Re: Tophat 2.0.6 is ready for upload
Le Mon, Nov 05, 2012 at 10:03:40AM -0500, Carlos Borroto a écrit : > On Sun, Nov 4, 2012 at 8:36 PM, Charles Plessy wrote: > > > > I just realised that tophat never made it into Wheezy befor the freeze. > > Therefore, 2.0.6 is perfectly suitable for Sid. > > > > I lost track of who is DM or not. Please let me know if you need somebody > > to upload (and apply to DM). > > I'm not a DM, so I will need sponsoring for this package. Uploaded. Something I like to with my packages, is to commit the logs in the source package's Git repository. But it would make quite a number of tags and branches, so I wonder if you would like me to refrain to do so with tophat ? In some rare cases, I found it useful for troubleshooting differences between architectures, or between buildd builds and QA mass-rebuilds. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- 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/20121106085751.gh12...@falafel.plessy.net
New metapackages just uploaded
Hi, I just want to let you know that I created new metapackages and uploaded these to unstable. The rationale is that I do not expect any changes in the dependencies any more since we fixed all RC bugs affecting testing. Once the packages are accepted I'll file an unblock request to the release team. Moreover I played / hacked a bit with matplotlib to get some graph of the development of the most important (regarding the number of dependencies) tasks and this very hackish script which is available in Git[1] enabled me to create some kind of reasonable output[2]. Thanks to all those people who contributed to packaging all this nice software which makes Debian Med a success Andreas. [1] http://anonscm.debian.org/gitweb/?p=blends/website.git;a=commit [2] http://anonscm.debian.org/gitweb/?p=blends/website.git;a=blob_plain;f=misc/team_analysis_tools/debian-med_1.12.pdf -- 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/20121106104634.ga12...@an3as.eu
Re: Packaging Ray for Debian Med
Hi Andreas, On 11/06/2012 02:18 AM, Andreas Tille wrote: Hi Sébastien, On Mon, Nov 05, 2012 at 06:59:27PM -0500, Sébastien Boisvert wrote: I want the ray-extra because ray contains the executable Ray whereas ray-extra has some R and python scripts which are not used in most Ray workflows. Thus, I don't want the ray package to require (or suggest) r-base-core or python. Right, avoiding some extra dependencies which are usually unneeded is a fair reason for a separate binary package. ray-doc contains documentation not required to operate Ray. The man page alone is sufficient. I understood this but as I previosely said I personally would not split these few bytes from the main package. But in any case it is your decision as the person responsible for the package. I just wanted to make sure you are aware about typical reasons for splitting and that your decision was not simply after having read in the docs that it is possible to split up into different binary packages. In the end it is a matter of taste but if you would decide to keep these packages they should be "Architecture: all" in any case. Fixed. Fine. I guess now you need to fire up lintian -i ray_2.1.0-1_amd64.changes I don't get anything when I run this command. I am on Squeeze. which tells you about some issues of your packaging. The explanation that are triggered in verbose mode (-i) should give you a reasonable clue what needs to be done but in any case feel free to ask here if you might stumble upon any issue you might not understand. Regarding W: ray: hardening-no-relro usr/bin/Ray W: ray: hardening-no-fortify-functions usr/bin/Ray Do you know why I don't see these warning with lintian ? I would recommend to simply try debian/compat: 9 and in Build-Depends: debhelper (>= 9) which gives you good chances that hardening will be switched on in case Ray has a properly crafted build system. Changed compat and debbuilder to 9. BTW, in debian/changelog you are using "stable" as target distribution. Besides the fact that you *never* can upload to stable and always have to target at "unstable" our convention is to use "UNRELEASED" in VCS as long as the package is not yet uploaded. Changed to UNRELEASED. Kind regards and thanks for your work on this Andreas. Sent from my IBM Blue Gene/Q Way cooler than any other booring "Sent from my ..." signatures. :-) -- 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/50991c17.5060...@ulaval.ca
Re: Tophat 2.0.6 is ready for upload
On Tue, Nov 6, 2012 at 3:57 AM, Charles Plessy wrote: > > Uploaded. > > Something I like to with my packages, is to commit the logs in the source > package's Git repository. But it would make quite a number of tags and > branches, so I wonder if you would like me to refrain to do so with tophat ? > > In some rare cases, I found it useful for troubleshooting differences between > architectures, or between buildd builds and QA mass-rebuilds. > Sure please, by all means go ahead and include them. Thanks for the quick upload, Carlos -- 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/cabgghbjsjs0r59whtfoawg4519hk7w4al5hwdnkemwj-ma2...@mail.gmail.com
Re: Packaging Ray for Debian Med
On Tue, Nov 06, 2012 at 09:17:59AM -0500, Sébastien Boisvert wrote: > >I guess now you need to fire up > > > > lintian -i ray_2.1.0-1_amd64.changes > > > > I don't get anything when I run this command. I am on Squeeze. For development I'd (strongly) suggest to do drop a file /etc/apt/preferences.d/01-lintian.pref containing Package: lintian Pin: release a=unstable Pin-Priority: 605 provided that Squeeze supports this /etc/apt/preferences.d way - if not add this to your normal /etc/apt/preferences that should contain something like Package: * Pin: release a=stable Pin-Priority: 501 Package: * Pin: release a=unstable Pin-Priority: 50 Package: * Pin: release a=experimental Pin-Priority: 5 Once you might have done this please check apt-cache policy lintian It should give lintian from unstable preference. Alternatively you can explicitely do sudo apt-get install -t unstable lintian (always provided your sources.list has an entry for unstable). Please check again the lintian report with a recent lintian. > >Regarding > > > > W: ray: hardening-no-relro usr/bin/Ray > > W: ray: hardening-no-fortify-functions usr/bin/Ray > > > > Do you know why I don't see these warning with lintian ? Because of using lintian from stable. > >I would recommend to simply try > > > > debian/compat: 9 > > > >and in Build-Depends: debhelper (>= 9) which gives you good chances that > >hardening will be switched on in case Ray has a properly crafted build > >system. > > > > Changed compat and debbuilder to 9. OK. > >BTW, in debian/changelog you are using "stable" as target distribution. > >Besides the fact that you *never* can upload to stable and always have > >to target at "unstable" our convention is to use "UNRELEASED" in VCS as > >long as the package is not yet uploaded. > > > > Changed to UNRELEASED. OK. 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 Archive: http://lists.debian.org/20121106150905.ga20...@an3as.eu
Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
X-Debbugs-Cc: debian-med@lists.debian.org X-Debbugs-Cc: debian-de...@lists.debian.org Package: wnpp Severity: wishlist Owner: debian-med@lists.debian.org * Package name: bamtools Version : 2.2 Upstream Author : Derek Barnett * URL : https://github.com/pezmaster31/bamtools * License : Expat Programming Lang: C++ Description : C++ API and toolkit for manipulating BAM (genome alignment) files -- 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/CAD=wrcla-be-tyforwnmbje0nwwyahyli+7-nbdabnmmrau...@mail.gmail.com
Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
And here's the package, https://github.com/mr-c/bamtools/tree/debian My packaging skills are a bit rusty, so your feedback would be appreciated. On Tue, Nov 6, 2012 at 1:28 PM, Michael Crusoe wrote: > X-Debbugs-Cc: debian-med@lists.debian.org > X-Debbugs-Cc: debian-de...@lists.debian.org > Package: wnpp > Severity: wishlist > Owner: debian-med@lists.debian.org > > * Package name: bamtools > Version : 2.2 > Upstream Author : Derek Barnett > * URL : https://github.com/pezmaster31/bamtools > * License : Expat > Programming Lang: C++ > Description : C++ API and toolkit for manipulating BAM (genome > alignment) files > > > -- > 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/CAD=wrcla-be-tyforwnmbje0nwwyahyli+7-nbdabnmmrau...@mail.gmail.com > -- 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/CAD=WrcKOjuoF6vCvGR_Bm7=we=Kbb7cu0eL=wNyB=srnmwo...@mail.gmail.com
Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
And here's the package, https://github.com/mr-c/bamtools/tree/debian My packaging skills are a bit rusty, so your feedback would be appreciated. On Tue, Nov 6, 2012 at 1:28 PM, Michael Crusoe wrote: > X-Debbugs-Cc: debian-med@lists.debian.org > X-Debbugs-Cc: debian-de...@lists.debian.org > Package: wnpp > Severity: wishlist > Owner: debian-med@lists.debian.org > > * Package name: bamtools > Version : 2.2 > Upstream Author : Derek Barnett > * URL : https://github.com/pezmaster31/bamtools > * License : Expat > Programming Lang: C++ > Description : C++ API and toolkit for manipulating BAM (genome > alignment) files > > > -- > 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/CAD=wrcla-be-tyforwnmbje0nwwyahyli+7-nbdabnmmrau...@mail.gmail.com > -- 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/CAD=WrcJisnn71ZtpE_1f=mzKSt52XGuzcJTQ5=wazovibq2...@mail.gmail.com
