[Debian-med-packaging] Bug#1045612: libgoby-java: Fails to build source after successful build
Lucas Nussbaum
lucas at debian.org
Sun Aug 13 20:20:52 BST 2023
Source: libgoby-java
Version: 3.3.1+dfsg2-9
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 libgoby-java
> dpkg-buildpackage: info: source version 3.3.1+dfsg2-9
> 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 -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo
> /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>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+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...
> [WARNING]
> [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
> [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
> [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
> [WARNING]
> [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
> [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
> [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
> [WARNING]
> [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
> [WARNING]
> [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
> [WARNING]
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Build Order:
> [INFO]
> [INFO] Goby Framework [pom]
> [INFO] Goby I/O [jar]
> [INFO] Goby Full Distribution [jar]
> [INFO]
> [INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
> [INFO] Building Goby Framework 3.3.1 [1/3]
> [INFO] --------------------------------[ pom ]---------------------------------
> [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) @ goby-framework ---
> [INFO] Deleting /<<PKGBUILDDIR>>/target
> [INFO]
> [INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
> [INFO] Building Goby I/O 3.3.1 [2/3]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO]
> [INFO] --- maven-clean-plugin:3.2.0:clean (default-clean) @ goby-io ---
> [INFO] Deleting /<<PKGBUILDDIR>>/goby-io/target
> [INFO]
> [INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
> [INFO] Building Goby Full Distribution 3.3.1 [3/3]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO]
> [INFO] --- maven-clean-plugin:3.2.0:clean (default-clean) @ goby-distribution ---
> [INFO] Deleting /<<PKGBUILDDIR>>/goby-distribution/target
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Summary for Goby Framework 3.3.1:
> [INFO]
> [INFO] Goby Framework ..................................... SUCCESS [ 0.259 s]
> [INFO] Goby I/O ........................................... SUCCESS [ 0.228 s]
> [INFO] Goby Full Distribution ............................. SUCCESS [ 0.204 s]
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD SUCCESS
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 0.996 s
> [INFO] Finished at: 2023-08-12T08:12:09Z
> [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 -plibgoby-io-java
> rm -f goby-distribution/test-data
> rm -rf test-results/
> 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 libgoby-java using existing ./libgoby-java_3.3.1+dfsg2.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: file libgoby-java-3.3.1+dfsg2/GOBY_COMMIT.properties has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to goby-distribution/test-results/alignments-splices/spliced-1.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/alignments-splices/spliced-1.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/alignments-splices/spliced-1.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/alignments-splices/spliced-1.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/alignments-splices/spliced-1.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/alignments-splices/spliced-1.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/alignments-splices/spliced-1.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/alignments/align-101-tmh.tmh: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/alignments/align-101-tmh.tmh in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/align-specific-sample.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/align-specific-sample.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/align-specific-sample.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/align-specific-sample.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/align-specific-sample.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/align-specific-sample.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/align-specific-sample.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen0-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen0-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen0-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen0-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen0-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen0-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen0-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen0.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen0.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen0.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen0.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen0.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen0.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen0.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen1-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen1-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen1-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen1-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen1-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen1-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen1-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen1.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen1.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen1.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen1.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen1.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen1.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen1.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen2-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen2-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen2-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen2-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen2-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen2-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen2-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen2.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen2.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen2.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen2.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen2.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen2.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen2.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen3-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen3-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen3-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen3-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen3-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen3-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen3-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen3.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen3.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen3.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen3.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen3.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen3.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen3.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen4-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen4-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen4-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen4-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen4-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen4-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen4-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen4.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen4.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen4.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen4.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen4.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen4.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen4.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen5-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen5-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen5-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen5-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen5-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen5-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen5-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen5.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen5.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen5.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen5.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen5.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen5.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen5.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen6-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen6-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen6-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen6-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen6-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen6-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen6-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen6.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen6.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen6.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen6.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen6.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen6.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen6.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen7-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen7-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen7-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen7-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen7-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen7-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen7-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen7.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen7.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen7.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen7.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen7.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen7.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen7.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen8-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen8-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen8-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen8-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen8-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen8-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen8-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen8.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen8.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen8.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen8.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen8.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen8.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen8.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen9-indels.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen9-indels.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen9-indels.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen9-indels.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen9-indels.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen9-indels.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen9-indels.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen9.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen9.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen9.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen9.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/discover-variants/basen9.index: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/discover-variants/basen9.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/discover-variants/basen9.stats' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/permutations/append-1.perm: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/permutations/append-1.perm in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/permutations/breakpoint-1.perm' will not be represented in diff
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/permutations/breakpoint-2.perm' will not be represented in diff
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/permutations/breakpoint-3.perm' will not be represented in diff
> dpkg-source: error: cannot represent change to goby-distribution/test-results/permutations/test-doubleLocal.perm: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/permutations/test-doubleLocal.perm in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/permutations/test-multipleChunks-1.perm: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/permutations/test-multipleChunks-1.perm in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/permutations/test-multipleChunks-2.perm: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/permutations/test-multipleChunks-2.perm in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/permutations/test-simple.perm: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/permutations/test-simple.perm in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: file libgoby-java-3.3.1+dfsg2/goby-distribution/test-results/read-sets/set-1.filter has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to goby-distribution/test-results/read-sets/set-2.filter: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/read-sets/set-2.filter in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/reads/written-101.bin: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/reads/written-101.bin in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/splicedsamhelper/tricky-spliced-17.entries: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/splicedsamhelper/tricky-spliced-17.entries in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/splicedsamhelper/tricky-spliced-17.header: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/splicedsamhelper/tricky-spliced-17.header in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to goby-distribution/test-results/splicedsamhelper/tricky-spliced-17.tmh: binary file contents changed
> dpkg-source: error: add goby-distribution/test-results/splicedsamhelper/tricky-spliced-17.tmh in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'goby-distribution/test-results/stats-writer/not-tested.vcf' will not be represented in diff
> dpkg-source: error: cannot represent change to test-data/alignments/pileup/1.entries: binary file contents changed
> dpkg-source: error: add test-data/alignments/pileup/1.entries 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-data/alignments/pileup/1.header: binary file contents changed
> dpkg-source: error: add test-data/alignments/pileup/1.header 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-data/alignments/pileup/1.index: binary file contents changed
> dpkg-source: error: add test-data/alignments/pileup/1.index in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: newly created empty file 'test-data/alignments/pileup/1.stats' will not be represented in diff
> dpkg-source: warning: newly created empty file 'test-data/seq-var-test/kevin-synth/sorted-seq-var-reads-gsnap.perm' will not be represented in diff
> 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/libgoby-java_3.3.1+dfsg2-9_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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