Bug#916715: toulbar2: What will happen if testing migration takes longer than removal from testing
> Hi Thomas, >> Dear Andreas, >> >> Thanks for taking care of toulbar2. I did spend some time to try to go >> around this #920459 bug but even a postprocessing of the LaTeX output of >> doxygen (removing inclusion of the xcolor package that generates the >> LaTeX compilation issue) did not work (another bug popped up, that was >> apparently already met by other people using doxygen using the same >> TexLive update but I found no workaround). > I think doxygen is severly broken and just skipping refman.pdf (finally > users can read other format) the only safe solution to keep the package > in. I added several FIXMEs to get it back for Buster+1. My current (partial) understanding is that TexLive/LaTeX is broken (not doxygen): TeXlive provides the tabu LaTeX package (https://ctan.org/pkg/tabu) that doxygen uses but this tabu package does not work anymore in TeXlive (not only for doxygen, but for all tabu users). See #920621/#921272 saying that "upstream is working on it". Probably this will not be fast as the README.md of tabu on CTAN says: The original author of tabu appears out of contact, and tabu had not been updated for several years, finally becoming unusable in 2019 as updates to other packages mean some of its patched code did not work as intended. The package is not being actively maintained however any major required fixes may be reported to the https://github.com/tabu-fixed/tabu repository and volunteers there (currently members of the LATEX3 Team) will attempt to update the package with any fixes required. Getting rid of the PDF output as you suggest for eg. HTML is probably best. Thomas
Bug#916715: toulbar2: What will happen if testing migration takes longer than removal from testing
Sorry, missed the Reply-All as Andreas pointed out. See attached mail. Thomas --- Begin Message --- Hi Thomas, On Tue, Feb 19, 2019 at 11:15:13AM +0100, Thomas Schiex wrote: > Dear Andreas, > > Thanks for taking care of toulbar2. I did spend some time to try to go > around this #920459 bug but even a postprocessing of the LaTeX output of > doxygen (removing inclusion of the xcolor package that generates the > LaTeX compilation issue) did not work (another bug popped up, that was > apparently already met by other people using doxygen using the same > TexLive update but I found no workaround). I think doxygen is severly broken and just skipping refman.pdf (finally users can read other format) the only safe solution to keep the package in. I added several FIXMEs to get it back for Buster+1. > If there is anything I can do, please do not hesitate to ask for > support. I'm not sure I'll be able to quickly allocate time, but I at > least I would be happy to try. I do not think that there is anything to do now but hoping that the package will be kicked for no good reason. Kind regards Andreas. PS: Its better to write in public - at least CCing the bug would have made sense. Feel free to quote me. > Le 19/02/2019 à 08:46, Andreas Tille a écrit : > > Hi, > > > > toulbar2 is > > > >Marked for autoremoval on 22 February: #916715 > > > > However, this bug was closed in > > > > > > toulbar2 (1.0.0+dfsg3-1.1) unstable; urgency=medium > > > > * Non-maintainer upload. > > * Add the missing build dependency on zlib1g-dev. (Closes: #916715) > > > > -- Adrian Bunk Fri, 11 Jan 2019 13:47:51 +0200 > > > > > > The problem is that the package did not migrated due to #920459 (doxygen > > currently breaks lots of packages and I wonder in general what will > > happen with those packages). I now uploaded > > > > > > toulbar2 (1.0.0+dfsg3-2) unstable; urgency=medium > > ... > > * Prevent generation of PDF documentation since otherwise toulbar2 does > > not build (see bug #920459). This means should be reverted once doxygen > > is fixed. > > ... > > -- Andreas Tille Mon, 18 Feb 2019 22:17:10 +0100 > > > > > > Which enabled the build on all release architectures. > > > > I'm simply wondering what will happen with toulbar2 (and other packages > > - I'm actually not that much involved in this, it is just a random > > Debian Science package) once it was removed from testing. As far as I > > understood there will be no migrations from unstable to testing any more > > if there is no version of that package in testing. Does that mean that > > the doxygen issues will kick several packages out of Buster or is there > > any way to prevent this? > > > > Kind regards > > > > Andreas. > > > -- http://fam-tille.de --- End Message ---
Bug#921272: texlive-latex-extra: package tabu broken when xcolor is used
Package: texlive-latex-extra
Version: 2018.20190131-1
Severity: important
Dear Maintainer,
*** Reporter, please consider answering these questions, where appropriate ***
* What led up to the situation?
Compiling the LaTeX doxygen-generated documentation for debian package
toulbar2 fails.
* What exactly did you do (or not do) that was effective (or
ineffective)?
A minimal latex file does not compile anymore on texlive (did previously)
* What was the outcome of this action?
An error (missing brace) is raised.
* What outcome did you expect instead?
A PDF file should be generated by pdflatex
*** End of the template - remove these template lines ***
-- Package-specific info:
IMPORTANT INFORMATION: We will only consider bug reports concerning
the packaging of TeX Live as relevant. If you have problems with
combination of packages in a LaTeX document, please consult your
local TeX User Group, the comp.text.tex user group, the author of
the original .sty file, or any other help resource.
In particular, bugs that are related to up-upstream, i.e., neither
Debian nor TeX Live (upstream), but the original package authors,
will be closed immediately.
*** The Debian TeX Team is *not* a LaTeX Help Desk ***
If you report an error when running one of the TeX-related binaries
(latex, pdftex, metafont,...), or if the bug is related to bad or wrong
output, please include a MINIMAL example input file that produces the
error in your report.
Please run your example with
(pdf)latex -recorder ...
(or any other program that supports -recorder) and send us the generated
file with the extension .fls, it lists all the files loaded during
the run and can easily explain problems induced by outdated files in
your home directory.
Don't forget to also include minimal examples of other files that are
needed, e.g. bibtex databases. Often it also helps
to include the logfile. Please, never send included pictures!
If your example file isn't short or produces more than one page of
output (except when multiple pages are needed to show the problem),
you can probably minimize it further. Instructions on how to do that
can be found at
http://www.minimalbeispiel.de/mini-en.html (english)
or
http://www.minimalbeispiel.de/mini.html (german)
##
minimal input file
\documentclass{article}
\usepackage{array}
\usepackage[table]{xcolor}
\usepackage{longtable}
\usepackage{tabu}
\begin{document}
\begin{longtabu}{X[-1]X[-1]}
\textbf{Cost Function Network Solver} & toulbar2
\end{longtabu}
\end{document}
##
other files
##
List of ls-R files
-rw-r--r-- 1 root root 1201 Feb 3 17:49 /var/lib/texmf/ls-R
lrwxrwxrwx 1 root root 29 Sep 2 12:32 /usr/share/texmf/ls-R ->
/var/lib/texmf/ls-R-TEXMFMAIN
lrwxrwxrwx 1 root root 31 Jan 31 03:53 /usr/share/texlive/texmf-dist/ls-R ->
/var/lib/texmf/ls-R-TEXLIVEDIST
lrwxrwxrwx 1 root root 31 Jan 31 03:53 /usr/share/texlive/texmf-dist/ls-R ->
/var/lib/texmf/ls-R-TEXLIVEDIST
##
Config files
-rw-r--r-- 1 root root 475 Feb 3 17:49 /etc/texmf/web2c/texmf.cnf
lrwxrwxrwx 1 root root 33 Jan 31 03:53 /usr/share/texmf/web2c/fmtutil.cnf ->
/var/lib/texmf/fmtutil.cnf-DEBIAN
lrwxrwxrwx 1 root root 32 Jan 31 03:53 /usr/share/texmf/web2c/updmap.cfg ->
/var/lib/texmf/updmap.cfg-DEBIAN
-rw-r--r-- 1 root root 2763 Feb 3 17:49
/var/lib/texmf/tex/generic/config/language.dat
##
Files in /etc/texmf/web2c/
total 8
-rw-r--r-- 1 root root 283 Aug 17 2017 mktex.cnf
-rw-r--r-- 1 root root 475 Feb 3 17:49 texmf.cnf
##
md5sums of texmf.d
ca40c66f144b4bafc3e59a2dd32ecb9c /etc/texmf/texmf.d/00debian.cnf
-- System Information:
Debian Release: buster/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.18.12-041812-generic (SMP w/4 CPU cores)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: unable to detect
Versions of packages texlive-latex-extra depends on:
ii preview-latex-style11.91-2
ii python 2.7.15-4
ii tex-common 6.10
ii texlive-base 2018.20190131-1
ii texlive-binaries 2018.20181218.49446-1
ii texlive-latex-recommended 2018.20190131-1
ii texlive-pictures 2018.20190131-1
Versions of packages texlive-latex-extra recommends:
ii texlive-fonts-recommended 2018.20190131-1
ii texlive-plain-generic 2018.20190131-1
Versions of packages texlive-latex-extra suggests:
pn icc-profiles
ii libfile-which-perl 1.23-1
pn libspreadsheet-parseexcel-perl
pn python-pygments
pn texlive-latex-extra-doc
Versions of packages tex-common
Bug#819391: RFS: toulbar2/0.9.8 debian-science [ITP]
Package: sponsorship-requests Severity: wishlist Dear mentors, We are looking for a sponsor for the "toulbar2" software, in the debian-science project. A current version of its git repository is available on alioth, in the debian- science/pkg-toulbar2 git repository. Toulbar2 is an open source exact discrete optimization software targeted at solving optimization problems that are described as "Graphical Models" including Cost Function Networks, aka Weighted cConstraint Satisfaction Problems, Markov Random Fields (MAP/MRF), Bayesian Nets (MPE), Weighted MaxSAT, pre linkage files and Quadratic Pseudo Boolean Optimization problems. On such problems, toulbar2 is often more efficient than expensive commercial ILP (Integer Linear Programming) solvers. Toulbar2 has won international solver competitions: the Weighted CSP competition (first, in 2007 and 2008), the Uncertainly in AI challenge (first, in 2010 and 2014) and the Pascal Inference challenge (second, in 2011). It has been used in several scientific publications in machine learning, theoretical computer science, statistical physics, genetics and structural biology. It has been developed for more than 10 years on our FusionForge server, hosted by the MIA (Applied mathematics and Computer Science) Departement of INRA, offering a stable and reliable environment. The forge also hosts the associated costfunctionlib benchmark library: https://mulcyber.toulouse.inra.fr/projects/toulbar2/ https://mulcyber.toulouse.inra.fr/projects/costfunctionlib As a preliminary test, a prerelease of a debian source package can be obtained at https://launchpad.net/~thomas-schiex/+archive/ubuntu/toulbar2 -- System Information: Debian Release: stretch/sid APT prefers xenial-updates APT policy: (500, 'xenial-updates'), (500, 'xenial-security'), (500, 'xenial'), (100, 'xenial-backports') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.4.0-14-generic (SMP w/4 CPU cores) Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system)
Bug#780516: ITP: toulbar2 -- An exact optimization solver for Graphical Models.
Package: wnpp Severity: wishlist Owner: Thomas Schiex empnes...@gmail.com * Package name: toulbar2 Version : 0.9.8 Upstream Author : Simon de Givry simon.degi...@toulouse.inra.fr * URL : https://mulcyber.toulouse.inra.fr/projects/toulbar2/ * License : GPL Programming Lang: C++ Description : An exact optimization solver for Graphical Models. Toulbar2 is an exact combinatorial optimization tool for problems defined as Graphical Models such as Cost Function Networks, Markov Random Fields, Weighted Constraint Satisfaction Problems and Bayesian Nets. It includes many recent state of the art algorithms, has won several optimization competitions and used to solve different real life scientific problems. This software is a scientific optimization software. It is unique in its capabilities, although it is related to software such as OpenGM2 (http://hci.iwr.uni-heidelberg.de/opengm2/) or daoopt (https://github.com/lotten/daoopt). It has been used to tackled different real life optimization problems especially in scientific areas such as genetics and computation protein design. As the most active developpers of toulbar2, we intend to maintain and package it. We do not need co-maintainers and don't know if a sponsor is needed. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
