Bug#901562: invesalius: Segmentation fault at startup

2018-06-22 Thread Andreas Tille
You could have done Control: reassign -1 python-vtk6 and the python-vtk6 maintainer can close it with the according upload. On Fri, Jun 22, 2018 at 01:16:42PM -0300, Thiago Franco Moraes wrote: > Hi Andreas, > > I reported the bug to the python-vtk6 package. Here the link > https://bugs.debian

Bug#896253: visionegg is marked for autoremoval from testing

2018-06-24 Thread Andreas Tille
On Sun, Jun 24, 2018 at 06:19:34PM +0200, Andreas Beckmann wrote: > > Given that this looks pretty much unfixable in stretch, should the > package be removed from stretch? ACK - I see no better chance for this. Kind regards Andreas. -- http://fam-tille.de

Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14

2018-06-25 Thread Andreas Tille
Hi Graham, On Sun, Jun 24, 2018 at 08:48:32PM +0200, Graham Inggs wrote: > Control: tags -1 + patch thanks for the patch. Since we are targeting in Git at version 1.4.2 I adapted the patch to this version and it works for this. I also fixed another issue in the test suite[1]. Unfortunately the

Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14

2018-06-25 Thread Andreas Tille
Hi Afif, On Mon, Jun 25, 2018 at 03:41:11AM -0400, Afif Elghraoui wrote: > >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: > >/tmp/tmpveTAsa.subreadset.xml > > > >Before I start diving into this: Afif, upstream seems to have released > >1.5.0 which might be worth a try. While I asked

Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14

2018-06-26 Thread Andreas Tille
On Mon, Jun 25, 2018 at 09:52:50AM -0400, Afif Elghraoui wrote: > I think we can give 1.5.0 a try, but it might have the same problem. Since it builds successfully I've just uploaded. > > (And what do you think about watch mode=git?) > > I don't know much about it, but I don't have any strong

Bug#894213: No clue yet for building snakemake since there are two dirs in .pybuild

2018-06-26 Thread Andreas Tille
Hi, meanwhile I upgraded snakemake to latest upstream in Salsa[1]. I keep on having trouble with building it: ... Building DAG of jobs... Using shell: /bin/bash Job counts: count jobs 1 1 1 Finished job 0. 1 of 1 steps (100%) done Complete log: /tmp/tmp3rl_vn12/

Bug#902592: New version does not build

2018-06-29 Thread Andreas Tille
Hi Ghislain, since one of the Debian Med packages seems to be affected I tried to upgrade h5py (see Git repository). Unfortunately it does not build: ... running build_ext Traceback (most recent call last): File "setup.py", line 168, in cmdclass = CMDCLASS, File "/usr/lib/python2.7/dist

Bug#902592: [Help] Potential Cython issue with new version of h5py (Was: Bug#902592: New version does not build)

2018-06-29 Thread Andreas Tille
; Looks Cython related from a first look. > > Ghis > > Le ven. 29 juin 2018 à 11:17, Andreas Tille a écrit : > > > Hi Ghislain, > > > > since one of the Debian Med packages seems to be affected I tried to > > upgrade h5py (see Git repository). Unfortunately

Bug#902592: [Help] Potential Cython issue with new version of h5py (Was: Bug#902592: New version does not build)

2018-06-29 Thread Andreas Tille
Hi Tristan, On Fri, Jun 29, 2018 at 01:31:31PM +0200, Tristan Seligmann wrote: > This is a cython bug; cython-dbg fails to ship the StringIOTree extension > module, so the regular non-debug module is found when doing a debug build > but fails to load. Are you refering to #902551? I'd consider to

Bug#902592: [Help] Potential Cython issue with new version of h5py (Was: Bug#902592: New version does not build)

2018-06-29 Thread Andreas Tille
Hi Tristan, On Fri, Jun 29, 2018 at 02:26:47PM +0200, Tristan Seligmann wrote: > On Fri, 29 Jun 2018 at 14:20 Andreas Tille wrote: > > > Hi Tristan, > > > > On Fri, Jun 29, 2018 at 01:31:31PM +0200, Tristan Seligmann wrote: > > > This is a cython bug; cython-d

Bug#790196: Rasmol needs severe contribution to stay in Debian

2018-07-03 Thread Andreas Tille
Hi, the bug log of #790196[1] shows that rasmol in its current state will not be distributable with Buster. Upstream is dead so if we want to keep it in Debian we have the option: 1) Port it to Gtk+ 3 (see porting guide [2]) 2) Find a Gtk+ 2 replacement for libvte 3) Give up and remove

Bug#902945: igraph: FTBFS with ARPACK 3.6

2018-07-03 Thread Andreas Tille
Control: forwarded -1 https://github.com/igraph/igraph/issues/1107 Control: tags -1 help Control: tags -1 upstream Hi, thanks for the bug report. I've forwarded the issue upstream. Kind regards Andreas. -- http://fam-tille.de

Bug#902470: influxdb-python: FTBFS in buster/sid (failing tests)

2018-07-03 Thread Andreas Tille
Control: tags -1 help Hi, the diff can be found here 'foo,hello=there 0="1",1=1i,2=1.1 0\nfoo,hello=there 0="2",1=2i,2=2.2 36000\n' != 'foo,hello=there 0="1",1=1i,2=1.111 0\nfoo,hello=there 0="2",1=2i,2=2.222 36000\n'

Bug#902516: [Help] Re: Bug#902516: python-matplotlib-venn: FTBFS in buster/sid (failing tests)

2018-07-04 Thread Andreas Tille
Control: tags -1 help Hi, I can confirm this problem in a pbuilder environment. Unfortunately I have no idea about the cause of the issue nor how to fix it. Any hint from the Debian Python team? Kind regards Andreas. On Wed, Jun 27, 2018 at 12:50:32PM +, Santiago Vila wrote: > Pac

Bug#903105: nlopt: FTBFS with to octave 4.4.0

2018-07-06 Thread Andreas Tille
Package: nlopt Severity: serious Justification: FTBFS Hi, when I team uploaded nlopt on Tue, 29 May 2018 it was building fine. At 2018-06-09 octave 4.4.0-3 was uploaded to unstable. When I build today the build fails with ... /build/nlopt-2.4.2+dfsg/octave/nlopt_optimize-oct.cc:82:36: error:

Bug#903105: nlopt: FTBFS with to octave 4.4.0

2018-07-06 Thread Andreas Tille
Control: tags -1 help No idea whether Debian Octave Group is read by a human beeing. To be sure Sébastien was always in CC. Kind regards Andreas. On Fri, Jul 06, 2018 at 09:59:46AM +0200, Andreas Tille wrote: > Package: nlopt > Severity: serious > Justification: FTBFS > >

Bug#901562: invesalius is marked for autoremoval from testing

2018-07-09 Thread Andreas Tille
Hi Thiago, any news about this? Note that bug #901377 is fixed so we need to concentrate only on #901562. Are you able to reproduce the issue or do you need more information from the bug reporter? Kind regards Andreas. On Tue, Jul 10, 2018 at 04:39:04AM +, Debian testing autoremov

Bug#901562: invesalius is marked for autoremoval from testing

2018-07-10 Thread Andreas Tille
Hi Thiago, On Tue, Jul 10, 2018 at 09:39:12PM -0300, Thiago Franco Moraes wrote: > I think the easiest way to fix this bug is to package the git version. > Also, the git version is already working with Python3. What do you > think? I have no opinion about what code works better - that's perfectly

Bug#901562: invesalius is marked for autoremoval from testing

2018-07-11 Thread Andreas Tille
On Wed, Jul 11, 2018 at 12:18:28PM -0300, Thiago Franco Moraes wrote: > > I was thinking the second option. I'll create a new version tag, > something like 3.1.9997, then I'll have a tarball with this version. > Also, I'll package it using Python3. Perfect. Kind regards Andreas. -- htt

Bug#890691: ruby-bio FTBFS with ruby 2.5

2018-07-16 Thread Andreas Tille
Hi, I'd love to fix this bug since this package is of relevance for Debian Med. It seems to boil down to Error: test_na_seqstat(Bio::TestShellPluginSeq): ArgumentError: incomplete format specifier; use %% (double %) instead which sounds pretty easy for somebody who speaks Ruby (which is not

Bug#903793: libgmap1-dev: broken symlink: /usr/lib/x86_64-linux-gnu/libgmap.so -> libgmap.so.1.0.0

2018-07-16 Thread Andreas Tille
Hi Alexandre, On Sat, Jul 14, 2018 at 11:41:01PM +0200, Andreas Beckmann wrote: > Depends: gmap (= 2017-11-15-1) | libgmap1 (= 2017-11-15-1) > > which does not sound like a good idea if gmap does not provide the required > shared library. I've fixed this in Git and also updated to the latest ups

Bug#908456: invesalius is no longer installable

2018-09-10 Thread Andreas Tille
Hi Thiago On Mon, Sep 10, 2018 at 08:41:27AM +0300, Adrian Bunk wrote: > Package: invesalius > Version: 3.1.1-1 > Severity: grave > > The following packages have unmet dependencies: > invesalius : Depends: python-gdcm but it is not going to be installed > Depends: python-vtkgdc

Bug#891994: epigrass: Depends on Qt4-only python-qwt5-qt4

2018-09-10 Thread Andreas Tille
Control: tags -1 help On Sat, Sep 08, 2018 at 09:38:25PM +0200, Gudjon I. Gudjonsson wrote: > There is a new package in Debian > https://tracker.debian.org/pkg/pyqt-qwt > > that builds on the Qt5 version of Qwt6. > It should not be difficult to upgrade the package from > PyQwt5 to PyQt-Qwt. I

Bug#908459: Bug#908459: theseus FTBFS with gcc 8

2018-09-10 Thread Andreas Tille
Cool. Das macht dann auf jeden Fall einen $drink wie in der anderen Mail versprochen. Dein einer commit zu pbbam ist auch einen Wert - da schreibe ich noch mal was dazu ... Erinner mich aber bitte, wenn wir uns sehen. ;-) Bis dann Andreas. On Mon, Sep 10, 2018 at 12:47:34PM +0200, Fabian K

Bug#908459: theseus FTBFS with gcc 8

2018-09-10 Thread Andreas Tille
On Mon, Sep 10, 2018 at 12:47:34PM +0200, Fabian Klötzl wrote: > Thanks for reporting. There were plenty of string related errors. Fixed in > git repo. Hmmm, the string related errors are gone - thanks /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -Wall -Wer

Bug#907806: How to disable tests for Python2 only?

2018-09-10 Thread Andreas Tille
Hi, looking at the bug log of scikit-learn[1] it seems to be a simple means to do --- a/debian/control +++ b/debian/control @@ -20,6 +20,7 @@ Build-Depends: debhelper (>= 9), dh-autoreconf, python3-pytest, python3-matplotlib, python3-joblib (>= 0.9.

Bug#907806: How to disable tests for Python2 only?

2018-09-10 Thread Andreas Tille
On Mon, Sep 10, 2018 at 10:54:02AM -0400, Yaroslav Halchenko wrote: > Outstanding few issues so far are reported/dealt with upstream: > https://github.com/scikit-learn/scikit-learn/issues?q=is%3Aopen+is%3Aissue+author%3Ayarikoptic+label%3ABlocker > updating packaging is in debian-0.20 branch at >

Bug#907806: How to disable tests for Python2 only?

2018-09-10 Thread Andreas Tille
On Mon, Sep 10, 2018 at 11:44:00AM -0400, Yaroslav Halchenko wrote: > > > ... sorry to repeat myself but having team maintained packages on > > github is not inviting to others. Is there any reason not to > > use Salsa? > > yeap, let's make a repo on salsa. Would you be ok to retain my weird >

Bug#891994: epigrass: Depends on Qt4-only python-qwt5-qt4

2018-09-10 Thread Andreas Tille
On Tue, Sep 11, 2018 at 06:58:03AM +0200, Gudjon I. Gudjonsson wrote: > Hi Andreas > > > > I would love if people would test this. Since it is not a Build-Depends > > where I could see whether the build breaks or not and there is no test > > suite to verify whether things work as expected I'm hes

Bug#908456: invesalius is no longer installable

2018-09-11 Thread Andreas Tille
Hi Thiago, On Tue, Sep 11, 2018 at 10:21:51AM -0300, Thiago Franco de Moraes wrote: > Hi Andreas, > > Done! I've just pulled the changes to Salsa. I created a new release > (3.1.2). Good. :-) > But I'm getting this warning: > dpkg-gencontrol: warning: Depends field of package invesalius:

Bug#908456: invesalius is no longer installable

2018-09-11 Thread Andreas Tille
On Tue, Sep 11, 2018 at 03:31:18PM -0300, Thiago Franco de Moraes wrote: > > > > This was easy - see my latest commit. > > Thanks! You are welcome. > I created a patch to remove the python2 shebangs. This patch was already > applied into the upstream. But there is other problem: Fine. > W:

Bug#902132: [Debian-med-packaging] Bug#902132: falcon: FTBFS since python-networkx version 2.1-1; fails in test suite

2018-09-12 Thread Andreas Tille
Hi Alex, On Wed, Sep 12, 2018 at 10:55:20AM +0200, Alex Mestiashvili wrote: > Well, according upstream, current repository is not active anymore: > > > Oh, sorry. We are no longer mirroring our internal FALCON repo here. In > fact, I think this Issues board will disappear soon too, in favor of >

Bug#908670: libundead: ftbfs on armhf

2018-09-12 Thread Andreas Tille
Control: tags -1 help Sorry, I have no idea what to do. Any help is welcome. Kind regards Andreas. On Wed, Sep 12, 2018 at 02:09:47PM +0200, Gianfranco Costamagna wrote: > Source: libundead > Severity: serious > Version 1.0.9-2 > > hello, recent ldc made the package FTBFS. > > Releva

Bug#908752: r-cran-stan: epends on version of libgdal-dev that doesn't exist

2018-09-13 Thread Andreas Tille
Control: tags -1 pending Control: block -1 by 898704 The package r-cran-rstan was accepted by ftpmaster before r-cran-stanheaders so it does not even build. I'll ping ftpmaster about this. On Thu, Sep 13, 2018 at 04:03:36PM +0300, Adrian Bunk wrote: > > > > The package depends on libgdal-dev >=

Bug#908670: libundead: ftbfs on armhf

2018-09-13 Thread Andreas Tille
Hi Peter, thanks a lot for your analysis. On Thu, Sep 13, 2018 at 01:27:58PM +0100, peter green wrote: > 4. Simply get libundead removed on armhf/raspbian. libundead seems to only > have two reverse build-dependencies neither of which has ever successfully > built on armhf. libbiod previously f

Bug#907819: I'm temped to drop python support from jellyfish - please help if you need this

2018-09-13 Thread Andreas Tille
Hi, while I was able to deal with bug #907819 the latest version of jellyfish in Git[1] does not build due to some issues with the python module. Scott and Michael did something for Python support in the past and I hope you can help out. The build breaks with ... dh_install -ppython3-dna-jelly

Bug#906337: Any clue how to circumvent issues with MPI on autobuilders

2018-09-14 Thread Andreas Tille
Control: tags -1 help Hi, in the bug log of #906337 the test suite aborts with ... -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI

Bug#906381: Issues possibly due to new pandas version

2018-09-14 Thread Andreas Tille
Control: tags -1 help Hi, I tried my luck by injecting the latest upstream version. This needs a new dependency python-asteval (#907283, just uploaded to new queue). Unfortunately this does not help at all and we surely should contact upstream about this and so it is better to refer to the lates

Bug#908786: mothur-mpi contains the same binary as mothur

2018-09-14 Thread Andreas Tille
Control: tags -1 pending Hi Adrian, On Fri, Sep 14, 2018 at 01:39:34AM +0300, Adrian Bunk wrote: > USEMPI seems to be no longer an upstream option, > so both builds produce the same binary. Very good catch! Thanks for this. In fact the MPI code was removed 2015-08-19 so we ship the non-functio

Bug#906337: Any clue how to circumvent issues with MPI on autobuilders

2018-09-14 Thread Andreas Tille
Control: tags -1 pending On Fri, Sep 14, 2018 at 10:33:28AM +0200, Johannes Ring wrote: > > In debian/rules in dolfin, we use the following to allow test programs to > run with OpenMPI: > > export OMPI_MCA_plm_rsh_agent=/bin/false > > Maybe that will fix your problem. This is set in bioperl-

Bug#905706: libpicard-java-doc: ships /usr/share/javascript/jquery/jquery.min.js

2018-09-17 Thread Andreas Tille
Control: tags -1 pending This issue should be fixed in https://salsa.debian.org/med-team/picard-tools/commit/4da851972983cee93a3cce27bfbb40f9648dcc3d While fixing the bug I also tried to upgrade the package to the latest upstream version. Unfortunately this failed with: Compiling build fi

Bug#902760: Two failed tests remaining in igraph which are arpack related

2018-09-17 Thread Andreas Tille
Control: tags -1 help Hi Adrian, I realised that you have set 908648: libarpack2 needs fix applied for igraph fixed. So I tried to build igraph from Git[1] with latest arpack but there are two remaining issues in the build time test which both are connected to arpack: ... 196: Eigenvector

Bug#902760: Two failed tests remaining in igraph which are arpack related

2018-09-17 Thread Andreas Tille
ollab/arpack-ng/commit/31854cadaff067e30b8715f10533c459a9b7d447 > > As far as I know, there was no official ARPACK release with the patch > above yet so it has to be applied manually. > > All the best, > Tamas > On Mon, 17 Sep 2018 at 21:44, Andreas Tille wrote: > > > > Control: tags

Bug#905706: [Debian-med-packaging] Bug#905706: libpicard-java-doc: ships /usr/share/javascript/jquery/jquery.min.js

2018-09-18 Thread Andreas Tille
Thanks for your work anyway Andreas. On Tue, Sep 18, 2018 at 10:38:31AM +0200, Olivier Sallou wrote: > > > On 09/18/2018 10:02 AM, Olivier Sallou wrote: > > > > On 09/17/2018 04:36 PM, Andreas Tille wrote: > >> Control: tags -1 pending > >> >

Bug#909120: camitk FTBFS: tests segfault (Bug #909120)

2018-09-20 Thread Andreas Tille
Control: tags -1 upstream Hi Bernhard, thanks a lot for your investigation. Emmanuel Promayon is Uploader and Upstream and I think he will come back to you and hopefully will implement the fix soon. Kind regards Andreas. On Thu, Sep 20, 2018 at 06:01:38PM +0200, Bernhard Übelacker wrot

Bug#907819: I'm temped to drop python support from jellyfish - please help if you need this

2018-09-21 Thread Andreas Tille
On Fri, Sep 14, 2018 at 08:15:26AM +0200, Andreas Tille wrote: > > If I will not get any help I'll consider removing the Python module > package to safe all other dependencies from jellyfish. Sorry, but we > are loosing currently more and more packages due to RC bugs and I

Bug#902760: Two failed tests remaining in igraph which are arpack related

2018-09-21 Thread Andreas Tille
On Mon, Sep 17, 2018 at 09:44:32PM +0200, Andreas Tille wrote: > Please send `tests/testsuite.log' and all information you think might help: > >To: >Subject: [igraph 0.7.1] testsuite: 196 197 failed with recent libarpack2-dev (3.6.3-1) we are down to one remaining erro

Bug#909120: camitk FTBFS: tests segfault (Bug #909120)

2018-09-21 Thread Andreas Tille
On Fri, Sep 21, 2018 at 07:05:40PM +0200, Emmanuel Promayon wrote: > Andreas, do you have any smart way to check the list of packages that have > changed/been uploaded in sid in the dependencies of a package during a > period of time (here from 9 Sep to 15 Sep)? This might help me finding how > to

Bug#907489: Trying sambamba pre-release but meson build needs adapting

2018-09-22 Thread Andreas Tille
Hi Matthias, to build sambamba you once added a patch that creates a meson.build file. I have no experience with meson at all. I tried to adapt meson.build to the move of main.d and the additional source files[1]. I admit the manual work for cases when upstream adds new source files is not real

Bug#907806: How to disable tests for Python2 only?

2018-09-23 Thread Andreas Tille
Hi Yaroslav, On Mon, Sep 10, 2018 at 09:39:38PM +0200, Andreas Tille wrote: > On Mon, Sep 10, 2018 at 11:44:00AM -0400, Yaroslav Halchenko wrote: > > > > > ... sorry to repeat myself but having team maintained packages on > > > github is not inviting to others.

Bug#908495: New upstream version should fix bugs

2018-09-24 Thread Andreas Tille
Control: tags -1 pending

Bug#909120: camitk FTBFS: tests segfault (Bug #909120)

2018-09-24 Thread Andreas Tille
On Mon, Sep 24, 2018 at 02:49:37PM +0200, Emmanuel Promayon wrote: > - if there is no (easy) way to go back to vtk6 in gdcm (or to support both > vtk6 and vtk7), does this means that we (upstream) need to update CamiTK to > be based on VTK7 in order to fix this bug? Disclaimer: I have no idea abou

Bug#907806: How to disable tests for Python2 only?

2018-09-24 Thread Andreas Tille
Hi Yaroslav, On Mon, Sep 24, 2018 at 09:40:49AM -0400, Yaroslav Halchenko wrote: > > On Mon, 24 Sep 2018, Andreas Tille wrote: > > > When you talked about new upstream version: Do you want to give 0.20rc1 > > I did give it a try... > > From the now empty list of

Bug#907806: How to disable tests for Python2 only?

2018-09-24 Thread Andreas Tille
Hi Yaroslav, On Mon, Sep 24, 2018 at 11:03:16AM -0400, Yaroslav Halchenko wrote: > > > You asked me to clone http://github.com/yarikoptic/scikit-learn to > > https://salsa.debian.org/science-team/scikit-learn which I did. In > > cool :-) > > *your* packaging repository is no branch 0.20rc1 t

Bug#907806: How to disable tests for Python2 only?

2018-09-26 Thread Andreas Tille
Hi Yaroslav, On Mon, Sep 24, 2018 at 11:32:03AM -0400, Yaroslav Halchenko wrote: > > > I confirm that there are cases where this workflow makes sense. We need > > to outweight pros and cons. > > To say the truth, I am no longer sure since it is possible to still have > regular upstream repo as

Bug#909767: salmon FTBFS with spdlog 1:1.1.0-1

2018-09-27 Thread Andreas Tille
Hi Adrian, thanks again for your tough QA work. On Thu, Sep 27, 2018 at 11:40:04PM +0300, Adrian Bunk wrote: > Source: salmon > Version: 0.7.2+ds1-3 > Severity: serious > Tags: ftbfs Salmon is heavily lagging behind upstream due to complex packaging. The latest version made it very high on my t

Bug#909763: hinge FTBFS with spdlog 1:1.1.0-1

2018-09-28 Thread Andreas Tille
Control: tags -1 help Hi, On Thu, Sep 27, 2018 at 11:28:04PM +0300, Adrian Bunk wrote: > Source: hinge > Version: 0.5.0-3 > Severity: serious > Tags: ftbfs > > https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/hinge.html > > ... > /build/1st/hinge-0.5.0/src/filter/filter.cpp:20

Bug#909766: rapmap FTBFS with spdlog 1:1.1.0-1

2018-09-28 Thread Andreas Tille
Control: tags -1 help On Thu, Sep 27, 2018 at 11:38:55PM +0300, Adrian Bunk wrote: > Source: rapmap > Version: 0.5.0+dfsg-3 > Severity: serious > Tags: ftbfs > > https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rapmap.html > > ... > In file included from /build/1st/rapmap-0.5.0

Bug#909761: porechop FTBFS: command 'PorechopClean' has no such option 'all'

2018-09-28 Thread Andreas Tille
Hi Mattia, I can confirm that I get the same result: Works on local machine (here running testing) and fails with that error in pbuilder. BTW, if I drop the --buildsystem pybuild this problem vanishes. So I guess pybuild is doing some magic. Kind regards Andreas. -- http://fam-

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

2017-11-08 Thread Andreas Tille
Dear Diane, On Wed, Nov 08, 2017 at 04:58:49PM -0800, Diane Trout wrote: > > Should I push these proposed changes to a clone of the htslib packaging > repository? A branch of the alioth repository, or just push it to the > alioth master? Thanks for your sane considerations and pleas push to alio

Bug#880245: Forwarded upstream

2017-11-09 Thread Andreas Tille
control: tags -1 upstream control: tags -1 help control: forwarded -1 https://github.com/statsmodels/statsmodels/issues/4116 Hi, I have forwarded the issue upstream (GitHub issue 4116). Kind regards Andreas. -- http://fam-tille.de

Bug#880245: ipython/jupyter issue [Was: RuntimeError: Kernel died before replying to kernel_info (#4116)]

2017-11-09 Thread Andreas Tille
: statsmodels/statsmodels Cc: Andreas Tille , Author Subject: Re: [statsmodels/statsmodels] RuntimeError: Kernel died before replying to kernel_info (#4116) This is a ipython/jupyter issue, and not related to statsmodels. You can ask at their issue tracker. -- You are receiving this because

Bug#880245: Not forwarded

2017-11-09 Thread Andreas Tille
control: notforwarded -1 -- http://fam-tille.de

Bug#881331: bcftools: needs a versioned dependency on libhts2

2017-11-10 Thread Andreas Tille
Hi, Graham commited according fixes in Git. Graham, I'm perfectly fine if you (or anybody else) would upload. Kind regards Andreas. control: tags -1 pending On Fri, Nov 10, 2017 at 01:27:48PM +0100, Mattia Rizzolo wrote: > Source: bcftools > Version: 1.5-3 > Severity: serious > Control:

Bug#880245: ipython/jupyter issue [Was: RuntimeError: Kernel died before replying to kernel_info (#4116)]

2017-11-10 Thread Andreas Tille
Hi, On Thu, Nov 09, 2017 at 08:48:02PM +0100, Gordon Ball wrote: > > I just built statsmodels 0.8.0-6 in and amd64 sbuild chroot without > encountering this issue. > > Looking at the trace in #880245, it looks like the key error is > > zmq.error.ZMQError: Address already in use > > and the

Bug#878498: snakemake FTBFS with Python 3.6 as default

2017-11-11 Thread Andreas Tille
Hi Chrysn, since nobody raised any veto and we finally will follow upstream anyway: Could you please push your changes to latest upstream version and than we try to work together from there? For instance it will help to contact upstream when refering to the latest upstream version. Kind regards

Bug#880245: Lowering severity (Was: ipython/jupyter issue [Was: RuntimeError: Kernel died before replying to kernel_info (#4116)])

2017-11-13 Thread Andreas Tille
:28, Andreas Tille wrote: > Hi, > > On Thu, Nov 09, 2017 at 08:48:02PM +0100, Gordon Ball wrote: >> >> I just built statsmodels 0.8.0-6 in and amd64 sbuild chroot without >> encountering this issue. >> >> Looking at the trace in #880245, it looks like the ke

Bug#881114: Transition to xerces-c 3.2

2017-11-16 Thread Andreas Tille
Hi, I just sponsored xsd yesterday and I wonder what your plan might be to upload xerces-c 3.2. For me it is a bit strange that you set severity of this bug to serious while nothing is broken as long as xerces-c sticks to version 3.1. Could you please either lower the severity to important or up

Bug#881368: fis-gtm: please switch build-dep from libconfig8-dev to libconfig-dev

2017-11-20 Thread Andreas Tille
Hi Mattia, On Fri, Nov 10, 2017 at 09:09:16PM +0100, Mattia Rizzolo wrote: > Version: 6.3-002-3 > Severity: serious > > I'm about to upload a libconfig dropping this transitional package, > please update fis-gtm. Fis-gtm Build-Depends: libconfig-dev | libconfig8-dev. In how far is it serious to

Bug#873417: pocl: Please update to llvm-toolchain 4.0 or, better, 5.0

2017-11-21 Thread Andreas Tille
Hi, I realised that there is a new upstream version 0.14 which seems to allow LLVM 4.0. I gave it a try in Git in the new branch 0.14 but faced build problems I was not able to solve. However, since I was hoping that the refreshed patches might help (please review!) I commited this branch. Hope

Bug#882430: libics FTBFS on 32bit: FAIL: test_strides3.sh

2017-11-22 Thread Andreas Tille
Control: forwarded -1 https://github.com/svi-opensource/libics/issues/6 Control: tags -1 upstream Hi, I've forwarded the issue upstream. Kind regards Andreas. -- http://fam-tille.de

Bug#842815: Re-opening: Please support HDF5 1.10

2016-11-22 Thread Andreas Tille
Hi Bernd, I'm hereby forwarding the main parts of the discussion of the bug report which might contain hints what to do to make jhdf5 compliant with hdf5 version 1.10. It would be nice if you could give us a hint if you were able to fix this. Kind regards Andreas. On Tue, Nov 15, 2016 at

Bug#842815: Re-opening: Please support HDF5 1.10

2016-11-22 Thread Andreas Tille
Hi Bernd, On Wed, Nov 23, 2016 at 06:54:21AM +0100, Bernd Rinn wrote: > the migration of JHDF5 to HDF5 1.10 is ongoing and mostly depend on me > having a block of time I can spend on it. Your analysis of the work that > needs to be done is right from what I can see. The plan is to switch to > usin

Bug#845505: sra-sdk 2.7.0-1 is broken libncbi-vdb2 2.8.0+dfsg-1

2016-11-23 Thread Andreas Tille
Hi Charles, On Thu, Nov 24, 2016 at 01:38:11PM +0900, Charles Plessy wrote: > Package: sra-sdk > Severity: grave > > Hi all, > > quick note from work; sorry to not being able to go deeper. > > A colleague has reported to me that sra-sdk 2.7.0-1 is broken > libncbi-vdb2 2.8.0+dfsg-1. For instan

Bug#845348: What is going on with gtkdatabox?

2016-11-23 Thread Andreas Tille
Hi Peter, On Thu, Nov 24, 2016 at 02:49:56AM +, peter green wrote: > As a derivative maintainer I noticed that there appears to be a gtkdatabox > transition going on. Looking at the list archives for debian-release I see > no mention of it on there. That might have been a race condition since

Bug#843712: Closing since this bug was possibly caused by broken Build-Depends

2016-11-24 Thread Andreas Tille
C.UTF-8 * Fix clean target * d/watch: do not report beta versions + * d/rules: tolerate test failures of biojava-core which happens in stretch +sbuild environments for no obvious reasons +Closes: #843712 -- Andreas Tille Thu, 24 Nov 2016 13:17:32 +0100 Index: rules ==

Bug#843712: Closing since this bug was possibly caused by broken Build-Depends

2016-11-24 Thread Andreas Tille
Hi Santiago, On Thu, Nov 24, 2016 at 03:10:27PM +0100, Santiago Vila wrote: > On Thu, Nov 24, 2016 at 02:37:46PM +0100, Andreas Tille wrote: > > > I do nit think that the issue can be explained by a missing > > Build-Depends - otherwise it would fail in pbuilder as w

Bug#845348: What is going on with gtkdatabox?

2016-11-24 Thread Andreas Tille
Hi Daniele, thanks for the quick response. On Thu, Nov 24, 2016 at 04:34:26PM +0100, Daniele E. Domenichelli wrote: > On 2016-11-24 08:24, Andreas Tille wrote: > >I'll checkout gtkdataboxmm myself since I was once sponsering this - no > >idea whether Daniele remains ac

Bug#840094: blends-dev: Does not recognize multiline dependencies

2016-11-24 Thread Andreas Tille
Hi Ole, sorry for my longer than planned silence but today I found the time to repeat all tests with your new version. On Tue, Nov 15, 2016 at 10:12:00AM +0100, Ole Streicher wrote: > Hi Andreas, Petter and all, > > > On 15.11.2016 07:09, Andreas Tille wrote: > >> Use o

Bug#840094: blends-dev: Does not recognize multiline dependencies

2016-11-24 Thread Andreas Tille
On Thu, Nov 24, 2016 at 08:39:54PM +0100, Petter Reinholdtsen wrote: > [Andreas Tille] > > I just want to hear confirmation from some Debian Edu developer > > whether the upload of blends-dev 0.6.95 is OK. > > As far as I can tell, these changes are intended and reflect

Bug#845752: ShortRead fails do build on armel architecture with C stack overflow

2016-11-26 Thread Andreas Tille
Hi, the Debian bug tracker contains a bug report that ShortRead fails to build on armel architecture (while any other Debian architecture seems to be fine). Please have a look here: https://bugs.debian.org/845752 I admit I have no idea how to track this issue down. Kind regards A

Bug#845753: Treescape fails to build on i386 and armhf architecture

2016-11-26 Thread Andreas Tille
Hi, in the Debian bug tracking system you can find a bug report about the build failure: https://bugs.debian.org/845753 The build log for i386 says: ** preparing package for lazy loading Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis' Warning in rgl

Bug#846002: blends-tasks must be priority:standard and not make a mess out of tasksel menu

2016-11-28 Thread Andreas Tille
Hi, On Mon, Nov 28, 2016 at 10:09:56AM +0100, Ole Streicher wrote: > ... > about the blends available during installation, and this makes the > package that provides this information "important". Therefore, it is not > a policy violation, which in turn removes your argument to make this bug > "ser

Bug#846078: [pycogent/pycogent] Random failures of test suite (#103)

2016-11-29 Thread Andreas Tille
Hi Gavin, On Mon, Nov 28, 2016 at 02:33:03PM -0800, GavinHuttley wrote: > Could you run the tests using the verbose flag, e.g. > > ```python > $ ./run_tests -v > ``` > That will show each test run, helping identify the exact test where the issue > occurs. My prediction is it will be in the struc

Bug#846002: blends-tasks must be priority:standard and not make a mess out of tasksel menu

2016-11-29 Thread Andreas Tille
Hi Holger, On Sun, Nov 27, 2016 at 05:38:27PM +0100, Holger Levsen wrote: > I also plan to NMU blends-dev to set blends-tasks back to priority:optional, > probably on Thursday or Friday this week. (To give some time to discussion, > but soon, to not let this slip for to long.) I wonder what your

Bug#846002: blends-tasks must be priority:standard and not make a mess out of tasksel menu

2016-11-29 Thread Andreas Tille
On Tue, Nov 29, 2016 at 05:52:01PM +, Holger Levsen wrote: > I'm sorry about not being able to reply right now. Gotta catch another > train in 30 or 90min… > > (I peeked into your replies very briefly and saw that I cannot reply quickly…) OK, take your time, have a nice travel - but please de

Bug#846078: [pycogent/pycogent] Random failures of test suite (#103)

2016-12-01 Thread Andreas Tille
Hi Santiago, (now in CC) On Tue, Nov 29, 2016 at 11:56:28PM +0100, Santiago Vila wrote: > On Tue, Nov 29, 2016 at 09:31:05AM +0100, Andreas Tille wrote: > > > Thanks a lot for this quick and helpful response. I've prepared a > > package featuring this verbose output

Bug#846078: [pycogent/pycogent] Random failures of test suite (#103)

2016-12-01 Thread Andreas Tille
On Thu, Dec 01, 2016 at 05:58:41PM +0100, Santiago Vila wrote: > On Thu, 1 Dec 2016, Andreas Tille wrote: > > > Version 1.9-6 is available now. While it does not build on mips and > > mips64el I'd like to hear from you before doing something about this > > which

Bug#921781: fis-gtm: FTBFS (dh_auto_configure fails)

2019-02-08 Thread Andreas Tille
Hi, that's caused by missing icu-config (#920900) On Sat, Feb 09, 2019 at 12:15:16AM +, Santiago Vila wrote: > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > > [... snipped ...] ... the relevant part

Bug#921781: fis-gtm: FTBFS (dh_auto_configure fails)

2019-02-09 Thread Andreas Tille
g/med-team/fis-gtm/blob/master/debian/patches/no_icu-config.patch but this does not help. :-( Any hints? Kind regards Andreas. On Sat, Feb 09, 2019 at 07:15:00AM +0100, Andreas Tille wrote: > Hi, > > that's caused by missing icu-config (#920900) > > > On Sat,

Bug#921843: discosnp has unsatisfiable dependencies

2019-02-09 Thread Andreas Tille
Control: tags -1 help moreinfo Hi, I really wonder why gatb-core should be missing. According to tracker[1] gatb-core is in testing and the build logs[2] are specifying exactly those architectures as successfully installed that you claim missing (in agreement with discosnp tracker page[3] admitt

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

2019-02-11 Thread Andreas Tille
Hi Carnë, On Mon, Feb 11, 2019 at 12:59:45PM +, Carnë Draug wrote: > On Wed, 6 Feb 2019 at 14:06, Andreas Tille wrote: > > This is what I've though about: Removing the files from bioperl-run > > (which would be 1.7.2-5 then) > > Upstream has released BioPerl-

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

2019-02-11 Thread Andreas Tille
On Mon, Feb 11, 2019 at 03:32:47PM +, Carnë Draug wrote: > > Well, all those regressions are because they can't install bioperl > which is their dependency. There is no issue on themselves or in > upstream bioperl. The issue is that Debian's bioperl claims to have > recommend dependency on b

Bug#921495: Bioperl 1.7.4 should not migrate to Buster

2019-02-12 Thread Andreas Tille
On Mon, Feb 11, 2019 at 04:15:21PM +, Carnë Draug wrote: > > What do you think? > > All packages that depend on bioperl are being affected by this. The > current situation is a bit awkward because packaging and testing in > sid fails even though it would be fine in testing. This will cause >

Bug#921779: cascade of FTBFS

2019-02-12 Thread Andreas Tille
710aa9e003982ee7 -- http://fam-tille.de >From b0a8a6a14c391fbc40489ab6df984435efaba1c4 Mon Sep 17 00:00:00 2001 From: Andreas Tille Date: Tue, 12 Feb 2019 16:02:57 +0100 Subject: [PATCH] Fix watch file --- debian/changelog | 4 debian/watch | 4 ++-- 2 files changed, 6 insertions(+), 2 de

Bug#882641: New version of statsmodels is out possibly fixing important bug - any volunteer

2019-02-12 Thread Andreas Tille
Hi, On Sun, Oct 28, 2018 at 07:32:43PM +0100, Andreas Tille wrote: > Hi Julian, > > On Sat, Oct 27, 2018 at 06:05:39PM +0200, Julian Taylor wrote: > > I have pushed an update to git that fixes the build for me and filed > > https://github.com/statsmodels/statsmodels/pull

Bug#921495: Does not affect testing

2019-02-13 Thread Andreas Tille
Control: tags -1 -help Control: notfound -1 1.7.2-3

Bug#921299: It is not caffe that is broken

2019-02-14 Thread Andreas Tille
Control: tags -1 moreinfo Control: reassign -1 doxygen Control: retitle -1 "Doxygen breaks caffe" Hi, I've build caffe with latest doxygen and can not confirm the result you wrote. The Build-Depends: doxygen-latex ensures that the style file `listofitems.sty' is available. I rather get a differ

Bug#921779: Bug#919413: cascade of FTBFS

2019-02-14 Thread Andreas Tille
On Thu, Feb 14, 2019 at 03:16:22PM +0100, Dominique Dumont wrote: > On Tuesday, 12 February 2019 16:54:12 CET Andreas Tille wrote: > > I'm > > not sure how to deal with the jquery.js one since this is potentially an > > issue with lots of dependencies - I remember discus

Bug#920459: Toulbar2 issue is caused by doxygen 'cascade of FTBFS'

2019-02-15 Thread Andreas Tille
Control: retitle -1 Doxygen breaks toulbar2 Control: affects 921779 toulbar2 Control: reassign -1 doxygen Hi, I've verified the situation of the build failure and it shows the typical problem caused by bug #921779. Thus I'm reassigning the bug to doxygen. Kind regards Andreas. -- http:

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