[Debian-med-packaging] Bug#1046827: snpsift: Fails to build source after successful build
Lucas Nussbaum
lucas at debian.org
Sun Aug 13 20:21:28 BST 2023
Source: snpsift
Version: 5.1+dfsg2-2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild
Hi,
This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).
This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.
More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> -------------------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package snpsift
> dpkg-buildpackage: info: source version 5.1+dfsg2-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Pierre Gruet <pgt at debian.org>
> dpkg-source --before-build .
> debian/rules clean
> dh clean --with javahelper
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 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]:[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)
>
> /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 clean
> 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-clean-plugin:jar:2.5 has been relocated to org.apache.maven.plugins:maven-clean-plugin:jar:3.2.0
> [INFO]
> [INFO] --- maven-clean-plugin:3.2.0:clean (default-clean) @ snpsift ---
> [INFO] Deleting /<<PKGBUILDDIR>>/target
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD SUCCESS
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 0.507 s
> [INFO] Finished at: 2023-08-12T12:43:42Z
> [INFO] ------------------------------------------------------------------------
> [0m[0m bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
> mh_unpatchpoms -plibsnpsift-java
> # Removing the unit tests we copied into a subdirectory of src/test.
> if [ -e src/test/java/org ]; then \
> rm -f -rf src/test/java/org; \
> fi
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> jh_clean
> dh_clean
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building snpsift using existing ./snpsift_5.1+dfsg2.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to test/ann/gnomad_db_multiple_entries.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/ann/gnomad_db_multiple_entries.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/annotate_multiple_allele.db.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/annotate_multiple_allele.db.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/annotate_multiple_allele_R.db.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/annotate_multiple_allele_R.db.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/annotate_oder_db.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/annotate_oder_db.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_06.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_06.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_09.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_09.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_1.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_1.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_10.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_10.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_11.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_11.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_12.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_12.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_13.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_13.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_16.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_16.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_2.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_2.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_20.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_20.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_21.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_21.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_23.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_23.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_24.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_24.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_26.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_26.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_27.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_27.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_28.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_28.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_29.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_29.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_31.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_31.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_32.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_32.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_33.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_33.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_34.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_34.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_35.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_35.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_36.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_36.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_38.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_38.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_39.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_39.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_40.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_40.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_41.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_41.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_42.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_42.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_43.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_43.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_chr22.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_chr22.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_index_01.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_index_01.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_index_02.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_index_02.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_large.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_large.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/db_test_multiline.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/db_test_multiline.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to test/test_annotate_18_db.vcf.sidx: binary file contents changed
> dpkg-source: error: add test/test_annotate_18_db.vcf.sidx in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/13/snpsift_5.1+dfsg2-2_unstable.log
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.
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