under Python 3.8 (Was: python-colormap: Python2 removal in sid/bullseye)

2019-11-15 Thread Andreas Tille
Control: tags -1 help Hi, I have dropped the Python2 package in Git[1] and tried to build which ended up in: ... I: pybuild base:217: cd /build/python-colormap-1.0.2/.pybuild/cpython3_3.8_colormap/build; python3.8 -m nose -v test nose.config: INFO: Ignoring files matching ['^\\.', '^_',

Bug#944042: Help needed to adapt python-skbio to Python3(?) / Pandas

2019-11-14 Thread Andreas Tille
Control: tags -1 help Control: tags -1 upstream Control: forwarded -1 https://github.com/biocore/scikit-bio/issues/1678 Hi Rebecca, thanks a lot for working on the Pandas migration. On Wed, Nov 13, 2019 at 10:19:56PM +, Rebecca N. Palmer wrote: > The ones that are blocking pandas [1] are

Bug#937330: Remove pyoptical from Debian, upgrade psychopy to latest upstream to enable Pandas migration

2019-11-13 Thread Andreas Tille
Hi, I stumbled upon pyoptical since its the only package that uses psychopy which in turn is blocking the python-pandas migration to Python3. Psychopy is extremely lagging behind upstream (which probably - not checked might have switched to Python3). From my point of view it makes sense to

Bug#874853: [cmtk] Future Qt4 removal from Buster

2019-11-11 Thread Andreas Tille
Done. Thanks for the patch, Andreas. On Sun, Nov 10, 2019 at 11:09:12PM +0100, Moritz Mühlenhoff wrote: > On Thu, Oct 31, 2019 at 08:11:31PM -0700, Torsten Rohlfing wrote: > > > > There hasn't been any followup on this bug since two years and we're now > > > moving > > > forward with the Qt4

Bug#940902: doesn't read the data

2019-11-10 Thread Andreas Tille
On Sun, Nov 10, 2019 at 05:32:48PM +0100, Ana Guerrero Lopez wrote: > > > > Welcome to the team, Andreas. > > Thanks! > Good news, I've tested and it works fine. I'm doing a team upload right now. > > I think we shouldn't give up in getting this ported to python3, but I think a > re-write

Bug#855494: Broken with different error - I'm going to ask for removal of the package soon

2019-11-08 Thread Andreas Tille
On Fri, Nov 08, 2019 at 06:00:08PM +0100, Michael Crusoe wrote: > > I got farther, but now the "dashboard" module won't load (no traceback). > The tests still fail spectacularly. > > This is very old and non-free code. I suggest that all mglools* and > autodocktools* packages be removed. I'm

Bug#874880: [freemedforms-project] Future Qt4 removal from Buster

2019-10-28 Thread Andreas Tille
3PM +0200, Andreas Tille wrote: > > Hi again, > > > > I'm sorry to repeat myself but please pretty please help finding some > > solution. Freemedform-project is about to be removed from Debian and > > I see no way to prevent this. > > Andreas, > can you fi

Bug#925745: libgtextutils is marked for autoremoval from testing

2019-10-15 Thread Andreas Tille
Hi Olivier, any solution? On Tue, Oct 15, 2019 at 04:39:04AM +, Debian testing autoremoval watch wrote: > libgtextutils 0.7-6 is marked for autoremoval from testing on 2019-10-25 > > It is affected by these RC bugs: > 925745: libgtextutils: ftbfs with GCC-9 > > >

Bug#875065: [odin] Future Qt4 removal from Buster -> odin is ready for Qt5

2019-10-12 Thread Andreas Tille
I can do so not before November 4th, Andreas. On Fri, Oct 11, 2019 at 11:08:02PM +0200, Moritz Mühlenhoff wrote: > On Wed, Jan 23, 2019 at 09:46:28AM +0100, thies wrote: > > Dear all, > > > > odin should compile on Buster without changes using the packages qt5-default > > and libqwt-qt5-dev. >

Bug#941638: autopkg tests still rely on removed python-schema

2019-10-11 Thread Andreas Tille
Hi, since I have no permissions to push my patches feel free to git am the attachments from my NMU. Kind regards Andreas. -- http://fam-tille.de >From 27ed7d0257f4487b2ef24709f5d7e87ecf2c66ba Mon Sep 17 00:00:00 2001 From: Andreas Tille Date: Fri, 11 Oct 2019 11:33:38 +0200 Subj

Bug#905206: Additional remark to: Status of rostlab software in Debian (Was: Bug#905206: Seems to crash in fortran lib)

2019-10-11 Thread Andreas Tille
ate replacements might be. We'd happily support you in packaging the latest and greatest code from your lab. Kind regards and thanks a lot for your cooperation Andreas. On Tue, Oct 08, 2019 at 04:47:12PM +0200, Andreas Tille wrote: > Hello, > > back in 2009 Laszlo Kajan did quite

Bug#905206: Status of rostlab software in Debian (Was: Bug#905206: Seems to crash in fortran lib)

2019-10-08 Thread Andreas Tille
+0200, Olivier Sallou wrote: > > 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 > >>> refe

Bug#874880: [freemedforms-project] Future Qt4 removal from Buster

2019-10-08 Thread Andreas Tille
Hi again, I'm sorry to repeat myself but please pretty please help finding some solution. Freemedform-project is about to be removed from Debian and I see no way to prevent this. Kind regards Andreas. On Sat, Sep 21, 2019 at 08:45:05AM +0200, Andreas Tille wrote: > Hi Eric, >

Bug#940564: [lbcb-sci/racon] Incompatible with latest spoa release (#6)

2019-10-08 Thread Andreas Tille
On Tue, Oct 08, 2019 at 03:51:47AM -0700, Robert Vaser wrote: > Hi Andreas, yes I have a plan how to deal with it but I am not available for > a week or more. Will let you know. Thanks a lot. Just take your time until end of October since I'll be not available until then. ;-)

Bug#941920: jellyfish: FTBFS on ppc64el

2019-10-07 Thread Andreas Tille
Control: tags -1 help > See https://buildd.debian.org/status/logs.php?pkg=jellyfish=ppc64el I see Testsuite summary for jellyfish 2.3.0 #

Bug#940564: Upstream tries to find a solution without liblogger

2019-10-05 Thread Andreas Tille
The current racon needs an extra dependency from liblogger (#940585). Upstream is working on a solution without this since it was rejected. -- http://fam-tille.de

Bug#939663: Usage of Debian Science Git repositories [Was: freefem++_3.61.1+dfsg1-5_source.changes ACCEPTED into unstable]

2019-10-05 Thread Andreas Tille
a nuisance and is demotivating to touch a package. Kind regards Andreas. - Forwarded message from Debian FTP Masters - Date: Sat, 05 Oct 2019 08:49:10 + From: Debian FTP Masters To: Debian Science Maintainers , Andreas Tille Subject: freefem++_3.61.1+dfsg1-5_source.change

Bug#905206: Seems to crash in fortran lib

2019-10-04 Thread Andreas Tille
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 fortran issue after an > upgrade (something that was working but not done the

Bug#935086: insighttoolkit4 REMOVED from testing

2019-10-03 Thread Andreas Tille
Hi Steve and Gert, since I have no idea about itk I have ignored this issue. Is there any chance to get this fixed soon to make sure this package and its rdepends will migrate back to testing soon? Kind regards Andreas. On Fri, Oct 04, 2019 at 04:39:19AM +, Debian testing watch

Bug#905206: Do you have some spare cycles to have a look at this (Was: profnet is marked for autoremoval from testing)

2019-10-02 Thread Andreas Tille
Hi Shayan, more pinging the bug to extend the period the package stays in testing but in case you might have any temporary results for this issue feel free to post these here. Kind regards, Andreas. On Sat, Sep 21, 2019 at 07:05:27PM +0200, Andreas Tille wrote: > Hi Shayan, > > On Sa

Bug#940902: doesn't read the data

2019-09-30 Thread Andreas Tille
On Mon, Sep 30, 2019 at 11:47:14PM +0200, Ana Guerrero Lopez wrote: > > Thanks to you. I'd be happy if you could check master[1] and confirm > > that it is OK. I can even give you commit permissions so you can change > > anything you feel sensible and do the team upload yourself. > > Please,

Bug#925745: Bug#925745: [Help] libgtextutils: ftbfs with GCC-9

2019-09-25 Thread Andreas Tille
Hi again, On Wed, Sep 11, 2019 at 02:16:04PM +0200, Andreas Tille wrote: > > commenting in text_line_reader.h: > > > >         // operator const std::string& () const { return > > line_string() ; } > > > > do the job and test pass > > > >

Bug#875150: Should we file a removal bug?

2019-09-25 Thread Andreas Tille
Hi, On Tue, Sep 24, 2019 at 10:48:24PM +0200, Moritz Mühlenhoff wrote: > On Tue, Sep 17, 2019 at 12:05:17PM -0300, Lisandro Damián Nicanor Pérez Meyer > wrote: > > Hi! It seems there is no activity on this bug, should we file a removal bug? > > Adding the last two uploaders to CC. ... as well

Bug#940902: doesn't read the data

2019-09-23 Thread Andreas Tille
Hi Ana, On Sun, Sep 22, 2019 at 11:11:47PM +0200, Ana Guerrero Lopez wrote: > > thanks a lot for thorough testing the package! > > > > The situation is as follows: Upstream is dead so we probably become > > upstream in Debian. I has done my best to port it to Python3 with the > > help of

Bug#905206: Do you have some spare cycles to have a look at this (Was: profnet is marked for autoremoval from testing)

2019-09-21 Thread Andreas Tille
Hi Shayan, On Sat, Sep 21, 2019 at 05:23:49PM +0100, Shayan Doust wrote: > This is new territory - I have spent some time looking at this and so far I > could only reproduce all of what was already mentioned above. It might become time consuming. > I will later go more in-depth and try using

Bug#940902: doesn't read the data

2019-09-21 Thread Andreas Tille
Control: tags -1 help Dear Ana, On Sat, Sep 21, 2019 at 05:41:27PM +0200, Ana Guerrero Lopez wrote: > This new version of cycle, ported to python3, doesn't read the data file > ( under .cycle) and prompts to create a new user. > > Not creating a new user and downgrading to the version in buster

Bug#874880: [freemedforms-project] Future Qt4 removal from Buster

2019-09-21 Thread Andreas Tille
at 11:41:33AM +0200, Andreas Tille wrote: > Hi, > > thanks to a patch by Michael Crusoe I'm a bit further now but there are > remaining errors. I have no idea about C++/Qt and thus need to ask for > help. Eric, are you up to safe your package inside Debian? > > ... > g++

Bug#875184: Help needed for medical imaging framework sofa (Was: Bug#875184: [sofa-framework] Future Qt4 removal from Buster)

2019-09-21 Thread Andreas Tille
Hi, On Fri, Sep 20, 2019 at 11:55:03PM +0200, Moritz Mühlenhoff wrote: > On Fri, Sep 20, 2019 at 06:41:05PM -0300, Lisandro Damián Nicanor Pérez Meyer > wrote: > > I've created a WIP merge request at > > > > https://salsa.debian.org/med-team/sofa-framework/merge_requests/1 > > > > I could

Bug#940611: fails to start because no wrapper missing

2019-09-19 Thread Andreas Tille
Hi Dylan, On Thu, Sep 19, 2019 at 05:08:28PM +0200, Dylan Aïssi wrote: > Le mar. 17 sept. 2019 à 23:08, Andreas Tille a écrit : > > Thanks for your bug report including the patch. I've pushed it the the > > packaging Git leaving the package for final inspection by Dylan. >

Bug#875184: Help needed for medical imaging framework sofa (Was: Bug#875184: [sofa-framework] Future Qt4 removal from Buster)

2019-09-19 Thread Andreas Tille
Hi Lisandro, On Wed, Sep 18, 2019 at 07:42:23PM -0300, Lisandro Damián Nicanor Pérez Meyer wrote: > On 19/09/17 10:17, Andreas Tille wrote: > > On Tue, Sep 17, 2019 at 01:26:17PM -0300, Lisandro Damián Nicanor Pérez > > Meyer wrote: > > > > > > Is

Bug#912077: Any chance to get libbiod compiling again?

2019-09-19 Thread Andreas Tille
Hi Matthias, On Thu, Sep 19, 2019 at 12:49:54AM +0200, Matthias Klumpp wrote: > > As I told you before: I have no idea about meson. It would be great if > > we could get it working but if we restrict the package to those > > architectures where it builds out of the box and save some manpower I

Bug#912077: Any chance to get libbiod compiling again?

2019-09-19 Thread Andreas Tille
Hi Pjotr, On Wed, Sep 18, 2019 at 05:43:08PM -0500, Pjotr Prins wrote: > Libundead was removed as dependency for biod, but it may be there are > some other issues now because the D ecosystem keeps moving. > > My main interest is sambamba and we are working on a fix for one of > the main

Bug#912077: Any chance to get libbiod compiling again?

2019-09-18 Thread Andreas Tille
Hi, [Pjotr as upstream in CC] On Wed, Sep 18, 2019 at 04:54:16PM +0200, Matthias Klumpp wrote: > Am Fr., 13. Sept. 2019 um 22:51 Uhr schrieb Andreas Tille : > > > > On Fri, Sep 13, 2019 at 03:37:32PM +0200, Matthias Klumpp wrote: > > > Am Fr., 13. Sept. 2019 um 15:21 U

Bug#940564: racon: FTBFS against libspoa3

2019-09-18 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/lbcb-sci/racon/issues/6

Bug#935349: Reviving maintenance of python-pyface

2019-09-18 Thread Andreas Tille
Hi, pyface was lagging extremely behind upstream. To cope with Qt5 and Python3 migration I simply pushed the latest upstream version to the packaging Git[1] == ERROR: pyface.action.tests.test_action_item

Bug#940611: fails to start because no wrapper missing

2019-09-17 Thread Andreas Tille
Control: tag -1 pending Hi Daniel, On Tue, Sep 17, 2019 at 09:31:13PM +0200, Daniel Baumann wrote: > tag 940611 + patch > thanks > > here's a patch: > https://git.progress-linux.org/distributions/engywuck/packages/beagle/commit/?id=dfd229f18e861f5107091be55b82770e961dd7dd Thanks for your bug

Bug#940564: racon: FTBFS against libspoa3

2019-09-17 Thread Andreas Tille
Hi again, On Tue, Sep 17, 2019 at 02:15:51PM +0200, Andreas Tille wrote: > Latest upstream needs liblogger[1] which needs to be packaged new. > I'm working on this (Python3 migration drained to many resources, > sorry) > > [1] https://salsa.debian.org/med-team/liblogger Th

Bug#875184: Help needed for medical imaging framework sofa (Was: Bug#875184: [sofa-framework] Future Qt4 removal from Buster)

2019-09-17 Thread Andreas Tille
On Tue, Sep 17, 2019 at 01:26:17PM -0300, Lisandro Damián Nicanor Pérez Meyer wrote: > > Is the embedded stuff all in extlibs/? or is there some other 3rdparty code? A lot is excluded in advance from the packaging Git: Files-Excluded: */libQGLViewer* */csparse

Bug#940564: racon: FTBFS against libspoa3

2019-09-17 Thread Andreas Tille
Latest upstream needs liblogger[1] which needs to be packaged new. I'm working on this (Python3 migration drained to many resources, sorry) [1] https://salsa.debian.org/med-team/liblogger -- http://fam-tille.de

Bug#874916: [imagevis3d] Future Qt4 removal from Buster

2019-09-16 Thread Andreas Tille
+0200, Moritz Mühlenhoff wrote: > On Mon, Sep 16, 2019 at 11:31:45AM +0200, Andreas Tille wrote: > > Hi Moritz, > > > > On Sun, Sep 15, 2019 at 11:19:32PM +0200, Moritz Mühlenhoff wrote: > > > > I have opened an issue on Github (#8) that a Qt5 port would be helpf

Bug#905206: Do you have some spare cycles to have a look at this (Was: profnet is marked for autoremoval from testing)

2019-09-16 Thread Andreas Tille
Hi Shayan, On Mon, Sep 16, 2019 at 04:39:03AM +, Debian testing autoremoval watch wrote: > profnet 1.0.22-6 is marked for autoremoval from testing on 2019-09-26 > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging This bug is quite some nuisance since several

Bug#874916: [imagevis3d] Future Qt4 removal from Buster

2019-09-16 Thread Andreas Tille
Hi Moritz, On Sun, Sep 15, 2019 at 11:19:32PM +0200, Moritz Mühlenhoff wrote: > > I have opened an issue on Github (#8) that a Qt5 port would be helpful > > to keep the imagevis3d package inside Debian. > > Given the radio silence in https://github.com/SCIInstitute/ImageVis3D/issues/8 > let's

Bug#912077: Any chance to get libbiod compiling again?

2019-09-13 Thread Andreas Tille
On Fri, Sep 13, 2019 at 03:37:32PM +0200, Matthias Klumpp wrote: > Am Fr., 13. Sept. 2019 um 15:21 Uhr schrieb Andreas Tille : > > /usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of > > '_d_execBssBegAddr' > > /usr/bin/ld.gold: contrib/undead/*/__main.o: pre

Bug#912077: Any chance to get libbiod compiling again?

2019-09-13 Thread Andreas Tille
Hi Matthias, since a ling time libbiod does not build and it also does not install. Current issue when trying to build it is: ... ldc2 -wi -g -relocation-model=pic -unittest -main -Icontrib/undead -L-lz -O0 -d-debug -link-debuglib contrib/undead/cstream.o contrib/undead/stream.o

Bug#938494: skimage (build-)depends on python-cloudpickle which has already been dropped

2019-09-13 Thread Andreas Tille
On Fri, Sep 13, 2019 at 11:09:58AM +0200, Ole Streicher wrote: > > Sure. But do you want to do team uploads of python-numpy and its > 300 > > rdepends as well? I was considering the amount of packages that are > > affected by RC bugs which is way lower if we leave skimage RC buggy > > rather

Bug#938494: skimage (build-)depends on python-cloudpickle which has already been dropped

2019-09-13 Thread Andreas Tille
Hi, as Peter Green found out the cloudpickle source package droped Python2 support which makes bug #938494 serious. I guess it would be even harder to drop python-skimage right now since this would affect python-numpy and according to $ apt-cache rdepends python-numpy | sort | uniq | wc -l

Bug#875184: Help needed for medical imaging framework sofa (Was: Bug#875184: [sofa-framework] Future Qt4 removal from Buster)

2019-09-12 Thread Andreas Tille
Control: tags -1 help On Sun, Sep 08, 2019 at 11:00:34PM +0200, Moritz Mühlenhoff wrote: > On Sun, Sep 08, 2019 at 08:41:40AM +0200, Andreas Tille wrote: > > On Sat, Sep 07, 2019 at 10:43:53PM +0200, Moritz Mühlenhoff wrote: > > > > > > The current releases on https:

Bug#925745: Bug#925745: [Help] libgtextutils: ftbfs with GCC-9

2019-09-11 Thread Andreas Tille
Hi Olivier, On Tue, Aug 20, 2019 at 05:57:50PM +0200, Olivier Sallou wrote: > > On 8/20/19 3:41 PM, Andreas Tille wrote: > > Hi Olivier, > > > > I'm just forwarding this to Debian Mentors list to get a wider audience. > > I'd prefer a fix over simply removing t

Bug#875184: [sofa-framework] Future Qt4 removal from Buster

2019-09-08 Thread Andreas Tille
On Sat, Sep 07, 2019 at 10:43:53PM +0200, Moritz Mühlenhoff wrote: > > The current releases on https://github.com/sofa-framework claim to be Qt5 > compatible. Is anyone working on updating the package or should it be removed? > > sofa-framework is one of the three remaining reverse dependencies

Bug#935345: microbegps: Qt4 removal from Bullseye

2019-09-06 Thread Andreas Tille
On Fri, Sep 06, 2019 at 04:21:10PM +0300, Dmitry Shachnev wrote: > > AttributeError: 'GPSAnalyzer' object has no attribute 'sgroups' > > self.sgroups is set in visualize() method. > > So maybe it works only when you actually have some data? E.g. if you open > a file and then save it, it should

Bug#935345: microbegps: Qt4 removal from Bullseye

2019-09-06 Thread Andreas Tille
On Fri, Sep 06, 2019 at 03:40:18PM +0300, Dmitry Shachnev wrote: > That is because resource_stream() returns stream in binary mode, not text: > > https://setuptools.readthedocs.io/en/latest/pkg_resources.html#basic-resource-access > > Try adding .decode('utf-8'): > > fields =

Bug#935345: microbegps: Qt4 removal from Bullseye

2019-09-06 Thread Andreas Tille
Hi Dmitry, On Fri, Sep 06, 2019 at 02:28:48PM +0300, Dmitry Shachnev wrote: > On Fri, Sep 06, 2019 at 01:18:33PM +0200, Andreas Tille wrote: > > since upstream is currently inactive I tried my best to do the > > porting of this package in Git[1]. The Python3 port went quite >

Bug#935345: microbegps: Qt4 removal from Bullseye

2019-09-06 Thread Andreas Tille
Control: tags -1 help Hi, since upstream is currently inactive I tried my best to do the porting of this package in Git[1]. The Python3 port went quite smoothly and I have the feeling I made quite some progress with Qt5 port. However, when I build HEAD from the packaging Git[1] install the

Bug#874880: [freemedforms-project] Future Qt4 removal from Buster

2019-09-06 Thread Andreas Tille
Hi, thanks to a patch by Michael Crusoe I'm a bit further now but there are remaining errors. I have no idea about C++/Qt and thus need to ask for help. Eric, are you up to safe your package inside Debian? ... g++ -c -pipe -g -O2 -fdebug-prefix-map=/build/freemedforms-project-1.0.0=.

Bug#874880: [freemedforms-project] Future Qt4 removal from Buster

2019-09-06 Thread Andreas Tille
Control: tags -1 help Hi Moritz, On Thu, Sep 05, 2019 at 11:26:12PM +0200, Moritz Mühlenhoff wrote: > I've downloaded 1.0.0 and the included README.md states "FreeMedForms > and derivatives are coded in C++ / Qt5", so I suppose the latest > version should now support Qt5. > > If that works

Bug#935293: rampler: FTBFS on amd64

2019-09-05 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/rvaser/rampler/issues/2 I think upstream has just addressed this and just forgot to tag a release. Just filed an issue to save the time to apply patches since upstream usually responds quickly. Kind regards, Andreas.

Bug#933527: snakemake: fails to install: SyntaxError: duplicate argument 'stay_on_remote' in function definition

2019-09-05 Thread Andreas Tille
to add themselves to the list of Uploaders and care for this package? Kind regards Andreas. On Mon, Sep 02, 2019 at 10:09:22AM +0200, Andreas Tille wrote: > Hi, > > On Wed, Jul 31, 2019 at 10:37:22AM +0200, Andreas Beckmann wrote: > > Version: 5.5.3-1 > > Severity: se

Bug#939002: Problem in test suite of sf since upgrade of proj

2019-09-04 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 Edzer Pebesma Hi Edzer, since the upgrade to proj (6.1.1-1) the autopkgtest for sf fails: $ LC_ALL=C.UTF-8 R --no-save < testthat.R R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical

Bug#933527: snakemake: fails to install: SyntaxError: duplicate argument 'stay_on_remote' in function definition

2019-09-02 Thread Andreas Tille
Hi, On Wed, Jul 31, 2019 at 10:37:22AM +0200, Andreas Beckmann wrote: > Version: 5.5.3-1 > Severity: serious > > during a test with piuparts I noticed your package failed to install. As > per definition of the release team this makes the package too buggy for > a release, thus the severity. > >

Bug#905206: Could you have a look at profnet test?

2019-08-27 Thread Andreas Tille
Hi Tatiana, since some time one of the profnet tests is failing with Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Do you have time to do some debugging on this? Kind regards Andreas. -- http://fam-tille.de

Bug#931948: r-cran-lwgeom: FTBFS with PROJ 6

2019-08-26 Thread Andreas Tille
Hi, On Fri, Jul 12, 2019 at 08:55:02PM +0200, Bas Couwenberg wrote: > Source: r-cran-lwgeom > Version: 0.1-5+repack-1 > Severity: important > Tags: upstream > User: debian-...@lists.debian.org > Usertags: proj-6 > > Your package FTBFS with PROJ 6 from experimental. > > It fails at configure

Bug#920545: python-intervaltree breaks python-intervaltree-bio autopkgtest

2019-08-21 Thread Andreas Tille
Hi Graham, On Wed, Aug 21, 2019 at 03:31:35PM +0200, Graham Inggs wrote: > > I uploaded to Ubuntu the fix that was already in git [1]. > At the bottom right of the package tracker [2] (or the old PTS) is a link to > patches in Ubuntu. So it seems you were just lucky. I checked again, the error

Bug#920545: python-intervaltree breaks python-intervaltree-bio autopkgtest

2019-08-21 Thread Andreas Tille
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 this might be. Any hint / patch / team upload that would fix the

Bug#925745: [Help] libgtextutils: ftbfs with GCC-9

2019-08-20 Thread Andreas Tille
Hi Olivier, I'm just forwarding this to Debian Mentors list to get a wider audience. I'd prefer a fix over simply removing the test ... Thanks for your analysis anyway Andreas. On Tue, Aug 20, 2019 at 03:36:48PM +0200, Olivier Sallou wrote: > > On 8/20/19 1:24 PM, Andreas Tille

Bug#925745: [Help] libgtextutils: ftbfs with GCC-9

2019-08-20 Thread Andreas Tille
Control: tags -1 help Hi, any hint how to deal with ... g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default

Bug#925731: libbpp-*: ftbfs with GCC-9

2019-08-20 Thread Andreas Tille
Hi Julien, On Tue, Aug 20, 2019 at 11:37:19AM +0200, Julien Dutheil wrote: > All packages compile without warning with gcc 9. I think the issue is (again) > the symbol files, which have to be regenerated. > Honestly, it seems to me that these symbol files brought more issues than > they solved

Bug#934600: gffread in cufflinks seems to be the same codebase but older

2019-08-19 Thread Andreas Tille
Hi Alexandre, it looks as if the gffread code in cufflinks would be the same code base but the code in gffread source seems to be more recent. What do you think? Kind regards Andreas. - Forwarded message from Debian testing autoremoval watch - Date: Tue, 20 Aug 2019 04:39:04

Bug#875075: Kido renamed to dart - waiting in new queue (Was: [openscenegraph] Future Qt4 removal from Buster)

2019-08-19 Thread Andreas Tille
Hi, I also checked kido. Thanks to Jose Luis Rivero who prepared the renamed version dart in Git[1] I now uploaded this to new with Build-Depends changed to libopenscenegraph-3.4-dev. Since I explained in my last mail that there is no point in waiting for opensurgsim there is no reason to wait

Bug#875075: [openscenegraph] Future Qt4 removal from Buster

2019-08-19 Thread Andreas Tille
Hi, as member of the opensurgsim maintainer team I confirm that there is no point in waiting for this package. If all fails it probably should be removed. Kind regards, Andreas. -- http://fam-tille.de

Bug#934370: r-cran-fs: autopkgtest regression

2019-08-19 Thread Andreas Tille
Control: forwarded -1 Jim Hester Hi Jim, as you can read below there is an issue with the test suite of fs version 1.3.1. Do you have any hint whether we might do something wrong in calling the tests via: for testfile in *.R; do LC_ALL=C.UTF-8 R --no-save < $testfile done or something

Bug#875026: marked as pending in libquazip

2019-08-18 Thread Andreas Tille
Control: tag -1 pending Hello, Bug #875026 in libquazip reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at:

Bug#875026: [libquazip] Future Qt4 removal from Buster

2019-08-17 Thread Andreas Tille
wrote: > > On 10 September 2017 at 03:25, Andreas Tille wrote: > > > libquazip builds both Qt4 and Qt5 interface. I could simply drop the > > > Qt4 interface to fix this bug by breaking nomacs and freemedforms build. > > > > I would first file proper bugs against th

Bug#934360: Bug#934360: r-cran-boolnet: autopkgtest regression

2019-08-11 Thread Andreas Tille
Can you please simply do team uploads if you found a patch. I'm busy with real life for the next 10 days. On Sun, Aug 11, 2019 at 01:17:40PM +0200, Graham Inggs wrote: > Control: tags -1 + patch > > The patch below got the test passing in Ubuntu. > > --- a/debian/tests/run-unit-test > +++

Bug#934281: r-bioc-metagenomeseq: Should not migrate to testing

2019-08-08 Thread Andreas Tille
Package: r-bioc-metagenomeseq Severity: grave Tags: upstream Justification: renders package unusable Hi, we can not upgrade r-bioc-metagenomeseq to the new upstream version since it got a new dependency from a non-free package. We are sorting this out with upstream but this might take time.

Bug#933937: biobambam2 | Name conflict with exonerate: fastaexplode is used by both software packages (#83)

2019-08-08 Thread Andreas Tille
Hello German, On Thu, Aug 08, 2019 at 07:56:41AM +, German Tischler wrote: > I have renamed the program in biobambam2 to fastaexplod. I hope this helps. This definitely solves the problem. Thanks a lot, Andreas.

Bug#933937: biobambam2: /usr/bin/fastaexplode is already provided by exonerate

2019-08-07 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://gitlab.com/german.tischler/biobambam2/issues/83, Guy St.C. Slater Hi Guy, as you can read in the bug report[1] against exonerate and biobambam2 there is a name space conflict between these two packages and thus the Debian packages can not

Bug#933937: Exonerate conflicts with biobambam

2019-08-05 Thread Andreas Tille
On Sun, Jul 28, 2019 at 01:40:33AM +0200, Steffen Möller wrote: > > Am 27.07.2019 um 20:09 schrieb Andreas Tille: > > On Sat, Jul 27, 2019 at 07:40:45PM +0200, Steffen Möller wrote: > > > dpkg: error processing archive > > > /var/cache/apt/archives/exonera

Bug#905206: profnet: autopkgtest regression

2019-08-02 Thread Andreas Tille
Control: tags -1 forwarded assist...@rostlab.org

Bug#905206: profnet: autopkgtest regression

2019-08-02 Thread Andreas Tille
Control: tags -1 upstream Control: tags -1 forwarded profnet: autopkgtest regression Hi, please have a look at a bug in the Debian package of profnet: https://bugs.debian.org/905206 There is an issue in profnet_snapfun: profnet_snapfun switch 385 55 10 46 100 PROFin.dat PROFacc_tst.jct

Bug#881555: Epydoc will be removed

2019-08-01 Thread Andreas Tille
OK, I think "removing the API doc" is a sufficient hint what should be done ... On Thu, Aug 01, 2019 at 07:51:44AM +0200, Andreas Tille wrote: > Hi Kenneth, > > if you provide a patch the package will be uploaded in less then 24 > hours. I'm fine without the API doc

Bug#881555: Epydoc will be removed

2019-07-31 Thread Andreas Tille
Hi Kenneth, if you provide a patch the package will be uploaded in less then 24 hours. I'm fine without the API doc. Thanks for your cooperation Andreas. On Wed, Jul 31, 2019 at 09:51:38PM -0500, Kenneth Pronovici wrote: > Hi, > > This is still one of 20+ packages in the archive that

Bug#927166: libbiod0: not installable in sid

2019-07-26 Thread Andreas Tille
Hi Shayan, On Fri, Jul 26, 2019 at 03:14:20PM +0100, Shayan Doust wrote: > Honestly never even heard of Dlang so I thought I'd give this a try. Let me say at first that's quite a brave approach. I need to admit that I als never heard before I had a package which actually needs that library. >

Bug#914731: r-bioc-biocparallel: autopkgtest regression - any idea

2019-07-22 Thread Andreas Tille
Hi folks, after each new upload of r-bioc-biocparallel the autopkgtest fails in a different way. Currently I have no good idea what might be the problem and currently its also urgent to fix it since if we don't our whole BioC stack will be removed from testing which we need to prevent. Any idea

Bug#920545: [Request for comments about Python3 migration] PbSuite

2019-07-21 Thread Andreas Tille
Hi folks, it is time to decide about some packages which are upstream Python2 and will probably not supported any more so we would become upstream for the Python3 migration. We probably need to confess that we do not have the capacity to do so. My first candidate for this decision is pbsuite.

Bug#932543: Please switch to Python 3

2019-07-20 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/PacificBiosciences/pbcommand/issues/189 On Sat, Jul 20, 2019 at 03:28:41PM +0200, Thomas Goirand wrote: > Your package is Python 2 only, please switch it to Python 3 (only), as I'm > removing Python 2 support in python-xmlbuilder

Bug#908662: r-cran-etm: autopkgtest regression: saved results mismatch

2019-07-20 Thread Andreas Tille
Sure I'll agree - just do whatever you consider sensible. Thanks, Andreas. On Sat, Jul 20, 2019 at 10:11:51AM +0200, Graham Inggs wrote: > Control: reopen -1 > Control: tags -1 + patch > > Hi Andreas > > Your patch fixed the autopkgtest on amd64 and armhf, but now it fails > on i386, arm64,

Bug#908662: r-cran-etm: autopkgtest regression: saved results mismatch

2019-07-17 Thread Andreas Tille
gonna play a bit with the state names > dd <- sir.cont I tend to ignore this for now but it would be really helpful if you could solve this in a future release. Kind regards Andreas. On Tue, Oct 02, 2018 at 07:09:38AM +0200, Andreas Tille wrote: > Hi, > > it is definitely a

Bug#929506: gbrowse FTBFS: tests fail

2019-07-09 Thread Andreas Tille
Hi Carnë, On Tue, Jul 09, 2019 at 04:53:31PM +0100, Carnë Draug wrote: > On Tue, 9 Jul 2019 at 10:33, Andreas Tille wrote: > > > > https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/gbrowse_2.56+dfsg-4.rbuild.log.gz > > I have checked the output from that

Bug#929506: gbrowse FTBFS: tests fail

2019-07-09 Thread Andreas Tille
Hi Carnë, I have not checked but I could imagine that this issue is somehow connected to the the new upstream version of bioperl. Since you intended to to restructure the bioperl packages I think this is a good point in time. Since you are way more involved in bioperl than I I'd be more than

Bug#930356: CVE-2019-12760

2019-06-21 Thread Andreas Tille
Hi Piotr, On Fri, Jun 21, 2019 at 01:15:23PM +0200, Piotr Ożarowski wrote: > >https://github.com/davidhalter/parso/issues/75 > > > > I understand that it is not fixed but the authors do not consider the > > issue serious. Could you please give some comment from an insiders > > point of view

Bug#930368: Bug#930727: unblock: gatb-core/1.4.1+git20181225.44d5a44+dfsg-3

2019-06-20 Thread Andreas Tille
On Thu, Jun 20, 2019 at 10:22:28AM +0200, Paul Gevers wrote: > On 19-06-2019 13:40, Andreas Tille wrote: > > - > > _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base > > 1.4.1+git

Bug#929720: hkl: FTBFS: ../../hkl/ccan/generator/generator.h:23:2: error: #error Generators require coroutines

2019-06-19 Thread Andreas Tille
Control: severity -1 important Hi Lucas, I confirm that I'm the third one who can not reproduce this issue. Can we agree that this bug is maximum of severity important (just set this - feel free to reset to serious if you have good reasons for it). Do you have any further hints how this FTBFS

Bug#930356: CVE-2019-12760

2019-06-19 Thread Andreas Tille
Hi Piotr > Please see https://bugzilla.redhat.com/show_bug.cgi?id=1718212 > > Patch is at https://gist.github.com/dhondta/f71ae7e5c4234f8edfd2f12503a5dcc7 I know you are usually pretty quick in solving serious issues. I tried to check the issue and think the link provided for a patch is just

Bug#929386: Can you please run `inject-into-salsa-git` on your local clone (Was: Bug#929386: r-cran-webgestaltr: FTBFS (missing builds-depends))

2019-05-22 Thread Andreas Tille
Hi Steffen, can you please run `inject-into-salsa-git` on your local clone. There is no Git repository at https://salsa.debian.org/r-pkg-team/r-cran-webgestaltr Kind regards Andreas. -- http://fam-tille.de

Bug#897109: fastqc: htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed

2019-05-21 Thread Andreas Tille
Hi Dylan, On Tue, May 21, 2019 at 02:32:48PM +0200, Dylan Aïssi wrote: > Control: severity -1 serious > > Hi, > I have tested the testsuite with the upstream binary (FastQC 0.11.8) > and there is no error, so the testsuite is fine. This bug was probably > hidden before we added the test of bam

Bug#888733: hyantesite: test failures on most architectures

2019-05-20 Thread Andreas Tille
On Mon, May 20, 2019 at 08:05:09PM +0100, Rebecca N. Palmer wrote: > On 19/05/2019 18:15, Andreas Tille wrote: > > So what is the plan to fix this bug? Create new references to craft > > a valid test or ignore these tests? > > ...or decide that something that's abandoned a

Bug#923433: 0x51063B3: EncoderStrategy::Flush() (encoderstrategy.h:156)

2019-05-20 Thread Andreas Tille
Hint, hint, hint: Feel free to do an NMU / team upload of RC buggy package. That's really welcome and will speed up the release. Thanks a lot, Andreas. On Mon, May 20, 2019 at 02:38:23PM +0200, Mathieu Malaterre wrote: > Control: severity -1 grave > Justification: Debian patches are introducing

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