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

2020-03-09 Thread Pierre Gruet
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

Bug#956232: sumaclust: Last sequence of input is skipped on arm64

2020-04-08 Thread Pierre Gruet
, which seems to solve the problem. I am waiting for its opinion on it. Best, Pierre From: Pierre Gruet Date: Wed, 8 Apr 2020 11:18:01 +0200 Subject: Reading only-ACGT sequences safely --- sumalibs/libfasta/sequence.c | 10 -- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git

Bug#956232: sumaclust: Last sequence of input is skipped on arm64

2020-04-08 Thread Pierre Gruet
Hi Andreas, Le 08/04/2020 à 21:35, Andreas Tille a écrit : > > Thanks again for your contribution. Would you mind commiting your patch > right to salsa to enable me sponsoring your second package version? > Done, I have committed version 1.0.35-3. Now autopkgtests pass on amd64 and arm64! >

Bug#953898: (no subject)

2020-04-17 Thread Pierre Gruet
tags 953898 pending thanks Hi, I have investigated: at some point, the result of an operation on integers is stored in a char variable. This result happens to be negative, which is a problem on arm64 where char type is unsigned by default. I will prepare an upload fixing the bug. Bye, Pierre

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

2020-04-20 Thread Pierre Gruet
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#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'

2020-04-20 Thread Pierre Gruet
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

Bug#958662: transition: bibutils

2020-04-24 Thread Pierre Gruet
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

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

2020-04-24 Thread Pierre Gruet
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/Bibutils.hsc

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

2020-04-26 Thread Pierre Gruet
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

Bug#957036: (no subject)

2020-04-22 Thread Pierre Gruet
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

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

2020-03-20 Thread Pierre Gruet
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,

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

2020-05-20 Thread Pierre Gruet
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

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

2020-05-20 Thread Pierre Gruet
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 >> >>

Bug#968308: src:cgview: fails to migrate to testing for too long: autopkgtest failure

2020-09-09 Thread Pierre Gruet
Hi Andreas, Le 09/09/2020 à 13:48, Andreas Tille a écrit : > Control: tags -1 help > > Hi, > > I wonder why this > > ... > autopkgtest [16:10:05]: test run-unit-test: [--- > [warning] /usr/bin/cgview: No java runtime was found > autopkgtest [16:10:06]: test run-unit-test:

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

2020-09-12 Thread Pierre Gruet
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 (charmap=UTF-8

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

2020-10-08 Thread Pierre Gruet
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 :

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

2020-10-20 Thread Pierre Gruet
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 :

Bug#969176: ITP: libdsiutils-java -- Java library of statistical and text data handling tools

2020-08-28 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: libdsiutils-java Version : 2.6.6 Upstream Author : Sebastiano Vigna * URL : http://dsiutils.di.unimi.it * License

Bug#969186: ITP: libreflections-java -- Java runtime metadata analysis library

2020-08-28 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: libreflections-java Version : 0.9.12 Upstream Author : ronmamo * URL : https://github.com/ronmamo/reflections * License

Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]

2020-08-21 Thread Pierre Gruet
Hi Andreas, Le 21/08/2020 à 11:05, Andreas Tille a écrit : > Hi again, > > I injected the latest upstream version into Git. It does not include so > many binary jar's any more but I think its trying to download these > instead. I gave up for the moment since I have no idea about gradle. >

Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]

2020-08-21 Thread Pierre Gruet
Hi Andreas, Le 21/08/2020 à 07:38, Andreas Tille a écrit : > Hi Pierre, > > do you have some spare cycles for this issue? > > BTW, I do not think that we should stick to that now outdated > version but while fixing the issue package latest upstream. > > On a more general note: Igv is another

Bug#845113: scala 2.12 released. Please upload version 2.12 ASAP into debian sid, so that it integrates into debian stable 9 stretch

2020-08-26 Thread Pierre Gruet
Dear Maintainers, For our information, do you know if it might be possible to unblock the situation soon? Is there some ongoing work on sbt? In Debian-med, we would be interested in having Scala 2.12 or 2.13 to package the pre-dependency akka. Thanks a lot in any case, Best regards, Pierre

Bug#968739: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]

2020-08-24 Thread Pierre Gruet
Hi, Le 21/08/2020 à 12:44, Andreas Tille a écrit : > Hi Pierre, > > On Fri, Aug 21, 2020 at 11:32:47AM +0200, Pierre Gruet wrote: >>> I injected the latest upstream version into Git. It does not include so >>> many binary jar's any more but I think its trying to dow

Bug#963396: jimfs: FTBFS: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project jimfs: Compilation failure

2020-08-07 Thread Pierre Gruet
for the attempt to help anyway > >Andreas. > All the best, Pierre Description: Providing Override of test method Author: Pierre Gruet Last-Update: 2020-08-07 --- a/jimfs/src/main/java/com/google/common/jimfs/PathService.java +++ b/jimfs/src/main/java/com/google/common

Bug#963630: ITP: libaparapi-java -- framework for executing native Java code on the GPU

2020-06-24 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian-med project * Package name: libaparapi-java Version : 2.0.0 Upstream Author : Gary Frost, Syncleus, Inc. * URL : http://aparapi.com/ * License : Apache-2.0 Programming Lang: Java Description : framework

Bug#963430: Any volunteer to spent some time on the new version of artemis (Was: Bug#963430: artemis: FTBFS: /bin/sh: 1: /usr/share/java/j2ssh-core.jar: Permission denied)

2020-06-22 Thread Pierre Gruet
Hi Emmanuel, Le 22/06/2020 à 16:30, Andreas Tille a écrit : > Hi Emmanuel, > > On Mon, Jun 22, 2020 at 10:57:15AM -0300, Emmanuel Arias wrote: >> I would be happy to help on artemis. Obviously I will need >> a more experienced developer helping me. :) > > I'll try hard to answer any question

Bug#966192: ITP: libcharts4j-java -- free, lightweight charts and graphs Java API

2020-07-24 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: libcharts4j-java Version : 1.3 Upstream Author : Julien Chastang * URL : https://github.com/julienchastang/charts4j *

Bug#966299: ITP: libapfloat-java -- high performance arbitrary precision arithmetic library for Java

2020-07-26 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian Java team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-j...@lists.debian.org * Package name: libapfloat-java Version : 1.9.1 Upstream Author : Mikko Tommila * URL : http://www.apfloat.org/apfloat_java * License

Bug#925745: libgtextutils is marked for autoremoval from testing

2020-07-28 Thread Pierre Gruet
Hello, C++11 introduced references on rvalues, which basically allows to use a non-constant reference on a temporary object (ie waiting for affectation). Before, temporary objects could only be references by a const reference. Thus, from there, it becomes a problem to have two implicit

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

2020-11-27 Thread Pierre Gruet
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

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

2020-11-26 Thread Pierre Gruet
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

2020-11-27 Thread Pierre Gruet
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

2020-12-06 Thread Pierre Gruet
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.

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

2020-12-06 Thread Pierre Gruet
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#977021: bus errors on armhf running on a 64bit kernel

2020-12-10 Thread Pierre Gruet
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

2020-12-10 Thread Pierre Gruet
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 Dear Bernd, In Debian we have received a bug report you

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

2020-12-13 Thread Pierre Gruet
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

2020-12-15 Thread Pierre Gruet
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

Bug#974437: Providing a non-superficial test

2020-11-12 Thread Pierre Gruet
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

2020-11-13 Thread Pierre Gruet
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

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

2020-11-15 Thread Pierre Gruet
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 :

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

2020-11-02 Thread Pierre Gruet
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

2020-11-02 Thread Pierre Gruet
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#973568: ITP: libpj-java -- API and middleware for parallel programming in Java

2020-11-01 Thread Pierre Gruet
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#970217: java-propose-classpath does not run as it does not find jcf-dump

2020-10-29 Thread Pierre Gruet
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#988279: ITP: libpf4j-java -- framework to turn monolithic Java applications into modular ones

2021-05-09 Thread Pierre Gruet
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

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

2021-05-10 Thread Pierre Gruet
ny 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#988144: google-auth-java: misses two version numbers in the pom of oauth2_http

2021-05-06 Thread Pierre Gruet
of 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#988531: ITP: libpf4j-update-java -- update mechanism for Java modular applications

2021-05-14 Thread Pierre Gruet
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 :

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

2021-05-14 Thread Pierre Gruet
is 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

2021-05-20 Thread Pierre Gruet
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 :

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

2021-05-02 Thread Pierre Gruet
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 :

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

2021-04-29 Thread Pierre Gruet
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 *

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

2021-03-30 Thread Pierre Gruet
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 :

Bug#982617: drop-seq: autopkgtest regression

2021-02-12 Thread Pierre Gruet
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

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

2021-02-07 Thread Pierre Gruet
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

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

2021-02-22 Thread Pierre Gruet
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

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

2021-08-27 Thread Pierre Gruet
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:" fi

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

2021-08-31 Thread Pierre Gruet
icons 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#992092: king: contains a file with a non-free "disparaging to Sun" license

2021-08-24 Thread Pierre Gruet
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#994477: Please consider removing the "Suggests: jmol-applet" clause in control file

2021-09-16 Thread Pierre Gruet
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#994715: RM: jmol-applet -- ROM; now unmaintained upstream

2021-09-19 Thread Pierre Gruet
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#992044: ITP: libgoby-java -- next-generation sequencing data and results analysis tool

2021-08-09 Thread Pierre Gruet
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 :

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

2021-08-07 Thread Pierre Gruet
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#992087: libfonts-java: contains a file with a non-free "disparaging to Sun" license

2021-08-11 Thread Pierre Gruet
ast 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

2021-08-11 Thread Pierre Gruet
paraging to Sun Microsystems" clause. Best regards, -- Pierre Gruet

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

2021-08-11 Thread Pierre Gruet
un Microsystems" clause. There is also another clause restricting the field of endeavor. Best regards, -- Pierre Gruet

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

2021-08-11 Thread Pierre Gruet
ing to Sun. This breaks at least DFSG-6, due to the "disparaging to Sun Microsystems" clause. Best regards, -- Pierre Gruet

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

2021-08-11 Thread Pierre Gruet
forbids modification of the artwork. Best regards, -- Pierre Gruet

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

2021-08-11 Thread Pierre Gruet
nner which is disparaging to Sun. This breaks at least DFSG-6, due to the "disparaging to Sun Microsystems" clause. Best regards, -- Pierre Gruet

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

2021-08-11 Thread Pierre Gruet
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

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

2021-10-19 Thread Pierre Gruet
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#996727: ITP: ciftools-java -- Java library to read and write CIF files

2021-10-17 Thread Pierre Gruet
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 *

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

2021-09-29 Thread Pierre Gruet
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

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

2021-08-28 Thread Pierre Gruet
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.

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

2021-10-21 Thread Pierre Gruet
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

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

2021-10-21 Thread Pierre Gruet
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 :

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

2021-12-04 Thread Pierre Gruet
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#976505: gkl: FTBFS on arm64: deflate.c:995:36: error: ‘x86_cpu_has_sse42’ undeclared (first use in this function)

2021-12-24 Thread Pierre Gruet
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

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

2021-12-22 Thread Pierre Gruet
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

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

2021-12-26 Thread Pierre Gruet
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]

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

2021-12-22 Thread Pierre Gruet
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#999424: ITP: geners -- generic serialization library for C++

2021-11-12 Thread Pierre Gruet
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#999424: ITP: geners -- generic serialization library for C++

2021-11-10 Thread Pierre Gruet
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#872418: Reproducible, forwarded

2021-11-27 Thread Pierre Gruet
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#1000261: RM: sepp/experimental -- ROM; architectures wrongly set to "all" instead of "any"

2021-11-20 Thread Pierre Gruet
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

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

2021-11-03 Thread Pierre Gruet
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#998200: transition: bibutils

2021-10-31 Thread Pierre Gruet
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

Bug#1001681: sight: FTBFS in unstable

2021-12-14 Thread Pierre Gruet
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#1003782: ITP: megan-ce -- interactive tool to explore and analyse microbiome sequencing data

2022-01-15 Thread Pierre Gruet
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#1005356: ITP: rockhopper -- system for analyzing bacterial RNA-seq data

2022-02-11 Thread Pierre Gruet
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#1006834: ITP: aeonbits-owner -- API to handle application configuration through Java properties file

2022-03-06 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@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

2022-02-26 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: snpsift Version : 5.1 Upstream Author : Pablo Cingolani * URL : https://pcingola.github.io/SnpEff/ss_introduction/ *

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

2022-02-11 Thread Pierre Gruet
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#1008128: ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code

2022-03-22 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: gatk-fermilite Version : 1.2.1 Upstream Author : Broad Institute * URL :

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

2022-03-26 Thread Pierre Gruet
Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@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#986474: NMU to DELAYED/5

2022-03-27 Thread Pierre Gruet
on libservlet3.1-java, which was +previously provided by libnetty9-java (Closes: #997213) + * Adding an explicit dependency of i2p-router on libecj-java +(Closes: #986474) + + -- Pierre Gruet Sun, 27 Mar 2022 22:11:17 +0200 + i2p (0.9.48-1) unstable; urgency=medium * New upstream release. diff

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

2022-03-28 Thread Pierre Gruet
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-...@lists.debian.org * Package name: http-nio Version

Bug#1008572: ITP: xgboost-predictor-java -- Java implementation of XGBoost predictor for online prediction tasks

2022-03-28 Thread Pierre Gruet
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: xgboost-predictor-java Version : 0.3.1 Upstream Author : KOMIYA Atsushi

Bug#1007923: maven-*-helper JAR placement seems to contradict Java policy

2022-03-29 Thread Pierre Gruet
Hello everyone, Le 29/03/2022 à 11:59, Markus Koschany a écrit : Am Montag, dem 28.03.2022 um 21:06 -0700 schrieb tony mancill: [...] I am interested to hear other opinions from the Debian Java Team. I have no objections with implementing this change and I agree that a versionless symlink is

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