Re: Last call for any other location than Berlin (Was: Any suggestions for next Debian Med sprint (in person meeting)?)

Hi all, Le 29/12/2023 à 14:07, Andreas Tille a écrit : Am Wed, Dec 27, 2023 at 09:43:19PM +0100 schrieb Steffen Möller: for teaching and meeting reasons. But as I just wrote, 17-18 also works. I'd opt for the earlier date, so we have a bit of a break before some of us I expect to bump into

Re: Last call for any other location than Berlin (Was: Any suggestions for next Debian Med sprint (in person meeting)?)

Hi all, Le 21/12/2023 à 16:15, Sascha Steinbiss a écrit : Hi, [...] How about Feb 10-11, for example? My weekends are still free for now so it's your choice. I admit I'd prefer Feb. 17-18 over 10-11.  Other opinions? I will be available on both weekends, although I prefer 10-11 over

[Advent bug squashing] Bug #1058683 : incompatibility between igv and htsjdk

Hello, I fixed bug #1058683, which showed up in igv after an important upgrade of htsjdk. Great idea to improve one's Advent bug squashing metrics: upgrade software, break things, fill bugs, fix them. Best, -- Pierre OpenPGP_signature.asc Description: OpenPGP digital signature

Re: Thanks a lot [ftpmas...@ftp-master.debian.org: ugene_49.1+dfsg-1_amd64.changes ACCEPTED into unstable]

To: Debian Med Packaging Team , Pierre Gruet Subject: ugene_49.1+dfsg-1_amd64.changes ACCEPTED into unstable Thank you for your contribution to Debian. Accepted: Format: 1.8 Date: Tue, 12 Dec 2023 14:49:53 +0100 Source: ugene Binary: ugene ugene-data ugene-dbgsym Architecture: source all amd64

Re: Could some SnpEff user from the community please ping authors

Hi Nilesh, Le 05/12/2023 à 21:30, Nilesh Patra a écrit : On Tue, Nov 28, 2023 at 05:54:30PM +0100, Andreas Tille wrote: I wonder whether some people from the community might be able to join our attempt to get this issue fixed and raise their voice inside the Github issue (or use other

[Advent bug squashing] 9 bugs

Hi, Fixing minor bugs #1043696, #1045612, #1046315, #1046647, #1046802, #1046809, #1047000, #1048408, #1049745. Not crucial, but they offer the opportunity to do some housekeeping in our packages! Best, -- Pierre OpenPGP_signature.asc Description: OpenPGP digital signature

Re: genomicsdb not migrating and new upstream version

Hi Andreas, Le 27/11/2023 à 11:31, Andreas Tille a écrit : Hi Pierre, I realised that you've fixed bug #1054675 (thanks for doinig so) but You're welcome! :) that several architectures are failing to build[1] which I do not understand when looking at the build logs. Since there was a new

Re: Any suggestions for next Debian Med sprint (in person meeting)?

Hi Andreas, Le 02/11/2023 à 17:27, Andreas Tille a écrit : Hi, its autumn so we should prepare for winter. For Debian Med winter is the time where we usually do our in person meeting. The last meetings were in a perfectly fitting location in Berlin and I for myself would be fine to meet

Re: Java help for bbmap needed

Hi Andreas, Le 18/10/2023 à 18:48, Andreas Tille a écrit : Hi Pierre (or whoever wants to take this task), I tried to upgrade bbmap but failed[1]. I stumbled upon the line: jh_build: error: find current -name '*.java' -and -type f -print0 | xargs -s 512000 -0

Re: New CamiTK 5.1.0 release

Hello Emmanuel, Le 29/08/2023 à 17:48, Emmanuel Promayon a écrit : Dear Pierre, On 25/08/2023 22:46, Pierre Gruet wrote: Sorry, it seems your questions have remained unanswered for quite some time. Vacations, summer, ...! No problem at all, vacations is really important! On my setup

Re: New CamiTK 5.1.0 release

to the LD_LIBRARY_PATH at the beginning of the two autopkgtest scripts (test/config-test.sh and cepgenerator-test.sh): export JAVA_HOME=/usr/lib/jvm/default-java export LD_LIBRARY_PATH=${JAVA_HOME}/lib/:${JAVA_HOME}/lib/server/ (btw, thanks to a lot to Pierre Gruet who had already done that in d

Re: Volunteer request

Hello Rakesh, Welcome! Le 25/08/2023 à 14:26, Andreas Tille a écrit : Hi, [...] Admittedly, I'm very busy with other things, so I defer MoM stuff to Andreas. I'd also delay past-DebConf but there is no good reason for Rakesh to wait. All communication is on the list and usually there are

Re: GATK

Hi Andreas, Le 14/07/2023 à 08:14, Andreas Tille a écrit : Hi Pierre, [...] Right now I am preparing the move of my family some hundreds of kilometers away, I expect to get more time to look at it closer afterwards. Sure, Real life should have preference over volunteer work. Is the

Re: GATK

Hi Andreas, Le 12/07/2023 à 15:01, Andreas Tille a écrit : Hi Pierre, I was wondering whether we might be able to package GATK for the next release. I've just fixed the watch file in Git. It would be great if you could have a look once you might find some spare cycles. Yeah, GATK is one of

Re: "Poll" for video conference date

Hi Andreas, Le 10/07/2023 à 10:03, Andreas Tille a écrit : Hi, I think we do not need any poll site to decide how to schedule our video conferences in future. IMHO it makes sense to do it in the beginning of each month and as far as I understood responses (private and public) it make sense to

Re: Do we want to have a video conference tomorrow or is a monthly meeting more appropriate

Hi all, Le 06/07/2023 à 11:04, Andreas Tille a écrit : Hi, last time we were wondering whether a monthly video meeting is more sensible. Its not that much we need to talk about (in case there is something we can perfectly do ad hoc meetings) and may be its enough to meet only once a month.

Re: pychopper has switched to a non-free license in new upstream version

Hi again, Le 17/06/2023 à 22:14, Pierre Gruet a écrit : Hi all, Le 17/06/2023 à 19:37, Nilesh Patra a écrit : On 06/17/2023 11:21 AM IST Andreas Tille wrote: ''' 1.10. "Research Purposes" means use for internal research and not intended for or directed towards commercial

Re: pychopper has switched to a non-free license in new upstream version

Hi all, Le 17/06/2023 à 19:37, Nilesh Patra a écrit : On 06/17/2023 11:21 AM IST Andreas Tille wrote: ''' 1.10. "Research Purposes" means use for internal research and not intended for or directed towards commercial advantages or monetary compensation; provided, however, that monetary

Re: Please review release notes patch

Hi all, Le 25/05/2023 à 09:51, Andreas Tille a écrit : Hi Nilesh, Am Wed, May 24, 2023 at 10:16:22PM +0530 schrieb Nilesh Patra: On Wed, May 24, 2023 at 11:28:13AM +0200, Pierre Gruet wrote: Le 24/05/2023 à 08:25, Andreas Tille a écrit : https://salsa.debian.org/med-team/community

Re: Please review release notes patch

Hello Andreas, Le 24/05/2023 à 08:25, Andreas Tille a écrit : Hi, as for every release we want to increase or visibility to show up in the release notes. I've drafted a patch https://salsa.debian.org/med-team/community/communication/-/blob/master/releasenotes/bookworm/release-notes.patch

Re: Nextflow - have just used it on our HPC cluster and liked it

Hi Andreas, Le 09/05/2023 à 18:36, Andreas Tille a écrit : Hi Pierre, Am Mon, May 08, 2023 at 10:50:54PM +0200 schrieb Pierre Gruet: It is very nice to hear from you on Nextflow, this is a motivation booster for the packaging! +1 I have indeed packaged many dependencies, and if I

Re: Nextflow - have just used it on our HPC cluster and liked it

Hi Steffen, Le 05/05/2023 à 22:16, Steffen Möller a écrit : Hello, I must admit that I am rather impressed - a series of images were auto-downloaded to function together with singularity and this then worked on a test data collection of the workflow. So, with singularity (or docker) in

Re: New version bali-phy 4.0-beta2

Hi Benjamin, Le 28/03/2023 à 03:52, Benjamin Redelings a écrit : Hi, I'd like to upload a new version 4.0-beta2 of bali-phy. It decreases memory usage over the existing 3.6.1 by > 20fold in some cases. The first question I have is about using uscan with the "-beta2" suffix.  I hacked the

Re: Snippy autopkgtest claims that snpeff is version 0

Hi Andreas, Le 03/02/2023 à 13:05, Andreas Tille a écrit : Hi Pierre, Am Fri, Feb 03, 2023 at 11:32:07AM +0100 schrieb Pierre Gruet: [16:13:15] Found snippy-vcf_to_tab - /usr/bin/snippy-vcf_to_tab [16:13:15] Found snippy-vcf_report - /usr/bin/snippy-vcf_report [16:13:15] Checking version

Re: Snippy autopkgtest claims that snpeff is version 0

Hi Andreas, Le 03/02/2023 à 11:17, Andreas Tille a écrit : Hi, I realised that snippy autopkgtest is failing for i386 and s390x[1] The log for i386[2] says: Get:310 http://deb.debian.org/debian testing/main i386 libsnpeff-java all 5.1+d+dfsg-3 [2,150 kB] ... [16:13:15] Found snpEff -

pplacer status (Was: Re: [RFH] aeonbits-owner and capsule-maven-nextflow)

Hi all, Le 22/12/2022 à 17:17, Andreas Tille a écrit : Am Thu, Dec 22, 2022 at 08:55:27PM +0530 schrieb Nilesh Patra: I see three options: 1. Revert mcl to past version From a user base point of view I do not consider this a good option. 2. Wait for upstream reaction on ocaml support

Re: Sprint can start Friday evening - who would like to join

Hi Andreas and everyone, Le 18/01/2023 à 11:28, Andreas Tille a écrit : Am Wed, Jan 18, 2023 at 07:56:55AM +0100 schrieb Andreas Tille: Hi, Am Tue, Jan 17, 2023 at 10:07:28PM +0100 schrieb Sascha Steinbiss: FYI the Vietnamese place (Viet Kitchen) around the corner has many vegan options and

Re: Sprint can start Friday evening - who would like to join

Hi all, Le 16/01/2023 à 19:27, Andreas Tille a écrit : Hi, on top of the small hotel at EUREF-Campus 22 there is a lounge for 8 persons. I can book this with Debian sponsored money for the evening - so we can meet there. Who would like to join and at what time do we want to meet? They hotel

[Advent bug squashing] #1026659 and #1026764 (Was: Re: [RFH] aeonbits-owner and capsule-maven-nextflow)

Hello, Le 22/12/2022 à 14:21, Nilesh Patra a écrit : Hi Pierre, all, Recent rebuilds have led to bug reports #1026659 and #1026764 for aeonbits-owner and capsule-maven-nextflow respectively. As you might have guessed, both of them are java packages and I've quite frankly been unable to

Re: [RFH] aeonbits-owner and capsule-maven-nextflow

Hi Nilesh and everyone, Le 22/12/2022 à 14:21, Nilesh Patra a écrit : Hi Pierre, all, Recent rebuilds have led to bug reports #1026659 and #1026764 for aeonbits-owner and capsule-maven-nextflow respectively. As you might have guessed, both of them are java packages and I've quite frankly

[Advent bug squashing] Fwd: Bug#1025953: marked as done (beast-mcmc: only usable with OpenCL)

, 16 Dec 2022 22:24:05 + De : Debian Bug Tracking System Répondre à : 1025...@bugs.debian.org Pour : Pierre Gruet Your message dated Fri, 16 Dec 2022 22:20:56 + with message-id and subject line Bug#1025953: fixed in libhmsbeagle 3.1.2+dfsg-13 has caused the Debian Bug report #1025953

[Advent bug squashing] This weekend: closed #1025887, eased testing migration, opened more bugs

Hello, I fixed bug #1025887 in biojava4-live thanks to a patch submitted along with the bug report. Also I eased the migration to testing of a few packages with long-standing failing migrations (autopkgtests and architectures problems essentially) and I opened some bugs -- so my contribution

Re: [help] vdjtools autopkgtest fails

Hi Andreas, Le 27/11/2022 à 07:07, Andreas Tille a écrit : Hi Pierre, when fixing the watch file I stumbled upon an autopkgtest error[1]. Do you have an idea what might be wrong here? At last I found classpath issues in the build, and I could provide a cleaner way to build the jar which was

Re: [help] vdjtools autopkgtest fails

Hi Andreas, Le 27/11/2022 à 07:07, Andreas Tille a écrit : Hi Pierre, when fixing the watch file I stumbled upon an autopkgtest error[1]. Do you have an idea what might be wrong here? My guess is there is a missing jar in the manifest of the jar shipped by libmilib-java, which I updated two

Re: [Help] Build issue of latest version of libsbml (probably Java compatibility issue)

Hi Andreas, Le 25/11/2022 à 10:57, Andreas Tille a écrit : Hi, I just realised that libsbml moved to Github. After fixing the watch file I tried to package the latest upstream version. Unfortunately the build fails and I see the lines

Re: Possibility of In-person sprints in 2023?

Hi, Le 22/11/2022 à 14:38, Andreas Tille a écrit : Hi Sascha, Am Tue, Nov 22, 2022 at 12:38:21AM +0100 schrieb Sascha Steinbiss: I have been in touch with our front desk and it looks like a meeting at my employer here is doable in principle, given the same conditions as last time. So I guess

Re: Possibility of In-person sprints in 2023?

Hi everyone, Le 29/10/2022 à 21:28, Nilesh Patra a écrit : Hi, I suppose sprints in 2021 and 2022 have been virtual so far due to COVID. There were some COVID related sprints in 2020 as well. Is there a possibilty to have an in-person debian-med sprint in 2023? Would someone be interested in

Re: Debian Med video conference tomorrow, Wednesday 2022-11-02 18:00 UTC

Hi everyone, Le 01/11/2022 à 16:35, Andreas Tille a écrit : Hi, this is the call for the next video conference of the Debian Med team [...] For those who are interested in hot topics we want to tackle, here are some items: - RC bugs - Pushing latest versions of our software While I

Re: gdcm: vtk[6,7] removal

Hi Andreas, Le 26/10/2022 à 11:24, Andreas Tille a écrit : Hi Pierre, Am Wed, Oct 26, 2022 at 10:41:51AM +0200 schrieb Pierre Gruet: [1] https://salsa.debian.org/med-team/gdcm/-/jobs/3427720 This is really just a missing include dir, as the problematic header is in /usr/lib/jvm/default-java

Re: gdcm: vtk[6,7] removal

Hi, Le 26/10/2022 à 10:35, Andreas Tille a écrit : Hi Mathieu, Am Wed, Oct 26, 2022 at 08:10:42AM +0200 schrieb Mathieu Malaterre: On Wed, Oct 26, 2022 at 7:53 AM Andreas Tille wrote: Hi, in the bug log there is some discussion to drop C# and Java VTK bindings. This would mean to drop

Re: Please have a look at beast2-mcmc in Git

Hi Andreas, Le 24/10/2022 à 09:58, Andreas Tille a écrit : Hi Pierre, I've updated beast2-mcmc in Git but the new upstream version fails to build[1] which has hopefully a simple fix. Thanks for drawing my attention on this issue. I pushed the effort forward, but now half of the tests are

Bug#1022258: ITP: libmjson-java -- lean JSON Library for Java with a compact API

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: libmjson-java Version : 1.4.0 Upstream Author : Miami-Dade County * URL : https://bolerio.github.io/mjson/ * License

Bug#1021934: ITP: biojava6-live -- Java API to biological data and applications (version 6)

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: biojava6-live Version : 6.0.5 Upstream Author : BioJava Developers * URL : https://biojava.org * License :

Re: Finishing ncbi-vdb and sra-sdk

Hi Aaron, Le 14/10/2022 à 02:05, Aaron M. Ucko a écrit : Pierre Gruet writes: I have just pushed some changes. I adopted the -- I believe -- least invasive solution by creating a new package libngs-jni which depends on the shared lib package (not the -dev one), only ships a symlink

Re: Finishing ncbi-vdb and sra-sdk

Hi Aaron, Le 12/10/2022 à 04:48, Aaron M. Ucko a écrit : Pierre Gruet writes: Indeed, this warning should be overridden, usually I do so and add a pointer to the discussion in https://lists.debian.org/debian-java/2018/06/msg00021.html in the comment in the .lintian-overrides file. Got

Re: Finishing ncbi-vdb and sra-sdk

Hi Aaron and Andreas, Le 11/10/2022 à 15:06, Aaron M. Ucko a écrit : Andreas Tille writes: I wanted to set you "Owner" of the Debian Med team repository since this is the maximum power. I realised you are owner. So either someone has beaten me and just did so or something is wrong if you

sight failing to build

Hello Flavien, We have just had this bug report on sight: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016276 My last upload of sight was 15 days ago with no issue. Anyway, if you have some time to look at it, it will be useful! Best wishes, -- Pierre OpenPGP_signature

Re: CMake help needed for tiddit

Hi Andreas, Le 26/07/2022 à 13:50, Andreas Tille a écrit : Hi, from my perspective the CMakeLists.txt of tiddit has not changed compared to the last upstream version. Unfortunately the build fails[1] with CMake Error at CMakeLists.txt:42 (add_executable): No SOURCES given

Bug#1016046: ITP: genomicsdb -- sparse array storage library for genomics

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: genomicsdb Version : 1.4.3 Upstream Author : Intel Health and Lifesciences * URL : https://www.genomicsdb.org/ * License

Bug#1014344: ITP: gatk-bwamem -- interface to call Heng Li's bwa mem aligner from Java code

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: gatk-bwamem Version : 1.0.4 Upstream Author : Broad Institute * URL : https://github.com/broadinstitute/gatk-bwamem-jni/ *

Re: milib moved to gradle build system - help needed

Hi Andreas and tony, Le 01/07/2022 à 19:13, tony mancill a écrit : On Thu, Jun 30, 2022 at 05:06:50PM +0200, Andreas Tille wrote: Hi Pierre (and others) I injected latest version of milib which moved to gradle even in some versions before. My extremely weak attempt to switch to gradle failed

Re: Removing myself from uploaders in (most) med-packages / Winding down involvement a little

Hi everyone, Le 24/06/2022 à 22:15, Étienne Mollier a écrit : [...] In the light of Andreas' own time shrinking, my id is also available if need be (disregarding the fact that I felt having the head underwater in the past few months myself). I'll try to add myself systematically when

Re: Upgrading biojava-live from 1.7 to 1.9

Hi Olivier, Andreas, Steffen, Le 28/03/2022 à 17:54, Steffen Möller a écrit : On 28.03.22 17:15, Andreas Tille wrote: Am Mon, Mar 28, 2022 at 04:42:15PM +0200 schrieb olivier sallou: ... that's fine for me Thanks a lot for this effort Many thanks - brings some memories back! Steffen

Upgrading biojava-live from 1.7 to 1.9

1-07 15:25:19.0 +0100 +++ artemis-18.1.0+dfsg/debian/changelog2022-02-28 18:24:58.0 +0100 @@ -1,3 +1,9 @@ +artemis (18.1.0+dfsg-7) UNRELEASED; urgency=medium + + * Changing coordinates of biojava, which is now Maven-packaged + + -- Pierre Gruet Mon, 28 Feb 2022 18:2

Bug#1008304: ITP: http-nio -- http/s file system provider for Java NIO.2

Hi Guillem, Le 28/03/2022 à 13:43, Guillem Jover a écrit : Hi! On Sat, 2022-03-26 at 14:59:17 +0100, Pierre Gruet wrote: Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: http-nio Version

Bug#1008304: ITP: http-nio -- http/s file system provider for Java NIO.2

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: http-nio Version : 0.1.0 Upstream Author : Daniel Gomez-Sanchez * URL : https://github.com/lbergelson/http-nio * License

Bug#1008128: ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: gatk-fermilite Version : 1.2.1 Upstream Author : Broad Institute * URL :

Re: Advice needed: building new gatk-bwamem-jni against another version of bwa

Hi Andrius, Thanks for looking at my issue. Le 14/03/2022 à 06:03, Andrius Merkys a écrit : Hi Pierre, On 2022-03-13 16:35, Pierre Gruet wrote: My proposal would be to design a multiple upstream tarball for gatk-bwamem-jni: original one + the sources at the tip of the Apache2 branch of bwa

Re: Advice needed: building new gatk-bwamem-jni against another version of bwa

Hi Nilesh, Thanks for the quick answer. Your advice is much appreciated, as always. Le 13/03/2022 à 15:46, Nilesh Patra a écrit : On 3/13/22 8:05 PM, Pierre Gruet wrote: What should I do? My proposal would be to design a multiple upstream tarball for gatk-bwamem-jni: original one

Advice needed: building new gatk-bwamem-jni against another version of bwa

Hello everyone, I need your advice on a packaging issue I am meeting right now. I am in the course of packaging gatk-bwamem-jni [0], providing a native interface which allows one to use bwa (Debian packaged [1]) from Java code. Fine. But the upstream of gatk-bwamem-jni relies on a version of

Bug#1006834: ITP: aeonbits-owner -- API to handle application configuration through Java properties file

Package: wnpp Severity: wishlist Owner: Debian med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: aeonbits-owner Version : 1.0.12 Upstream Author : Luigi R. Viggiano * URL : http://owner.aeonbits.org/ * License :

Bug#1006501: ITP: snpsift -- tool to annotate and manipulate genome variants

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: snpsift Version : 5.1 Upstream Author : Pablo Cingolani * URL : https://pcingola.github.io/SnpEff/ss_introduction/ *

Re: Datasets to design autopkgtests for our packages

Hi Andrius, Le 18/02/2022 à 17:21, Andrius Merkys a écrit : Hi Pierre, On 2022-02-18 17:52, Pierre Gruet wrote: To give a bit of context: I am currently writing autopkgtests for htsjdk, which is one Java library we maintain in the team. Those autopkgtests should test reverse-dependencies

Datasets to design autopkgtests for our packages

Hi everyone, To give a bit of context: I am currently writing autopkgtests for htsjdk, which is one Java library we maintain in the team. Those autopkgtests should test reverse-dependencies to ease upgrades of htsjdk. When designing such tests, I would need data to run, let's say, artemis

Bug#1005356: ITP: rockhopper -- system for analyzing bacterial RNA-seq data

Hi, Le 12/02/2022 à 06:42, Andreas Tille a écrit : Very cool! You're welcome! Eventually, all the .class files in the archive were just igv and its dependencies, so that I could remove all of them and have igv as the sole dependency of the binary package :-) Best regards, -- Pierre

Bug#1005356: ITP: rockhopper -- system for analyzing bacterial RNA-seq data

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: rockhopper Version : 2.0.3 Upstream Author : Brian Tjaden * URL : https://cs.wellesley.edu/~btjaden/Rockhopper * License

Re: New version of snpeff in Git (Was: snpeff_4.3t+dfsg1-1_amd64.changes REJECTED)

Hi again, Le 03/02/2022 à 22:22, Andreas Tille a écrit : Am Thu, Feb 03, 2022 at 02:42:40PM +0100 schrieb Pierre Gruet: Yes, just before looking at king/libpdfbox-graphics2d-java I was updating snpeff and seeing if I could turn some unit tests into autopkgtests -- and I trust I can

Re: New version of snpeff in Git (Was: snpeff_4.3t+dfsg1-1_amd64.changes REJECTED)

Hi Andreas, Le 03/02/2022 à 10:31, Andreas Tille a écrit : Hi, Am Sat, Jan 22, 2022 at 09:49:32PM +0100 schrieb Pierre Gruet: I did the upload -- I agree autopkgtests would be valuable, still. Yet I remember the tests I did when designing the package last Spring, and I feel providing

Re: Java help for king needed

Hi, Le 28/01/2022 à 22:42, Andreas Tille a écrit : Am Fri, Jan 28, 2022 at 10:11:27PM +0100 schrieb pgtdeb...@free.fr: If you want, I would be happy to package pdfbox-graphics2d. I can do that very soon. Else, please tell me if you start something :-) I've pushed

Re: Java help for king needed

Hi Andreas, Le 28/01/2022 à 22:42, Andreas Tille a écrit : Am Fri, Jan 28, 2022 at 10:11:27PM +0100 schrieb pgtdeb...@free.fr: If you want, I would be happy to package pdfbox-graphics2d. I can do that very soon. Else, please tell me if you start something :-) I've pushed

Re: Java help for king needed

Hi Andreas, Le 28/01/2022 à 22:30, Andreas Tille a écrit : Am Fri, Jan 28, 2022 at 10:11:27PM +0100 schrieb pgtdeb...@free.fr: If you want, I would be happy to package pdfbox-graphics2d. I can do that very soon. Else, please tell me if you start something :-) I've just collected a basic

Re: 20 years of Debian Med list :-) and suggested sprint date

Dear all, Le 24/01/2022 à 16:09, Andreas Tille a écrit : Hi folks, on Mon, 21 Jan 2002 11:59:11 +0100 the first mail to this list was sent[1]. So somehow we can celebrate some anniversary. :-) Great :-) Happy to celebrate this! Since 11 years we are doing team sprints - preferably face

Re: snpeff_4.3t+dfsg1-1_amd64.changes REJECTED

Hi again Andreas, Le 22/01/2022 à 21:24, Andreas Tille a écrit : Hi Pierre, Am Sat, Jan 22, 2022 at 08:37:54PM +0100 schrieb Pierre Gruet: Le 22/01/2022 à 16:43, Andreas Tille a écrit : Thanks a lot Pierre for fixing it quickly in a new upload. Its a great step forward if we have

Re: snpeff_4.3t+dfsg1-1_amd64.changes REJECTED

[redirecting to debian-med@lists.debian.org for information] Hi Andreas, Le 22/01/2022 à 16:43, Andreas Tille a écrit : Thanks a lot Pierre for fixing it quickly in a new upload. Its a great step forward if we have this package. Thanks also to Thorsten for checking You're welcome! Thanks

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+

Bug#1003782: ITP: megan-ce -- interactive tool to explore and analyse microbiome 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: megan-ce Version : 6.21.1 Upstream Author : Daniel Huson * URL : https://github.com/danielhuson/megan-ce * License

Re: [Advent bug squashing] Pierre Gruet fixed: Bug#1002155: marked as done (libgoby-java: FTBFS: [WARNING] /<>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaT

Hi Andreas, On 23/12/2021 19:42, Andreas Tille wrote: Hi Pierre, Am Thu, Dec 23, 2021 at 05:42:24PM +0100 schrieb Pierre Gruet: You're welcome! Thanks for your help on this. That's team work, isn't it? ;-) Sure ! :) BTW, if you are seeking new challanges: It would be great to have

Re: [Advent bug squashing] Pierre Gruet fixed: Bug#1002155: marked as done (libgoby-java: FTBFS: [WARNING] /<>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaT

Hi Andreas, On 23/12/2021 17:27, Andreas Tille wrote: Thanks Pierre for your work. :-) Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Closes: 1002155 Changes: libgoby-java (3.3.1+dfsg2-6) unstable; urgency=medium . * Adding --no-parallel flag to dh_auto_test to avoid

Re: libgoby-java: FTBFS: [WARNING] /<>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist

Control: tags -1 unreproducible help Hi, Currently I am not able to reproduce the issue on my computer nor on several machines of the Debian project. I shall investigate further a bit later, but so far looking at a diff between the provided build log and mine has not helped. The warning

Re: autopkgtest requiring large data sets (pique, hinge)

Hello Lance, On 21/12/2021 14:33, Lance Lin wrote: Debian Medical Team, I have started looking at adding autopkgtest suites for a variety of packages. Two of the packages (hinge, pique) require very large data sets to run their included examples. The sizes are several GB. It also looks like

Re: Scala error when trying to build latest version of pilon

Hi Andreas, On 18/12/2021 08:52, Andreas Tille wrote: Hi Pierre, Am Fri, Dec 17, 2021 at 11:27:50PM +0100 schrieb Pierre Gruet: I have just uploaded latest upstream version of pilon to unstable, together with a fix for the scala issues showing up. Normally we would have had to update scala

Re: Scala error when trying to build latest version of pilon

Hi Andreas, On 09/09/2021 14:21, Andreas Tille wrote: Hi Pierre, thanks a lot for your educated answer. On Thu, Sep 09, 2021 at 12:48:33PM +0200, Pierre Gruet wrote: Any hint how to fix this? Well, /maybe/ we could patch this last pilon version to use Scala 2.11 with it... but I see

[Advent bug squashing] Fwd: Bug#1001681: marked as done (sight: FTBFS in unstable)

RC bug in sight is now fixed! Forwarded Message Subject: Bug#1001681: marked as done (sight: FTBFS in unstable) Date: Thu, 16 Dec 2021 06:21:03 + From: Debian Bug Tracking System Reply-To: 1001...@bugs.debian.org To: Pierre Gruet Your message dated Thu, 16 Dec 2021 06

[Advent bug squashing] Bugs #989328 and #989961 : newest picard-tools in unstable

Hi, Newest picard-tools is in unstable, and I fixed the two bugs the source package had! Best, Pierre

Re: RM profphd?

Hi Nilesh, Le 23/11/2021 à 19:11, Nilesh Patra a écrit : Hi, It looks like profphd has a open RC bug for a little over two years by now, and upstream looks dead. It has only reverse-recommends, no reverse-(build-)depends $ reverse-depends profphd Reverse-Recommends * norsnet * norsp *

Re: libjung-java needs some love

Hi, Le 10/11/2021 à 15:14, Andreas Tille a écrit : Hi, I realised that libjung-java "smells"[1] and in fact it was not uploaded a long time and has some maintenance issues. I tried to build the current state in Git but it fails the API fails to build. I hope this is not a big issue for a

Re: Thanks a lot for enabling igv in main [Was: igv_2.6.3+dfsg2-1_amd64.changes ACCEPTED into unstable, unstable]

Hi Andreas, Le 09/11/2021 à 18:29, Andreas Tille a écrit : Hi Pierre, Am Tue, Nov 09, 2021 at 06:02:39PM +0100 schrieb Pierre Gruet: If you are not able to reproduce I can send a full build log. It would be fine for me if you would just fix - build - upload yourself. I just wanted to help

Re: Thanks a lot for enabling igv in main [Was: igv_2.6.3+dfsg2-1_amd64.changes ACCEPTED into unstable, unstable]

Hi Andreas, Le 09/11/2021 à 07:55, Andreas Tille a écrit : Hi Pierre, thanks a lot for all your work on this. You are welcome! Indeed I am very pleased this long-term target of mine is now reached! I intended to do a source-only upload and when doing so at least fixing the watch file (I

Bug#996993: ITP: biojava5-live -- Java API to biological data and applications (version 5)

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: biojava5-live Version : 5.4.0 Upstream Author : BioJava Developers * URL : https://www.biojava.org/ * License :

Re: New upstream version of drop-seq does not build

Hi Andreas, Le 13/10/2021 à 07:38, Andreas Tille a écrit : Hi Pierre, Am Tue, Oct 12, 2021 at 09:13:49PM +0200 schrieb Pierre Gruet: Cool. I also think we should pimp biojava4 watch file to return the last upstream source of biojava4 and than also provide biojava5. We will soon see

Re: New upstream version of drop-seq does not build

Hi again, Le 12/10/2021 à 18:58, Andreas Tille a écrit : Hi Pierre, Am Tue, Oct 12, 2021 at 03:29:33PM +0200 schrieb Pierre Gruet: I have added biojava4 as a dependency, then some paths had to be changed because upstream relies on a far outdated version of biojava, and then I had to revise

Re: New upstream version of drop-seq does not build

Hi again, Le 12/10/2021 à 15:24, Andreas Tille a écrit : Am Tue, Oct 12, 2021 at 12:12:43PM +0200 schrieb Pierre Gruet: Thanks for pointing this out; I looked at it and saw biojava has not been a dependency of drop-seq until now. It seems version 2.4.1 is the first to need biojava. So I

Re: New upstream version of drop-seq does not build

Hi Andreas, Le 12/10/2021 à 09:59, Andreas Tille a écrit : Hi Pierre, I realised that you updated Git of drop-seq to fix the watch file. I simply uploaded basically as is to have a proper signal in our tools that there is a new upstream version. Unfortunately I realised that there seems to

Re: Pilon might need newer scala

Hi, Le 01/10/2021 à 16:52, Andreas Tille a écrit : Hi, I intended to update pilon to its latest upstream version but got: scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar src/main/scala/org/broadinstitute/pilon/* src/main/scala/org/broadinstitute/pilon/BamFile.scala:24: error:

Re: Do users know about README.Debian and /usr/share/doc/packagename (Was: libcifpp)

Hi Andreas, Thanks for forking the thread and launching this conversation. Le 01/10/2021 à 08:48, Andreas Tille a écrit : Hi, Am Thu, Sep 30, 2021 at 02:10:50PM +0200 schrieb Pierre Gruet: My concern with this is the average user might not even know about the README.Debian file and could

Re: libcifpp

Hi Maarten, Le 29/09/2021 à 17:28, Andreas Tille a écrit : Should I add a call to this update script in the post install hook? Having 500MB of data in Debian that's probably updated the very next day after installation seems very inconvenient, right? I'm not sure whether we have example

Re: Upgrading IGV

HI Andreas, Le 28/09/2021 à 07:11, Andreas Tille a écrit : Hi Pierre, On Mon, Sep 27, 2021 at 08:38:34PM +0200, Pierre Gruet wrote: Actually the situation is a bit complicated with igv: - I am waiting for libgoby-java to exit NEW so that I can upload the version currently packaged to main

Bug#995294: ITP: tipp -- taxonomic identification and abundance profiling tool

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: tipp Version : 1.0 Upstream Author : Siavash Mirarab * URL : https://github.com/TeraTrees/TIPP * License : GPL-3

Re: Upgrading IGV

Hi Andreas, Le 27/09/2021 à 17:26, Andreas Tille a écrit : Hi Pierre, I was running routine-update on igv and as usually some patches did not applied. There is no urgent pressure to upgrade the package but its raising a signal that the watch file is not working (due to changes on github).

Re: Any volunteer to verify autopkgtest of spades?

Hi Tony, Le 23/09/2021 à 22:06, Tony Travis a écrit : On 23/09/2021 17:16, Steffen Möller wrote: [...] You would install both the source tree (with the Debian folder) and install the binary. Then run sh debian/tests/run-unit-test from the source directory. Hi, Steffen. Please forgive my

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