Re: [Emc-developers] LinuxCNC is in Debian!

2022-02-28 Thread Steffen Möller
On 28.02.22 19:44, gene heskett wrote: On Monday, February 28, 2022 12:53:21 PM EST Steffen Möller wrote: On 28.02.22 18:40, gene heskett wrote: On Monday, February 28, 2022 8:28:36 AM EST andy pugh wrote: On Mon, 28 Feb 2022 at 13:22, Steffen Möller wrote: ie, "rtapi" i

Re: [Emc-developers] LinuxCNC is in Debian!

2022-02-28 Thread Steffen Möller
On 28.02.22 18:40, gene heskett wrote: On Monday, February 28, 2022 8:28:36 AM EST andy pugh wrote: On Mon, 28 Feb 2022 at 13:22, Steffen Möller wrote: ie, "rtapi" is relevant to uspace and rt builds. Can you guide me (or someone else surfacing) towards what would be requir

[Emc-developers] EtherCAT - would not be a prob with free membership in EtherCAT Technology Group Re: LinuxCNC is in Debian!

2022-02-28 Thread Steffen Möller
Hello again, On 28.02.22 14:28, andy pugh wrote: On Mon, 28 Feb 2022 at 13:22, Steffen Möller wrote: Personally I know nothing about EtherCAT. I have always been a little afraid of the licensing complexities mentioned here: https://etherlab.org/en/ethercat/ Etherlab itself is GPLv2

Re: [Emc-developers] LinuxCNC is in Debian!

2022-02-28 Thread Steffen Möller
On 28.02.22 14:28, andy pugh wrote: On Mon, 28 Feb 2022 at 13:22, Steffen Möller wrote: ie, "rtapi" is relevant to uspace and rt builds. Can you guide me (or someone else surfacing) towards what would be required to have LinuxCNC readily compatible with that external EtherC

Re: [Emc-developers] LinuxCNC is in Debian!

2022-02-28 Thread Steffen Möller
On 28.02.22 13:44, andy pugh wrote: On Mon, 28 Feb 2022 at 12:20, Steffen Möller wrote: +rtapi_timespec_advance(task->nextstart, task->nextstart, task->period + task->pll_correction); which patches LinuxCNC's src/rtapi/rtapi.h and I have no idea if we can just ignore this fo

Re: [Emc-developers] LinuxCNC is in Debian!

2022-02-28 Thread Steffen Möller
ter *1300 896 832* +61 435 765 611 Vehicle Modifications Network www.vehiclemods.net.au On Mon, 28 Feb 2022 at 10:38, Steffen Möller wrote: I have asked this myself. Why did I want this to happen - and I think the answer is two-fold: a) community-forming - not necessarily I am after contributors

Re: [Emc-developers] LinuxCNC is in Debian!

2022-02-27 Thread Steffen Möller
I have asked this myself. Why did I want this to happen - and I think the answer is two-fold: a) community-forming - not necessarily I am after contributors to LinuxCNC but I see the extra stimulus to package other CNC-related software for Debian from which then LinuxCNC benefits b) less stress

Re: Question about building a deb package

2022-02-26 Thread Steffen Möller
On 25.02.22 07:32, Andrey Rahmatullin wrote: On Fri, Feb 25, 2022 at 11:44:46AM +0800, Yunmei Li wrote: I am new to building deb packages, and I would like some help with a question. I am trying to build a deb package for Milvus(https://milvus.io/) on Ubuntu18.04 or Ubuntu 20.04. Building

Re: Google Summer of Code, Debian Science

2022-02-22 Thread Steffen Möller
You are aware of https://wiki.debian.org/DebianScience/ROOT ? On 22.02.22 17:19, Stephan Lachnit wrote: On Mon, Feb 21, 2022 at 5:43 PM Anton Gladky wrote: If somebody wants to be a co-mentor or if you have better ideas for the project, please let me know. I would love to have a student to

Re: q2-emperor - flagged as "RFS"ed

2022-02-17 Thread Steffen Möller
On 17.02.22 22:01, Nilesh Patra wrote: On 2022-02-18 01:34, Steffen Möller wrote: Hello, q2-emperor is flagged as "RFS" in https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1986383821 and late January, its dependency EM

q2-emperor - flagged as "RFS"ed

2022-02-17 Thread Steffen Möller
Hello, q2-emperor is flagged as "RFS" in https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=1986383821 and late January, its dependency EMPEROR made it into the distribution. I have not seen any rejection email in my inbox (and it should be flagged as

[Emc-developers] [Hosted Weblate] New comment in LinuxCNC/LinuxCNC

2022-02-13 Thread Steffen Möller via Emc-developers
# Comment added [ smoe](https://hosted.weblate.org/user/smoe/ "Steffen Möller"): [Hosted Weblate](https://hosted.weblate.org) / [LinuxCNC](https://hosted.weblate.org/projects/linuxcnc/) / [LinuxCNC](https://hosted.weblate.org/projects/linuxcnc/linuxcnc/) / [English](https://hosted.w

Re: RFS faber - build dependency for boost-python

2022-02-11 Thread Steffen Möller
Fantastic - thank you tons! Steffen On 11.02.22 11:44, Étienne Mollier wrote: Hi Steffen, Steffen Möller, on 2022-02-08: https://salsa.debian.org/python-team/packages/faber I had asked the Debian boost folks already to comment on that package but have not heard back. Faber is a build tool

Re: [Emc-developers] How to contribute?

2022-02-10 Thread Steffen Möller
Hi Andy, On 10.02.22 22:49, Andy Howell wrote: On 2/10/22 06:10, Steffen Möller wrote: On 10.02.22 07:28, Phill Carter wrote: On 10 Feb 2022, at 4:14 pm, Andy Howell wrote: On 2/9/22 14:46, andy pugh wrote: On Wed, 9 Feb 2022 at 20:21, Andy Howell wrote: My background is in c/c

Re: [Emc-developers] linuxcnc_2.9.0~pre0-1+git20211120.a2b87d299-1_amd64.changes REJECTED

2022-02-10 Thread Steffen Möller
On 10.02.22 22:12, Sebastian Kuzminsky wrote: On 2/10/22 09:06, Steffen Möller wrote: On 10.02.22 17:00, Thorsten Alteholz wrote: This version does not appear in latest changelog anymore ... Thorsten just rejected the first of two submissions, the second was a smallish correction

Re: [Emc-developers] linuxcnc_2.9.0~pre0-1+git20211120.a2b87d299-1_amd64.changes REJECTED

2022-02-10 Thread Steffen Möller
On 10.02.22 17:00, Thorsten Alteholz wrote: This version does not appear in latest changelog anymore ... Thorsten just rejected the first of two submissions, the second was a smallish correction that indeed is agnostic about the version from the day before. Best, Steffen

Re: [Emc-developers] How to contribute?

2022-02-10 Thread Steffen Möller
There should be a section on man pages, I tend to agree. My concern is that while we are typing there is Petter active on getting weblate (https://hosted.weblate.org/projects/linuxcnc/linuxcnc/) to also function with the documentation. I lost touch a bit,

Re: [Emc-developers] How to contribute?

2022-02-10 Thread Steffen Möller
On 10.02.22 07:28, Phill Carter wrote: On 10 Feb 2022, at 4:14 pm, Andy Howell wrote: On 2/9/22 14:46, andy pugh wrote: On Wed, 9 Feb 2022 at 20:21, Andy Howell wrote: My background is in c/c++ development under UNIX/Linux. I know bit of python. I don't have the experience to work on

RFS faber - build dependency for boost-python

2022-02-08 Thread Steffen Möller
Hello, This is about https://salsa.debian.org/python-team/packages/faber I had asked the Debian boost folks already to comment on that package but have not heard back. Faber is a build tool that the upstream boost community has elevated as the next thing for their Python interface. But it can

Re: [Emc-developers] Need help with sourcecode-highlighting in .adoc and xsltproc parse error

2022-02-07 Thread Steffen Möller
/attribute-colon.conf -a "scriptdir=docs/src/" -d book -o- -b docbook ../testme.adoc http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd;>    sectionname Bla moeller@ On 07.02.22 17:31, Steffen Möller wrote: Dear all, I am lost. And since git-bisect is not an eye-opener

[Emc-developers] Need help with sourcecode-highlighting in .adoc and xsltproc parse error

2022-02-07 Thread Steffen Möller
Dear all, I am lost. And since git-bisect is not an eye-opener for me, maybe someone on the list can help. I created this minimalistic file - removing any single line makes the problem go away. ``` :ini: {basebackend@docbook:'':ini} [source,{ini}] the source code goes here - likely as a ---

does anyone know of its whereabouts? Fwd: r-bioc-progeny_1.14.0+ds-1_amd64.changes REJECTED

2022-02-07 Thread Steffen Möller
Hello, I just checked but could not find any info on r-bioc-progeny. Andreas has fixed the missing license info for https://afeld.github.io/bootstrap-toc/ (which looks good btw) . @Andreas do you happen to recall if you have uploaded this again? Or was this rejected with a request to provide

Re: [Emc-developers] thinking about the next LinuxCNC release

2022-02-06 Thread Steffen Möller
Steffen Möller: Heya, On 06.02.22 11:43, Jérémie Tarot wrote: Le mer. 2 févr. 2022 à 19:18, Sebastian Kuzminsky a écrit : What are the big projects that need to get finished for the next release?  Some things I know vaguely about, but don't know the status of: ... * Transition docs translations

Re: [Emc-developers] thinking about the next LinuxCNC release

2022-02-06 Thread Steffen Möller
Heya, On 06.02.22 11:43, Jérémie Tarot wrote: Le mer. 2 févr. 2022 à 19:18, Sebastian Kuzminsky a écrit : What are the big projects that need to get finished for the next release? Some things I know vaguely about, but don't know the status of: ... * Transition docs translations to po4a

[Emc-developers] LinuxCNC Participation in Google Summer of Code 2022?

2022-02-03 Thread Steffen Möller
Hello, There may be are a couple of developments in the LinuxCNC source tree that would benefit from having a trainee work on full-time for a couple of weeks. A quick web search found that LinuxCNC was adopted by BRL-CAD for previous GSoCs but have not heard about 2021 - is anything happening

[Emc-developers] I also see a LinuxCNC Python problem on bullseye Re: latency-test period - (return) problem

2022-02-01 Thread Steffen Möller
Hi Gene, I just ran into the problem below which I expect to be at the root of what then kills it further down. I'll investigate this a bit more and then create a github issue or a pull request ... or both :) Steffen "~/Github/linuxcnc$ linuxcnc LINUXCNC - 2.9.0~pre0 Machine configuration

Re: [Emc-developers] latency-test period - (return) problem

2022-01-31 Thread Steffen Möller
On 01.02.22 01:57, gene heskett wrote: On Monday, January 31, 2022 12:45:27 PM EST Steffen Möller wrote: On 31.01.22 18:28, gene heskett wrote: On Monday, January 31, 2022 6:14:42 AM EST Steffen Möller wrote: latency-test 100 500 And it works! This is great to hear! Thank you

Re: [Emc-developers] latency-test period - (return) problem

2022-01-31 Thread Steffen Möller
On 31.01.22 18:28, gene heskett wrote: On Monday, January 31, 2022 6:14:42 AM EST Steffen Möller wrote: latency-test 100 500 And it works! This is great to hear! Thank you! This is 32bits now, right? Where are you at? Maybe Rod can compare with his 64bit findings. The man page sorta

Re: [Emc-developers] latency-test period - (return) problem

2022-01-31 Thread Steffen Möller
Dear Gene, I just tried this locally and it seems like the number conversion is broken in latency-test. Also there should not be a prefix like base-period in the command line. First thought it was just the capital "S" but it wasn't.  Good news: you don't need them, please try again with

Re: [Emc-developers] @Seb, can we please have an RPi bullseye buildbot? Re: signed arm64 bullseye (armbian) binaries for download Re: trying to install linuxcnc built on buster on a bullseye system

2022-01-29 Thread Steffen Möller
dpkg -c linuxcnc-uspace_2.9.0~pre0_arm64.deb | grep -i preemp and this showed no such file, so, I still hope nothing was omitted and you indeed refer to the kernel. Many thanks and greetings! Steffen On Sun, 30 Jan 2022 at 08:01, Steffen Möller wrote: On 29.01.22 22:08, Sebastian Kuzmins

Re: [Emc-developers] @Seb, can we please have an RPi bullseye buildbot? Re: signed arm64 bullseye (armbian) binaries for download Re: trying to install linuxcnc built on buster on a bullseye system

2022-01-29 Thread Steffen Möller
On 29.01.22 22:08, Sebastian Kuzminsky wrote: On 1/29/22 10:44 AM, Steffen Möller wrote: 32 or 64 bits, well, I think we want to see packages for both. Let's wait for what Sebastian replies. I just saw on his page http://buildbot.linuxcnc.org/buildslave-admin-guide.html that there are buildbot

[Emc-developers] @Seb, can we please have an RPi bullseye buildbot? Re: signed arm64 bullseye (armbian) binaries for download Re: trying to install linuxcnc built on buster on a bullseye system

2022-01-29 Thread Steffen Möller
On 29.01.22 05:14, gene heskett wrote: On Friday, January 28, 2022 9:15:18 PM EST Steffen Möller wrote: On 28.01.22 23:25, gene heskett wrote: On Friday, January 28, 2022 2:21:50 PM EST gene heskett wrote: On Friday, January 28, 2022 1:32:52 PM EST gene heskett wrote: On Friday, January 28

Re: [Emc-developers] signed arm64 bullseye (armbian) binaries for download Re: trying to install linuxcnc built on buster on a bullseye system

2022-01-28 Thread Steffen Möller
On 28.01.22 23:25, gene heskett wrote: On Friday, January 28, 2022 2:21:50 PM EST gene heskett wrote: On Friday, January 28, 2022 1:32:52 PM EST gene heskett wrote: On Friday, January 28, 2022 10:18:38 AM EST Steffen Möller wrote: ... Processing linuxcnc-uspace_2.9.0~pre0_arm64.deb

Re: [Emc-developers] signed arm64 bullseye (armbian) binaries for download Re: trying to install linuxcnc built on buster on a bullseye system

2022-01-28 Thread Steffen Möller
... Processing linuxcnc-uspace_2.9.0~pre0_arm64.deb... ... Install them on a pi, and run latency-test please. Are you running on 64bit? Then the packages should work. ___ Emc-developers mailing list Emc-developers@lists.sourceforge.net

Re: [Emc-developers] signed arm64 bullseye (armbian) binaries for download Re: trying to install linuxcnc built on buster on a bullseye system

2022-01-28 Thread Steffen Möller
2022 at 22:30, Steffen Möller wrote: Hello again, I built the arm64 packages on an odroid that runs armbian's bullseye variant. Placed it on https://drive.google.com/drive/folders/1kTr7uigCQY3c-layLJKdXqN5sRsXJnWo?usp=sharing It worked just fine, except that armbian apparently does not have that

[Emc-developers] signed arm64 bullseye (armbian) binaries for download Re: trying to install linuxcnc built on buster on a bullseye system

2022-01-28 Thread Steffen Möller
Hello again, I built the arm64 packages on an odroid that runs armbian's bullseye variant. Placed it on https://drive.google.com/drive/folders/1kTr7uigCQY3c-layLJKdXqN5sRsXJnWo?usp=sharing It worked just fine, except that armbian apparently does not have that gpl2-variant of the readline

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-28 Thread Steffen Möller
On 28.01.22 02:15, gene heskett wrote: On Thursday, January 27, 2022 7:17:10 PM EST Steffen Möller wrote: On 28.01.22 00:31, gene heskett wrote: On Thursday, January 27, 2022 2:22:43 PM EST Steffen Möller wrote: On 27.01.22 20:03, gene heskett wrote: On Thursday, January 27, 2022 9:54:54 AM

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-27 Thread Steffen Möller
On 28.01.22 00:31, gene heskett wrote: On Thursday, January 27, 2022 2:22:43 PM EST Steffen Möller wrote: On 27.01.22 20:03, gene heskett wrote: On Thursday, January 27, 2022 9:54:54 AM EST Steffen Möller wrote: Fresh start! Dear Gene, I would like to catch the problem before you start

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-27 Thread Steffen Möller
of time building the debs. Which for the RPi and he SD card underneath would be good. Next time. Best, Steffen On Fri, 28 Jan 2022 at 05:23, Steffen Möller wrote: On 27.01.22 20:03, gene heskett wrote: On Thursday, January 27, 2022 9:54:54 AM EST Steffen Möller wrote: Fresh start! Dear

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-27 Thread Steffen Möller
On 27.01.22 20:03, gene heskett wrote: On Thursday, January 27, 2022 9:54:54 AM EST Steffen Möller wrote: Fresh start! Dear Gene, I would like to catch the problem before you start building and also exclude the possibility that somehow the code base of yours is affected by your previous

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-27 Thread Steffen Möller
Fresh start! Dear Gene, I would like to catch the problem before you start building and also exclude the possibility that somehow the code base of yours is affected by your previous checkout - just because I cannot inspect your machine from here. Once that was successful, yes, then this can be

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-27 Thread Steffen Möller
On 27.01.22 14:31, gene heskett wrote: On Tuesday, January 25, 2022 8:27:27 PM EST gene heskett wrote: Greetings all; I built a fresh pull of master earlier today, which makes installable debs. I normally run this shell script to install them, and on buster it Just Works. But, now I have

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-26 Thread Steffen Möller
On 27.01.22 00:35, gene heskett wrote: On Wednesday, January 26, 2022 5:22:10 PM EST Steffen Möller wrote: Seems like you have done something to your git repository and it cannot just go and fetch the newer version. It could be that these are just some changes that have been made during

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-26 Thread Steffen Möller
oving previous repository of linuxcnc-dev to 'linuxcnc-dev-$d'"    mv linuxcnc-dev "linuxcnc-dev-$d" fi mkdir linuxcnc-dev so everything is clean - you do not run that script too often, I presume. Best, Steffen On 26.01.22 22:57, gene heskett wrote: On Wednesday, January 26, 2022 3:49:58 PM

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-26 Thread Steffen Möller
On 26.01.22 22:30, gene heskett wrote: On Wednesday, January 26, 2022 3:49:58 PM EST Steffen Möller wrote: On 26.01.22 02:27, gene heskett wrote: Greetings all; I built a fresh pull of master earlier today, which makes installable debs. I normally run this shell script to install them

Re: [Emc-developers] trying to install linuxcnc built on buster on a bullseye system

2022-01-26 Thread Steffen Möller
Hi Gene, On 26.01.22 02:27, gene heskett wrote: Greetings all; I built a fresh pull of master earlier today, which makes installable debs. I normally run this shell script to install them, and on buster it Just Works. And that is how things should also behave on Bullseye. Let's find out what

Re: sambamba and freebayes new releases

2022-01-21 Thread Steffen Möller
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

Bug#1003968: [Pkg-electronics-devel] Bug#1003968: fpga-icestorm: icetime looking in wrong directory for chipdb files

2022-01-18 Thread Steffen Möller
Uploaded. On 18.01.22 20:41, Daniel Gröber wrote: Hi Scott, Thanks, for the report. On Tue, Jan 18, 2022 at 05:50:58PM +, Scott Ashcroft via Pkg-electronics-devel wrote: icetime seems to be looking in /usr/local/share/icebox and /usr/bin/../share/icebox for chipdb files instead of

Re: alphafold Debian packaging ?

2022-01-12 Thread Steffen Möller
On 12.01.22 17:24, M. Zhou wrote: Even more complicated is the underlying software dependency tree. alphafold depends on dm-haiku, jax, tensorflow. dm-haiku depends on jax. jax depends on XLA from tensorflow. tensorflow still in NEW. Long way to go. Mhhh. That is what I had thought, too.

Re: alphafold Debian packaging ?

2022-01-12 Thread Steffen Möller
I am only aware of someone who got it to run on Debian :)  I agree that it would be nice to have. Very nice. Cheers, Steffen On 11.01.22 14:47, PICCA Frederic-Emmanuel wrote: Hello guyes, I would like to know if you are aware of an effort to package alphafold[1] on Debian ? Cheers Frederic

Re: Contributing to yosys maintenance

2021-12-30 Thread Steffen Möller
Hi Daniel, On 30.12.21 22:38, Daniel Gröber wrote: Hi Anton and Steffen, On Thu, Dec 30, 2021 at 10:11:26PM +0100, Anton Gladky wrote: I have just added you to the group. Welcome on board! You can commit directly in git, but please coordinate your work with an active uploaders of this

Re: Contributing to yosys maintenance

2021-12-30 Thread Steffen Möller
Hi Daniel, On 30.12.21 21:08, Daniel Gröber wrote: I'm working on packaging the latest version of yosys and related packages for Debian. Nice. I was not aware of the many new releases - clifford.at seems down and https://github.com/YosysHQ/yosys is the new home? What's the procedure in

Re: RF peer review: r-other-ibi-disgenet2r freshly injected into salsa

2021-12-22 Thread Steffen Möller
On 22.12.21 14:32, Andreas Tille wrote: Hi Steffen, Am Wed, Dec 22, 2021 at 01:47:35PM +0100 schrieb Steffen Möller: https://salsa.debian.org/r-pkg-team/r-other-ibi-disgenet2r just arrived. It needs r-cran-sparql that Andreas kindly uploaded yesterday. I've added a watch file, renamed

RF peer review: r-other-ibi-disgenet2r freshly injected into salsa

2021-12-22 Thread Steffen Möller
Hello again, https://salsa.debian.org/r-pkg-team/r-other-ibi-disgenet2r just arrived. It needs r-cran-sparql that Andreas kindly uploaded yesterday. Many thanks and regards, Steffen

RFS: r-cran-sparql - dependency for a more typical Med package

2021-12-21 Thread Steffen Möller
Dear Andreas, dear Nilesh, dear all, I would appreciate some extra scrutiny for https://salsa.debian.org/r-pkg-team/r-cran-sparql Please kindly upload if you consider this "ready-enough" or pass the token back to me, please. This https://www.disgenet.org/disgenet2r is why I (and Debian at

Re: Moving python-bioblend to med-team?

2021-12-21 Thread Steffen Möller
Please go ahead - thank you both. If there is any particular action for me to perform then please ping me, preferably with a respective tag in the subject line. Best Steffen On 19.12.21 12:05, Andreas Tille wrote: Hi Nilesh and Steffen, Am Sun, Dec 19, 2021 at 01:36:50PM +0530 schrieb Nilesh

r-bioc-txdb.hsapiens.ucsc.hg19.knowngene on salsa Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with

2021-12-13 Thread Steffen Möller
Hi all, On 10.12.21 17:46, Andreas Tille wrote: Am Fri, Dec 10, 2021 at 11:57:49AM +0100 schrieb Steffen Möller: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1001436 for r-bioc-txdb.hsapiens.ucsc.hg19.knowngene and when I wanted to inject it found that it is already existing at https

Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with

2021-12-10 Thread Steffen Möller
On 10.12.21 07:15, Andreas Tille wrote: Am Fri, Dec 10, 2021 at 03:07:51AM +0530 schrieb Nilesh Patra: On Thu, Dec 09, 2021 at 08:32:46PM +0100, Steffen Möller wrote: Hello this goes out to Andreas in particular, I hope you do not mind me taking over (have a few spare cycles) I definitely

please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with

2021-12-09 Thread Steffen Möller
Hello this goes out to Andreas in particular, I completed the packaging of r-bioc-fishpond earlier this afternoon. This is a suggestion for r-bioc-tximport with some other interesting reverse-dependencies - and tximport makes problems with my rabbit data that I yet do not understand. The

Re: [Emc-developers] Status of Weblate translations

2021-12-09 Thread Steffen Möller
On 09.12.21 10:52, Petter Reinholdtsen wrote: [Steffen Möller] I think the format-adjustments between French and English are good to go. We should just not both edit the English in parallel. My French is catastrophique but I can read it, so we could have a joint shot at the first few *_fr.adoc

Re: [Emc-developers] Status of Weblate translations

2021-12-08 Thread Steffen Möller
Hello, On 08.12.21 20:19, Jérémie Tarot wrote: Hello Hans, Le mar. 7 déc. 2021 à 20:31, Hans Unzner a écrit : ... @smoe has made an amazing work on es translation as well as sanitizing en source files. Only were the the po4a script to automated the sync to Spanish bailed out. I'm lagging

[Emc-developers] missing anyone in debian/copyright? Re: linuxcnc_2.9.0~pre0+git20211108.cf14c89a9-1_amd64.changes REJECTED

2021-11-18 Thread Steffen Möller
things going. Best, Steffen On 15.11.21 14:57, Steffen Möller wrote: Hello, I thought I should possibly comment on the rejection email for those who read this the first time. We can fix this and reupload. It is just this first version of the packaging that is rejected, not the software per se

Bug#999632: r-bioc-isoformswitchanalyzer FTBFS: ERROR: dependencies ‘DRIMSeq’, ‘tximeta’ are not available

2021-11-18 Thread Steffen Möller
On 14.11.21 08:47, Andreas Tille wrote: Control: blocked -1 by 995252 Hi Steffen ERROR: dependencies ‘DRIMSeq’, ‘tximeta’ are not available for package ‘IsoformSwitchAnalyzeR’ r-bioc-tximeta is in Debian and just needs to be mentioned in Build-Depends. However, Git seems not to be up to

Bug#999632: r-bioc-isoformswitchanalyzer FTBFS: ERROR: dependencies ‘DRIMSeq’, ‘tximeta’ are not available

2021-11-18 Thread Steffen Möller
On 14.11.21 08:47, Andreas Tille wrote: Control: blocked -1 by 995252 Hi Steffen ERROR: dependencies ‘DRIMSeq’, ‘tximeta’ are not available for package ‘IsoformSwitchAnalyzeR’ r-bioc-tximeta is in Debian and just needs to be mentioned in Build-Depends. However, Git seems not to be up to

Re: Debian Med video conference tomorrow, Wednesday 2021-11-17 18:00 UTC

2021-11-16 Thread Steffen Möller
Heya, On 16.11.21 19:58, Nilesh Patra wrote: For those who are interested in hot topics we want to tackle, here are some action items to be done: - Coordinating work for bioconductor transition (to be started soon) Nice! I am traveling and cannot join you. From my side I can only report

Re: [Emc-developers] linuxcnc_2.9.0~pre0+git20211108.cf14c89a9-1_amd64.changes REJECTED

2021-11-15 Thread Steffen Möller
Hello, I thought I should possibly comment on the rejection email for those who read this the first time. We can fix this and reupload. It is just this first version of the packaging that is rejected, not the software per se. On 15.11.21 12:00, Thorsten Alteholz wrote: Hi Sebastian,

Re: [Emc-developers] linuxcnc_2.9.0~pre0+git20211108.cf14c89a9-1_amd64.changes REJECTED

2021-11-15 Thread Steffen Möller
Hello, I thought I should possibly comment on the rejection email for those who read this the first time. We can fix this and reupload. It is just this first version of the packaging that is rejected, not the software per se. On 15.11.21 12:00, Thorsten Alteholz wrote: Hi Sebastian,

Re: [Emc-developers] linuxcnc_2.9.0~pre0+git20211108.cf14c89a9-1_amd64.changes REJECTED

2021-11-15 Thread Steffen Möller
Hello, I thought I should possibly comment on the rejection email for those who read this the first time. We can fix this and reupload. It is just this first version of the packaging that is rejected, not the software per se. On 15.11.21 12:00, Thorsten Alteholz wrote: Hi Sebastian,

Re: [Emc-developers] RFC: doc translations

2021-11-14 Thread Steffen Möller
Good evening also to you, Jérémie! I think I can quickly top-post and thank you for your very encouraging reply. This reads all (surprisingly) nice and encouraging. Steffen On 14.11.21 21:23, Jérémie Tarot wrote: Good evening Steffen, Le dim. 14 nov. 2021 à 15:51, Steffen Möller a écrit

Re: [Emc-developers] RFC: doc translations

2021-11-14 Thread Steffen Möller
Hi Jérémie, On 14.11.21 11:32, Jérémie Tarot wrote: Hi Sebastian and all, Le lun. 8 nov. 2021 à 20:41, Sebastian Kuzminsky a écrit : Hello LinuxCNC people, there's a possible change brewing that I'd like to ask for your feedback on. The translations of our documentation into non-English

Re: [Emc-developers] RFC: doc translations

2021-11-09 Thread Steffen Möller
On 10.11.21 00:29, andy pugh wrote: On Tue, 9 Nov 2021 at 23:19, Steffen Möller wrote: Maybe Andy could outline how his system differs from what po4a would come up with. The thing I was trying to address is that the HAL components that are derived from .comp files are self-documenting. You

Re: [Emc-developers] RFC: doc translations

2021-11-09 Thread Steffen Möller
Hello, I have looked at https://techbase.kde.org/Localization but failed to take too much from their site. Maybe Andy could outline how his system differs from what po4a would come up with. The difficulty I see is that the synchronisation between the original and its translations is not

LinuxCNC in New Queue - upstream as an alternative to teams on salsa

2021-11-09 Thread Steffen Möller
Hello, LinuxCNC.org has its own Debian repository since a couple of decades. and I have worked as DDs with upstream over the past few weeks to eliminate a series of lintian errors and sidetracked ourselves here and there, but yesterday LinuxCNC arrived in the New Queue. Its runtime (suggested)

Re: [Emc-developers] RFC: doc translations

2021-11-09 Thread Steffen Möller
Hello, On 08.11.21 20:40, Sebastian Kuzminsky wrote: Hello LinuxCNC people, there's a possible change brewing that I'd like to ask for your feedback on. The translations of our documentation into non-English languages has been handled in an unusual and cumbersome way, and a new developer has

Re: [Emc-developers] Processing of linuxcnc_2.9.0~pre0+git20211108.cf14c89a9-1_amd64.changes

2021-11-09 Thread Steffen Möller
+git20211108.cf14c89a9-1_amd64.deb linuxcnc-uspace_2.9.0~pre0+git20211108.cf14c89a9-1_amd64.deb linuxcnc_2.9.0~pre0+git20211108.cf14c89a9-1_amd64.buildinfo Greetings, Your Debian queue daemon (running on host usper.debian.org) Wooo h! Huge thanks to Steffen Möller and Petter

Re: no report generation, likely not only for pigx-rnaseq Re: What happened to r-cran-jquerylib ?

2021-11-03 Thread Steffen Möller
On 03.11.21 15:55, Andreas Tille wrote: Hi Steffen, Am Wed, Nov 03, 2021 at 12:58:53PM +0100 schrieb Steffen Möller: Hi Andreas et al., We should think about what it means for us not to have a current version of the DT cran package. For one, it kills the PIGX RNA-seq workflow. What do you

no report generation, likely not only for pigx-rnaseq Re: What happened to r-cran-jquerylib ?

2021-11-03 Thread Steffen Möller
to not create extra hassle for ftpmaster. Kind regards Andreas. Am Tue, Nov 02, 2021 at 09:43:07PM +0100 schrieb Andreas Tille: Hi Am Sun, Oct 31, 2021 at 07:16:44PM +0100 schrieb Steffen Möller: On 31.10.21 19:14, Nilesh Patra wrote: On 10/31/21 11:30 PM, Steffen Möller wrote: Hello

Re: Debian Math Team

2021-10-30 Thread Steffen Möller
While I agree, this may also be good thing. There will be more Sprints (I hope) with then more people that are brought to our community at large. And Debian so far does very well in keeping all those fragments together. Best, Steffen On 30.10.21 01:55, Anton Gladky wrote: Hi Doug, well, I

Bug#984243: Help: mothur: ftbfs with GCC-11

2021-10-21 Thread Steffen Möller
On 21.10.21 20:21, Étienne Mollier wrote: Hi Andreas, Andreas Tille, on 2021-10-21: In file included from addtargets2.cpp:3: myutils.h:176:1: error: reference to 'byte' is ambiguous Since C++ 2017, the std::byte type is defined: 176 | byte *ReadAllStdioFile(FILE *f, off_t ); |

Bug#984243: Help: mothur: ftbfs with GCC-11

2021-10-21 Thread Steffen Möller
On 21.10.21 20:21, Étienne Mollier wrote: Hi Andreas, Andreas Tille, on 2021-10-21: In file included from addtargets2.cpp:3: myutils.h:176:1: error: reference to 'byte' is ambiguous Since C++ 2017, the std::byte type is defined: 176 | byte *ReadAllStdioFile(FILE *f, off_t ); |

Re: snakemake-dependency Fwd: Bug#996868: ITP: python-connection-pool -- thread-safe connection pool for python

2021-10-20 Thread Steffen Möller
On 20.10.21 14:08, Nilesh Patra wrote: On 20 October 2021 6:26:29 am IST, "Steffen Möller" wrote: Snakemake is working for me with python3-connection-pool installed, so I have uploaded. Best, Steffen I had uploaded with my hack, and autopkgtests work in salsa CI. I think

snakemake-dependency Fwd: Bug#996868: ITP: python-connection-pool -- thread-safe connection pool for python

2021-10-19 Thread Steffen Möller
Snakemake is working for me with python3-connection-pool installed, so I have uploaded. Best, Steffen Forwarded Message Subject:Bug#996868: ITP: python-connection-pool -- thread-safe connection pool for python Resent-Date:Wed, 20 Oct 2021 00:33:01 +

Re: snakemake_6.9.1+dfsg1-1_source.changes ACCEPTED into unstable

2021-10-19 Thread Steffen Möller
I just ran into this. Will package this with the Python team now. On 19.10.21 23:40, Nilesh Patra wrote: On Wed, 20 Oct 2021 at 00:57, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote: On 19.10.21 21:12, Nilesh Patra wrote: > On 10/20/21 12:40 AM, Steffen Möl

Re: snakemake_6.9.1+dfsg1-1_source.changes ACCEPTED into unstable

2021-10-19 Thread Steffen Möller
On 19.10.21 21:12, Nilesh Patra wrote: On 10/20/21 12:40 AM, Steffen Möller wrote: Update follows. There is an uninstallable file in the tests folders. I am now separating -tests and -doc. Thanks, but that'd go a trip to NEW. It'd be nice if you can fix it in the single-source package only

Re: snakemake_6.9.1+dfsg1-1_source.changes ACCEPTED into unstable

2021-10-19 Thread Steffen Möller
Update follows. There is an uninstallable file in the tests folders. I am now separating -tests and -doc . And these .snakemake folders come from installdocs, which is why all these removals failed. Getting there. Best, Steffen On 19.10.21 20:17, Nilesh Patra wrote: > Many thanks, Steffen :-) >

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-18 Thread Steffen Möller
On 18.10.21 18:41, Rebecca N. Palmer wrote: On 18/10/2021 08:15, Nilesh Patra wrote: On Mon, Oct 18, 2021 at 01:32:30AM +0200, Steffen Möller wrote: Is anyone continuing the update of snakemake now? @Rebecca, could you look into it now that pulp is done? Currently, there is just a very few

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-17 Thread Steffen Möller
Hi Nilesh, On 17.10.21 23:27, Nilesh Patra wrote: Hi Steffen, On Mon, 18 Oct 2021 at 01:41, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote: On 17.10.21 21:39, Nilesh Patra wrote: Hi Steffen, On Mon, 18 Oct 2021 at 01:06, Steffen Möller mailto:steffen_moel...@

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-17 Thread Steffen Möller
On 17.10.21 21:39, Nilesh Patra wrote: Hi Steffen, On Mon, 18 Oct 2021 at 01:06, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote: On 17.10.21 21:19, Nilesh Patra wrote: Yeah, snakemake has now moved to pulp 2.0. pulp had another rev-dep on congress which is now remove

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-17 Thread Steffen Möller
to it, though. I Just paste our exchange below (don't expect anyone to mind). On 6/8/21 1:40 PM, Steffen Möller wrote: Hi Thomas, Am 07.06.2021 um 09:05 schrieb Thomas Goirand: On 6/5/21 7:52 PM, Steffen Möller wrote: Hello, pulp is outdated. Would you mind updating it or having me update

Bug#969416: LinuxCNC is coming to Debian

2021-10-13 Thread Steffen Möller
Petter kindly got in touch about me supporting the LinuxCNC developers in their packaging and an eventual upload to Debian. So, it is happening and we happily close this RFP with the upload. The package will be maintained by the LinuxCNC developers as DMs with me (or Petter, I presume) sponsoring

Bug#969416: LinuxCNC is coming to Debian

2021-10-13 Thread Steffen Möller
Petter kindly got in touch about me supporting the LinuxCNC developers in their packaging and an eventual upload to Debian. So, it is happening and we happily close this RFP with the upload. The package will be maintained by the LinuxCNC developers as DMs with me (or Petter, I presume) sponsoring

Bug#995723: r-cran-dbscan_1.1-8+ds-1_amd64.changes REJECTED

2021-10-11 Thread Steffen Möller
Hello, I admit not to recall if I had responded, but I had "-sa"-uploaded a fixed version -2. Many thanks to you all Steffen On 11.10.21 16:47, Andreas Tille wrote: Hi Thorsten, just in case Steffen had not responded and to have a record in the ITP bug: A fixed package was uploaded to new.

Bug#995723: r-cran-dbscan_1.1-8+ds-1_amd64.changes REJECTED

2021-10-11 Thread Steffen Möller
Hello, I admit not to recall if I had responded, but I had "-sa"-uploaded a fixed version -2. Many thanks to you all Steffen On 11.10.21 16:47, Andreas Tille wrote: Hi Thorsten, just in case Steffen had not responded and to have a record in the ITP bug: A fixed package was uploaded to new.

salsa-ci initiation for Debian Med - suspended?

2021-10-01 Thread Steffen Möller
Hi all, I just got + PROJECT_ID=64711 + set +x Error GETing https://salsa.debian.org/api/v4/user (HTTP 401): Unauthorized {"error":"invalid_token","error_description":"Toke... at /usr/share/perl5/Devscripts/Salsa/update_repo.pm line 114. W: Could not initiate CI for long-read-assembler, please

Nature Methods article on worfklows

2021-09-24 Thread Steffen Möller
Wratten, Laura et al.: Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers Nature Methods. 2021 https://doi.org/10.1038/s41592-021-01254-9 They kindly cited the "Reproducible workflows"-paper. Steffen

Re: Any volunteer to verify autopkgtest of spades?

2021-09-23 Thread Steffen Möller
Hi Tony, On 23.09.21 15:07, Tony Travis wrote: On 23/09/2021 13:53, Andreas Tille wrote: Hi, some time ago I've pushed a packaging update for Spades. Unfortunately the autopkgtest fails with [...] I'm willing to volunteer, but I don't know how to run "autopkgtest": Can I just download your

Re: Any reason to wait with qiime upgrades? (Was: Bug#994470: please update dependency on openblas)

2021-09-20 Thread Steffen Möller
On 20.09.21 13:34, Andreas Tille wrote: Control: tags -1 pending On Thu, Sep 16, 2021 at 11:54:18AM +0200, Sébastien Villemot wrote: q2-types depends on libopenblas-base, which is a transitional dummy package. Please replace it by libopenblas0. I did this in Git (please leave distribution

Datasets downloaded by scikit-learn as separate packages?

2021-09-19 Thread Steffen Möller
Hello, This goes out to the good fellas who care about scikit-learn. There is tutorial for the qiime package that has classifier prepared that only works with the latest stable version (0.24.2). We are at 0.23.2 in Debian. I gave an update of Scikit-Learn a shot and while the main build was

Re: Is pigx-rnaseq ready to be uploaded?

2021-09-16 Thread Steffen Möller
On 15.09.21 23:27, Nilesh Patra wrote: Hi Steffen, On 9/15/21 5:31 PM, Steffen Möller wrote: I don't know about the software myself, if you could take a look and push what you deem sensible, that'd be very cool. Done. Also eliminated some lintian warnings. All dependencies have been

RFS: r-bioc-stringdb and deps r-cran-gsubfn,r-cran-sqldf

2021-09-15 Thread Steffen Möller
I needed the STRINGdb package locally. Was a bit surprised that we did not have it already in our archive, I must admit. It comes with some interesting dependencies. Steffen

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