Re: debian/upstream/metadata: registry item for the Blends' task pages?

Hi, 2017-08-12 13:25 GMT+02:00 Steffen Möller : > > On 12.08.17 11:31, Charles Plessy wrote: >> >> I wonder if this metadata would be even more useful via AppStream. From >> https://appstream.debian.org/: >> >> AppStream is a cross-distro XML format to provide metadata for software >>

Re: References to registries -> debian-med policy?

Hi Steffen, 2017-09-16 18:37 GMT+02:00 Steffen Möller : > > I have added a sentence to the Debian Med policy and also pushed > the "Registry:" entry for the UpstreamMetadata wiki page that our > policy is pointing to. > Thank you for this. After a discussion with Fabien (from OMICtools) in Augus

Re: Proposal for Registry-display on task pages

Hi Andreas, 2017-10-19 8:29 GMT+02:00 Andreas Tille : > On Mon, Oct 09, 2017 at 04:10:59PM +0200, Steffen Möller wrote: >> "OMICtools" => "https://duckduckgo.com/?q=\\"; (a single backslash at the >> end is what I want) > > The link > > https://duckduckgo.com/?q=\OMIC_6 > > should lead

Re: Proposal for Registry-display on task pages

Hi Andreas, 2017-10-19 12:40 GMT+02:00 Andreas Tille : > > Well, it might be that we have some typos in our data but this > duckduckgo.com detour seems very suspicious to me and I would love to > avoid this. > The solution will come from OMICtools, they will provide an API that will permit to dir

Re: A common group on salsa.debian.org for R packages ?

Hi, I just transferred the dh-r package from debian-science to r-pkg-team [1-2]. But I don't have right to remove the repository at debian-science. Can someone do it for me? Best, Dylan [1] https://salsa.debian.org/r-pkg-team/dh-r [2] https://salsa.debian.org/salsa/AliothRewriter/merge_requests/

Re: r-pkg-team page on wiki.d.o.

Hi, 2018-01-10 12:59 GMT+01:00 Charles Plessy : > > I just drafted a r-pkg-team page on wiki.debian.org: > > https://wiki.debian.org/Teams/r-pkg-team > Thanks Charles for this. It could be useful to add this link in the description of the team in the salsa page. Like this someone who arrives on

Re: Salsa migration of Debian Med team packages

Hi Sascha, Thanks for the migration. I think all R packages (r-*) can be removed from the Debian Med repository, they moved into the Debian R team repository [1] some weeks ago [2]. Best, Dylan [1] https://salsa.debian.org/r-pkg-team [2] https://lists.debian.org/debian-med/2018/01/msg00026.html

Re: Salsa migration of Debian Med team packages

Hi, 2018-02-13 14:00 GMT+01:00 Andreas Tille : > No objections and thanks to Dylan for bringing this up (I just missed > this). I just did a pull request [1] to fix Alioth redirections for these packages. Best, Dylan [1] https://salsa.debian.org/salsa/AliothRewriter/merge_requests/152

Re: Depends available in other PPA's

Hi Tony, 2018-02-12 16:06 GMT+01:00 Tony Travis : > Is it possible to refer to dependencies like this available in other > PPAs when building packages? It seems possible [1] but for the whole PPA not for an individual package. Not sure that it is reasonable to add dependency to other PPA here.

RFS: python-fitbit

Hi, I updated python-fitbit, the new version builds new binary packages, so it should go into the NEW queue. Can someone sponsor it? python-fitbit (0.3.0-2) UNRELEASED; urgency=medium * Move documentation into a new package python-fitbit-doc. * Bump Standards-Version: 4.1.3 (no changes neede

RFS: jheatchart -- Heat map charting library for Java

Hi, Could someone upload it? Thanks. Best, Dylan Package name: jheatchart URL: http://www.javaheatmap.com/ License: LGPL-3+ Description: Heat map charting library for Java The JHeatChart library provides a simple API for generating Java heat maps. Output heat maps as .png, .jpg or .gif images

Re: Depends available in other PPA's

Hi Tony, 2018-03-07 19:29 GMT+01:00 Tony Travis : > > Do you or anyone else object if I add the ToolChain test PPA dependency? > >> ppa:ubuntu-toolchain-r/test > I don't use the Debian Med PPA so I am probably not the most concerned person here. I would like to say it is not a problem for me to a

Some R packages are still present in the Debian Med repository

Hi, I moved pvclust and permute from Debian Med salsa repository to Debian R team (respectively r-cran-pvclust and r-cran-permute). Could someone remove them from the Debian Med team? Thanks, Dylan

Re: Some R packages are still present in the Debian Med repository

2018-03-10 0:10 GMT+01:00 Andreas Tille : > > Done. I wonder whether we should fix the entries in AliothRewriter > accordingly. > Thanks Andreas. About AliothRewriter, it is already done ;-) https://salsa.debian.org/salsa/AliothRewriter/merge_requests/231/ Best, Dylan

RFS: ChromHMM -- Chromatin state discovery and characterization

Hi, Could someone upload it? Thanks. Best, Dylan Package name: chromhmm URL: http://compbio.mit.edu/ChromHMM/ License: GPL-3+ Description: Chromatin state discovery and characterization ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chro

Re: RFS: ChromHMM -- Chromatin state discovery and characterization

Hi Andreas, 2018-03-12 10:00 GMT+01:00 Andreas Tille : > I've asked upstream for release tags[1]. May be upstream will set those > tags and you do not need a get-orig-source script any more but if not it > makes sense to use such a script. I've provided an example that even > removes Files-Excl

RFS: bioSyntax -- Syntax highlighting for computational biology

Hi, Could someone review and upload it? Thanks. Best, Dylan Package name: biosyntax URL: https://biosyntax.org/ License: GPL-3 Description: Syntax Highlighting for Computational Biology (gedit) Syntax highlighting for computational biology to bring you intuitively close to your data. BioSynta

Re: RFS: bioSyntax -- Syntax highlighting for computational biology

Hi Andreas, 2018-03-24 17:46 GMT+01:00 Andreas Tille : > Uploaded. Could you please make some suggestion in what task > (=metapackage) we should put what binary package? I'm undecided between > med-bio and med-bio-dev and which binary package should be mentioned in > that task(s). Thanks for th

Re: RRID update on salsa on packages starting with A+B

Hi Steffen, hi Andreas, 2018-03-28 14:16 GMT+02:00 Andreas Tille : > >> Via salsa, though, well, not. Should lintian invoke yamllint, possibly? > > As far as I know syntax errors in upstream files are fetched by lintian. > Its the downside of just using the not yet uploaded commits as data > input

RFS: ChromImpute -- Large-scale systematic epigenome imputation

Hi, Could someone upload it? Thanks. Best, Dylan Package name: chromimpute URL: http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/ License: GPL-2 Description: Large-scale systematic epigenome imputation ChromImpute takes an existing compendium of epigenomic data and uses it to predict signa

Re: TR: Debian has RRID SCR_006638

Hi all, 2018-04-19 14:16 GMT+02:00 Andreas Tille : >> To answer Andreas, we, at OMICtools, could publish every month, the list of >> new packages available in Debian Med on our blog : >> https://omictools.com/blog, if you feel it can helps. Thanks Fabien for this. :-) >> We just need a list of

Re: TR: Debian has RRID SCR_006638

Hi Fabien, 2018-04-25 8:37 GMT+02:00 Fabien Pichon : > > If what Dylan proposed is convenient for a majority of persons (and if the > list and script he sent are correct) I can have something ready this week or > the next one. Of course, they are not correct :-) I will have another look today but

Re: OMICS ID

Hi Andreas, 2018-04-26 9:10 GMT+02:00 Andreas Tille : > I noticed several commits of yours doing something like: > > - Entry: OMIC_04161 > + Entry: OMICS_04161 I did it when I tried to sort out which packages should be reported in the OMICtools newsletter. I think, all OMICtools IDs in our da

Re: TR: Debian has RRID SCR_006638

Hi all, 2018-04-25 12:21 GMT+02:00 Fabien Pichon : > As I said in my previous e-mail : YOU tell me what you want WE publish. > > It is YOUR communication **NOT** OMICtools' one. > > I just offered a "media" support after an Andreas' suggestion. No more. > > You should maybe discuss all together in

RFS: chromhmm and r-cran-metamix

Hi, Could I get upload rights for chromhmm? r-cran-metamix is ready to be sent to the NEW queue. Thanks. Best, Dylan

Re: RFS: chromhmm and r-cran-metamix

:27 GMT+02:00 Dylan Aïssi : > Hi, > > Could I get upload rights for chromhmm? > > r-cran-metamix is ready to be sent to the NEW queue. > > Thanks. > > Best, > Dylan

AppStream file to store upstream metadata: registry and bibliography references

Hi all, I started discussions with AppStream devs to add new tags in the AppStream file. This file contains upstream metadata and it is cross distro in contrary to our d/upstream/metadata. If you are using the d/u/metadata to store bibliography references or registry refences you can take part of

RFS: bolt-lmm and gemma

Hi, I fixed FTBFS for bolt-lmm and gemma, could someone give me upload rights? Thanks. Best, Dylan

Re: RFS: bolt-lmm and gemma

Hi Andreas, 2018-06-06 21:11 GMT+02:00 Andreas Tille : > > I've done gemma since I've seen your tag pending, bolt-lm was done right now. > Thanks. Oups, I didn't see the notification for gemma because I received it on another email address. Best, Dylan

Request for review: minimac4 and libstatgen

Hi, I finished packages for minimac4 and one of its dependency libstatgen. Could I have a review of them before to upload to NEW? Especially for libstatgen, because the upstream makefile does not generate a shared library, so it is the first time that I have to manually generate a shared library

RFS: python-colormath, python-spectra and python-lzstring

Hi, Could someone upload them? (colormath is a dependency of spectra). Thanks. These packages are dependencies for MultiQC [1] which still need some work before to be uploaded. Best, Dylan [1] http://multiqc.info/

RFS: python-ratelimiter

Hi, Snakemake, a package from Debian Med, is blocked in unstable (among others) because python-ratelimiter is not available anymore in testing. So, I fixed the RC bug and I did some minor updates for python-ratelimiter [1]. Could you review/merge this [1] and upload the package? Thanks. Best, D

RFS: biosyntax.

Hi, I have updated biosyntax which should go to the NEW queue due to new binary packages. Thanks. Best, Dylan

Upload rights request

Hi, Can someone give me the upload rights for these packages? - minimac4 - r-cran-leaps - r-cran-shinythemes - r-cran-rlumshiny dcut dm --uid "bob.dyb...@gmail.com" --allow minimac4 r-cran-leaps r-cran-shinythemes r-cran-rlumshiny Thanks, Dylan PS: this should be my last request of upload right

Re: Upload rights request

Hi Mattia, Le ven. 28 sept. 2018 à 14:38, Mattia Rizzolo a écrit : > In which case, this should happen very soon, the keyring-maint team is > having some troubles, but I'd expect this to happen at most in the > upcoming weekend (should have happened 4 days ago…) Thanks for these news :-) Best,

Re: Debian Med Badge - just like Conda has it?

Le sam. 15 sept. 2018 à 21:30, Steffen Möller a écrit : > > https://bioconda.github.io/_static/badge-generator/ Not as pretty but we have those ones: https://badges.debian.net/ Dylan

Re: Too many hands on MultiQC Fwd: Bug#925304: Acknowledgement (ITP: multiqc -- output gathering for RNA sequencing across tools and samples)

Hi Andreas, hi Steffen, Unfortunately, MultiQC is not DFSG compatible because its main component is Highcharts (CC BY-NC 3.0). https://github.com/ewels/MultiQC/issues/800 But this tool is very useful, so maybe we can push it in non-free. Best, Dylan

Re: multiqc | Add more registries (074d642d)

Hi Steffen, Le lun. 25 mars 2019 à 23:23, Steffen Möller a écrit : > Ooops! Well done! It was quite easy, I tried to merge my packaging attempt into yours :-). Le sam. 23 mars 2019 à 12:22, Steffen Möller a écrit : > That escaped me. Many thanks. And, amazingly, we apparently had even > more h

Re: Please help with Conda packaging [Was: Bug#926416: ITP: conda -- OS-agnostic, system-level binary package manager and ecosystem]

Hi, If we have some questions regarding conda, we can ask to upstream, they should be happy to help us. https://github.com/conda/conda/issues/1235 Best, Dylan

Re: FW: Bio linux download

Hi Graham, Le mer. 24 avr. 2019 à 21:19, Graham Inggs a écrit : > > Is this LP: #1777165 [1]? Let's get this fixed, I'm happy to sponsor > a SRU [2] upload. > I am preparing the fix [1], I will ping you when it is ready. Best, Dylan [1] https://salsa.debian.org/med-team/metaphlan2/commits/ubu

Re: FW: Bio linux download

Hi Tony, Le lun. 20 mai 2019 à 22:21, Tony Travis a écrit : > Hi, Dylan. > > I've installed the "metaphlan2" package from Ubuntu "bionic-proposed" > successfully, with no errors reported. If "metaphlan2" is installed, > "med-bio" will install without errors in Ubuntu-MATE 18.04.2 LTS: > Thanks f

fastqc: htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed

Control: severity -1 serious Hi, I have tested the testsuite with the upstream binary (FastQC 0.11.8) and there is no error, so the testsuite is fine. This bug was probably hidden before we added the test of bam and sam files. Currently, fastqc from our package is unable to process bam and sam fil

Migration to testing of optimir is blocked - why?

Hi, The migration of optimir [1] to testing was blocked during the freeze for Buster. But since the freeze is over, optimir never moved to testing and I don't know why. He has some dependencies which are available only in amd64, so could this be a problem for the migration? Should I restrict the a

Re: Migration to testing of optimir is blocked - why?

Hi Andreas, Le mer. 17 juil. 2019 à 16:49, Andreas Tille a écrit : > > The Excuses link[2] is your friend. The Architecture all package > expects to be able to run on *all* architectures but it can't since some > Depends are only available on amd64 this is a problem. I try to > remember what th

Re: Migration to testing of optimir is blocked - why?

Hi Mattia, Le mer. 17 juil. 2019 à 18:15, Mattia Rizzolo a écrit : > Just mentioning: arch:all needs to be installable on amd64 and i386, the > other archs are there only for reference. If that isn't possible you can > contact the release team to ask for a "force"-hint and make that migrate >

Please allow optimir to migrate to testing

Hi release team, I guess the summer break period (+ debconf2019) was not the best time for my request. I try it again :-), could you allow optimir to migrate to testing? Thank you. Best, Dylan -- Forwarded message - De : Dylan Aïssi Date: jeu. 18 juil. 2019 à 10:15 Subject

Re: RFS or upload permissions for python-pomegranate

Le jeu. 2 janv. 2020 à 10:35, Michael Crusoe a écrit : > > Thank you Dylan Aïssi ! You are welcome! Best, Dylan

Re: RoSA ante portas - happily pass this on

Hi Andreas, Le sam. 4 juil. 2020 à 09:43, Andreas Tille a écrit : > @Dylan: Any idea how to fix > > E: r-other-rosa: requires-r-api \o/ this tag is finally useful :-) I pushed a change that should fix this issue. I was not able to test because r-cran-lsd is not available (still in NEW). Could y

Re: RoSA ante portas - happily pass this on

Le sam. 4 juil. 2020 à 11:27, Andreas Tille a écrit : > > While I think your changes are pretty sensible it does not solve the > problem. > :-( I will investigate this again later today Dylan

Re: RoSA ante portas - happily pass this on

Hi Andreas, hi Steffen, Le sam. 4 juil. 2020 à 12:30, Steffen Möller a écrit : > Lintian still is > lintian ../rosa_1.0-1_amd64.changes > E: r-other-rosa: requires-r-api This tag is now fixed using a workaround to a problem I guess in dh-r. We had a similar problem some times ago: https://bugs.d

Re: What happened to r-bioc-complexheatmap?

Hi Andreas, Le mer. 8 juil. 2020 à 15:16, Andreas Tille a écrit : >E: r-cran-getoptlong: requires-r-api > > Dylan, any idea what might be wrong here? By looking into the git repo, I have no idea why this tag is emitted. I will investigate it this evening ( I am at work without a root access

False positive lintian tag: requires-r-api

Hi Andreas, hi Felix Le mer. 8 juil. 2020 à 15:16, Andreas Tille a écrit : >E: r-cran-getoptlong: requires-r-api > > Dylan, any idea what might be wrong here? This seems to be a false positive from lintian, this tag seems to be always emitted even when the binary package has correct dependen

Re: False positive lintian tag: requires-r-api

Hi Felix, Thanks for your prompt answer! Le jeu. 9 juil. 2020 à 02:34, Felix Lechner a écrit : > Yes. At least for the package r-cran-getopt, the package depends on > r-api-X.X, (4.0 for arch all) but the regular expression includes no > period (yet has a plus): > > Please just let me know which

Re: shapeit4 and AVX2

Dear Giulio, I am CCing the public Debian Med mailing list and Michael Crusoe who can help to improve the Debian package in order to have an AVX2 binary optimized. Le jeu. 5 nov. 2020 à 15:20, Giulio Genovese a écrit : > > I have noticed you are the author of the following patch for the shapeit4

Re: Help for optimir autopkgtest needed

Hi Andreas, My laptop has decided to die last week, so I can do only minor edits through the salsa web interface. Le ven. 4 déc. 2020 à 23:58, Andreas Tille a écrit : > > I updated the packaging of optimir in Git[1] but its autopkgtest > fails with > > > Starting Library preparation... > Error

Bug#991919: transition: r-api-bioc-3.13

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition X-Debbugs-CC: debia...@lists.debian.org, debian-med@lists.debian.org Hi, Bioconductor 3.13 was released in May [1]. All r-bioc-* packages need a manual upgrade (after the release of bull

Re: Bioconductor API Bump to 3.13

Hi Steffen, hi Andreas, Le jeu. 5 août 2021 à 06:18, Andreas Tille a écrit : > Sure. We need a transition. Dylan (in CC) was kind enough to trigger > this in the past and we should do so right after the release (I'm > announcing here pseudo-VAC due to personal reasons on one hand as well > as D

Re: Bug#991919: Bioconductor API Bump to 3.13

Hi, Le jeu. 26 août 2021 à 09:49, Paul Gevers a écrit : > > If this question is to the release team, than the following question we > asked earlier requires an answer: > > What's the status wrt. to the reverse dependencies. Do those that are > > binNMU-able build against the new version? > No, a

Re: Bioconductor API Bump to 3.13

Hi Nilesh, Le mar. 31 août 2021 à 09:07, Nilesh Patra a écrit : > > I just happened to see this commit[1]. Has the transition begun? > If so, can I do anything to help? > Yep :-) See https://bugs.debian.org/991919#44 I don't have too much free time. So, Feel free to upload all packages you can

Re: Bug#1040500: routine-update: Don't create d/salsa-ci.yml file

Hi Andreas, Le ven. 7 juil. 2023 à 11:24, Andreas Tille a écrit : > > Thanks for your opinion about this. What I mean with de facto standard: We > have about 2000 repositories configured to check debian/salsa-ci.yml. I have > not yet found a way to set the according field via gitlab API to som