RFS: andi

Hi, A new version of andi (v0.9.6.1-1) is ready for upload. Thanks in advance, Fabian http://anonscm.debian.org/cgit/debian-med/andi.git/

Mentioning EDAM files in DebianMed Policy

Hi all, The new edam files should also be mentioned in our team policy. Below is a quick mock up; But we might also need to write a proper spec. Best, Fabian ## debian/upstream/edam This is a machine-readable file to categorize where in life-science this package has its application. The cate

RFS: indelible 1.03-2

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, I updated indelible to feature a brand new man page. Now the package should be lintian-free. Would someone kindly sponsor? Just wondering, which timestamp is supposed to be under a changelog entry, the day I started a new version, or its uplo

Re: RFS: indelible 1.03-2

-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Afif, On 2016-02-14 06:21, Afif Elghraoui wrote: > على الجمعـة 12 شباط 2016 ‫02:40، كتب Fabian Klötzl: >> Just wondering, which timestamp is supposed to be under a >> changelog entry, the day I started a new version, or its upl

Re: Mentioning EDAM files in DebianMed Policy

-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi Jon, Andreas mentioned, that some refactoring of the policy is going on. So when that is done, we should double-check we use the right EDAM version. Best, Fabian On 2016-02-14 18:07, ji...@cbs.dtu.dk wrote: > Thanks Fabian > > Anyway, the link

transtermhp ready for review and upload

-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi all, I moved transtermhp packaging from SVN to Git [1]. Also, I fixed the GCC-6 bug (#811614), made the package lintian-clean again and did some more housekeeping. Though, I did not yet remove the SVN repo in case I got something wrong in the tra

libgtextutils: sym links

Hi all, I have been fixing some issues in libgtextutils and now I am left with a single lintian warning: W: libgtextutils0v5: dev-pkg-without-shlib-symlink usr/lib/x86_64-linux-gnu/libgtextutils-0.7.so.0.0.0 usr/lib/x86_64-linux-gnu/libgtextutils-0.7.so I guess, there are a thousand and one ways

Request for Sponsoring: spaced

Hi all, I have prepared a package for spaced (words). The remaining issues are due to upstream not releasing proper source tarballs (binaries are included and no versioning). While I sort out these minor issues with the authors I guess we can already upload the current version into the new queue.

Re: Request for Sponsoring: spaced

Hi, > ... and should be used if there are no good reasons to do otherwise. Unfortunately I can't use uscan because the upstream website does not provide proper links. So I used the basic idea of Sascha's and implemented it in a get-orig-source script. It is not beautiful, but probably better than

Re: Request for Sponsoring: spaced

On 24.03.2016 14:37, Andreas Tille wrote: > On Thu, Mar 24, 2016 at 12:46:21PM +0100, Fabian Klötzl wrote: >>> ... and should be used if there are no good reasons to do otherwise. >> >> Unfortunately I can't use uscan because the upstream website does not >>

Re: Request for Sponsoring: spaced

Hi, Good thing this wasn't sponsored yet. Reawaking from the holiday inflicted drowsiness, I realized the ITP bug number was wrong. I hope that was the last issue and someone will kindly sponsor. http://anonscm.debian.org/cgit/debian-med/spaced.git/ Best, Fabian

Re: Request for Sponsoring: spaced

Hi Afif, On 29.03.2016 06:43, Afif Elghraoui wrote: > Hi, Fabian, > > Unfortunately, this code built an empty package. I noticed that you > haven't activated the autotools plugin for debhelper for the build to > work. How the fuck, did I miss this one? > Other points for future reference: > >

Re: Proposal to start link time optimisation for Debian Med packages

Hi all, On 30.03.2016 22:28, Sascha Steinbiss wrote: >> The promotion of this enhancement I consider to be exceptionally >> important, especially so if we can tie this up with the continuous >> integration testing and some benchmarking. For all the folks that wait >> over some NGS data set to be a

libgtextutils

Hi Charles, A while ago I made some changes to the libgtextutils package, see git [1] for details. Since I am on a new machine, I can no longer reproduce the lintian warning which may (or may not) explain the problems appearing in the wild [2]. However, I cannot reproduce that problem, either. Co

Re: Mugsy (Was: Seqan knowledge needed (Was: Help needed in C++ / seqan issue))

Hi Andreas, I spent the last few weeks meandering in the murky marshes of the mugsy source code; It is a monstrosity. Before answering to your individual points I'd like to stress that I *literally* spend days trying to compile mugsy with seqan 1.3 which comes with Ubuntu 14.04 LTS. A hundred cha

Re: Mugsy (Was: Seqan knowledge needed (Was: Help needed in C++ / seqan issue))

Hi, On 19.04.2016 14:03, Andreas Tille wrote: > On Tue, Apr 19, 2016 at 12:29:59PM +0200, Fabian Klötzl wrote: >> Hi Andreas, >> >> I spent the last few weeks meandering in the murky marshes of the mugsy >> source code; It is a monstrosity. >> >> [ … lots o

Re: Mugsy (Was: Seqan knowledge needed (Was: Help needed in C++ / seqan issue))

On 19.04.2016 14:53, Andreas Tille wrote: > On Tue, Apr 19, 2016 at 02:40:34PM +0200, Fabian Klötzl wrote: >>>> I have some extra patches for those tools, making them up to ten times >>>> faster. Will commit in due course. >>> >>> Cool. Just ping me

mummer patches

Hi all, So I finally got round to submit my patches for MUMmer. One can be found in the repo, half of the other is attached to this mail. Unfortunately, the other half got lost in a code reindentation. Applying the changes requires refactoring src/tigr/sw_align.cc for the changes in the header. If

Re: mummer patches

Hi Sascha, On 05.08.2016 16:27, Sascha Steinbiss wrote: >> So I finally got round to submit my patches for MUMmer. One can be found >> in the repo, half of the other is attached to this mail. Unfortunately, >> the other half got lost in a code reindentation. Applying the changes >> requires refact

Re: bwa Segmentation fault issue

Hi, I much prefer an interesting coding challenge to cleaning out my flat, so I tackled this problem. On 01.07.2017 00:04, Nadiya Sitdykova wrote: > > 2) negative argument for malloc size > ==10017== Thread 13: > ==10017== Argument 'size' of function malloc has a fishy (possibly > negative) valu

Sponsoring request: andi and libdivsufsort

Hi all, The andi package has been updated to incorporate the latest upstream version; Sponsoring kindly requested (debian/0.11-1). I also tackled some issues with libdivsufsort (debian/2.0.1-3). However, the lintian page shows some errors with ldconfig which I can't reproduce. Maybe they were fixe

Re: Please fix bugs

Hi, On 27.06.2017 21:34, Andreas Tille wrote: > I have the feeling we are currently receiving way more > than we are fixing. I tried to do my part and applied an available patch to trimmomatic. Not sure if you want to upload a new version for such a tiny change, though. I also had a look at the j

Sponsoring request: figtree

Hi all, With the last release of figtree upstream switched to a proper release and naming scheme, which the old watch file didn't catch. I fixed that, imported the new version and did a bit of housekeeping (tag: debian/1.4.3+dfsg-1). Many thanks in advance, Fabian https://anonscm.debian.org/cgit

Re: Sponsoring request: figtree

Hi Andreas, On 14.07.2017 15:04, Andreas Tille wrote: >> (tag: debian/1.4.3+dfsg-1). > > Please leave the tagging for the uploader (or tag *after* the upload). > I had two further corrections - so please git pull and make sure you > remove the tag inside your local repository since I changed the

Re: EDFlib 1.12 (new version available)

Hi all, So I tackled this one. The packaging has been moved from SVN to Git [1]. For the sponsor I left the task of tagging and deleting the old repo. Best, Fabian [1]: https://anonscm.debian.org/cgit/debian-med/edflib.git/

Re: CWL workflow as Debian package

Hi all, On 11.08.2017 17:57, Steffen Möller wrote: > I had an exchange with Stian yesterday about what CWL workflow of his > database he would propose to use as an experience-gathering example. He > proposed the GATK workflow by Farah Zaib Khan et al. for being good to > cite about workflows and r

Re: EDFlib 1.12 (new version available)

Hi Andreas, On 10.08.2017 00:59, Andreas Tille wrote: > Sponsored and removed from SVN. Thanks a lot for the complete job As far as I can tell, the package didn't make it into the new queue. Would you mind uploading it again? Best, Fabian

Re: EDFlib 1.12 (new version available)

Hi, Because of a bad feature check, the build failed on hurd. I tried to properly fix it using cmake, which I have no previous experience with. Please review and dput again. ☺ Fabian

Re: Any idea how to fix freebayes? [Was: Bug#866646: freebayes FTBFS with libhts-dev 1.4.1-2]

Hi Andreas, On 02.09.2017 14:54, Andreas Tille wrote: > The htslib issue remains the same but I have no idea how to fix it. The problem is that Allele.h defines a friend function called `json` residing in global namespace. However, hts.h already defined a value of an enum with the same name, thus

Re: Any idea how to fix freebayes? [Was: Bug#866646: freebayes FTBFS with libhts-dev 1.4.1-2]

On 04.09.2017 13:20, Andreas Tille wrote: > Fully ACK. Would you volunteer to create an issue in htslib bug tracker. > >> Btw, I had to add -std=c++11 for a successful build. > > Seems you have build the package locally. Would you mind pushing your > changes to Git? Will do. Forgot to mentio

Re: Any idea how to fix freebayes? [Was: Bug#866646: freebayes FTBFS with libhts-dev 1.4.1-2]

On 04.09.2017 13:38, Fabian Klötzl wrote: > > On 04.09.2017 13:20, Andreas Tille wrote: >> Fully ACK. Would you volunteer to create an issue in htslib bug tracker. >> >>> Btw, I had to add -std=c++11 for a successful build. >> >> Seems you have bui

Re: Issue with new version of Bowtie

Hi Andreas, I am having trouble reproducing the issue locally, but reading between the lines of the template mess, the solution might be as simple as defining ~KarkkainenBlockwiseSA as noexcept: ~KarkkainenBlockwiseSA() noexcept { … } The compiler complains, because in C++11 autom

Re: Issue with new version of Bowtie

Hi, On 05.09.2017 09:44, Andreas Tille wrote: > On Mon, Sep 04, 2017 at 05:26:15PM +0200, Fabian Klötzl wrote: >> I am having trouble reproducing the issue locally, > > So bowtie 1.2.1.1 builds at your side in a sid chroot? Should have been more specific: It builds fine on my

Re: Issue with new version of Bowtie

Hi all, On 05.09.2017 09:56, Fabian Klötzl wrote: > I will setup a proper sid chroot and ping you again, when I have > committed a patch. Done and done. Compiles fine now, but the tests hit the known issue on example 5‽ Best, Fabian

RFS: arb

Hi all, Andreas wanted us to fix more bugs, so that's what I did: arb is now managed in git [1] and the two bugs from the BTS are fixed. Please review, tag and sponsor. I also left the SVN repo alive, incase I did something severly wrong and we need to go back (*). Best, Fabian [1] git+ssh://git

RFS: indelible

Hi all, indelible has accumulated some changes. It would be great if someone could tag + sponsor a new update. Thanks, Fabian https://anonscm.debian.org/cgit/debian-med/indelible.git/tree/

Re: RFS: indelible

Hi Alex, On 02.10.2017 17:03, Alex Mestiashvili wrote: > I usually run lintian this way: > lintian -Iivc --pedantic $pkg.changes Wow, now lintian produces way more output than before. Thanks for the hint, will try to fix the issues ASAP. Fabian

Re: RFS: indelible

Hi, On 02.10.2017 17:03, Alex Mestiashvili wrote: > A few notes to the package - lintian complains about non-https VCS > fields, a couple of typos and a hardening issue - > indelible: hardening-no-bindnow usr/bin/indelible Fixed the VCS URL, some typos (my lintian doesn't actually complain) and

Re: RFS: indelible

Hi, On 03.10.2017 08:30, Andreas Tille wrote: > This also tells you about spelling errors (which I fixed quickly - no > idea whther upstream might be alive - please forward if you think so). > I sure hope, they are alive; but they are unresponsive. > The only remaining lintian "issue" is now th

Re: figtree autopkgtest

Hi Kate, Thanks for starting tests for figtree. It is my favourite way to produce a phylogeny. On 29.11.2017 21:56, ka lou wrote: > I made my first attempt on providing a simple autopkgtest for the > 'figtree' package , referring to the 879621 >  bug. It successful

Re: figtree autopkgtest

Ho, On 30.11.2017 10:07, Andreas Tille wrote: > thanks for your comments. I'd really love if more people become > involved in autopkgtests and teaching newcomers! I am also a newcomer with respect to autopackage tests. > On Wed, Nov 29, 2017 at 10:30:14PM +0100, Fabian Klötzl

Re: figtree autopkgtest

On 30.11.2017 10:39, Andreas Tille wrote: >> GIF works just fine on my Ubuntu LTS‽ > > $ figtree -graphic GIF -width 320 -height 320 test.tree test.gif | head -n5 > > Argument, -graphic has a bad string value: GIF > > > FigTree v1.4.3, 2006-2016 > > > > What version of fig

Re: figtree autopkgtest

Hi Andreas, On 30.11.2017 10:59, Andreas Tille wrote: > On Thu, Nov 30, 2017 at 10:42:36AM +0100, Fabian Klötzl wrote: >> The output is a well rendered phylogeny. > > Yes, but may be the GIF format was droped for pretty good reasons > replaced by PNG without adapting the docs.

December: tophat

Hi all, I just pushed some changes to build tophat with our version of libbam. Not sure if the previously mentioned issue in [1] is fixed; can't test, because my cowbuild just broke. :( Best, Fabian [1]: https://lists.debian.org/debian-med/2014/10/msg4.html

Re: [Debian-med-packaging] Bug#780816: December: tophat

On 04.12.2017 17:33, Andreas Tille wrote: > Thanks to the test suite we now know that the issue is not solved yet: > > $ sh run-unit-test > > [2017-12-04 17:28:54] Beginning TopHat run (v2.1.1) > --- > [2017-12-04 17:28:54] Checking for Bowtie >

Re: December: tophat

Hi Andreas, On 04.12.2017 17:33, Andreas Tille wrote: > On Mon, Dec 04, 2017 at 02:09:48PM +0100, Fabian Klötzl wrote: >> I just pushed some changes to build tophat with our version of libbam. >> Not sure if the previously mentioned issue in [1] is fixed; can't test, > >

Re: December: tophat

On 06.12.2017 16:20, Andreas Tille wrote: > Hi Fabian, > > On Wed, Dec 06, 2017 at 03:53:09PM +0100, Fabian Klötzl wrote: >> On 04.12.2017 17:33, Andreas Tille wrote: >>> >>> Thanks to the test suite we now know that the issue is not solved yet: >>> &g

Re: removing tophat from Debian

Hi, On 16.12.2017 15:40, geo...@marsel.is wrote: > There are **plenty** of bioinformaticians and sysadmins, especially > downstream of Debian who will say “I need tophat”, without being able to > explain why they do. > >   > > Migration path, big announcement, large time path so everybody gets >

RFS: andi

Hi all, I prepared a new package for andi, now on salsa [1]. However, I am sure, I must have done something wrong, because the packaging was surprisingly smooth. Best, Fabian [1]: https://salsa.debian.org/med-team/andi

Re: RFS: andi

Hi Sascha, On 26.02.2018 16:42, Sascha Steinbiss wrote: > I can sponsor this, but it seems that the 0.12 orig tarball is missing > in the pristine-tar branch. Could you please push this as well -- thanks :) Forgot to push --all. Done! Thanks for sponsering. Fabian

Re: RFS: andi

Hi, In order to fix the random build failures, I added a patch to make the unit tests reproducible. I would be happy, if someone could sponsor again. Thanks in advance, Fabian

Re: RFS: andi

Spend all of yesterday debugging the remaining build failures. Hope I got it fixed now. Would someone care to tag+sponsor again? Fabian On 05.03.2018 16:50, Andreas Tille wrote: > Done. Thanks for your work on it, Andreas.

Re: RFS: andi

Hi Andreas, On 07.03.2018 15:02, Andreas Tille wrote: > BTW, if andi has a build time test do you think it is feasible to run > this as autopkgtest as well? Some of the build time tests are not *unit* tests at all but verify the functionality of the whole program. So yeah, these could be ported t

Figtree on Ubuntu

Hi all, Currently, figtree crashes on Ubuntu due to a simple bug [1]. I have opened a bug on launchpad some time ago but nobody has yet volunteered to integrate the debian version into ubuntu (and backport it to 18.04). Does someone on this mailinglist have the permissions and leisure to do s

Re: Figtree on Ubuntu

Hi Graham, On 17.10.2018 15:49, Graham Inggs wrote: As it happened, figtree 1.4.3+dfsg-6 was uploaded to Debian after Ubuntu 18.10 was already frozen for automatic imports from Debian [1], and no sync request [2] was filed. Once figtree has been fixed in the development version of Ubuntu, I c

Re: Figtree on Ubuntu

Hi Graham, Thank you very much for your effort. I updated the bug description and added a debdiff based on your changes. Hope that is alright and you can upload without issues. Best, Fabian

RFS: libmurmurhash 1.3

Hi all, The latest version should fix the few remaining build issues on big-endian systems. Furthermore, I added some man page links. I also wanted to remove some private functions from the .symbols file. However, that resulted in a lintian error. So if, as per the documentation, someone want

Re: RFS: libmurmurhash 1.3

Hi Andreas, On 11.02.19 15:41, Andreas Tille wrote: Furthermore, I added some man page links. I also wanted to remove some private functions from the .symbols file. However, that resulted in a lintian error. Could you be more verbose about what you did and what lintian error was issued? Norm

Re: RFS: libmurmurhash 1.3

On 11.02.19 22:24, Andreas Tille wrote: I had a look on the build logs[1] and at least mips and s390x keep on failing (some archs are not yet build). Sorry for keeping you busy with this That's fine, because it is entirely my fault; Wouldn't have happened if I had merged your automake sugge

libmurmurhash: help required before RFS

Hi all, It's been a while, but I finally managed to package v1.5 of libmurmurhash. The most important changes is that upstream now comes with autotools. Furthermore, I marked a few functions as private (PMurHash_*). This changes the public API and thus required a SONAME bump. Is it ok to just

Re: libmurmurhash: help required before RFS

Ho, On 09.07.19 13:44, Andreas Tille wrote: In theory, libmurmurhash also supports an auto package test but I have yet to figure out how that is done. You mean how that is done in general or for this specific package? More like, in general. The debian/tests might be a good start. I will ta

Re: libmurmurhash: help required before RFS

Hi, On 10.07.19 07:59, Andreas Tille wrote: > Since it was not to much work I added the autopkgtest and uploaded. Thanks a lot. Could you also push your changes to salsa so that I can have a look? Best, Fabian

libmurmurhash debcheck

Hi all, libmurmurhash has issues in testing and unstable according to debcheck [1]. > Package declares a build time dependency on debhelper-compat (= 12) which cannot be satisfied on ppc64el. Package libmurmurhash does not exist on ppc64el. The package itself builds fine on my computer. I re

Re: Bug#944299: ITP: phylonium -- Fast and Accurate Estimation of Evolutionary Distances

an do it? Best Fabian https://salsa.debian.org/med-team/phylonium On 07.11.19 13:34, Fabian Kloetzl wrote: Package: wnpp Severity: wishlist Owner: Fabian Klötzl * Package name: phylonium Version : 1.1 Upstream Author : Fabian Klötzl * URL : https://github.com/

RFS: phylonium

Hi all, So I prepared a preliminary package for phylonium [1]. It is not perfect yet, but I am mostly interested whether it builds correctly on non-x86 architectures. I would be very grateful if someone could sponsor an upload to trigger builds. Have a nice Monday, Fabian 1: https://salsa.d

Re: RFS: phylonium

Thanks for the reminder. Done. Fabian

Re: Sponsering libdivsufsort?

Hi, > you have injected libdivsufsort into Debian Med Git. If you confirm > that the package is ready I could sponsor the package. As far as I can tell, the package is ready. But as this is my first Debian package, I might be wrong. If you would sponsor libdivsufsort that would be great. Steffe

Re: Sponsering libdivsufsort?

Hi, On 28.07.2015 17:08, Andreas Tille wrote: > I did two aditional commits: One removing an unusued get-orig-source > template and more importantly I fixed the clean target that tried to > remove not existing files (please test such things using pbuilder and > `gbp buildpackage` next time). Oh y

Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, On 06.08.2015 08:32, Andreas Tille wrote: > Hi Fabian, > > I hope you read the mailing list > debian-med-packag...@lists.alioth.debian.org or at least have > subscribed this package in the Debian Package Tracker. If not > please do either of on

Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, On 06.08.2015 10:09, Andreas Tille wrote: > On Thu, Aug 06, 2015 at 09:46:51AM +0200, Tomasz Buchert wrote: >> My packaging branch has also this bug + section problem (but my >> parallel collab-maint repo is ok :D ). I've pushed two more >> commi

Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, I will be on a week-long vacation, starting tomorrow. Please, feel free to continue committing so we can release an improved package, soon. On 06.08.2015 20:01, Andreas Tille wrote: > On Thu, Aug 06, 2015 at 05:43:47PM +0200, Tomasz Buchert wrote

Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]

-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi, Am 22.08.2015 um 12:28 schrieb Tomasz Buchert: > I've pushed another change to libdivsufsort which, to my knowledge, > is "The Right Thing To Do". I still needed to apply a custom patch > for "include" directory because header files are generate

Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]

-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi, Am 22.08.2015 um 16:44 schrieb Tomasz Buchert: > Wrt the bug: as the dependency is now explicit, you can close in > the next release. More genrally, you need to format the changelog > with a nice summary of all changes. I wrote up a changelog e

Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, Would someome be so kind as to sponser another upload for libdivsufsort? Thanks in advance. Fabian ps. Thanks to Andreas for the reminder. On 23.08.2015 17:48, Tomasz Buchert wrote: > On 23/08/15 17:11, Fabian Klötzl wrote: &g

Bug#800932: ITP: andi -- Efficient Estimation of Evolutionary Distances

Package: wnpp Severity: wishlist Owner: "Fabian Klötzl" * Package name: andi Version : 0.9.4 Upstream Author : Fabian Klötzl * URL : https://github.com/EvolBioInf/andi * License : GPL Programming Lang: C Description : Efficient Est

Re: Bug#800932: ITP: andi -- Efficient Estimation of Evolutionary Distances

t, Fabian On 05.10.2015 10:02, Fabian Klötzl wrote: > Package: wnpp Severity: wishlist Owner: "Fabian Klötzl" > > > * Package name : andi Version : 0.9.4 Upstream Author : > Fabian Klötzl * URL : > https://github.com/EvolBioInf/andi

Re: Bug#800932: ITP: andi -- Efficient Estimation of Evolutionary Distances

On 05.10.2015 10:55, Andreas Tille wrote: > I guess for non-German speakers andy might be a random 4 letter > combination and nobody will confuse it with the tyical nickname of > a German Andreas. :-) Great, I'll stick with "andi" then and continue packaging. Thanks for the quick advice Fabian

Request for Sponsoring: andi

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, As far as I can tell, andi is already ready for sponsoring: `gbp buildpackage` ran through and lintian did not report any issues. git+ssh://git.debian.org/git/debian-med/andi.git Thanks in advance, Fabian -BEGIN PGP SIGNATURE- Versi

Sponsoring request: andi-0.9.5

Hi all, I have updated the andi package to the upstream version 0.9.5. I hope it is correct w.r.t. the ongoing GSL transition. http://anonscm.debian.org/cgit/debian-med/andi.git/ Best, Fabian

Re: Sponsoring request: andi-0.9.5

On 09.12.2015 10:52, Andreas Tille wrote: > Please make sure you provide the according pristine-tar for the > new upstream version by using > > gbp import-orig --pristine-tar > > as described in our policy document. Ok, I executed that command and push the pristine branch. I hope that was the r

Bug#807486: ITP: INDELible -- A powerful and flexible simulator of biological evolution

Package: wnpp Severity: wishlist Owner: "Debian Med Team" * Package name: INDELible Version : 1.03 Upstream Author : William Fletcher * URL : http://abacus.gene.ucl.ac.uk/software/indelible/ * License : GPL Programming Lang: C++ Description : A powerful

Almost ready: indelible

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, indelible [1] is almost ready for sponsoring. However there are two more issues bothering me. 1) There is not proper upstream URL for watching. The actual download URL contains a string looking like a hash to me and thus may be subject to cha

Re: Almost ready: indelible

Hi Andreas, On 22.12.2015 15:59, Andreas Tille wrote: > On Tue, Dec 22, 2015 at 03:15:21PM +0100, Fabian Klötzl wrote: >> 1) There is not proper upstream URL for watching. The actual download >> URL contains a string looking like a hash to me and thus may be >> subject t

Re: Almost ready: indelible

Hi all, On 22.12.2015 19:09, Andreas Tille wrote: >>> Once you are using a get-orig-source script you can decide to strip the >>> files there. Or you can use Files-Excluded in debian/copyright to let >>> uscan do its work. >> >> Thanks for the pointers. I'll try my best. > > Our package template

RFS: indelible

Hi Andreas, On 2015-12-25 23:50, Andreas Tille wrote: Unfortunately upstream does provide a proper download page, only a form that forwards to the download. Thus I couldn't get uscan to run (and no Files-Excluded). So instead I used the above script, download via wget and remove the binaries.

Re: RFS: indelible

Hi, On 2015-12-26 07:32, Andreas Tille wrote: Hi Fabian, uploaded after some commits. Please check these and make sure you will apply these in future packages similarly. Sure thing, will do. Thanks for sponsoring, Fabian

Re: RFS: phylonium

=945133 On 11.11.19 10:41, Fabian Klötzl wrote: Hi all, So I prepared a preliminary package for phylonium [1]. It is not perfect yet, but I am mostly interested whether it builds correctly on non-x86 architectures. I would be very grateful if someone could sponsor an upload to trigger builds

Re: Request for feedback: adding additional arch support to libssw using the SIMDE headers

Hi Michael, On 12.12.19 13:05, Michael Crusoe wrote: Specifically I'm interested in seeing more of our packages for the latest RaspberryPI systems (arm64). Likewise I am interested in testing things on arm. However, remote debugging is not a lot of fun and I am busy writing my dissertation an

Re: Help with autopkgtest for package andi

Hi, Adding autopackagetests for andi has been on my TODO list for a long time, as I am both its upstream author and maintainer. However, as my dissertation is due in two weeks, that currently takes priority. If you want to go forward with the tests, here are some pointers: The package comes with

Re: Help with autopkgtest for package andi

see below. > Following error was encountered: > > autopkgtest [00:00:12]: test run-unit-test: [--- > Triggering low homology failed > a_low.fa:>S0 (base_seed: 744030346) > a_low.fa:>S1 (base_seed: 744030346) > b_low.fa:>S0 (base_seed: 2613208344) > b_low.fa:>S1 (base_seed: 261

Re: Help with autopkgtest for package andi

mailing list. As I have some free time on my hand now, I will look closer at the autopkgtests. We can then add them in a -2. Best, Fabian On 07.03.20 20:12, Samyak Jain wrote: > Hey Fabian, > Thank you for the follow-ups :D > > On Sat, Mar 7, 2020 at 9:56 PM Fabian Klötzl

RFS: andi

Hi all, Samyak updated andi to its latest upstream release. I reviewed the changes and pushed them to the repo. Could somepne sponsor an upload [1]? I will look at the autopkgtests in the next weeks. Thanks in advance, Fabian 1: https://salsa.debian.org/med-team/andi

Re: RFS: andi

Hi, On 27.03.20 19:05, Andreas Tille wrote: > On Fri, Mar 27, 2020 at 06:20:50PM +0100, Fabian Klötzl wrote: >> I will look at the autopkgtests in the next weeks. > > That would be great. Been there, pushed that. It *should* work fine. After all, the tests have already b

Re: Help with autopkgtest for package andi

Oops, fixed. :) Thanks! On 05.04.20 23:36, Andreas Tille wrote: > Hi Fabian, > > sponsored - but since you are upstream please fix > > I: andi: spelling-error-in-binary usr/bin/andi exlusive exclusive > > in your next release. > > Thank you for your preparation > > Andreas. >

Re: Help with autopkgtest for package andi

Double oops. Forgot to add build-essential as a dependency for the autopkgtests. Could you sponsor again? Have a nice Monday, Fabian On 06.04.20 09:09, Fabian Klötzl wrote: > Oops, fixed. :) > Thanks! > > > On 05.04.20 23:36, Andreas Tille wrote: >> Hi Fabian, >> &

Re: [RFC] Update libssw? (Needed by parasail)

Hi, The error in parasail complains that some structure doesn't have a `saturated` property. However, the libssw repository you linked to doesn't contain that word either. Thus, the version you deleted has some crucial changes, I guess. There are a few ways you could go. 1) Judging from the name

Re: RFS: indelible

Hi Pranav, Thank you for your work on this. I have just two comments. For one the repo now contains a file log.txt which I think you might have added by accident. Secondly, your test check whether the program runs. However, they don't actually check whether it runs correctly. You could add a rando

Re: RFS: indelible

Hi Pranav, Wow, you have quite the bash skills. I can't run things locally at the moment, but I think it looks fine. Fingers crossed, it works consistently across architectures. Can s.o. please sponsor an upload? Best, Fabian On 11.06.20 23:51, Pranav Ballaney wrote: > Hi Fabian, > I added log

Re: shapeit4 and AVX2

Hi all, I agree that most CPUs used for scientific computing these days support AVX2. However, that is going to change. For instance, Apple is switching to ARM based CPUs. MacBooks are quite popular among bioinformaticians so so any tool author would want to support non-x86 CPUs. I also believ

Re: shapeit4 and AVX2

vious experience the author has been quite non-responsive. Giulio On Thu, Nov 5, 2020 at 2:46 PM Fabian Klötzl <mailto:kloe...@evolbio.mpg.de>> wrote: Hi all, I agree that most CPUs used for scientific computing these days support AVX2. However, that is going to change. For inst

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