Re: FOSDEM 2013
Hi Sebastien, On Wed, Jan 30, 2013 at 08:46:12AM +0100, Sebastien Jodogne wrote: > >I saw that Andreas is giving 2 talks [0] at FOSDEM this Saturday, I'll > >be present, wondering if there would be other Debian Med members > >around to meet? > > I will also give a talk about Orthanc [1] in the FOSS for Scientists > devroom [2]. Ahh, forgot to mention that I will speak about Debian Med twice. In the 15min talk in the FOSS for Scientists track[3] I will explicitely advertise your talk as well as Filippo Rusconi's talk about mass spectroscopy and I will also mention the talk inbetween about AMEBA[4] which could potentially be included into Debian (Med) as well. BTW, I will try to not beeing boring by talking twice about the same thing in different talks - so the talk in the science field is more about the relation to sciences (mentioning our effort about publications etc) while in the distribution track I will try to make Debian Med an example worth following also in very different fields like GIS, Edu, Multimedia etc. Kind regards Andreas. > [1] https://code.google.com/p/orthanc/ > [2] https://fosdem.org/2013/schedule/event/orthanc/ [3] https://fosdem.org/2013/schedule/event/debian_med/ [4] https://fosdem.org/2013/schedule/event/ameba/ -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130130082949.gb27...@an3as.eu
Re: Flexbar source code?
Hi Andreas, ok, the plan sounds reasonable. Besides these issues, I consider to include the tbb lib in the source tarball to make it easy for those who download it for compilation. As far as I understood the tbb could be dropped by the patch for packaging based on tarball, right? Or would this complicate the packaging process or be against conventions? Thank you a lot for the help! Best, Johannes On Jan 29, 2013, at 8:29 AM, Andreas Tille wrote: > Hi Johannes, > > thanks again for your very helpful clarification. After reading this I > think it might be the best idea if we try to package flexbar as it is > (including seqan copy) for the experimental branch in Debian which helps > Toni for the moment and once there might be some new seqan library > release we will build flexbar using this new release and move it to main > Debian. I guess for the moment this helps those who need flexbar now > and is technically OK. > > Toni, do you consider it reasonable if we do this together at the Debian > Med Sprint in Kiel? > > Johannes, thanks again for sharing your insight and also for providing > flexbar as free software > > Andreas. > > On Mon, Jan 28, 2013 at 04:09:08PM +0100, Johannes Röhr wrote: >> Hi Andreas, >> >> it is completely clear to me that one should use as many packaged libraries >> as possible. I'm simply not sure if it works with the older SeqAn package >> apart from modifications. I would have to test this first, and for reasons >> of consistency I would then go back to this release also on sourceforge. >> Since I know that a lot changes were introduced in the recent year, >> especially in the align module and the argument parser, this could cause >> problems and I also prefer to rely on the recent implementations. >> >> Therefore, I propose to wait for the next SeqAn package release. I will then >> use it also for the Flexbar version on sourceforge and will try to come >> along without modifications. Since I applied only very slight modifications, >> I am optimistic that it works out and I will discuss it with SeqAn >> developers. I definitely prefer to use an official and unmodified release, >> and see it as an aim for coming versions. Besides from cleaner sources and >> packaging, it would then also become obsolete to adjust new SeqAn libs to >> modifications for inclusion in Flexbar. However, I am not sure how fast a >> new packaged release will be provided. >> >> Best regards >> Johannes > > -- > http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/ba2990d1-7d53-4664-b7d8-4d362fd16...@users.sourceforge.net
Re: Flexbar source code?
Hi Johannes, On Wed, Jan 30, 2013 at 09:47:48AM +0100, Johannes Röhr wrote: > ok, the plan sounds reasonable. OK. > Besides these issues, I consider to > include the tbb lib in the source tarball to make it easy for those who > download it for compilation. As far as I understood the tbb could be > dropped by the patch for packaging based on tarball, right? Or would > this complicate the packaging process or be against conventions? We do often find tarballs containing convenience copies of certain libraries. In most cases it is possible to use a configuration option to use this copy or a system library. Debian currently has version 4.0+r233 (package libtbb-dev). If this is the same / a compatible version as you intend to include there should be no problems to expect. In the specific case of flexbar I'm lacking enough knowledge for cmake build system. I would consider the following options (prefered in this ranking): 1. Let cmake check whether libtbb is installed on the system and use this if yes 2. Provide a switch that enables forcing the usage of libtbb installed on the system 3. Patch CMakeLists.txt to ignore the convenience copy and take the system libtbb Options 1. and 2. enable us the packaging without applying extra patches which would simplify things on our side but might possibly put some extra work on your shoulders (which you would not have otherwise when ignoring our packaging attempt.) As I said I have no cmake experience and can not tell how much work this might be but in any case I could ask on some other list (debian-mentors) for the changes that might be needed. So if you would be willing to distribute flexbar source implementing 1. or 2. I could try to work out a patch that does exactly this. If you think 3. should be the way to go this is a fallback option for us. > Thank you a lot for the help! Thanks for your cooperation Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130130091045.gd27...@an3as.eu
Re: strap, strap-base, lintian warnings solved
Hi Christoph, thanks for your continuous work on strap. On Tue, Jan 29, 2013 at 10:04:28PM +0100, Dr. med. Christoph Gille wrote: > Made a README.Debian explaining the classpath issue and why the jar > file is in /usr/shar/strap-base/ rather than in /usr/share/java/ I need to admit that the explanation does not fit the problem. The JAR file in the strap-base package ends up in /usr/lib/strap-base ^^^ but JAR files are arch-indep files. I guess your intended to move it rather to /usr/share/strap-base ^ at least according to your explanation in README.Debian. If you really do so the lintian warning should vanish. The other problem you are listing in README.Debian (Java-Class-path) should rather be put into an overrides file to *really* suppress the warning. Please read man dh_lintian if you have no idea about these lintian-overrides. > Still get the lintian warning "newer-standards-version 3.9.4 " > even though I updated with apt-get -t > unstable install build-essential debhelper dh-make lintian > Can I ignore this? You can perfectly ignore this. If you are really bored by this warning you might like to install lintian from unstable via sudo apt-get -t unstable install lintian > Can I ignore this warning: P: strap: no-upstream-changelog Yes. I admit I do not verify 'P:' type lintian messages. > I did not manage to reproduce the lintian > warning "jar-not-in-usr-share" even not with options -I -i --pedantic > Has it vanished? Why? $ lintian strap-base_1.1.1-1_amd64.deb W: strap-base: hardening-no-relro usr/lib/strap-base/nativeTools_unix2 W: strap-base: hardening-no-fortify-functions usr/lib/strap-base/nativeTools_unix2 W: strap-base: jar-not-in-usr-share usr/lib/strap-base/strap-protein-alignment-1.jar W: strap-base: missing-classpath libcommons-httpclient-java, libcommons-compress-java, libhttpmime-java, libjavatar-java, libhttpclient-java, libgeronimo-activation-1.1-spec-java Kind regards and see you in Kiel Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130130105215.ga31...@an3as.eu
Re: FOSDEM 2013
Hi all, Thanks for your involvement in the FOSDEM 2013 (specially to Andreas and Sébastien). Unfortunately, I will not be able to join your talks. But I wish you a very good time. I'll probably be present at the LSM 2013 in Brussels too (july 2013) to present the FreeMedForms project. Thanks Eric Le 29 janv. 2013 à 22:33, Emilien Klein a écrit : > Hi team, > > I saw that Andreas is giving 2 talks [0] at FOSDEM this Saturday, I'll > be present, wondering if there would be other Debian Med members > around to meet? > > See you in Brussels! > +Emilien > > [0] https://fosdem.org/2013/schedule/speaker/andreas_tille -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/71b16418-7e64-47e6-8375-813b79311...@gmail.com
[MoM] Debian Med MoM for February
Hi, Just thought I should introduce myself -- I am the student for Debian Med MoM for February and Andreas Tille is my mentor. So to start, I am going to package the `hunspell-en-med' word list. A quick question: should the package be called `hunspell-en-med' or `openmedspel'? [0]. I have also sent a request to join the Debian Med group on Alioth. Please feel free to comment and contribute to the future discussions that will take place during the MoM! [0] - http://debian-med.alioth.debian.org/tasks/tools#prospective-debs -- Sukhbir -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130131020923.gd11...@gmail.com
