Re: PhyML error - does that ring any bell? Re: RFS: python-biopython

Hi Étienne, On Tue, Jun 16, 2020 at 10:41:28PM +0200, Étienne Mollier wrote: > I pushed a little change in the d/control file of the package > python-biopython in version 1.77+dfsg-2. This was the suggested > way to address the bug #962944: > > https://bugs.debian.org/cgi-bin/bugreport.cgi

Re: Can someone else check and sponsor (Was: nanofilt ready for upload)

Hi Shayan, On Tue, Jun 16, 2020 at 10:37:17PM +0100, Shayan Doust wrote: > > on the screen and than my screen froze. No ssh login possible any more. > > Waiting for more than 10min. I switched power-off and reboot worked > > fine (so no harm done) but I'm tired now and want to go to bed. I do >

Re: Can someone else check and sponsor (Was: nanofilt ready for upload)

Hi Andrius, On Wed, Jun 17, 2020 at 08:05:59AM +0300, mer...@debian.org wrote: > Why do you need to install these files as examples? Doing so unnecessarily > bloats packages. Autopkgtests are always run inside the source tree, so you > find your files in debian/tests/expected/. You need to blame

Re: Can someone else check and sponsor (Was: nanofilt ready for upload)

Hi Nilesh, On 2020-06-17 00:47, Nilesh Patra wrote: Add those files to say "debian/tests/expected/" and install these files as examples and take diff with what you get when you run-unit-test. Why do you need to install these files as examples? Doing so unnecessarily bloats packages. Autopkgte

RFS: pilon

Hi, I've added autopkgtests to pilon. Please review and sponsor. https://salsa.debian.org/med-team/pilon Regards, Pranav ᐧ

Re: What is the best way to refresh a 2to3 patch ?

Andreas Tille writes: > the short answer is: Convincing upstream to write Python3 and removing > the 2to3 patch at all is the best way. Meanwhile, if you do need to patch in Python 3 support, you may be able to reduce the opportunity for bitrot by doing so in the form of *two* patches: one for t

Uploaded Re: RFS: flash

Many thanks! On 17.06.20 02:38, Pranav Ballaney wrote: Hi, I've added autopkgtests to flash. Please review and sponsor. https://salsa.debian.org/med-team/flash Regards, Pranav ᐧ

[covid-19] r-bioc-beachmat

Hello, I just went through https://salsa.debian.org/r-pkg-team/r-bioc-beachmat which is contributing to several single-cell RNA-seq suites on BioConductor. Builds with cowbuilder. Please kindly comment/upload. Many thanks! Steffen

RFS: flash

Hi, I've added autopkgtests to flash. Please review and sponsor. https://salsa.debian.org/med-team/flash Regards, Pranav ᐧ

Re: Can someone else check and sponsor (Was: nanofilt ready for upload)

On Wed, 17 Jun 2020, 03:08 Shayan Doust, wrote: > Hello Andreas, > > > I've done some minor changes and was building the package. Unfortunately > > my computer crashed when ... or rather after(!) ... running the test. > I've > > seen > > > > [1] PASS > > > > on the screen and than my screen

Re: Can someone else check and sponsor (Was: nanofilt ready for upload)

Hello Andreas, > I've done some minor changes and was building the package. Unfortunately > my computer crashed when ... or rather after(!) ... running the test. I've > seen > > [1] PASS > > on the screen and than my screen froze. No ssh login possible any more. > Waiting for more than 10mi

Re: Can someone else check and sponsor (Was: nanofilt ready for upload)

Hi Étienne, hmmm, while checking all other activities of my computer while crashing I stumbled upon ... test_SeqIO_Insdc ... /build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/Scanner.py:304: BiopythonParserWarning: Non-standard feature line wrapping (didn't break o wa

Can someone else check and sponsor (Was: nanofilt ready for upload)

Hi Shayan, On Tue, Jun 16, 2020 at 08:48:51PM +0100, Shayan Doust wrote: > > I believe nanofilt[1] is ready. Please check and, if green light given, > upload :) I've done some minor changes and was building the package. Unfortunately my computer crashed when ... or rather after(!) ... running t

Re: What is the best way to refresh a 2to3 patch ?

Hi Charles, the short answer is: Convincing upstream to write Python3 and removing the 2to3 patch at all is the best way. On Wed, Jun 17, 2020 at 04:31:38AM +0900, Charles Plessy wrote: > Hello everybody, > > I was trying to update LAST (fortunately I saw I will not have to do so > anymore), but

Re: PhyML error - does that ring any bell? Re: RFS: python-biopython

Howdy, I pushed a little change in the d/control file of the package python-biopython in version 1.77+dfsg-2. This was the suggested way to address the bug #962944: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962944 I couldn't reproduce any particular problem with the few last rou

What is the best way to refresh a 2to3 patch ?

Hello everybody, I was trying to update LAST (fortunately I saw I will not have to do so anymore), but struggled for half an hour on the 2to3 patch... I fixed it partly by hand, and partly with "quilt refresh". But when I inspected the patch, I realised that this approach just makes it bitrot: t

Re: [covid-19] RFS: scrappie

On 16.06.20 19:59, Andreas Tille wrote: On Tue, Jun 16, 2020 at 07:17:08PM +0200, Steffen Möller wrote: On 16.06.20 18:40, mer...@debian.org wrote: Hi Steffen, On 2020-06-16 19:37, Steffen Möller wrote: Please kindly review and - either tell me to upload it or .. just upload. debian/copyri

Re: [covid-19] RFS: scrappie

On Tue, Jun 16, 2020 at 07:17:08PM +0200, Steffen Möller wrote: > > On 16.06.20 18:40, mer...@debian.org wrote: > > Hi Steffen, > > > > On 2020-06-16 19:37, Steffen Möller wrote: > > > Please kindly review and - either tell me to upload it or .. just upload. > > debian/copyright seems to contain

Re: [RFS] yanosim

On Tue, Jun 16, 2020 at 09:44:42PM +0530, Nilesh Patra wrote: > > I've packaged a NEW module: shovill - Assemble bacterial isolate genomes > > from Illumina paired-end reads > > > > OOPS!!! It's yanosim - Read simulator nanopore DRS datasets > Pardon me :P I've got it from the subject. ;-) Ple

Re: RFS: ivar

drop-seq and ivar are uploaded. yamllint d/u/metadata was not happy, which I have fixed. But that was something ancient. As another sidenote - lintian warns about W: ivar-doc: privacy-breach-generic usr/share/doc/ivar/html/cookbookpage.html [https://raw.githubusercontent.com/andersen-lab/ivar/ma

Re: [covid-19] RFS: scrappie

On 16.06.20 18:40, mer...@debian.org wrote: Hi Steffen, On 2020-06-16 19:37, Steffen Möller wrote: Please kindly review and - either tell me to upload it or .. just upload. debian/copyright seems to contain dh-make templates: Upstream-Contact: Source: Otherwise looks good. Thank you, An

Re: PhyML error - does that ring any bell? Re: RFS: python-biopython

Étienne Mollier, on 2020-06-16 18:51:52 +0200: > I'm on it. I'm a bit unsure of the maximum possible, but having > left my machine compute rosetta jobs for more than 80 > consecutive days, all I can say is that the limit is well over > the million. It is pid_max according to Linux documentation,

Re: PhyML error - does that ring any bell? Re: RFS: python-biopython

Hi Andrius, mer...@debian.org, on 2020-06-16 19:46:00 +0300: > Hi Étienne, > > On 2020-06-16 19:41, Étienne Mollier wrote: > > As a side note, I remarked that t_coffee dislikes it when its > > PID is greater than 26: > > > > $ t_coffee -version > > PROGRAM: T-COFFEE Version_13.41.0.28

Re: PhyML error - does that ring any bell? Re: RFS: python-biopython

Hi Étienne, On 2020-06-16 19:41, Étienne Mollier wrote: > As a side note, I remarked that t_coffee dislikes it when its > PID is greater than 26: > > $ t_coffee -version > PROGRAM: T-COFFEE Version_13.41.0.28bdc39 (2019-11-30 10:21:53 - > Revision 5d5a1c1 - Build 465) > >

Re: [covid-19] RFS: scrappie

Hi Steffen, On 2020-06-16 19:37, Steffen Möller wrote: > Please kindly review and - either tell me to upload it or .. just upload. debian/copyright seems to contain dh-make templates: Upstream-Contact: Source: Otherwise looks good. Best, Andrius

Re: PhyML error - does that ring any bell? Re: RFS: python-biopython

Greetings, mer...@debian.org, on 2020-06-15 14:48:07 +0300: > On 2020-06-12 20:40, Steffen Möller wrote: > > I found this > > > > Bio.PDB.mmtf docstring test ... skipped, missing Python dependency > > Bio.PDB.mmtf.DefaultParser docstring test ... skipped, missing Python > > dependency > > Bio.PDB

[covid-19] RFS: scrappie

Hi, I've packaged scrappie, i.e. an Open Source basecaller for the Nanopore. Here the paper accompanying it: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y I digress - there the tool: https://salsa.debian.org/med-team/scrappie Please kindly review and - either tell m

Re: RFS: ivar

And that, too. On 16.06.20 18:30, Pranav Ballaney wrote: Hi, I've added autopkgtests to ivar. Please review and sponsor. https://salsa.debian.org/med-team/ivar Regards, Pranav ᐧ

Re: RFS: drop-seq

I'll do that. On 16.06.20 18:29, Pranav Ballaney wrote: Hi, I've added autopkgtests to drop-seq. Please review and sponsor. https://salsa.debian.org/med-team/drop-seq Regards, Pranav ᐧ

RFS: ivar

Hi, I've added autopkgtests to ivar. Please review and sponsor. https://salsa.debian.org/med-team/ivar Regards, Pranav ᐧ

RFS: drop-seq

Hi, I've added autopkgtests to drop-seq. Please review and sponsor. https://salsa.debian.org/med-team/drop-seq Regards, Pranav ᐧ

Re: [RFS] yanosim

On Tue, 16 Jun 2020 at 21:43, Nilesh Patra wrote: > Hi, > I've packaged a NEW module: shovill - Assemble bacterial isolate genomes > from Illumina paired-end reads > OOPS!!! It's yanosim - Read simulator nanopore DRS datasets Pardon me :P It builds in a clean chroot. There are no autopkgtests

[RFS] yanosim

Hi, I've packaged a NEW module: shovill - Assemble bacterial isolate genomes from Illumina paired-end reads It builds in a clean chroot. There are no autopkgtests yet - since I'm not very sure of the exact data this needs. I've pushed my changes to team-repo[1]. This needs review and sponsorship.

Re: [RFS] streamz

On Tue, Jun 16, 2020 at 04:09:05PM +0530, Nilesh Patra wrote: > Hi, > I've packaged a NEW module: streamz - Helps build pipelines to manage > continuous streams of data. > It builds in a clean chroot with passing tests. > I've pushed my changes to team-repo[1]. > > *NB: The license on the repo loo

Re: [RFS] shovill

On Tue, Jun 16, 2020 at 07:08:04PM +0530, Nilesh Patra wrote: > Hi, > I've packaged a NEW module: shovill - Assemble bacterial isolate genomes > from Illumina paired-end reads > It builds in a clean chroot. I've not added autopkgtests at the moment > since some of the dependencies are still in NEW,

Re: RFS: seirsplus [ITP]

Dear Sao, On Tue, Jun 16, 2020 at 08:14:36PM +0900, Sao I Kuan wrote: > I'm looking for a sponsor for the package: > * seirsplus (#962942) > > The package is on: > https://salsa.debian.org/med-team/seirsplus > > The package is lintian-clean. > > Please consider reviewing and sponsoring th

[RFS] shovill

Hi, I've packaged a NEW module: shovill - Assemble bacterial isolate genomes from Illumina paired-end reads It builds in a clean chroot. I've not added autopkgtests at the moment since some of the dependencies are still in NEW, and it would be better suited (for me) to add these once the dependenci

Re: RFS: insilicoseq [ITP]

Hi Sao, On Tue, Jun 16, 2020 at 08:09:39PM +0900, Sao I Kuan wrote: > Thanks for your careful review. The main thanks goes to you for the tough work. > On Thu, Jun 11, 2020 at 2:16 AM Andreas Tille wrote: > > I patched argument error and forwarded the bug to upstream[1]. > [1] https://github.

Re: Tandem Repeats Finder License Terms

Hi again, in my talk I simply assumed that Tandem Repeats Finder will be released soon with a free license. The Debian Med team is now running the second COVID-19 sprint. So more packaging power is available for this week and it would be really great if you could put some part of it into trf. A

RFS: seirsplus [ITP]

Hi, I'm looking for a sponsor for the package: * seirsplus (#962942) The package is on: https://salsa.debian.org/med-team/seirsplus The package is lintian-clean. Please consider reviewing and sponsoring this. Any kind of suggestions are appreciated. Thank you! Sincerely, Sao I Kuan sao

Re: RFS: insilicoseq [ITP]

Hi, Andreas, Thanks for your careful review. On Thu, Jun 11, 2020 at 2:16 AM Andreas Tille wrote: > > Ahhh and please check calling /usr/bin/iss without any > argument throws a strange warning... I patched argument error and forwarded the bug to upstream[1]. [1] https://github.com/HadrienG/InSi

[RFS] streamz

Hi, I've packaged a NEW module: streamz - Helps build pipelines to manage continuous streams of data. It builds in a clean chroot with passing tests. I've pushed my changes to team-repo[1]. *NB: The license on the repo looks like an exact copy of BSD-3-clause license. However, it has some missing