Source: snpeff Version: 5.2.e+dfsg-1 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org 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>>' > # 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="@1728161934" +"%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-5.2.e\+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]:[117,21] > 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]:[117,21] > 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-5.2.e\+dfsg > -Dclassworlds.conf=/etc/maven/m2-debian.conf > org.codehaus.plexus.classworlds.launcher.Launcher > -s/etc/maven/settings-debian.xml > -Ddebian.dir=/<<BUILDDIR>>/snpeff-5.2.e\+dfsg/debian > -Dmaven.repo.local=/<<BUILDDIR>>/snpeff-5.2.e\+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. > [INFO] Scanning for projects... > [INFO] > [INFO] -------------------------< org.snpeff:snpeff > >-------------------------- > [INFO] Building SnpEff 5.2 > [INFO] from pom.xml > [INFO] --------------------------------[ jar > ]--------------------------------- > [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:3.1.2 > has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 > [WARNING] The POM for org.biojava:biojava-structure:jar:6.x is invalid, > transitive dependencies (if any) will not be available: 1 problem was > encountered while building the effective model > [FATAL] Non-parseable POM > /<<PKGBUILDDIR>>/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom: > start tag unexpected character $ (position: TEXT seen > ...org.jgrapht.jgrapht-core.originalVersion>\n\t\t\n\t\t\t<debian.org.rcsb.$... > @117:22) @ line 117, column 22 > > [WARNING] The POM for org.sharegov:mjson:jar:debian is missing, no dependency > information available > [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: 0.417 s > [INFO] Finished at: 2024-12-28T09:10:40Z > [INFO] > ------------------------------------------------------------------------ > [ERROR] Failed to execute goal on project snpeff: Could not resolve > dependencies for project org.snpeff:snpeff:jar:5.2 > [ERROR] dependency: org.sharegov:mjson:jar:debian (compile) > [ERROR] Cannot access maven (https://repo1.maven.org/maven2/) in > offline mode and the artifact org.sharegov:mjson:jar:debian has not been > downloaded from it before. > [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] Cannot access hadoop-bam > (https://hadoop-bam.sourceforge.net/maven/) in offline mode and the artifact > org.sharegov:mjson:jar:debian has not been downloaded from it before. > [ERROR] Cannot access ncimvn-public > (https://ncimvn.nci.nih.gov/nexus/content/groups/public/) in offline mode and > the artifact org.sharegov:mjson:jar:debian has not been downloaded from it > before. > [ERROR] Cannot access typesafe > (https://repo.typesafe.com/typesafe/releases/) 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>>/snpeff-5.2.e\+dfsg > -Dclassworlds.conf=/etc/maven/m2-debian.conf > org.codehaus.plexus.classworlds.launcher.Launcher > -s/etc/maven/settings-debian.xml > -Ddebian.dir=/<<BUILDDIR>>/snpeff-5.2.e\+dfsg/debian > -Dmaven.repo.local=/<<BUILDDIR>>/snpeff-5.2.e\+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/2024/12/28/snpeff_5.2.e+dfsg-1_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20241228;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20241228&fusertaguser=lu...@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.
