If you are using Debian Med packages please ask your upstream to mention Debian in install instructions (Was: Upstream CI: send patches to use Debian packages when existing?)

On Fri, Jun 19, 2020 at 02:55:38AM +0200, Steffen Möller wrote: > > On 18.06.20 20:12, Andreas Tille wrote: > > On Thu, Jun 18, 2020 at 03:51:15PM +0200, Steffen Möller wrote: > > > ... > > > > > > Opinions? > > Isn't this a question you should ask upstream whether they like > > patches or not?

Re: What is the relation ncbi-magicblast and magicblast

Hi Aaron, On Thu, Jun 18, 2020 at 03:54:19PM -0400, Aaron M. Ucko wrote: > Please try adding --with-mbedtls to the configure command line to request > use of system mbed TLS. > > Also, I found that c++/src/objtools/data_loaders/genbank/gicache/gicache.c > ran afoul of -Werror=format-security, whi

Re: [RFS] paryfor

The paryfor-examples package does not make sense IMHO. What we > really want to test is whether test.cpp will build on the user > machine. > > So you rather should move test.cpp to > /usr/share/doc/libparyfor-dev/examples > accompanied by a short Makefile or script that should reproduce the > pa

Re: [RFS] paryfor

Also I'm not sure if arch should be changed to 'any' here. Please check :-) On Fri, 19 Jun 2020, 14:08 Nilesh Patra, wrote: > > > The paryfor-examples package does not make sense IMHO. What we >> really want to test is whether test.cpp will build on the user >> machine. >> >> So you rather shou

Re: [RFS] paryfor

On Fri, Jun 19, 2020 at 02:15:21PM +0530, Nilesh Patra wrote: > Also I'm not sure if arch should be changed to 'any' here. Please check :-) Arg, too late. I've fixed in Git for source-only upload. Thanks for your work on this Andreas. > On Fri, 19 Jun 2020, 14:08 Nilesh Patra, wrote: >

Re: RFH pychopper - test in cowbuilder does not find tests

@Emmanuel, I presume (home) you worked on an outdated source tree. If you pull again, the patch shall be undone. The Debian default had the tests performed from within the .pybuild tree structure. When Nilesh started the tests from the root of the source tree, this fixed everything. :o) But thank

[RFS] ncls

Please review and sponsor :) https://salsa.debian.org/med-team/ncls Regards, Nilesh

Re: [RFS] ncls

Ooops - this is already done. https://salsa.debian.org/med-team/python-ncls https://ftp-master.debian.org/new/python-ncls_0.0+git20200225.f9894b0+ds-1.html :o/ Sorry. On 19.06.20 16:18, Nilesh Patra wrote: Please review and sponsor :) https://salsa.debian.org/med-team/ncls

Re: [RFS] ncls

On Fri, 19 Jun 2020, 20:19 Steffen Möller, wrote: > Ooops - this is already done. > Aw, I should have been careful !! Sorry for the noise :-( > > https://salsa.debian.org/med-team/python-ncls > > https://ftp-master.debian.org/new/python-ncls_0.0+git20200225.f9894b0+ds-1.html > > :o/ Sorry.

Re: RFH pychopper - test in cowbuilder does not find tests

On Fri, Jun 19, 2020 at 04:18:13PM +0200, Steffen Möller wrote: > @Andreas, > > I liked your changes. Is more coming? Otherwise I would like to send > this off. I think I'm ready. I somehow lost it out of sight so uploading should be fine. Kind regards Andreas. PS: Videoconference in

Parallel packaging attempts

We just had a first redundant packaging.  This happened a few times before between Andreas and me. Have no exact idea how to stop that. This live-editing Excel table I find helpful at https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?usp=sharing - I typically

Re: Parallel packaging attempts

On Fri, Jun 19, 2020 at 05:00:07PM +0200, Steffen Möller wrote: > We just had a first redundant packaging.  This happened a few times > before between Andreas and me. Have no exact idea how to stop that. This > live-editing Excel table I find helpful at > https://docs.google.com/spreadsheets/d/1tAp

Re: What is the relation ncbi-magicblast and magicblast

Andreas Tille writes: > Thanks for these helpful hints which I implemented and pushed. No problem. I alas don't have time to take this package on fully, but am happy to offer more hints. > Unfortunately I'm now running into an error of the test suite: Declaring a build dependency on the time

[RFS] pyrle

Hi, I've packaged pyrle - that's a new module. I've ensured that this looks good. The repo is here[1] Needs review and sponsorship. [1]: https://salsa.debian.org/med-team/pyrle Thanks and regards Nilesh

RFS: prinseq-lite: prinseq-graphs with PCA support

Greetings, With the adjonction of libstatistics-pca-perl to the repository, thanks to the Debian Perl team for its help, I finally took some time to enable support for PCA graphs in prinseq-lite 0.20.4-5. The package is pushed on salsa, ready for review, and upload hopefully: https://sal

Re: Bug#963052: ITP: pairtools -- Framework to process sequencing data from a Hi-C experiment

Hi, pairtools is getting closser to be ready. https://salsa.debian.org/med-team/pairtools On Thu, Jun 18, 2020 at 02:35:24PM +0200, Andreas Tille wrote: > Hi Antoni, > > On Thu, Jun 18, 2020 at 12:02:06PM +, Antoni Villalonga wrote: > > Done. > > > > Python problems at tests... > > https

RFH: vienna-rna - Pushed changes back for you all to inspect

Hello, it builds, it tests, but it does not build in cowbuilder and I am [after some trying] left clueless why this is. Many thanks! Steffen

pplacer - and undefined mclgUnionv reference

Hello, I had a look at the MCL package and found that it is very much focused on the MCL library but apparently does not feature the impala library that ships the implementation of mclgUnionv. Proof below, I compiled MCL myself and copied libimpala.a to the ocaml directory. I am mostly clueless