Bug#1078882: Fixing also in experimental

Control: found -1 3.0.9+dfsg-4 Control: fixed -1 3.0.9+dfsg-5 Control: forwarded -1 https://github.com/ncbi/sra-tools/issues/958 Hi, This also touches experimental, so I uploaded a new version there. I forwarded the issue upstream so that they can add the CPP flag. Best, -- Pierre OpenPGP

Bug#1079015: Breaks other packages' build: Malformed jar [eclipse-jdt-core-3.35.0.jar] found on classpath

Control: reassign -1 src:libsis-jhdf5-java Control: tags -1 + ftbfs Control: retitle -1 FTBFS: please add eclipse-jdt-core-compiler-batch.jar to the classpath Hi Emmanuel, Le 20/08/2024 à 12:19, Emmanuel Bourg a écrit : Hi Pierre, On 19/08/2024 11:52, Pierre Gruet wrote: The latest upload

Bug#1055194: transition: openturns

Dear Release Team, I think this bug can be closed now, as the transition has been done. I am not doing it myself in case I might have missed something... Best, -- Pierre OpenPGP_signature.asc Description: OpenPGP digital signature

Bug#1081166: RM: ants/experimental -- ROM; Upstream stopped supporting i386

Package: ftp.debian.org Severity: normal X-Debbugs-Cc: a...@packages.debian.org Control: affects -1 + src:ants User: ftp.debian@packages.debian.org Usertags: remove Dear FTP team, Could you please remove ants from experimental? The version in unstable is higher, but it remains there because t

Bug#982111: [b...@debian.org: Bug#982111: r-cran-rcdk: autopkgtest failure]

Hi Andreas, Le 07/02/2021 à 12:42, Andreas Tille a écrit : Control: tags -1 help Hi Pierre, do you have some idea how to fix this? Good news: Yes, I forgot to add libcdkr-java as a runtime dependency last time I looked at this package: adding libcdkr-java to the Depends field of t

Bug#988312: libslf4j-java: misses liblog4j1.2-java as a dependency

Hi Emmanuel, On Mon, 10 May 2021 12:41:36 +0200 Emmanuel Bourg wrote: > Le 2021-05-10 11:23, Pierre Gruet a écrit : > > > Version 1.7.30-1 of libslf4j does not declare liblog4j1.2-java as a > > dependency, > > it is only declared within the "Suggests:" field

Bug#992087: libfonts-java: contains a file with a non-free "disparaging to Sun" license

Control: tags -1 pending Hello, After a deeper examination, I see the file with the non-free contents is useless anyway, none of the files it attempts to patch exists. I think this file got lost here as it obviously comes from itext, not libfonts. I offer to team-upload the package soon. Be

Bug#993406: bullseye-pu: package king/2.23.161103+dfsg1-4

ns to .png that can be used by the software. - d/rules and a patch have been updated to ensure the new icons can be included at build time. - I added copyright information about the new DFSG-free icons in d.copyright. [ Other info ] Thank you for your help on this. Best, -- Pierre Gruet di

Bug#994477: Please consider removing the "Suggests: jmol-applet" clause in control file

constraints this is not a problem and it can be postponed a bit, but as we will have to proceed to the removal one day because of the deprecation of the Java Applet class, I would appreciate to do it sooner rather than later. Thanks for your help, Best regards, -- Pierre Gruet [0] https

Bug#988144: google-auth-java: misses two version numbers in the pom of oauth2_http

oauth2_http + + -- Pierre Gruet Thu, 06 May 2021 15:49:25 +0200 + google-auth-java (0.18.0-1) unstable; urgency=high * New upstream release diff -Nru google-auth-java-0.18.0/debian/patches/adding_version_of_http_client_for_oauth2.patch google-auth-java-0.18.0/debian/patches

Bug#988279: ITP: libpf4j-java -- framework to turn monolithic Java applications into modular ones

Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: libpf4j-java Version : 3.6.0 Upstream Author : Decebal Suiu * URL : https://pf4j.org/ * License : Apache-2.0 Pro

Bug#988312: libslf4j-java: misses liblog4j1.2-java as a dependency

classes in slf4j-migrator.jar, slf4j-log4j12.jar, log4j-over-slf4j.jar. log4j:log4j is also a declared dependency with scope runtime in slf4j-log4j12/pom.xml. For this reason, other projects depending on the artifact slf4j-log4j12 fail to resolve log4j:log4j:1.2.x. Thanks for your help, Pierre Gruet

Bug#988531: ITP: libpf4j-update-java -- update mechanism for Java modular applications

Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: libpf4j-update-java Version : 2.3.0 Upstream Author : Decebal Suiu * URL : https://pf4j.org * License : Apache-2.0

Bug#988532: junit5: junit-platform-console-standalone.jar does not embed its declared Main-Class

org.junit.platform.console.ConsoleLauncher, this class is not embedded in the jar. It is thus not possible to run tests from the command line as indicated in the JUnit5 documentation, at https://junit.org/junit5/docs/5.3.0-M1/user-guide/index.html#running-tests-console-launcher for instance. Thanks for your help, Best regards, Pierre

Bug#988879: ITP: grengine -- engine for running and embedding Groovy in a Java virtual machine

Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: grengine Version : 3.0.0 Upstream Author : Alain Stalder * URL : https://www.artecat.ch/grengine * License : Apach

Bug#982617: drop-seq: autopkgtest regression

Control: tags -1 confirmed pending Hi, On Fri, 12 Feb 2021 16:43:24 +0200 Adrian Bunk wrote: > Source: drop-seq > Version: 2.4.0+dfsg-5 > Severity: serious > > https://ci.debian.net/data/autopkgtest/testing/amd64/d/drop-seq/10416045/log.gz > > ... > autopkgtest [07:18:29]: test run-unit-test

Bug#983347: lintian-brush: postrm is skipped by the fixer of maintainer-script-without-set-e

Package: lintian-brush Version: 0.97 Severity: normal Dear Maintainer, I launched lintian-brush 0.97 in the tree of my package jalview and it fixed the maintainer-script-without-set-e by modifying debian/config and debian/postinst but not debian/postrm, although the three of them were starting wi

Bug#986141: ITP: snpeff -- genetic variant annotation and effect prediction toolbox

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: snpeff Version : 4.3t Upstream Author : Pablo Cingolani * URL : https://pcingola.github.io/SnpEff/ * License : LGPL

Bug#991980: libjsap-java: does not incorporate /usr/share/java/xstream.jar in the jar manifest

Exception in thread "main" java.lang.NoClassDefFoundError: com/thoughtworks/xstream/XStream in some code using /usr/share/java/jsap.jar. As the package is team-maintained, I intend to fix this myself in a few days, right after the bullseye release. Best regards, Pierre Gruet -- System I

Bug#992044: ITP: libgoby-java -- next-generation sequencing data and results analysis tool

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: libgoby-java Version : 3.3.1 Upstream Author : Institute for Computational Biomedicine * URL : https://github.com/CampagneLa

Bug#992087: libfonts-java: contains a file with a non-free "disparaging to Sun" license

ast DFSG-6, due to the "disparaging to Sun Microsystems" clause. Best regards, -- Pierre Gruet

Bug#992088: wims: contains two files with a non-free "disparaging to Sun" license

r which is disparaging to Sun. This breaks at least DFSG-6, due to the "disparaging to Sun Microsystems" clause. Best regards, -- Pierre Gruet

Bug#992089: xemacs21-packages: contains a file with a non-free "disparaging to Sun" license

Sun. This breaks at least DFSG-6, due to the "disparaging to Sun Microsystems" clause. Best regards, -- Pierre Gruet

Bug#992090: libskinlf-java: contains a file with a non-free "disparaging to Sun" license

paraging to Sun Microsystems" clause. Best regards, -- Pierre Gruet

Bug#992092: king: contains a file with a non-free "disparaging to Sun" license

modification of the artwork. Best regards, -- Pierre Gruet

Bug#992093: cccc: contains a file with a non-free "disparaging to Sun" license

un Microsystems" clause. There is also another clause restricting the field of endeavor. Best regards, -- Pierre Gruet

Bug#992087: libfonts-java: contains a file with a non-free "disparaging to Sun" license

Hi Tony, Thanks for looking at this! Le 11/08/2021 à 20:40, tony mancill a écrit : On Wed, Aug 11, 2021 at 02:25:45PM +0200, Pierre Gruet wrote: Source: libfonts-java Version: 1.1.6.dfsg-3 Severity: serious Tags: bullseye sid stretch buster Justification: Policy 2.2.1 Dear Maintainer, The

Bug#992092: king: contains a file with a non-free "disparaging to Sun" license

Control: tag -1 confirmed Hi, For the record, this text concerns 12 icons that are in king/resource/king/images. The problematic text is also in a file in this folder. I offer to create DFSG-free icons to replace those ones. Best, -- Pierre

Bug#970217: java-propose-classpath does not run as it does not find jcf-dump

input. Thanks for your attention, Pierre Gruet -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 5.8.0-1-amd64 (SMP w/4 CPU threads) Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (cha

Bug#961158: ITP: distlib -- Java library of statistical distribution functions

Package: wnpp Severity: wishlist Owner: Debian-med project * Package name: distlib Version : 0.9.1 Upstream Author : Peter N. Steinmetz * URL : https://sourceforge.net/projects/statdistlib * License : GPL-2 Programming Lang: Java Description : Java libr

Bug#961158: ITP: distlib -- Java library of statistical distribution functions

Control: retitle -1 ITP: libdistlib-java -- Java library of statistical distribution functions Hi Scott and Andreas, Le 21/05/2020 à 06:44, Scott Kitterman a écrit : > On Thursday, May 21, 2020 12:08:44 AM EDT Andreas Tille wrote: >> At least the name of the binary package should be >> >> l

Bug#971870: ITP: sepp -- methods using ensembles of Hidden Markov Models (HMM)

Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: sepp Version : 4.3.10 Upstream Author : Siavash Mirarab * URL : https://github.com/smirarab/sepp/ * License : GP

Bug#972554: ITP: icb-utils -- Java library of utilities to manage files and compute statistics

Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: icb-utils Version : 2.0.1+git20161002.afee1d9 Upstream Author : Fabien Campagne * URL : https://github.com/CampagneLabora

Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'

Hi Andreas, I gave it a try this morning but was not able to reproduce your issue in a sid chroot, with the most recent version of python-cobra that is packaged in the Salsa repository. The test session can be successfully launched in my chroot. Yet, I see that some tests do not pass, which is may

Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'

Hi Andreas, Le 20/04/2020 à 12:08, Andreas Tille a écrit : > > Thanks a lot for checking. The issue is that we can not build the recent > upstream version as I wrote in > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656#10 > > Most probably that's *not* a problem of python-cobra

Bug#957036: (no subject)

Control: tags -1 + confirmed fixed-upstream fixed-in-experimental Hi, For the record, this bug was found in version 6.2-1 currently in unstable. Version 6.10-1, currently in experimental as it includes a library that will follow a transition procedure soon, builds with gcc-10/g++-10. As is requi

Bug#958662: transition: bibutils

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Dear Release Team, I am preparing the transition from libbibutils6 to libbibutils7, which is in experimental and builds well. This change is needed as the ABI has encountered many chang

Bug#958663: libghc-hs-bibutils-dev: FTBFS with new libbibutils7 (library transition)

soon as libbibutils7 enters unstable, you will be able to package the new upstream version and everything should be OK. Best regards, Pierre Description: Changes for the transition to libbibutils7 Author: Pierre Gruet Last-Update: 2020-04-18 --- a/src/Text/Bibutils.hsc +++ b/src/Text/Bibutil

Bug#958663: libghc-hs-bibutils-dev: FTBFS with new libbibutils7 (library transition)

Control: severity 958663 serious Hi, The transition of libbibutils6 to libbibutils7 has begun as the new library is now in unstable. The package can now be updated with the new upstream or the patch enclosed to my initial message https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=958663#

Bug#977021: bus errors on armhf running on a 64bit kernel

you already met this issue and do you see how it might be fixed? Thanks a lot, Pierre Gruet On Thu, 10 Dec 2020 07:15:24 +0100 Matthias Klose wrote: > Package: src:libsis-base-java > Version: 18.09~pre1+git20180928.45fbd31+dfsg-2 > Severity: important > Tags: sid bullseye > > bu

Bug#977021: bus errors on armhf running on a 64bit kernel

31%2Bdfsg-2&stamp=1607325724&raw=0 I hope this can help. If you think it is worth investigating further the architecture of the failing machine please tell me! All the best, Bernd Best regards, Pierre On 12/10/20 5:45 PM, Pierre Gruet wrote: Control: forwarded -1 br...@ethz.ch Dea

Bug#977021: bus errors on armhf running on a 64bit kernel

this bus error. I can see two changes to my test > setup: > > - JDK 11 instead of JDK 8 > - 64bit OS instead of 32 bit OS > > The 64bit platoform is more likely to be the change that uncovers this > bug. Which hardware did you get the error on? > > All the best, > Bernd

Bug#977021: bus errors on armhf running on a 64bit kernel

Dear Bernd, Le 14/12/2020 à 00:41, Bernd Rinn a écrit : Dear Pierre, Thanks for digging into it. Indeed the tests check whether unaligned memory access works. Unfortunately, that is used in the NativeTaggedArray for 64bit primitive types and even ranks, see e.g. line 267 in NativeTaggedArray

Bug#957310: Proposal to add extern qualifier on problematic lines

s/gui-installer/dist/installer.jar is expected but absent... All the best, Pierre Gruet --- a/source/libs/japi/drmaa2_list_dict.h +++ b/source/libs/japi/drmaa2_list_dict.h @@ -10,7 +10,7 @@ struct _drmaa2_node *next; } _drmaa2_Node; -/* static */ struct drmaa2_list_s +/* static */ extern

Bug#956838: r-cran-rcdk_3.5.0+dfsg-1_amd64.changes REJECTED

Hi Andreas, Le 27/11/2020 à 10:07, Andreas Tille a écrit : Control: block -1 by 975945 Hi Pierre, On Sat, Nov 21, 2020 at 10:00:08PM +, Joerg Jaspert wrote: The statement from upstream in their txt file beside is --- Sources for the utility JAR file included with this package can be foun

Bug#956838: r-cran-rcdk_3.5.0+dfsg-1_amd64.changes REJECTED

Hi again, Le 27/11/2020 à 10:07, Andreas Tille a écrit : Control: block -1 by 975945 Hi Pierre, On Sat, Nov 21, 2020 at 10:00:08PM +, Joerg Jaspert wrote: The statement from upstream in their txt file beside is --- Sources for the utility JAR file included with this package can be found

Bug#976679: commons-io: Fails to delete a symlink pointing to a non-existing file

Source: commons-io Version: 2.8.0 Severity: normal Tags: patch Hi, Since version 2.8.0, commons-io fails at deleting a symlink when it points to nothing. Such situation was met in some tests of libsis-base-java (temporarily deactivated in order to face this issue), leading to bug #976490. This

Bug#976681: bad-jar-name: false positive for version numbers with a tilde

have overridden the warning); - libjsr305-java version 0.1~+svn49, of which jar is named jsr305-0.1~+svn49.jar . Thanks for considering and for all the work done on Lintian, Pierre Gruet [0] https://www.debian.org/doc/packaging-manuals/java-policy/ch02.html

Bug#974437: Providing a non-superficial test

Control: tags -1 pending Hi, I have marked the test as superficial and provided another one, which runs some of the build-time tests. Upload to come soon. Best, Pierre

Bug#974680: artemis: Wrong homepage

Control: tags -1 pending Hi, On Fri, 13 Nov 2020 17:55:43 +0100 Davide Prina wrote: > Package: artemis > Version: 18.1.0+dfsg-1 > Severity: normal > > I have see that the homepage > https://www.sanger.ac.uk/science/tool/artemis > do not respond anymore > Thanks for pointing this out! I see this

Bug#974879: ITP: intervalstorej -- Java implementation of the Nested Containment List data structure

Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: intervalstorej Version : 1.2 Upstream Author : Mungo Carstairs, Barton Group * URL : https://github.com/bartongroup/Interv

Bug#970217: java-propose-classpath does not run as it does not find jcf-dump

Control: severity -1 important Hi, I am raising the sevrity to important as I tested java-propose-classpath on several other jars and naver had it work. Feel free to contact me if I can provide further information. Bye, Pierre

Bug#973568: ITP: libpj-java -- API and middleware for parallel programming in Java

Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: libpj-java Version : 20150107 Upstream Author : Alan Kaminsky * URL : https://www.cs.rit.edu/~ark/pj.shtml * License

Bug#963630: RFS-ing libaparapi-java due to licensing issues at the moment

considering packaging aparapi itself, but it would impose restrictions on other software that might be bundled with it. We will discuss it with upstream and consider packaging later. Pierre Gruet

Bug#963630: RFP-ing libaparapi-java due to licensing issues at the moment

not seem to be harming when considering packaging aparapi itself, but it would impose restrictions on other software that might be bundled with it. We will discuss it with upstream and consider packaging later. Pierre Gruet

Bug#953481: dmaths: Sources are no more available from upstream

Source: dmaths Severity: serious Justification: Policy 2.3 Hello, While visiting the upstream website [1], I saw a financial contribution has to be paid in order to be able to download dmaths. This violates 2.3 in the Debian policy. No link for downloading the source can be found on the website

Bug#954346: libcgal-dev: does not depend on the runtime library

Package: libcgal-dev Version: 5.0.2-3 Severity: normal Dear Maintainer, According to 8.5 in Debian Policy, this development package should depend on the runtime package, as was the case e.g. in version 4.13-1. Else, packages depending on libcgal-dev cannot build. This is the case for rheolef, f

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-...@lists.debian.org * Package name: rockhopper Version : 2.0.3 Upstream Author : Brian Tjaden * URL : https://cs.wellesley.edu/~btjaden/Rockhopper * License

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#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-...@lists.debian.org * Package name: megan-ce Version : 6.21.1 Upstream Author : Daniel Huson * URL : https://github.com/danielhuson/megan-ce * License

Bug#994715: RM: jmol-applet -- ROM; now unmaintained upstream

now be removed from this field in unstable, and this will also be the case in testing in a few days. Thanks for your help on this, Best wishes, - -- Pierre Gruet [0] https://alioth-lists.debian.net/pipermail/debichem-devel/2021-September/012755.html [1] https://alioth-lists.debian.net/pipermail

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-...@lists.debian.org * Package name: tipp Version : 1.0 Upstream Author : Siavash Mirarab * URL : https://github.com/TeraTrees/TIPP * License : GPL-3 P

Bug#1000261: RM: sepp/experimental -- ROM; architectures wrongly set to "all" instead of "any"

Package: ftp.debian.org Severity: normal Hello, When working on sepp in experimental, I wrongly set the architecture of version 4.5.1+really4.5.1+dfsg-1~exp1 to "all", it should have been "any". Since then, version 4.5.1+really4.5.1+dfsg-2 has been uploaded to unstable with the right architectur

Bug#872418: Reproducible, forwarded

Control: forwarded -1 https://sourceforge.net/p/jmol/bugs/621/ Hello, I have just been able to reproduce the bug with version 14.30.2+dfsg-2 on an xfce desktop. Besides, I have forwarded the issue to the upstream bug tracker. -- Pierre

Bug#1001099: ITP: stopt -- library for stochastic optimization problems

Package: wnpp Severity: wishlist Owner: Pierre Gruet X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: stopt Version : 4.2 Upstream Author : Xavier Warin * URL : https://gitlab.com/stochastic-control/StOpt/ * License : LGPL-3 Programming Lang: C

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-...@lists.debian.org * Package name: malt Version : 0.5.2 Upstream Author : Daniel Huson * URL : https://github.com/danielhuson/malt * License : GPL-3+

Bug#1001922: supertuxkart: It doesn't load at init

Package: supertuxkart Version: 1.3+dfsg1-2 Followup-For: Bug #1001922 Hi, I also have this problem, seemingly randomly. Sometimes it starts well, sometimes it just fails. The log says nothing more: -8<--- ... [info ] [Fi

Bug#1004554: ITP: libpdfbox-graphics2d-java -- Java library to embed graphics as vector drawing in a PDF

Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-de...@lists.debian.org, pkg-java-maintain...@lists.alioth.debian.org * Package name: libpdfbox-graphics2d-java Version : 0.34 Upstream Author : Emmeran Seehuber * URL : https://github.com/ro

Bug#998244: lists.debian.org: request for debian-math mailing list

Hello, I would like to subscribe to the debian-math ML when it exists, as I am packaging maths-related software and I would like to be able to discuss about the common goals of the Debian Math team. Best regards, -- Pierre Gruet OpenPGP_signature Description: OpenPGP digital signature

Bug#999424: ITP: geners -- generic serialization library for C++

Package: wnpp Severity: wishlist Owner: Pierre Gruet X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: geners Version : 1.12.0 Upstream Author : Igor Volobouev * URL : https://geners.hepforge.org/ * License : Expat Programming Lang: C

Bug#999424: ITP: geners -- generic serialization library for C++

Hello Thaddeus, Le 10/11/2021 à 22:13, Thaddeus H. Black a écrit : On Wed, Nov 10, 2021 at 09:34:36PM +0100, Pierre Gruet wrote: Package: wnpp Severity: wishlist Owner: Pierre Gruet X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: geners Version : 1.12.0 Upstream

Bug#996727: ITP: ciftools-java -- Java library to read and write CIF files

Package: wnpp Severity: wishlist Owner: Debian java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: ciftools-java Version : 3.0.0 Upstream Author : Sebastian Bittrich * URL : https://github.com/rcsb/ciftools-java * License

Bug#996865: ITP: jheaps -- Java library with various heap implementations

Package: wnpp Severity: wishlist Owner: Debian-java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: jheaps Version : 0.14 Upstream Author : Dimitrios Michail * URL : https://github.com/d-michail/jheaps * License :

Bug#996991: ITP: jgrapht -- Java library of graph theory data structures and algorithms

Package: wnpp Severity: wishlist Owner: Pierre Gruet User: debian-scie...@lists.debian.org Usertags: field..science X-Debbugs-Cc: debian-de...@lists.debian.org, debian-scie...@lists.debian.org * Package name: jgrapht Version : 1.5.1 Upstream Author : Abdallah Atouani and

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-...@lists.debian.org * Package name: biojava5-live Version : 5.4.0 Upstream Author : BioJava Developers * URL : https://www.biojava.org/ * License : LGP

Bug#1001681: sight: FTBFS in unstable

Hello, On Tue, 14 Dec 2021 17:51:06 +0100 Flavien Bridault wrote: > Understood, I just wanted to avoid any overlap. I'll have a look asap. :) > > > *Dr. Flavien BRIDAULT* > Director of Software Development > IRCAD France & IRCAD Africa > > flavien.brida...@ircad.fr

Bug#1002155: 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 me

Bug#1002155: 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

Hi Andreas, On 22/12/2021 19:45, Andreas Tille wrote: Hi, Am Wed, Dec 22, 2021 at 06:17:21PM +0100 schrieb Pierre Gruet: The warning mentioned in the bug title is issued by the Javadoc builder, which we do not use. It does not trigger the failure of the build. The real issue is in the tests

Bug#976505: gkl: FTBFS on arm64: deflate.c:995:36: error: ‘x86_cpu_has_sse42’ undeclared (first use in this function)

Control: tags -1 wontfix Well, I guess it is fair to tag the bug with wontfix. The architecture of libgkl-jni is correctly indicated in the debian/control file, I think it is enough. Also, with current version (0.8.9+dfsg), the original error message that triggered this bug report is not sho

Bug#930333: ITP: xerial-sqlite-jdbc -- Xerial's SQLite JDBC Driver

Control: forwarded -1 https://github.com/xerial/sqlite-jdbc/issues/705 Hello, I filed an issue in the upstream repository [0]. I am also interested in having sqlite-jdbc packaged, would be ready to help about it, but of course we cannot do anything at the moment. Best, -- Pierre [0] https

Bug#987771: ITP: capsule-nextflow -- packaging and deployment tool for Java applications

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: capsule-nextflow Version : 1.1.0 Upstream Author : Paolo di Tommaso * URL : https://github.com/nextflow-io/capsule * Licens

Bug#987946: ITP: capsule-maven-nextflow -- packaging tool for Java applications with Maven coordinates

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: capsule-maven-nextflow Version : 1.0.3.1 Upstream Author : Paolo di Tommaso * URL : https://github.com/nextflow-io/capsule-

Bug#998200: transition: bibutils

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Dear Release Team, I am preparing the transition from libbibutils7 to libbibutils8, which is in experimental and builds well. This change is needed as the ABI has encountered many chang

Bug#1010553: transition: dlib

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Dear Release team, I would like to request a transition slot for dlib, which has been accepted in experimental and builds well inside. I changed the name of the binary lib package after

Bug#1010553: Providing information on the result of the transition

Hi, Although the tracker page [0] indicates ``?!'' for all architectures of all involved packages except plastimatch, I inform you that everything went well: all builds succeeded. This is not true for plastimatch, but no big issue as a RM request (for unstable) has recently been filed for this

Bug#1011068: ITP: spectra -- library for large scale eigenvalue problems

Package: wnpp Severity: wishlist Owner: Pierre Gruet X-Debbugs-Cc: debian-de...@lists.debian.org, team+m...@tracker.debian.org * Package name: spectra Version : 1.0.1 Upstream Author : Yixuan Qiu * URL : https://spectralib.org/ * License : MPL-2.0

Bug#1011468: FTBFS with OpenJDK 17 due to com.sun.javadoc removal

Source: barclay Version: 2.1.0-3.1 Severity: important Tags: ftbfs bookworm sid User: debian-j...@lists.debian.org Usertags: default-java17 barclay fails to build with Java 17 because it uses classes from the com.sun.javadoc package which was removed: /<>/src/main/java/org/broadinstitute/barclay/

Bug#1004971: pythonpy: diff for NMU version 0.4.11b-3.1

Control: tags 1004971 + patch Control: tags 1004971 + pending Control: tags 1009115 + patch Control: tags 1009115 + pending Dear maintainer, I've prepared an NMU for pythonpy (versioned as 0.4.11b-3.1) and uploaded it to DELAYED/3. Please feel free to tell me if I should cancel it. Best, --

Bug#1004971: pythonpy: diff for NMU version 0.4.11b-3.1

@@ +pythonpy (0.4.11b-3.1) unstable; urgency=medium + + * Non-maintainer upload. + * Importing Collections abstract classes from collections.abc +(Closes: #1004971, #1011468) + + -- Pierre Gruet Tue, 24 May 2022 20:37:28 +0200 + pythonpy (0.4.11b-3) unstable; urgency=medium * Avoid

Bug#1011557: ITP: pagmo -- library for massively parallel optimisation

Package: wnpp Severity: wishlist Owner: Pierre Gruet User: debian-scie...@lists.debian.org Usertags: field..science X-Debbugs-Cc: debian-de...@lists.debian.org, debian-scie...@lists.debian.org * Package name: pagmo Version : 2.18.0 Upstream Author : Francesco Biscani * URL

Bug#1009294: Upcoming biojava-live transition

Source: artemis Version: 18.1.0+dfsg-6 Severity: important Tags: fixed-in-experimental Hi, This is to inform you that the auto-biojava-live transition will start soon, as biojava-live 1:1.9.5+dfsg will enter unstable. Currently your package would ftbfs with this new biojava-live, yet I worke

Bug#1009296: Upcoming biojava-live transition

Source: alien-hunter Version: 1.7-8 Severity: important Tags: fixed-in-experimental Hi, This is to inform you that the auto-biojava-live transition will start soon, as biojava-live 1:1.9.5+dfsg will enter unstable. Currently your package would ftbfs with this new biojava-live, yet I worked on i

Bug#1009295: Upcoming biojava-live transition

Source: logol Version: 1.7.9+dfsg-3 Severity: important Tags: fixed-in-experimental Hi, This is to inform you that the auto-biojava-live transition will start soon, as biojava-live 1:1.9.5+dfsg will enter unstable. Currently your package would ftbfs with this new biojava-live, yet I worked on i

Bug#1009297: Upcoming biojava-live transition

Source: mauve-aligner Version: 2.4.0+4736-4 Severity: important Tags: fixed-in-experimental Hi, This is to inform you that the auto-biojava-live transition will start soon, as biojava-live 1:1.9.5+dfsg will enter unstable. Currently your package would ftbfs with this new biojava-live, yet I wor

Bug#1009298: transition: biojava-live

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Dear Release team, I would like to request a transition slot for biojava-live. This would be a small transition with 4 reverse-dependencies. The reason is upstream changed the interface

Bug#1009361: Unchecked use of __BIG_ENDIAN__ leads to an error

Package: libtbb-dev Version: 2022.3-1 Severity: normal Dear Maintainer, libtbb-dev installs the file /usr/include/tbb/machine/gcc_generic.h, of which line 39 reads: #if __BIG_ENDIAN__ || (defined(__BYTE_ORDER__) && __BYTE_ORDER__==__ORDER_BIG_ENDIAN__) I think it should instead start with somet

Bug#1009835: transition: hmat-oss

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Dear Release team, I would like to request a transition slot for hmat-oss. This would be a tiny transition with only 1 reverse dependency. The reason is upstream changed the interface qu

Bug#1017527: acceptance-* tests should be marked as 'flaky'

Source: patroni Version: 2.1.4-1 Severity: normal Control: affects -1 src:zookeeper src:psycopg2 Dear Maintainer, The three autopkgtests acceptance-consul, acceptance-etcd and acceptance-zookeeper began failing at a significant frequency recently, at least on armhf, independently of each other. T

Bug#1017563: RM: theseus [arm64 armel armhf mips64el mipsel ppc64el s390x alpha hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 m68k powerpc ppc64 riscv64 sh4 sparc64 x32] -- ROM; has a dependency av

Package: ftp.debian.org Severity: normal X-Debbugs-Cc: debian-med-packag...@lists.alioth.debian.org -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, theseus depends on muscle, which is only available on Intel architectures at the moment, see bug #1006161 which led to the removal of muscle on

Bug#1013178: transition: ceres-solver

Hi Emilio, On Tue, 21 Jun 2022 09:49:32 +0200 Emilio Pozuelo Monfort wrote: > [...] > > > All reverse dependencies are building fine at least on amd64 [2]. > > That link doesn't tell me if the rdeps build against the new SONAME. Have you > tested that? If so, go ahead. Thanks for looking at

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