Your message dated Sun, 05 Feb 2023 15:07:26 +0000
with message-id <[email protected]>
and subject line Bug#1030430: fixed in biojava6-live 6.1.0+dfsg-3
has caused the Debian Bug report #1030430,
regarding snpsift: FTBFS: [ERROR] Failed to execute goal on project snpsift:
Could not resolve dependencies for project org.snpsift:snpsift:jar:5.1: The
following artifacts could not be resolved:
org.apache.logging.log4j:log4j-to-slf4j:jar:debian,
org.apache.logging.log4j:log4j-api:jar:debian,
org.apache.logging.log4j:log4j-core:jar:debian: Cannot access maven
(https://repo1.maven.org/maven2/) in offline mode and the artifact
org.apache.logging.log4j:log4j-to-slf4j:jar:debian has not been downloaded from
it before. -> [Help 1]
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1030430: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1030430
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: snpsift
Version: 5.1+dfsg2-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: [email protected]
Usertags: ftbfs-20230203 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --with javahelper
> dh_update_autotools_config
> dh_autoreconf
> dh_auto_configure
> mh_patchpoms -plibsnpsift-java --debian-build --keep-pom-version
> --maven-repo=/<<BUILDDIR>>/snpsift-5.1\+dfsg2/debian/maven-repo
> Failed to parse
> /<<PKGBUILDDIR>>/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom
> javax.xml.stream.XMLStreamException: ParseError at [row,col]:[129,21]
> Message: Element type "debian.org.rcsb." must be followed by either attribute
> specifications, ">" or "/>".
> at
> java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652)
> at org.debian.maven.repo.POMReader.readPom(POMReader.java:82)
> at org.debian.maven.repo.POMReader.readPom(POMReader.java:57)
> at org.debian.maven.repo.Repository.scan(Repository.java:397)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:201)
> at org.debian.maven.repo.Repository.scanOnce(Repository.java:196)
> at
> org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107)
> at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779)
>
> Failed to parse
> /<<PKGBUILDDIR>>/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom
> javax.xml.stream.XMLStreamException: ParseError at [row,col]:[129,21]
> Message: Element type "debian.org.rcsb." must be followed by either attribute
> specifications, ">" or "/>".
> at
> java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652)
> at org.debian.maven.repo.POMReader.readPom(POMReader.java:82)
> at org.debian.maven.repo.POMReader.readPom(POMReader.java:57)
> at org.debian.maven.repo.Repository.scan(Repository.java:397)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:394)
> at org.debian.maven.repo.Repository.scan(Repository.java:201)
> at org.debian.maven.repo.Repository.scanOnce(Repository.java:196)
> at
> org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107)
> at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779)
>
> jh_linkjars
> 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>>/snpsift-5.1\+dfsg2
> -Dclassworlds.conf=/etc/maven/m2-debian.conf
> org.codehaus.plexus.classworlds.launcher.Launcher
> -s/etc/maven/settings-debian.xml
> -Ddebian.dir=/<<BUILDDIR>>/snpsift-5.1\+dfsg2/debian
> -Dmaven.repo.local=/<<BUILDDIR>>/snpsift-5.1\+dfsg2/debian/maven-repo
> --batch-mode package javadoc:jar javadoc:aggregate -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.
> [0m[0m[INFO] Scanning for projects...
> [INFO]
> [INFO] ------------------------< org.snpsift:snpsift
> >-------------------------
> [INFO] Building SnpSift 5.1
> [INFO] --------------------------------[ jar
> ]---------------------------------
> [WARNING] The artifact
> org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated
> to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3
> [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:2.4 has
> been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0
> [WARNING] The POM for org.apache.logging.log4j:log4j-to-slf4j:jar:debian is
> missing, no dependency information available
> [WARNING] The POM for org.apache.logging.log4j:log4j-api:jar:debian is
> missing, no dependency information available
> [WARNING] The POM for org.apache.logging.log4j:log4j-core:jar:debian is
> missing, no dependency information available
> [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid,
> transitive dependencies (if any) will not be available, enable debug logging
> for more details
> [INFO]
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Skipping SnpSift
> [INFO] This project has been banned from the build due to previous failures.
> [INFO]
> ------------------------------------------------------------------------
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 0.347 s
> [INFO] Finished at: 2023-02-04T02:54:11Z
> [INFO]
> ------------------------------------------------------------------------
> [ERROR] Failed to execute goal on project snpsift: Could not resolve
> dependencies for project org.snpsift:snpsift:jar:5.1: The following artifacts
> could not be resolved: org.apache.logging.log4j:log4j-to-slf4j:jar:debian,
> org.apache.logging.log4j:log4j-api:jar:debian,
> org.apache.logging.log4j:log4j-core:jar:debian: Cannot access maven
> (https://repo1.maven.org/maven2/) in offline mode and the artifact
> org.apache.logging.log4j:log4j-to-slf4j:jar:debian has not been downloaded
> from it before. -> [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
> [0m[0mdh_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>>/snpsift-5.1\+dfsg2
> -Dclassworlds.conf=/etc/maven/m2-debian.conf
> org.codehaus.plexus.classworlds.launcher.Launcher
> -s/etc/maven/settings-debian.xml
> -Ddebian.dir=/<<BUILDDIR>>/snpsift-5.1\+dfsg2/debian
> -Dmaven.repo.local=/<<BUILDDIR>>/snpsift-5.1\+dfsg2/debian/maven-repo
> --batch-mode package javadoc:jar javadoc:aggregate -DskipTests
> -Dnotimestamp=true -Dlocale=en_US returned exit code 1
> make: *** [debian/rules:11: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2023/02/03/snpsift_5.1+dfsg2-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230203;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230203&[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: biojava6-live
Source-Version: 6.1.0+dfsg-3
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
biojava6-live, 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 biojava6-live 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: Sun, 05 Feb 2023 14:34:29 +0100
Source: biojava6-live
Architecture: source
Version: 6.1.0+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1030430
Changes:
biojava6-live (6.1.0+dfsg-3) unstable; urgency=medium
.
* Ignoring log4j artifacts during the build and the publish phase
(Closes: #1030430)
* Updating Maven rules
* Updating the classpaths of the built jars
Checksums-Sha1:
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33bca0dd7e8e75871dd4a4ed0cffae695201084f 26816
biojava6-live_6.1.0+dfsg-3.debian.tar.xz
07261e0a82a0ecba87ff5aa093b88ff1e1ea6ed1 18899
biojava6-live_6.1.0+dfsg-3_amd64.buildinfo
Checksums-Sha256:
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biojava6-live_6.1.0+dfsg-3.dsc
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biojava6-live_6.1.0+dfsg-3.debian.tar.xz
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biojava6-live_6.1.0+dfsg-3_amd64.buildinfo
Files:
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biojava6-live_6.1.0+dfsg-3.dsc
af9015f34e782614b320b5d9c2a8551a 26816 java optional
biojava6-live_6.1.0+dfsg-3.debian.tar.xz
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biojava6-live_6.1.0+dfsg-3_amd64.buildinfo
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