Your message dated Sun, 12 May 2024 20:38:04 +0000
with message-id <[email protected]>
and subject line Bug#1046827: fixed in snpsift 5.1+dfsg2-3
has caused the Debian Bug report #1046827,
regarding snpsift: Fails to build source after successful build
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.)
--
1046827: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1046827
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: snpsift
Version: 5.1+dfsg2-2
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: [email protected]
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 <[email protected]>
> 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.
--- End Message ---
--- Begin Message ---
Source: snpsift
Source-Version: 5.1+dfsg2-3
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
snpsift, 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 snpsift 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, 12 May 2024 22:08:30 +0200
Source: snpsift
Architecture: source
Version: 5.1+dfsg2-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1046827
Changes:
snpsift (5.1+dfsg2-3) unstable; urgency=medium
.
* Fixing the clean target (Closes: #1046827)
* Raising Standards version to 4.7.0 (no change)
* Updating the Lintian override for embedded JS
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