Your message dated Sun, 03 Dec 2023 09:19:17 +0000
with message-id <[email protected]>
and subject line Bug#1045612: fixed in libgoby-java 3.3.1+dfsg2-10
has caused the Debian Bug report #1045612,
regarding libgoby-java: 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.)
--
1045612: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1045612
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libgoby-java
Version: 3.3.1+dfsg2-9
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 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 <[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 -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.
--- End Message ---
--- Begin Message ---
Source: libgoby-java
Source-Version: 3.3.1+dfsg2-10
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libgoby-java, 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 libgoby-java 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, 03 Dec 2023 08:03:09 +0100
Source: libgoby-java
Architecture: source
Version: 3.3.1+dfsg2-10
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1045612
Changes:
libgoby-java (3.3.1+dfsg2-10) unstable; urgency=medium
.
* Fixing the clean target (Closes: #1045612)
* Update standards version to 4.6.2, no changes needed.
Checksums-Sha1:
9d7d0c8bd45e580c159c89594561922f187543bd 3011 libgoby-java_3.3.1+dfsg2-10.dsc
46a6a881da114175ba247880ac918fbd443d60ce 29336
libgoby-java_3.3.1+dfsg2-10.debian.tar.xz
c2afee0008161fe1e7ac807f8d61097a7f2ba44a 19596
libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo
Checksums-Sha256:
4d4462efbc6b413916371d1fdbd2939ff1c086b6f5eead56b241d0a7aa411a1e 3011
libgoby-java_3.3.1+dfsg2-10.dsc
89a405303356305fe1c53dafd4cab5ddf599f2d8e73ed203956b648fb1cef8cf 29336
libgoby-java_3.3.1+dfsg2-10.debian.tar.xz
5ed2232983a045209adb48c33fcbe6b8e62c4f61182b9e2b46585165f3edcc35 19596
libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo
Files:
b71a1e36cea88c91dc53f39de99cbead 3011 science optional
libgoby-java_3.3.1+dfsg2-10.dsc
c593b3185449e6d893941b7e40b7daf9 29336 science optional
libgoby-java_3.3.1+dfsg2-10.debian.tar.xz
3820d20b40b39a0480ccbe079c6b6f76 19596 science optional
libgoby-java_3.3.1+dfsg2-10_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=rKvN
-----END PGP SIGNATURE-----
--- End Message ---
