Bug#820060: Debian Bug#820060: python-biom-format: broken on big-endian architectures

Hi Andreas, It looks like the upstream fixed the issue in some recent version, as according to the logs [1], the package builds now for big-endians as well. Do you agree, that we can close the bug as well as the issue? Best regards, Liubov [1] http://buildd.debian.org/python-biom-format

Bug#942404: Tests seem to work again

Hi Paul, I tried hard but wasn't able to reproduce the bug (in a clean chroot). Even for the stable version (2.3.0-2) tests are passing (several times in a row). Looking at the debci logs [1], tests are passing for quite some time. Do you think, it makes sense to keep it longer? Best regards,

Bug#936802: kmer: Python2 removal in sid/bullseye

Hi Andreas, As I mentioned during today's Jitsi meeting, kmer builds and all the tests passed in a clean sbuild schroot. Should we close the bug and make a release then? Regards, Liubov

Bug#950842:

Control: tags -1 upstream Control: forwarded -1 https://github.com/qiime2/qiime2/issues/520

Bug#950931: [rebecca_pal...@zoho.com: Bug#950931: q2templates: FTBFS with pandas 1.0: test failures]

Hello, The error seems to be related to this issue: https://github.com/qiime2/q2templates/issues/41. We could possibly work on it but the upstream is already going to fix the issue in the next release. Best, Liubov

Bug#940290: q2-types: triangular dependency with q2-types, q2cli

Hi Andreas, On Tue, 17 Sep 2019 at 14:39, Andreas Tille wrote: > Control: reassign -1 qiime > > Hi Liubov, > > On Tue, Sep 17, 2019 at 12:19:51PM +0200, Liubov Chuprikova wrote: > > > This is the case if neither q2-types or q2cli are totally broken if > > > qiim

Bug#940290: q2-types: triangular dependency with q2-types, q2cli

Hi Andreas, On Tue, 17 Sep 2019 at 07:54, Andreas Tille wrote: > Hi Liubov, > > On Sun, Sep 15, 2019 at 12:18:45PM +0200, Bill Allombert wrote: > > Package: q2-types > > Version: 2019.7.0-1 > > Severity: important > > > > Hello Debian Med Packaging Team, > > > > There is a trianglar dependency

Bug#932050: ITP: q2-taxa -- QIIME 2 plugin for working with feature taxonomy annotations

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-taxa Version : 2019.4.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME 2 plugin

Bug#932001: ITP: q2-feature-table -- QIIME 2 plugin supporting operations on feature tables

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-feature-table Version : 2019.4.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME 2

Bug#931887: ITP: q2-feature-classifier -- QIIME 2 plugin supporting taxonomic classification

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-feature-classifier Version : 2019.4.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description

Bug#931885: ITP: q2-quality-filter -- QIIME2 plugin for PHRED-based filtering and trimming

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-quality-filter Version : 2019.4.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME2

Bug#931249: ITP: q2-cutadapt -- QIIME 2 plugin to work with adapters in sequence data

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-cutadapt Version : 2019.4.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME 2

Bug#930976: ITP: python-dnaio -- Python 3 library for fast parsing of FASTQ and FASTA files

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: python-dnaio Version : 0.3 Upstream Author : Marcel Martin * URL : https://github.com/marcelm/dnaio * License : MIT Programming Lang: Python Description : Python 3 library

Bug#930755: ITP: q2-metadata -- QIIME 2 plugin for working with and visualizing Metadata

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-metadata Version : 2019.4.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME 2

Bug#930152: ITP: q2-demux -- QIIME 2 plugin for demultiplexing of sequence reads

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-demux Version : 2019.4.1 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME 2 plugin

Bug#930151: ITP: q2templates -- Design template package for QIIME 2 Plugins

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2templates Version : 2019.4.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : Design

Bug#925909: [Help] Re: pbgenomicconsensus: autopkgtest regression

Hi, On Sun, 7 Apr 2019 at 11:30, Graham Inggs wrote: > Hi Andeas > > On Sun, 7 Apr 2019 at 07:50, Andreas Tille wrote: > > I have no idea why command1 is failing. Anybody who can reproduce > > this test result and can fix this test? > > The output of command1 is the following: > > autopkgtest

Bug#925983: ITP: q2-alignment -- QIIME 2 plugin for generating and manipulating alignments

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-alignment Version : 2019.1.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME 2

Bug#925931: ITP: q2-types -- QIIME 2 plugin defining types for microbiome analysis

Package: wnpp Owner: Liubov Chuprikova Severity: wishlist * Package name: q2-types Version : 2019.1.0 Upstream Author : QIIME 2 development team * URL : https://qiime2.org/ * License : BSD-3-clause Programming Lang: Python Description : QIIME 2 plugin

Bug#925400: Processed: Bug#925400: ITP: q2cli -- Click-based command line interface for QIIME 2

for > QIIME 2 > > Owner changed from Liubov Chuprikova to Debian > Med team . > > While I think there is no harm done by changing the owner of this ITP > bug its rather unusual. Sorry for this mess! In the beginning, I set the bug owner to "Debian Med Packaging Team "

Bug#922486: python3-sbml5: libsbml fails to import

Hi Andreas, On Sat, 2 Mar 2019 at 07:07, Andreas Tille wrote: > Hi Liubov, > > I've lost this a bit out of sight. Today is the last day for uploading > anything without asking the release team for migration. I definitely > will not be able to work on the issue myself (sponsoring could be an >

Bug#907898: gmap: autopkgtest regression

Hi Andreas, I have just found the easiest bug to solve :-) This one was solved in the very next version 2018-07-04-4 and since then the autopkgtest is passing everywhere [1]. With regards, Liubov [1] https://ci.debian.net/packages/g/gmap/

Bug#912586: python-cobra still fails it's autopkg tests

Hi, I have just pushed a fix for this. In fact, the solution was proposed in one of the previous messages [1]: the test suite was returning True some time ago, but now it returns the exit code instead. Some tests are `xfail`-ing (in the beginning I thought that's was the problem) but as I

Bug#922486: python3-sbml5: libsbml fails to import

Hi Andreas, On Sat, 16 Feb 2019 at 22:43, Andreas Tille wrote: > > If you see any chance to hunt this issue in libsbml down this would be > really welcome. I would like to fix this if I have time in the following week. I can't say right now. JFI: Just looking onto the files installed with

Bug#922486: python3-sbml5: libsbml fails to import

Package: python3-sbml5 Version: 5.17.2+dfsg-3 Severity: normal Hi, After installing python3-sbml5, it is not possible to import libsbml module: Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'libsbml' I have found it when I was looking into

Bug#917143: t-coffee autopkgtest regression

Hi Andreas, On Sun, 27 Jan 2019 at 16:23, Andreas Tille wrote: > Control: tags -1 help upstream > Control: forwarded -1 https://github.com/cbcrg/tcoffee/issues/13 > > Hi Liubov, > > On Sun, Jan 27, 2019 at 04:06:51PM +0100, Liubov Chuprikova wrote: > > I was trying

Bug#917143: t-coffee autopkgtest regression

Hi, I was trying to figure out the reason for the failure but without any success. It appeared that the error is reproducible with the upstream's source version, so I have just opened an issue [1] to inform the upstream about this bug. [1] https://github.com/cbcrg/tcoffee/issues/13 With

Bug#908599: ITP: unicycler -- hybrid assembly pipeline for bacterial genomes

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: unicycler Version : 0.4.7 Upstream Author : Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt * URL : https://github.com/rrwick/Unicycler * License : GPL-3+

Bug#906980: kmer: autopkgtest fails with segfault in testing/unstable while it passes in stable

Hi Andreas, On Mon, 27 Aug 2018 at 17:02 Andreas Tille wrote: > > Ah, finally a pretty simple solution for a quite hidden problem. > I admit I have expected something more serious :-) > BTW, I wonder whether there are tools that would warn about issues > described in[1] - I think there

Bug#906980: kmer: autopkgtest fails with segfault in testing/unstable while it passes in stable

Hi Andreas, On Thu, 23 Aug 2018 at 08:58 Andreas Tille wrote: > > On Wed, Aug 22, 2018 at 09:42:13PM +0200, Liubov Chuprikova wrote: > > An autopkgtest fails with segfault in testing and unstable [1]. > > > > ``` > > /usr/bin/../lib/atac/bin/statsGenerator -a &

Bug#906980: kmer: autopkgtest fails with segfault in testing/unstable while it passes in stable

Package: kmer Version: 0~20150903+r2013-4 Severity: serious Justification: reproducibility An autopkgtest fails with segfault in testing and unstable [1]. ``` /usr/bin/../lib/atac/bin/statsGenerator -a /tmp/autopkgtest-lxc.epng5fx9/downtmp/autopkgtest_tmp/results/EcolivsSent.atac -p

Bug#890787: (Bug#890787) fastdnaml: Please provide autopkgtest

Hi Andreas, I have just pushed an autopkgtest and other minor changes for *fastdnaml* . Please, take a look at the commits [1]! With regards, Liubov [1] https://salsa.debian.org/med-team/fastdnaml/commits/master

Bug#890785: (Bug#890785) autodock-vina: Please provide autopkgtest

Hi Andreas, I pushed an autopkgtest for autodock-vina and also fixed some lintian warnings as usual. By the way, lintian says that the newest version of Debian Policy (4.1.5) should be indicated. I did so, is it OK? On Sat, 7 Jul 2018 at 09:37 Andreas Tille wrote: > Let me know if you need

Bug#900752: ITP: genometester -- toolkit for performing set operations on k-mer lists

Package: wnpp Severity: wishlist Owner: Liubov Chuprikova * Package name: genometester Version : 4.0 Upstream Author : University of Tartu * URL : https://github.com/bioinfo-ut/GenomeTester4 * License : GPL-3+ Programming Lang: C Description : toolkit

Bug#890993: (Bug#890993) primer3 FTBFS on big endian: test failure

Hi Andreas, Hi all, I tried to figure out what exactly could cause the failure. The error refers to the test files in the kmer_lists directory that are in binary format. It seems they were generated on a little-endian architecture, that is why the test fails on big-endian when it tries to verify

Bug#879619: Autopkgtest for ncbi-tools6

Hi Aaron, On Wed, 23 May 2018 at 20:36 Aaron M. Ucko <u...@debian.org> wrote: > Liubov Chuprikova <chuprikov...@gmail.com> writes: > > > Please, have a look at my two last commits ( > > https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually, >

Bug#879619: Autopkgtest for ncbi-tools6

On Wed, 23 May 2018 at 20:36 Aaron M. Ucko <u...@debian.org> wrote: > Liubov Chuprikova <chuprikov...@gmail.com> writes: > > > Please, have a look at my two last commits ( > > https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually, > > the fir

Bug#894781: bedtools: autopkgtest fails while it succeeded in the past

Hi Andreas, I have just pushed some changes to run-unit-test that are supposed to fix the problem. Please, check my commit . It seems that upstream test/test.sh has been updated so that now it returns an

Bug#879619: Autopkgtest for ncbi-tools6

Hi Aaron, Hi Andreas, Please, have a look at my two last commits ( https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually, the first one was made a month ago. On Tue, 17 Apr 2018 at 03:48 Aaron M. Ucko <u...@debian.org> wrote: > Liubov Chuprikova <chuprikov...@gmail

Bug#879619: Autopkgtest for ncbi-tools6

Hi Aaron, On Fri, 13 Apr 2018 at 02:04 Aaron M. Ucko <u...@debian.org> wrote: > Liubov Chuprikova <chuprikov...@gmail.com> writes: > > > On Thu, 12 Apr 2018 at 17:30 Aaron M. Ucko <u...@debian.org> wrote: > > > >> > >> That said, you did catc

Bug#879619: Autopkgtest for ncbi-tools6

On Thu, 12 Apr 2018 at 17:30 Aaron M. Ucko wrote: > > That said, you did catch a bug in taxblast; I'll push a fix this > evening. (The binary will still require a network connection, just > actually be able to use it now). > Ok, thank you! With regards, Liubov

Bug#879619: Autopkgtest for ncbi-tools6

On Thu, 12 Apr 2018 at 16:40 Andreas Tille wrote: > > Just from reading the shell script it looks fine. Requiring bash is > also OK. > Ok, thanks! SSL I'm getting suspicious: The test suite needs to be run in a machine > that is disconnected from the internet (similarly

Bug#879619: Autopkgtest for ncbi-tools6

Hi Aaron, On Thu, 5 Apr 2018 at 23:30 Aaron M. Ucko <a...@alum.mit.edu> wrote: > Liubov Chuprikova <chuprikov...@gmail.com> writes: > > > the same directory. What do you think about the whole test at this stage? > > Great, thanks! I suppose you could check for s

Bug#879619: Autopkgtest for ncbi-tools6

Hi Aaron, Hi Andreas, On Wed, 4 Apr 2018 at 01:41 Aaron M. Ucko <u...@debian.org> wrote: > Liubov Chuprikova <chuprikov...@gmail.com> writes: > > > Last two days I have been figuring out how to test *tbl2asn* and > > *asnmacro*. Please, take a look

Bug#894781: bedtools: autopkgtest fails while it succeeded in the past

Hi Andreas, hi Charles, On Thu, 5 Apr 2018 at 09:34 Andreas Tille wrote: > Hi, > > I confirm that the tests are throwing errors (despite I can not > reproduce the issue uncovered at ci.debian.net[1]) when running the also > user accessible script

Bug#879619: Autopkgtest for ncbi-tools6

Dear Andreas, dear Aaron, On Thu, 29 Mar 2018 at 18:14 Andreas Tille <andr...@an3as.eu> wrote: > On Thu, Mar 29, 2018 at 02:35:01PM +0000, Liubov Chuprikova wrote: > > > > Thanks a lot for your attention to my work on the project! > > I'd like to confirm that this is

Bug#879619: Autopkgtest for ncbi-tools6

Dear Andreas, dear Aaron, ср, 28 мар. 2018 г. в 5:07, Aaron M. Ucko <u...@debian.org>: > Liubov Chuprikova <chuprikov...@gmail.com> writes: > > > Thanks a lot for helping me out with this project! I saw your messages to > > Aaron and it was a relief for me t

Bug#879619: Autopkgtest for ncbi-tools6

Dear Andreas, вт, 27 мар. 2018 г. в 12:49, Andreas Tille <andr...@an3as.eu>: > Dear Liubov, > > On Sat, Mar 24, 2018 at 06:45:42PM +, Liubov Chuprikova wrote: > > > I once had the idea in the figtree package to use xvfb-run[1]. It was > > > not really succes

Bug#890783: Autopkgtest for prodigal (#890783)

Dear Andreas, пн, 19 мар. 2018 г. в 14:14, Andreas Tille <andr...@an3as.eu>: > Dear Liubov, > > On Mon, Mar 19, 2018 at 12:47:38PM +, Liubov Chuprikova wrote: > > > I have tried to find the information that should be placed in > d/copyright, > > but unfortuna

Bug#890783: Autopkgtest for prodigal (#890783)

Hi Andreas, > On Fri, Mar 16, 2018 at 05:48:35PM +0100, Andreas Tille wrote: > > > > I included a genome sequence from NCBI as test data. Should I indicate > the > > > source of this data somewhere in the package (e.g., in Readme.tests)? > > > > I think the best place would be debian/copyright

Bug#890786: Question about adding autopkgtest for coils (#890786)

Sorry, I've just realized that I've forgotten to specify the subject. вт, 13 мар. 2018 г. в 20:26, Liubov Chuprikova <chuprikov...@gmail.com>: > Hi Andreas, > > I have just added an autopkgtest to *coils* (commit > <https://salsa.debian.org/