[Help] librostlab-blast fails its autopkgtest with C++ issue

Hi, I did some cleanup in packages with uscan errors which affected all packages once created by members of rostlab. According to popcon these packages have remaining users anyway I refreshed the packages but stumbled upon librostlab-blast which fails its autopkgtest[1] which is a real bug since

Re: Bug#1004152: ITP: malt -- sequence alignment and analysis tool to process sequencing data

Thanks a lot Pierre! Am Fri, Jan 21, 2022 at 09:25:13PM +0100 schrieb Pierre Gruet: > Package: wnpp > Severity: wishlist > Owner: Debian-med team > X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org > > * Package name: malt > Version : 0.5.2 > Upstream

Bug#1004152: ITP: malt -- sequence alignment and analysis tool to process sequencing data

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: malt Version : 0.5.2 Upstream Author : Daniel Huson * URL : https://github.com/danielhuson/malt * License : GPL-3+

Re: New version of muscle contains asm statements which prevent building on non-Intel architectures

On Fri, Jan 21, 2022 at 5:05 PM Andreas Tille wrote: > > Hi, > > I've checked the build logs of muscle version 5.1[1] and noticed that > for instance on arm64 the build fails with: > > g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 > -ffile-prefix-map=/<>=. -fstack-protector-strong

New version of muscle contains asm statements which prevent building on non-Intel architectures

Hi, I've checked the build logs of muscle version 5.1[1] and noticed that for instance on arm64 the build fails with: g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o

Re: [Help] Any idea how to patch cmake code of terraphast properly to get shared libraries

Andreas Tille writes: > But there is some remaining syntax error[1]: [...] > [1] https://salsa.debian.org/med-team/terraphast/-/jobs/2386305#L857 Ah, yeah, it looks like you should also extend the GMP settings (around line 90); sorry for missing that earlier. In principle, I suppose the

Snap-aligner: Autopkgtest does not reproduce results from version 1.0.0

Hi, I upgraded snap-aligner in Git. The autopkgtest does not reproduce the results that were obtained with version 1.0.0. I have no idea with this is OK and we should simply adapt the reference data or whether this is an issue we should care about. Kind regards Andreas. --

Re: [Help] Any idea how to patch cmake code of terraphast properly to get shared libraries

Hi Aaron, Am Fri, Jan 21, 2022 at 08:09:03AM -0500 schrieb Aaron M. Ucko: > > Any hint how to fix this would be welcome > > I see some more target-specific settings towards the bottom of > CMakeLists.txt; please try extending the use of > TERRAPHAST_PLATFORM_INCLUDE and TERRAPHAST_COMPILE_FLAGS

Re: [Help] Any idea how to patch cmake code of terraphast properly to get shared libraries

Andreas Tille writes: > Any hint how to fix this would be welcome I see some more target-specific settings towards the bottom of CMakeLists.txt; please try extending the use of TERRAPHAST_PLATFORM_INCLUDE and TERRAPHAST_COMPILE_FLAGS to the new targets. -- Aaron M. Ucko, KB1CJC (amu at

Re: sambamba and freebayes new releases

Am Fri, Jan 21, 2022 at 12:20:49PM +0100 schrieb Steffen Möller: > Also many thanks to you both and greetings from my side! BTW, please let us know if you think backports are helpful for users of Debian stable. I do not do this automatically - but at request it is fine. Kind regards

Re: sambamba and freebayes new releases

Also many thanks to you both and greetings from my side! Best, Steffen On 21.01.22 12:17, Andreas Tille wrote: Am Fri, Jan 21, 2022 at 11:45:48AM +0100 schrieb Pjotr Prins: We release sambamba and freebayes with updated meson build systems. It should work for Debian. If not I am happy to

Re: sambamba and freebayes new releases

Am Fri, Jan 21, 2022 at 11:45:48AM +0100 schrieb Pjotr Prins: > We release sambamba and freebayes with updated meson build systems. It > should work for Debian. If not I am happy to troubleshoot. $ apt policy sambamba sambamba: Installed: (none) Candidate: 0.8.2+dfsg-1 Version table:

sambamba and freebayes new releases

Dear all, We release sambamba and freebayes with updated meson build systems. It should work for Debian. If not I am happy to troubleshoot. Pj.

Re: Sight needs to be ported to insighttoolkit5 [Fwd: sight is marked for autoremoval from testing]

Hi Flavien, Am Fri, Jan 21, 2022 at 10:16:19AM +0100 schrieb Flavien Bridault: > Well, sorry I assumed this module was not built for a reason... It is > actually an experimental module for algorithms, that may be promoted in a > real category if they are judged good enough. > > See

[Help] Any idea how to patch cmake code of terraphast properly to get shared libraries

Hi, terraphast is a precondition for raxml-ng and I've found a code copy also in iqtree. Thus it makes sense to release what is prepared in Salsa but I wanted to provide also a shared library. Without my cmake patch[1] the package builds a proper package with static library. If I activate the

Re: Sight needs to be ported to insighttoolkit5 [Fwd: sight is marked for autoremoval from testing]

Hi Andreas, Well, sorry I assumed this module was not built for a reason... It is actually an experimental module for algorithms, that may be promoted in a real category if they are judged good enough. See https://itk.org/Doxygen/html/group__ITKReview.html. So I have no idea if Debian wants