Re: New upstream version available type bugs for advent calendar use

Hi, Andreas, على الخميس 1 كانون الأول 2016 ‫01:16، كتب Andreas Tille: > I'll file a series of "New version available" > bugs here and will CC the list to enable everybody picking from the > list. I'll also give comments whether its an easy upgrade (for > beginners!) or whether its a hard one.

Re: pyBigWig

Hello, على الخميس 1 كانون الأول 2016 ‫16:32، كتب Diane Trout: > And instead of building a shared library, they just add the C files to > the python C extension. See: > https://github.com/dpryan79/pyBigWig/blob/master/setup.py#L14 > > I believe this is a violation of Debian packaging policy, but

pyBigWig

Hi, We needed to use pyBigWig for some of our processing. https://pypi.python.org/pypi/pyBigWig/0.3.2 or https://github.com/dpryan79/pyBigWig Being able to read bigBed or bigWig and to be able to directly write bigwig files seemed useful to us. The package is MIT/Expat licensed I made a

Re: [MoM] deepnano getting info from maintainer

Hi Andreas, I already started to make poretools-data package. Had to make some practice on split packaging . It's almost done. When I finished I will upload them both. Regards. 2016-12-01 16:00 GMT+03:00 Andreas Tille : > Hi Çağrı, > > I wonder whether Afif's hint how to get

Re: Macsyfinder Test Issues

Hello Andreas, Due to my exams i can not find any time to look this issue i will take care of it and return to you. Best Regards Canberk Koç [image: https://]about.me/canberkkoc 2016-12-01

Re: Problems to import origtar with gbp import-orig (Was: ncbi-blast+ new upstream version git import merge error)

On Thu, Dec 01, 2016 at 07:21:32PM +0500, Andrey Rahmatullin wrote: > As there is not enough data in the message, I'm assuming it's about the > published repo. > The upstream/2.4.0 tag is not merged into master so the debian/2.4.0-* > tags are not its descendants. This will not work properly. >

Re: ncbi-tools6: How to write a watch file with version encoded in _ftp_ directory

Hi Aaron, On Thu, Dec 01, 2016 at 09:39:42AM -0500, Aaron M. Ucko wrote: > Eriberto writes: > > > There are three problems here. > > Thanks for taking a look! You are welcome. :-) > > 1. The current FTP address is > > ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/,

Problems to import origtar with gbp import-orig (Was: ncbi-blast+ new upstream version git import merge error)

Hi, forwarding issue to debian-mentors On Thu, Dec 01, 2016 at 01:37:04PM +, olivier sallou wrote: > HI, > I have updated (locally) patches for the new release of ncbi-blast+. > However I face an error during import of new sources in git: > > gbp import-orig --pristine-tar

Re: Watch file for rnahybrid: Is redirection to jsf page messing confusing uscan?

Hi Eriberto, On Thu, Dec 01, 2016 at 11:48:12AM -0200, Eriberto wrote: > > https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_view_download > redirects to https://bibiserv2.cebitec.uni-bielefeld.de/sessionTimeout.jsf, > that shows the following message: > > > ERROR - Session

Re: ncbi-blast+ new upstream version git import merge error

Hi Olivier, On Thu, Dec 01, 2016 at 02:39:49PM +0100, Olivier Sallou wrote: > On 12/01/2016 02:37 PM, olivier sallou wrote: > > HI, > > I have updated (locally) patches for the new release of ncbi-blast+. > > However I face an error during import of new sources in git: > > > > gbp import-orig

Bug#846487: src:hhsuite: New version available

Package: src:hhsuite Severity: normal Hi, I noticed that hhsuite moved to Github[1] and version 3.0-beta.2 is available there. Its not fully clear whether beta.2 is ready for our users (compared to the current but outdated and probably unsupportet version 2.0.16). In any case we should start

Re: plastimatch/1.6.4+dfsg1-1 follow-up

Hi Gregory, could you possibly answer this question: On Thu, Dec 01, 2016 at 10:35:39AM +, Ghislain Vaillant wrote: > I did not notice this yesterday. May I ask why plastimatch is enabled for > x86 only? Is there a specific constrain for it? I admit if there was an explicit reason I simply

Re: ncbi-blast+ new upstream version git import merge error

On 12/01/2016 02:37 PM, olivier sallou wrote: > HI, > I have updated (locally) patches for the new release of ncbi-blast+. > However I face an error during import of new sources in git: > > gbp import-orig --pristine-tar ../ncbi-blast+_2.5.0.orig.tar.gz > > Upstream version is 2.5.0 >

ncbi-blast+ new upstream version git import merge error

HI, I have updated (locally) patches for the new release of ncbi-blast+. However I face an error during import of new sources in git: gbp import-orig --pristine-tar ../ncbi-blast+_2.5.0.orig.tar.gz Upstream version is 2.5.0 Merging to 'master' Automatic merge failed Error detected, will roll

Bug#846486: src:mothur: New version available

Package: src:mothur Severity: normal Tags: newcomer Hi, upgrading mothur to the latest version 1.38.1.1 should be pretty easy and thus a nice target for the advent bug squashing party. Kind regards Andreas. -- System Information: Debian Release: 8.6 APT prefers stable-updates APT

Re: Macsyfinder Test Issues

Hi Canberk, any news? Its *really* high time to get this issue settled. It would be extremely helpful if you could at least submit your test suite to Git to let me reproduce the test results if you do not manage to check the issue yourself. BTW, adding tests to packages could als made part of

Re: [MoM] deepnano getting info from maintainer

Hi Çağrı, I wonder whether Afif's hint how to get the example files might have been helpful for you. I admit I'm not keen to stick to the monthly boundaries of the MoM projects but if deepnano should make it into stretch we need to hurry up a bit. Kind regards Andreas. On Wed, Nov 16,

Re: Considerations for pird (Was: pirs/2.0.2+dfsg-2 follow-up)

On Thu, Dec 01, 2016 at 12:48:15PM +, Ghislain Vaillant wrote: > > > >I admit that loosing performance on amd64 where people will use the > >software in reality is not acceptable just for beeing able to compile it > >on random architecture that are not relevant for practical work. So if >

Re: Considerations for pird (Was: pirs/2.0.2+dfsg-2 follow-up)

On 01/12/16 12:33, Andreas Tille wrote: Hi Ghislain, thanks for your bug fixes and the tracking whether everything went fine afterwards. On Thu, Dec 01, 2016 at 10:31:30AM +, Ghislain Vaillant wrote: Looks like there are more non-portable options being used in pirs according to the build

Considerations for pird (Was: pirs/2.0.2+dfsg-2 follow-up)

Hi Ghislain, thanks for your bug fixes and the tracking whether everything went fine afterwards. On Thu, Dec 01, 2016 at 10:31:30AM +, Ghislain Vaillant wrote: > > Looks like there are more non-portable options being used in pirs according > to the build logs, -mtune=generic in particular.

Bug#846477: src:ncbi-tools6: New version available

Package: src:ncbi-tools6 Severity: normal Hi, there was a new release of ncbi-tools6 released which was not catched by its watch file since it is not able to parse ftp directory names properly. Please have a look at the download site[1] to find the latest version. (I've just sent a mail to

Bug#846474: src:igv: New version available

Package: src:igv Severity: normal Hi, updating igv to latest upstream (2.3.88) should not be that hard to do. If you want to do a really great job you could separate all its JARs and free the package itself - which is time consuming but definitely worth doing it. Kind regards Andreas.

Bug#846471: src:python-cutadapt: New version available

Package: src:python-cutadapt Severity: normal Hi, version 1.12 is available and usually this package has no pitfalls. Feel free to join our advant calender bug squashing party with preparing an update of this package and ping here if you need a sponsor. Kind regards Andreas. -- System

Re: December

On Wed, Nov 30, 2016 at 08:54:57AM +0100, Andreas Tille wrote: > BTW, I hope closed ITPs will be counted as well - finally we have a team > member in the ftpmaster team. :-P And for sure ROM requests which enable migration of packages to testing ... :-) Kind regards Andreas. --

Bug#846466: src:ncbi-blast+: New version available

Package: src:ncbi-blast+ Severity: normal Hi, since some time version 2.5.0 is available which should definitely distributed in Stretch. I made some noise about it before[1] but the usual Uploaders seem to be quite busy these days. The package needs usually adaptation of patches and is

New upstream version available type bugs for advent calendar use (Was: Bug#846461: src:sra-sdk: New version available)

Hi folks, at about Christmas the window for package upgrades will close and thus we should not only fix those bugs in existing packages but tackle important version upgrades as well to deliver the greatest software collection in Stretch. I'll file a series of "New version available" bugs here

Re: Shall we develop a Debian Med Tutorial? Fwd: [BC2-conference] Call for workshop and tutorial proposals open now.

Hi, On Thu, Dec 01, 2016 at 07:54:23AM +, Preussner, Jens wrote: > I think it would be a great idea to have a tutorial on Debian Med on the BC2 > or ISMB. I also would love to see something "hands-on", because knowing the > wealth of software packages that are readily available and also

Bug#846461: src:sra-sdk: New version available

Package: src:sra-sdk Severity: normal Hi, it would be really great to have sra-sdk in stretch. Any help for this not simple upgrade is welcome. Kind regards Andreas. -- System Information: Debian Release: 8.6 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500,

RE: Shall we develop a Debian Med Tutorial? Fwd: [BC2-conference] Call for workshop and tutorial proposals open now.

Hello, I think it would be a great idea to have a tutorial on Debian Med on the BC2 or ISMB. I also would love to see something "hands-on", because knowing the wealth of software packages that are readily available and also having the intention to participate in the packaging itself is one