Your message dated Thu, 08 Sep 2022 07:49:14 +0000 with message-id <e1owchi-007wl6...@fasolo.debian.org> and subject line Bug#1013591: fixed in oscar4 5.2.0+dfsg-1 has caused the Debian Bug report #1013591, regarding oscar4: FTBFS: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-resources-plugin:3.1.0:resources 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 ow...@bugs.debian.org immediately.) -- 1013591: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1013591 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: oscar4 Version: 5.1.2+dfsg-1 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20220624 ftbfs-bookworm Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > ln -fs /usr/share/EMBOSS/data/OBO/chebi.obo > oscar4-obo/src/main/resources/uk/ac/cam/ch/wwmm/oscar/obo/terms/chebi.obo > ln -s oscar4-tokeniser oscar4-tokenizer > dh_auto_configure > mh_patchpoms -pliboscar4-java --debian-build --keep-pom-version > --maven-repo=/<<BUILDDIR>>/oscar4-5.1.2\+dfsg/debian/maven-repo > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > dh_auto_build > /usr/lib/jvm/default-java/bin/java -noverify -cp > /usr/share/maven/boot/plexus-classworlds-2.x.jar > -Dmaven.home=/usr/share/maven > -Dmaven.multiModuleProjectDirectory=/<<BUILDDIR>>/oscar4-5.1.2\+dfsg > -Dclassworlds.conf=/etc/maven/m2-debian.conf > org.codehaus.plexus.classworlds.launcher.Launcher > -s/etc/maven/settings-debian.xml > -Ddebian.dir=/<<BUILDDIR>>/oscar4-5.1.2\+dfsg/debian > -Dmaven.repo.local=/<<BUILDDIR>>/oscar4-5.1.2\+dfsg/debian/maven-repo > --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US > [INFO] Scanning for projects... > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Build Order: > [INFO] > [INFO] oscar4-parent > [pom] > [INFO] oscar4-core > [jar] > [INFO] Chemical Name Dictionaries > [jar] > [INFO] oscar4-obo > [jar] > [INFO] oscar4-tokenizer > [jar] > [INFO] oscar4-recogniser-core > [jar] > [INFO] oscar4-memmrecogniser > [jar] > [INFO] oscar4-patternrecogniser > [jar] > [INFO] oscar4-opsin > [jar] > [INFO] oscar4-api > [jar] > [INFO] oscar4-preprocessor > [jar] > [INFO] oscar4-formatter > [jar] > [INFO] oscar4-data > [jar] > [INFO] > [INFO] -------------------< uk.ac.cam.ch.wwmm.oscar:oscar4 > >------------------- > [INFO] Building oscar4-parent 5.1.2 > [1/13] > [INFO] --------------------------------[ pom > ]--------------------------------- > [INFO] > [INFO] --- maven-enforcer-plugin:3.0.0-M2:enforce (enforce-maven) @ oscar4 --- > [INFO] > [INFO] ----------------< uk.ac.cam.ch.wwmm.oscar:oscar4-core > >----------------- > [INFO] Building oscar4-core 5.1.2 > [2/13] > [INFO] --------------------------------[ jar > ]--------------------------------- > [INFO] > [INFO] --- maven-enforcer-plugin:3.0.0-M2:enforce (enforce-maven) @ > oscar4-core --- > [INFO] > [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ > oscar4-core --- > [INFO] Using 'UTF-8' encoding to copy filtered resources. > [INFO] Copying 11 resources > [INFO] > [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ > oscar4-core --- > [INFO] Changes detected - recompiling the module! > [INFO] Compiling 29 source files to > /<<PKGBUILDDIR>>/oscar4-core/target/classes > Use of target 1.6 is no longer supported, switching to 7 > Use of source 1.6 is no longer supported, switching to 7 > [INFO] > /<<PKGBUILDDIR>>/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NamedEntity.java: > > /<<PKGBUILDDIR>>/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NamedEntity.java > uses or overrides a deprecated API. > [INFO] > /<<PKGBUILDDIR>>/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NamedEntity.java: > Recompile with -Xlint:deprecation for details. > [INFO] > [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) > @ oscar4-core --- > [INFO] Using 'UTF-8' encoding to copy filtered resources. > [INFO] Copying 6 resources > [INFO] > [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ > oscar4-core --- > [INFO] Changes detected - recompiling the module! > [INFO] Compiling 14 source files to > /<<PKGBUILDDIR>>/oscar4-core/target/test-classes > Use of target 1.6 is no longer supported, switching to 7 > Use of source 1.6 is no longer supported, switching to 7 > [INFO] > [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ oscar4-core --- > [INFO] Tests are skipped. > [INFO] > [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ oscar4-core --- > [INFO] Building jar: /<<PKGBUILDDIR>>/oscar4-core/target/oscar4-core-5.1.2.jar > [INFO] > [INFO] ------------< uk.ac.cam.ch.wwmm.oscar:oscar4-chemnamedict > >------------- > [INFO] Building Chemical Name Dictionaries 5.1.2 > [3/13] > [INFO] --------------------------------[ jar > ]--------------------------------- > [INFO] > [INFO] --- maven-enforcer-plugin:3.0.0-M2:enforce (enforce-maven) @ > oscar4-chemnamedict --- > [INFO] > [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ > oscar4-chemnamedict --- > [INFO] Using 'UTF-8' encoding to copy filtered resources. > [INFO] Copying 3 resources > [INFO] > [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ > oscar4-chemnamedict --- > [INFO] Changes detected - recompiling the module! > [INFO] Compiling 26 source files to > /<<PKGBUILDDIR>>/oscar4-chemnamedict/target/classes > Use of target 1.6 is no longer supported, switching to 7 > Use of source 1.6 is no longer supported, switching to 7 > [INFO] > /<<PKGBUILDDIR>>/oscar4-chemnamedict/src/main/java/uk/ac/cam/ch/wwmm/oscar/chemnamedict/core/ImmutableChemNameDict.java: > Some input files use or override a deprecated API. > [INFO] > /<<PKGBUILDDIR>>/oscar4-chemnamedict/src/main/java/uk/ac/cam/ch/wwmm/oscar/chemnamedict/core/ImmutableChemNameDict.java: > Recompile with -Xlint:deprecation for details. > [INFO] > [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) > @ oscar4-chemnamedict --- > [INFO] Using 'UTF-8' encoding to copy filtered resources. > [INFO] Copying 1 resource > [INFO] > [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ > oscar4-chemnamedict --- > [INFO] Changes detected - recompiling the module! > [INFO] Compiling 10 source files to > /<<PKGBUILDDIR>>/oscar4-chemnamedict/target/test-classes > Use of target 1.6 is no longer supported, switching to 7 > Use of source 1.6 is no longer supported, switching to 7 > [INFO] > [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ > oscar4-chemnamedict --- > [INFO] Tests are skipped. > [INFO] > [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ oscar4-chemnamedict --- > [INFO] Building jar: > /<<PKGBUILDDIR>>/oscar4-chemnamedict/target/oscar4-chemnamedict-5.1.2.jar > [INFO] > [INFO] -----------------< uk.ac.cam.ch.wwmm.oscar:oscar4-obo > >----------------- > [INFO] Building oscar4-obo 5.1.2 > [4/13] > [INFO] --------------------------------[ jar > ]--------------------------------- > [INFO] > [INFO] --- maven-enforcer-plugin:3.0.0-M2:enforce (enforce-maven) @ > oscar4-obo --- > [INFO] > [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ > oscar4-obo --- > [INFO] Using 'UTF-8' encoding to copy filtered resources. > [INFO] Copying 6 resources > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary for oscar4-parent 5.1.2: > [INFO] > [INFO] oscar4-parent ...................................... SUCCESS [ 0.265 > s] > [INFO] oscar4-core ........................................ SUCCESS [ 2.015 > s] > [INFO] Chemical Name Dictionaries ......................... SUCCESS [ 0.748 > s] > [INFO] oscar4-obo ......................................... FAILURE [ 0.023 > s] > [INFO] oscar4-tokenizer ................................... SKIPPED > [INFO] oscar4-recogniser-core ............................. SKIPPED > [INFO] oscar4-memmrecogniser .............................. SKIPPED > [INFO] oscar4-patternrecogniser ........................... SKIPPED > [INFO] oscar4-opsin ....................................... SKIPPED > [INFO] oscar4-api ......................................... SKIPPED > [INFO] oscar4-preprocessor ................................ SKIPPED > [INFO] oscar4-formatter ................................... SKIPPED > [INFO] oscar4-data ........................................ SKIPPED > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILURE > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 3.178 s > [INFO] Finished at: 2022-06-24T05:47:03Z > [INFO] > ------------------------------------------------------------------------ > [ERROR] Failed to execute goal > org.apache.maven.plugins:maven-resources-plugin:3.1.0:resources > (default-resources) on project oscar4-obo: > /<<PKGBUILDDIR>>/oscar4-obo/target/classes/uk/ac/cam/ch/wwmm/oscar/obo/terms/chebi.obo: > Operation not permitted -> [Help 1] > [ERROR] > [ERROR] To see the full stack trace of the errors, re-run Maven with the -e > switch. > [ERROR] Re-run Maven using the -X switch to enable full debug logging. > [ERROR] > [ERROR] For more information about the errors and possible solutions, please > read the following articles: > [ERROR] [Help 1] > http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException > [ERROR] > [ERROR] After correcting the problems, you can resume the build with the > command > [ERROR] mvn <args> -rf :oscar4-obo > dh_auto_build: error: /usr/lib/jvm/default-java/bin/java -noverify -cp > /usr/share/maven/boot/plexus-classworlds-2.x.jar > -Dmaven.home=/usr/share/maven > -Dmaven.multiModuleProjectDirectory=/<<BUILDDIR>>/oscar4-5.1.2\+dfsg > -Dclassworlds.conf=/etc/maven/m2-debian.conf > org.codehaus.plexus.classworlds.launcher.Launcher > -s/etc/maven/settings-debian.xml > -Ddebian.dir=/<<BUILDDIR>>/oscar4-5.1.2\+dfsg/debian > -Dmaven.repo.local=/<<BUILDDIR>>/oscar4-5.1.2\+dfsg/debian/maven-repo > --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US returned > exit code 1 > make: *** [debian/rules:4: binary] Error 25 The full build log is available from: http://qa-logs.debian.net/2022/06/24/oscar4_5.1.2+dfsg-1_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220624;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220624&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please marking 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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--- Begin Message ---Source: oscar4 Source-Version: 5.2.0+dfsg-1 Done: Andrius Merkys <mer...@debian.org> We believe that the bug you reported is fixed in the latest version of oscar4, 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 1013...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andrius Merkys <mer...@debian.org> (supplier of updated oscar4 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 08 Sep 2022 03:22:21 -0400 Source: oscar4 Architecture: source Version: 5.2.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Changed-By: Andrius Merkys <mer...@debian.org> Closes: 1013591 Changes: oscar4 (5.2.0+dfsg-1) unstable; urgency=medium . * New upstream release 5.2.0+dfsg. * Copy chebi.obo from EMBOSS instead of symlinking, as the build process possibly attempts to modify it (Closes: #1013591) Checksums-Sha1: 71fee72896bb618cac83e967761668bd90a42160 2224 oscar4_5.2.0+dfsg-1.dsc 24337dab12b20ff3baa17164ae0f1639fcc5e359 5974620 oscar4_5.2.0+dfsg.orig.tar.xz 6cf0bf93ce70988c540803afaa880920810b02f4 12564 oscar4_5.2.0+dfsg-1.debian.tar.xz 7a44d78fd004566e35c9c8fa825ca6e423fb94ae 14463 oscar4_5.2.0+dfsg-1_source.buildinfo Checksums-Sha256: 870e2b6bb2d8c5cd2a3c6aafc9b7e3b168711caa48dd90c01cc7f3feb0771bd0 2224 oscar4_5.2.0+dfsg-1.dsc 300b19a45641aa1f5600c3ce09f8fcef85082654be4230df294b367fc85358ee 5974620 oscar4_5.2.0+dfsg.orig.tar.xz fef974c8edf11db02c1603e8249718340cfd01647bba03b5462c4461431bed5a 12564 oscar4_5.2.0+dfsg-1.debian.tar.xz 732615137fcc402199e80a244b818c9bac06520877448e7a017ef98a14a070b4 14463 oscar4_5.2.0+dfsg-1_source.buildinfo Files: 255f657774268d0aac20f8be18e75456 2224 science optional oscar4_5.2.0+dfsg-1.dsc e2cef7a9b6101c4e9ed33ec6f4362e7e 5974620 science optional oscar4_5.2.0+dfsg.orig.tar.xz 14e3698d82cd3d2206e608e6ad5e17d7 12564 science optional oscar4_5.2.0+dfsg-1.debian.tar.xz 97c2841c7643483e94bbc2b5f829bad8 14463 science optional oscar4_5.2.0+dfsg-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmMZmJcSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHPmcP/23glvF5GYFTEY4lA3hO8AGre2HDzxJs DRO+8tCiA5jYHGqP5/tQBAiv/mfcb1rZP8P5+T7v81tGcigRHW7Xzy0typ65mkly 8A47Xnd8eZhxp5xIeY5aGfevjiKM1y3Rzrqa9cZp9RfuK87yNZZgziyJaTIFF/Nt CVpFpu9a1/B6m3cPDSn7triijglyiIZS9hqRF0YLn83FlHa/Pjw2LChbu8kCHXsI LQKhddHH76WNH1r40LXf7jDvWTTJqYGryVq9pewI3Y39OguzeF2HTCmwQq6yM+sW D4VXL8AND5WBUcJgDcA+7INyOid3oKwm4KDQIQInp4UIbpA0rkXdg1gBGRJIJdnQ IbJPXOlt5GymI0xxk4JY24qU6fXqPCdGRgW9xHHJ7BO3zjD1x8124DXh+U/498fu Wy9D0rAYqlsAHP5B0nvNwO2GPcDVHmXsxAmYjLGoZewYcLpPAzLna6Di6VRlnkVv GlA/pLldlZ8gTKZhmi5LAc7JsttUHZ4TCVZdoLGjpua5YjRD+D2WgkAErElUQ1Ox WFVBWaaCCSMNr0ufw+5LrRSavzVQS76XyViCQmDUGKC+C/b8pFFO9lDotV/BdxWj yDPaoDBeGmub16kBJgrxFmUaJh6qjnOduUHUlSU2FBGaR3TerOoF17Kbm52YjkkB 0SYrbUZp9Rio =4TQb -----END PGP SIGNATURE-----
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