Your message dated Mon, 30 Dec 2024 11:06:48 +0000
with message-id <[email protected]>
and subject line Bug#1091589: fixed in htsjdk 4.1.3+dfsg-2
has caused the Debian Bug report #1091589,
regarding Wrongly requires mjson in its POM file
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1091589: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1091589
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: artemis
Version: 18.2.0+dfsg-4
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-20241228 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_build
> /usr/lib/jvm/default-java/bin/java -noverify -cp
> /usr/share/maven/boot/plexus-classworlds-2.x.jar
> -Dmaven.home=/usr/share/maven
> -Dmaven.multiModuleProjectDirectory=/<<BUILDDIR>>/artemis-18.2.0\+dfsg
> -Dclassworlds.conf=/etc/maven/m2-debian.conf
> org.codehaus.plexus.classworlds.launcher.Launcher
> -s/etc/maven/settings-debian.xml
> -Ddebian.dir=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian
> -Dmaven.repo.local=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian/maven-repo
> --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US
> OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were
> deprecated in JDK 13 and will likely be removed in a future release.
> [INFO] Scanning for projects...
> [WARNING]
> [WARNING] Some problems were encountered while building the effective model
> for uk.ac.sanger:artemis:jar:18.2.0
> [WARNING] 'dependencies.dependency.systemPath' for org.emboss:jemboss:jar
> should use a variable instead of a hard-coded path
> /usr/share/EMBOSS/jemboss/lib/jemboss.jar @ line 200, column 16
> [WARNING] 'dependencies.dependency.systemPath' for
> com.github.broadinstitute:picard:jar should use a variable instead of a
> hard-coded path /usr/share/java/picard.jar @ line 253, column 16
> [WARNING]
> [WARNING] It is highly recommended to fix these problems because they
> threaten the stability of your build.
> [WARNING]
> [WARNING] For this reason, future Maven versions might no longer support
> building such malformed projects.
> [WARNING]
> [INFO]
> [INFO] ------------------------< uk.ac.sanger:artemis
> >------------------------
> [INFO] Building Artemis 18.2.0
> [INFO] from pom.xml
> [INFO] --------------------------------[ jar
> ]---------------------------------
> [WARNING] The POM for org.sharegov:mjson:jar:debian is missing, no dependency
> information available
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 0.454 s
> [INFO] Finished at: 2024-12-28T09:19:01Z
> [INFO]
> ------------------------------------------------------------------------
> [ERROR] Failed to execute goal on project artemis: Could not resolve
> dependencies for project uk.ac.sanger:artemis:jar:18.2.0
> [ERROR] dependency: org.sharegov:mjson:jar:debian (compile)
> [ERROR] Cannot access central (https://repo.maven.apache.org/maven2) in
> offline mode and the artifact org.sharegov:mjson:jar:debian has not been
> downloaded from it before.
> [ERROR] -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e
> switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please
> read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
> dh_auto_build: error: /usr/lib/jvm/default-java/bin/java -noverify -cp
> /usr/share/maven/boot/plexus-classworlds-2.x.jar
> -Dmaven.home=/usr/share/maven
> -Dmaven.multiModuleProjectDirectory=/<<BUILDDIR>>/artemis-18.2.0\+dfsg
> -Dclassworlds.conf=/etc/maven/m2-debian.conf
> org.codehaus.plexus.classworlds.launcher.Launcher
> -s/etc/maven/settings-debian.xml
> -Ddebian.dir=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian
> -Dmaven.repo.local=/<<BUILDDIR>>/artemis-18.2.0\+dfsg/debian/maven-repo
> --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US returned
> exit code 1
> make[1]: *** [debian/rules:9: override_dh_auto_build] Error 25
The full build log is available from:
http://qa-logs.debian.net/2024/12/28/artemis_18.2.0+dfsg-4_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20241228;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20241228&[email protected]&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: htsjdk
Source-Version: 4.1.3+dfsg-2
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
htsjdk, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (supplier of updated htsjdk package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 30 Dec 2024 10:33:32 +0100
Source: htsjdk
Architecture: source
Version: 4.1.3+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1091589
Changes:
htsjdk (4.1.3+dfsg-2) unstable; urgency=medium
.
* Updating the classpath of the built jar
* Updating the installed POM file (Closes: #1091589)
Checksums-Sha1:
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htsjdk_4.1.3+dfsg-2.debian.tar.xz
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htsjdk_4.1.3+dfsg-2_amd64.buildinfo
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Files:
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d4560ab16fc82bf09b30ad5dce1b565c 38280 science optional
htsjdk_4.1.3+dfsg-2.debian.tar.xz
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htsjdk_4.1.3+dfsg-2_amd64.buildinfo
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