Sat Feb 4 07:28:36 GMT 2023

Source: snpeff
Version: 5.1+d+dfsg-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230203 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # We replace the compiling timestamp by the one in d/changelog to enhance
> # build reproducibility.
> cp src/main/java/org/snpeff/SnpEff.java SnpEff.java.old
> sed "s/Gpr\.compile.*/\"$(date --utc --date="@1674244532" +"%Y-%m-%d %H:%M" )\";/" SnpEff.java.old > src/main/java/org/snpeff/SnpEff.java
> dh_auto_configure
> 	mh_patchpoms -plibsnpeff-java --debian-build --keep-pom-version --maven-repo=/<<BUILDDIR>>/snpeff-5.1\+d\+dfsg/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)
> 
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    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>>/snpeff-5.1\+d\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/snpeff-5.1\+d\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/snpeff-5.1\+d\+dfsg/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.snpeff:snpeff >--------------------------
> [INFO] Building SnpEff 5.1
> [INFO] --------------------------------[ jar ]---------------------------------
> [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 SnpEff
> [INFO] This project has been banned from the build due to previous failures.
> [INFO] ------------------------------------------------------------------------
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time:  1.143 s
> [INFO] Finished at: 2023-02-04T02:53:09Z
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal on project snpeff: Could not resolve dependencies for project org.snpeff:snpeff: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>>/snpeff-5.1\+d\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/snpeff-5.1\+d\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/snpeff-5.1\+d\+dfsg/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/snpeff_5.1+d+dfsg-3_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230203;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230203&fusertaguser=lucas@debian.org&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.