Attempt to remove treetool
Hi, after having updated several of our packages I try to target at removal candidates. When trying to take a screeshot - hey, anybody elso who wants to support Debian Med by doing screenshots??? - from treetool I realised that any action freezes my X server. I had to switch to console and kill the treetool process. I do not think that we need to care about bugs of packages that were orphaned upstream for 15 years and has very low popcon (6 user, 0 updated). Any active treetool user should please speek up now, prove the need for treetool inside Debian by providing a screenshot and thus give some motivation for us to keep this inside Debian. If this not happens I'll ask ftpmaster for removal. Kind regards 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
Re: Status of BioRuby
Hi, I'm an upstream author of BioRuby. On Mon, 5 Oct 2009 19:56:10 +0200 Andreas Tille wrote: > Well, BioRuby was not updated for a long time and nobody complained > until now. So the upload does not seem to be urgent. But we will have > a Debian freeze in December (at least this is the plan) and having our > packages ready 6-8 weeks before to give people time for updates and > reporting problems seems to be OK. So if you think you can have a look > in October and we upload at end of October / beginning of November seems > to be reasonable. If you know now that you are busy the next four weeks > I might upload the current status to have more chance for other testers. There were a complain in BioRuby mailing list. http://lists.open-bio.org/pipermail/bioruby/2009-April/000893.html -- Naohisa Goto ng...@gen-info.osaka-u.ac.jp / n...@bioruby.org -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Status of BioRuby
On Tue, Oct 06, 2009 at 06:10:13PM +0900, Naohisa GOTO wrote: > I'm an upstream author of BioRuby. Thanks for contacting Debian Med about this. > There were a complain in BioRuby mailing list. > http://lists.open-bio.org/pipermail/bioruby/2009-April/000893.html So this would give one more point for a quick upload. Do you have by chance any way to test the Debian package once it is uploaded? Kind regards 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
Status of axparafit (ITP #463219)
Hi, locking at Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/axparafit David has finished the package which closes #463219 and changelog says "Wed, 30 Jan 2008 11:52:11 +0100". But there is no visible sign of this package. If there is nothing I might have overlooked I would update the packaging to recent "state of art" and try uploading again. Kind regards 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
Tkmelting for Debian
Le Thu, Oct 01, 2009 at 10:05:57PM +0200, Andreas Tille a écrit : > > the Debian Med team has packaged melting for Debian - at least the > versions < 5. We now are considering to package the latest version and Dear Nicolas and Marine, I would like to add to what Andreas already wrote that we experienced problems on the upgrade of tkmelting from 4.2 to 4.3, as in this version tkmelting.pl executes `./melting4_4-linuxi386 $options -v -q 2>&1` instead of `melting $options -v -q 2>&1`. We are preparing a patched version to solve that problem, but in the course of testing tkmelting, I experienced more difficulties. In particular, after computing one melting temperature, I could not compute a second one. Lastly, do you by chance have an icon to suggest for the Melting gui? It would enhance the look of the entry in the GNOME/KDE menus. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Status of BioRuby
On Tue, 6 Oct 2009 12:11:10 +0200 Andreas Tille wrote: > On Tue, Oct 06, 2009 at 06:10:13PM +0900, Naohisa GOTO wrote: > > I'm an upstream author of BioRuby. > > Thanks for contacting Debian Med about this. > > > There were a complain in BioRuby mailing list. > > http://lists.open-bio.org/pipermail/bioruby/2009-April/000893.html > > So this would give one more point for a quick upload. > Do you have by chance any way to test the Debian package once it > is uploaded? Yes. I'm also a debian user, and I'm glad if I can help. Naohisa Goto ng...@gen-info.osaka-u.ac.jp -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Status of BioRuby
On Tue, Oct 06, 2009 at 08:05:59PM +0900, Naohisa GOTO wrote: > Yes. I'm also a debian user, and I'm glad if I can help. Ahh, that's really great. One word beforehand and to everybody (perhaps I'll compose a separate mail as well): Please install the package popularity-contest and answer the question whether your data can be sended to Debian with "Yes" if no specific local policy disallows this. This helps really to know which packages are used and which not. For instance according to http://qa.debian.org/popcon.php?package=libbio-ruby1.8 there is no single user of this package. We know that popularity contest does not reflect the real number of users. But it would be helpful - specifically for speciallised applications like Debian Med is providing - to know at least of some users. Otherwise there is the chance that we might drop a package with no users which would be a shame for those who are actually happy about Debian packages of the applications they are using. Now one minor issue addressed to upstream. When building the package some lintian issues are left. These are: W: libbio-ruby1.8: binary-without-manpage usr/bin/bioruby N: N:Each binary in /usr/bin, /usr/sbin, /bin, /sbin or /usr/games should N:have a manual page N: N:Note that though the man program has the capability to check for several N:program names in the NAMES section, each of these programs should have N:its own manual page (a symbolic link to the appropriate manual page is N:sufficient) because other manual page viewers such as xman or tkman N:don't support this. N: N:If the name of the man page differs from the binary by case, man may be N:able to find it anyway; however, it is still best practice to make the N:case of the man page match the case of the binary. N: N:If the man pages are provided by another package on which this package N:depends, lintian may not be able to determine that man pages are N:available. In this case, after confirming that all binaries do have man N:pages after this package and its dependencies are installed, please add N:a lintian override. N: N:Refer to Debian Policy Manual section 12.1 (Manual pages) for details. N: N:Severity: normal, Certainty: possible N: W: libbio-ruby1.8: image-file-in-usr-lib usr/lib/ruby/1.8/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif N: N:This package installs a pixmap or a bitmap within /usr/lib. According to N:the Filesystem Hierarchy Standard, architecture-independent files need N:to be placed within /usr/share instead. N: N:Severity: normal, Certainty: certain N: W: libbio-ruby1.8: image-file-in-usr-lib usr/lib/ruby/1.8/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png W: libbio-ruby1.8: image-file-in-usr-lib usr/lib/ruby/1.8/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif W: libbio-ruby1.8: image-file-in-usr-lib usr/lib/ruby/1.8/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif I think it would be great if you would provide a man page bioruby.1. The image-file-in-usr-lib issue is probably minor, but if I where you I would probably adapt to FHS and move the files to /usr/share. I do not see a point in changing this for the current Debian package but if you see a chance to change it for the next BioRuby release this would be nice. Finally I just uploaded the new package to unstable and it will be available after 12 hours at all mirrors. So you are able to test and report problems (preferably with patches, because you know we are not really the Ruby experts or our Ruby experts have time issues). You might also consider maintaining the package by becoming a member of the Debian Med team. In principle it is not that hard to update an existing package once the packaging stuff is written. Just let us know if you might consider this. We always are happy about upstream developers in our team and I hope people here agree with me that we are quite helpful once it comes to technical Debian details. We would also welcome if you might announce the existance of the new Debian packages at BioRuby lists to get more testers. (Also propagating the populatity-contest hint would be great.) Kind regards 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
Maintaining praat in Debian Med team?
Hi Rafael, your package praat was included in the Psychology task of the Debian Med Blend[1]. I realised that the packaged version is some minor versions behind upstream (Debian has 5.1.7, upstream has 5.1.17). I wonder whether this has some technical reason or whether you might struggle with other tasks and you just not find time for this package. In case you might need a backup maintainer you might consider joining the Debian Med team. I have seen that you are using git to maintain praat and we did not yet updated our policy to mention the freshly created git archive. So I will not point you to our packaging policy which might be not that relevant for you but just want to hear whether you are interested at all. Kind regards and thanks for maintaining praat Andreas. [1] http://debian-med.alioth.debian.org/tasks/psychology -- 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
Re: Maintaining praat in Debian Med team?
Sorry for answering my own mail: An alternative option for team maintenance might be Experimental Psychology Maintainers for sure - but this team might comment on this themselves. Kind regards Andreas. On Tue, Oct 06, 2009 at 03:54:54PM +0200, Andreas Tille wrote: > Hi Rafael, > > your package praat was included in the Psychology task of the Debian Med > Blend[1]. I realised that the packaged version is some minor versions > behind upstream (Debian has 5.1.7, upstream has 5.1.17). I wonder whether > this has some technical reason or whether you might struggle with other > tasks and you just not find time for this package. > > In case you might need a backup maintainer you might consider joining > the Debian Med team. I have seen that you are using git to maintain > praat and we did not yet updated our policy to mention the freshly > created git archive. So I will not point you to our packaging policy > which might be not that relevant for you but just want to hear whether > you are interested at all. > > Kind regards and thanks for maintaining praat > > Andreas. > > > [1] http://debian-med.alioth.debian.org/tasks/psychology > > -- > 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 > > -- 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
Re: Maintaining praat in Debian Med team?
Hi, On Tue, Oct 06, 2009 at 03:58:53PM +0200, Andreas Tille wrote: > Sorry for answering my own mail: > > An alternative option for team maintenance might be > >Experimental Psychology Maintainers > > > for sure - but this team might comment on this themselves. If there is need for assistance just drop us a note. We use git for almost all packages (look for 'pkg-exppsy' on git.debian.org). Cheers, Michael > On Tue, Oct 06, 2009 at 03:54:54PM +0200, Andreas Tille wrote: > > Hi Rafael, > > > > your package praat was included in the Psychology task of the Debian Med > > Blend[1]. I realised that the packaged version is some minor versions > > behind upstream (Debian has 5.1.7, upstream has 5.1.17). I wonder whether > > this has some technical reason or whether you might struggle with other > > tasks and you just not find time for this package. > > > > In case you might need a backup maintainer you might consider joining > > the Debian Med team. I have seen that you are using git to maintain > > praat and we did not yet updated our policy to mention the freshly > > created git archive. So I will not point you to our packaging policy > > which might be not that relevant for you but just want to hear whether > > you are interested at all. > > > > Kind regards and thanks for maintaining praat > > > > Andreas. > > > > > > [1] http://debian-med.alioth.debian.org/tasks/psychology > > > > -- > > 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 > > > > > > -- > 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 -- GPG key: 1024D/3144BE0F Michael Hanke http://mih.voxindeserto.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Maintaining praat in Debian Med team?
On Tue, Oct 06, 2009 at 10:29:02AM -0400, Michael Hanke wrote: > Hi, > > On Tue, Oct 06, 2009 at 03:58:53PM +0200, Andreas Tille wrote: > > Sorry for answering my own mail: > > > > An alternative option for team maintenance might be > > > >Experimental Psychology Maintainers > > > > > > for sure - but this team might comment on this themselves. > > If there is need for assistance just drop us a note. We use git for > almost all packages (look for 'pkg-exppsy' on git.debian.org). I'd prefer this. Unfortunately the address bounced. So perhaps we might reach Rafael via a bug report "new version available"? Kind regards 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
Re: kalign: Please enable bash-completion
Hi David, once you provided a patch which solves this problem. Unfortunately I'm not positively sure, how to apply this. Would you mind injecting it into the just updated packaging to let us finish the kalign packaging and fix all open bugs? Kind regards 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
Re: kalign: Please enable bash-completion
On Tue, Oct 06, 2009 at 04:52:17PM +0200, Andreas Tille wrote: > once you provided a patch which solves this problem. Unfortunately I'm > not positively sure, how to apply this. Would you mind injecting it into > the just updated packaging to let us finish the kalign packaging and fix > all open bugs? Sorry, for the noise, I just got the clue and can surely fix the problem. On the other hand: David, could you do us a favour and also find a patch for #441063 ? Kind regards 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
Re: Attempt to remove treetool
Le Tue, Oct 06, 2009 at 09:50:16AM +0200, Andreas Tille a écrit : > > after having updated several of our packages I try to target at removal > candidates. When trying to take a screeshot - hey, anybody elso who > wants to support Debian Med by doing screenshots??? - from treetool I > realised that any action freezes my X server. I had to switch to > console and kill the treetool process. I do not think that we need to > care about bugs of packages that were orphaned upstream for 15 years and > has very low popcon (6 user, 0 updated). > > Any active treetool user should please speek up now, prove the need for > treetool inside Debian by providing a screenshot and thus give some > motivation for us to keep this inside Debian. If this not happens I'll > ask ftpmaster for removal. Hi Andreas, you scared me with your freeze story, so I have not tried to reproduce it ;) But I am all for removing treetool. With NJplot being a bit superseded by the lastest SeaView, that unfortunately non-free now, and TreeView X being in difficulty because it does not compile with latest wxwidgets, we may fall short of tree viewers. I found a possible emergency plan B: jstreeview. http://www.sanger.ac.uk/Users/lh3/treeview.shtml It is a javascript program, but we can simply use it as a local web page and write a desktop entry that starts a browser on it. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Please review the copyright file of bwa.
user debian-le...@lists.debian.org usetags 548719 copyright-review-requested thanks Dear all, in order to lower our rejection rate from the new queue, I propose to do more systematically peer-review of Debian copyright files before the upload of new packages. I proposed a method in the following URL: http://wiki.debian.org/CopyrightReview For your convenience, I have uploaded the new “bwa” packages on mentors.debian.net. But of course, its debian directory is also in our repository. http://mentors.debian.net/debian/pool/main/b/bwa svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/ Could anybody have a look at its Debian copyright file? In exchange, I will review dicomscope. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Attempt to remove treetool
On Wed, Oct 07, 2009 at 01:40:23PM +0900, Charles Plessy wrote: > But I am all for removing treetool. OK. > With NJplot being a bit superseded by the lastest SeaView, that unfortunately > non-free now, and TreeView X being in difficulty because it does not compile > with latest wxwidgets, we may fall short of tree viewers. :-( > I found a possible emergency plan B: jstreeview. > http://www.sanger.ac.uk/Users/lh3/treeview.shtml > > It is a javascript program, but we can simply use it as a local web page and > write a desktop entry that starts a browser on it. Hmmm, I'd rather regard this as plan C because for purposes like this I would not prefer a browser based solution. I added it to our tasks file anyway to have this idea recorded somewhere. Kind regards 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
Re: Please review the copyright file of bwa.
On Wed, Oct 07, 2009 at 02:20:13PM +0900, Charles Plessy wrote: > Could anybody have a look at its Debian copyright file? In exchange, I will > review dicomscope. I had a look and do not have any additions regarding the content. However I'm curious about the formatting. If the copyright information should be expressed in RFC822 format you need to connect the paragraphs by a line conteining "^ .$" to make sure it will be machine parseable. Further comment: If you replace your rules file content by %: dh $@ You can spare the cdbs build dependency. Kind regards 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
