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 Thanks for your quick answers, let's go then! Bye, -- Pierre
Re: Upgrading biojava-live from 1.7 to 1.9
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
Re: Upgrading biojava-live from 1.7 to 1.9
Am Mon, Mar 28, 2022 at 04:42:15PM +0200 schrieb olivier sallou: > ... > that's fine for me Thanks a lot for this effort Andreas. -- http://fam-tille.de
Re: Upgrading biojava-live from 1.7 to 1.9
Le lun. 28 mars 2022 à 16:24, Pierre Gruet a écrit : > > Hello everyone, > > Recently I worked on biojava-live (locally, pushed nothing to Salsa), > which currently has version 1.7.1. Upstream is active and published > version 1.9.5 of this "legacy" biojava, which is still used by many > software: four reverse dependencies in Debian (alien-hunter, artemis, > logol, mauve-aligner), which cannot depend on modern biojava5-live > because classes have changed so much in between. > , biojava3, 4 etc... broke many things and required to create biojava3, biojava4 deb packages but we could expect that version 1 does not break things between versions > > I would like to upgrade to version 1.9.5, which would mean: > - keeping the same source package but pushing new binary package > libbiojava1.9-java to NEW, conflicting with and replacing > libbiojava1.7-java; > - making a source upload of the four reverse dependencies afterwards. > > About this last point: I am able to build the four reverse dependencies > against this biojava 1.9.5, few changes are necessary: mainly the names > of the jars, which have changed between 1.7.1 and 1.9.5. Enclosed are > the source debdiffs of the needed changes for the four reverse > dependencies. > > > Is it OK for you if I upgrade to 1.9.5 and then I take care of the > reverse dependencies? > that's fine for me Olivier > > I am explicitly CC-ing the current uploaders of biojava-live, and I plan > to add myself to this list of uploaders. > > Best regards, > > -- > Pierre > > > -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Upgrading biojava-live from 1.7 to 1.9
Hello everyone, Recently I worked on biojava-live (locally, pushed nothing to Salsa), which currently has version 1.7.1. Upstream is active and published version 1.9.5 of this "legacy" biojava, which is still used by many software: four reverse dependencies in Debian (alien-hunter, artemis, logol, mauve-aligner), which cannot depend on modern biojava5-live because classes have changed so much in between. I would like to upgrade to version 1.9.5, which would mean: - keeping the same source package but pushing new binary package libbiojava1.9-java to NEW, conflicting with and replacing libbiojava1.7-java; - making a source upload of the four reverse dependencies afterwards. About this last point: I am able to build the four reverse dependencies against this biojava 1.9.5, few changes are necessary: mainly the names of the jars, which have changed between 1.7.1 and 1.9.5. Enclosed are the source debdiffs of the needed changes for the four reverse dependencies. Is it OK for you if I upgrade to 1.9.5 and then I take care of the reverse dependencies? I am explicitly CC-ing the current uploaders of biojava-live, and I plan to add myself to this list of uploaders. Best regards, -- Pierre diff -Nru artemis-18.1.0+dfsg/debian/artemis.manifest artemis-18.1.0+dfsg/debian/artemis.manifest --- artemis-18.1.0+dfsg/debian/artemis.manifest 2021-11-06 14:44:49.0 +0100 +++ artemis-18.1.0+dfsg/debian/artemis.manifest 2022-02-28 18:24:58.0 +0100 @@ -1,15 +1,15 @@ usr/share/java/artemis.jar: - Class-Path: /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar + Class-Path: /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava-core.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar Main-Class: uk.ac.sanger.artemis.components.ArtemisMain usr/share/java/act.jar: - Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar + Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava-core.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar Main-Class: uk.ac.sanger.artemis.components.ActMain usr/share/java/bamview.jar: - Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar + Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava-core.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar Main-Class: uk.ac.sanger.artemis.components.alignment.BamView
Processed: retitle 1008304 to ITP: libhttp-nio-java -- http/s file system provider for Java NIO.2
Processing commands for cont...@bugs.debian.org: > retitle 1008304 ITP: libhttp-nio-java -- http/s file system provider for Java > NIO.2 Bug #1008304 [wnpp] ITP: http-nio -- http/s file system provider for Java NIO.2 Changed Bug title to 'ITP: libhttp-nio-java -- http/s file system provider for Java NIO.2' from 'ITP: http-nio -- http/s file system provider for Java NIO.2'. > thanks Stopping processing here. Please contact me if you need assistance. -- 1008304: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1008304 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
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 : 0.1.0 Upstream Author : Daniel Gomez-Sanchez * URL : https://github.com/lbergelson/http-nio * License : BSD-3-Clause Programming Lang: Java Description : http/s file system provider for Java NIO.2 This package provides a http or https file system that can be used in conjunction with Java NIO.2. This lightweight library provides a few classes related to file systems and paths. It is provided by the developers of gatk, which is a long-term packaging target of Debian-med team. I am packaging it as a reverse dependency of gatk. For this reason, it will be team-maintained inside Debian-med team. The http-nio name seems rather generic to be used as either source or binary package name. Could you namespace it? I don't see a very clear naming convention in the archive for Java packages, but then I have not checked the java-policy, TBH. What I see is either -jave or lib-java, either would work here. Thanks for your advice on this; the lib-java pattern seems wholly appropriate here, as it matches the name of the binary package that will be built by this source package. I will make the change as you suggest. Thanks, Guillem Best regards, -- Pierre OpenPGP_signature Description: OpenPGP digital signature
Bug#1008304: ITP: http-nio -- http/s file system provider for Java NIO.2
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 : 0.1.0 > Upstream Author : Daniel Gomez-Sanchez > * URL : https://github.com/lbergelson/http-nio > * License : BSD-3-Clause > Programming Lang: Java > Description : http/s file system provider for Java NIO.2 > > This package provides a http or https file system that can be used in > conjunction with Java NIO.2. This lightweight library provides a few classes > related to file systems and paths. > > It is provided by the developers of gatk, which is a long-term packaging > target > of Debian-med team. I am packaging it as a reverse dependency of gatk. > For this reason, it will be team-maintained inside Debian-med team. The http-nio name seems rather generic to be used as either source or binary package name. Could you namespace it? I don't see a very clear naming convention in the archive for Java packages, but then I have not checked the java-policy, TBH. What I see is either -jave or lib-java, either would work here. Thanks, Guillem
