[Debichem-devel] Bug#1093348: oscar4: FTBFS: Could not resolve dependencies for project uk.ac.cam.ch.wwmm.oscar:oscar4-recogniser-core:jar:5.2.0
Santiago Vila
sanvila at debian.org
Fri Jan 17 18:53:53 GMT 2025
Package: src:oscar4
Version: 5.2.0+dfsg-2
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
dh_auto_clean
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 -pliboscar4-java
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp /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>>/oscar4-5.2.0\+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>>/oscar4-5.2.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/oscar4-5.2.0\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/oscar4-5.2.0\+dfsg/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US
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.
[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 5.2.0 [1/13]
[INFO] from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[INFO]
[INFO] --- enforcer:3.5.0:enforce (enforce-maven) @ oscar4 ---
[INFO] Rule 0: org.apache.maven.enforcer.rules.version.RequireMavenVersion passed
[INFO]
[INFO] ----------------< uk.ac.cam.ch.wwmm.oscar:oscar4-core >-----------------
[INFO] Building oscar4-core 5.2.0 [2/13]
[INFO] from oscar4-core/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:3.1.2 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0
[INFO]
[INFO] --- enforcer:3.5.0:enforce (enforce-maven) @ oscar4-core ---
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ oscar4-core ---
[INFO] Copying 11 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ oscar4-core ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 29 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[WARNING] /<<PKGBUILDDIR>>/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NamedEntity.java:[286,16] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NamedEntity.java:[296,16] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NamedEntity.java:[307,16] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NamedEntity.java:[317,16] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ oscar4-core ---
[INFO] Copying 6 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ oscar4-core ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 14 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ oscar4-core ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar:3.3.0:jar (default-jar) @ oscar4-core ---
[INFO] Building jar: /<<PKGBUILDDIR>>/oscar4-core/target/oscar4-core-5.2.0.jar
[INFO]
[INFO] ------------< uk.ac.cam.ch.wwmm.oscar:oscar4-chemnamedict >-------------
[INFO] Building Chemical Name Dictionaries 5.2.0 [3/13]
[INFO] from oscar4-chemnamedict/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- enforcer:3.5.0:enforce (enforce-maven) @ oscar4-chemnamedict ---
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ oscar4-chemnamedict ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ oscar4-chemnamedict ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 26 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[INFO] /<<PKGBUILDDIR>>/oscar4-chemnamedict/src/main/java/uk/ac/cam/ch/wwmm/oscar/chemnamedict/core/ChemNameDictRegistry.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/ChemNameDictRegistry.java: Recompile with -Xlint:deprecation for details.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ oscar4-chemnamedict ---
[INFO] Copying 1 resource from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ oscar4-chemnamedict ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 10 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ oscar4-chemnamedict ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar:3.3.0:jar (default-jar) @ oscar4-chemnamedict ---
[INFO] Building jar: /<<PKGBUILDDIR>>/oscar4-chemnamedict/target/oscar4-chemnamedict-5.2.0.jar
[INFO]
[INFO] -----------------< uk.ac.cam.ch.wwmm.oscar:oscar4-obo >-----------------
[INFO] Building oscar4-obo 5.2.0 [4/13]
[INFO] from oscar4-obo/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- enforcer:3.5.0:enforce (enforce-maven) @ oscar4-obo ---
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ oscar4-obo ---
[INFO] Copying 6 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ oscar4-obo ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 7 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ oscar4-obo ---
[INFO] Copying 4 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ oscar4-obo ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 4 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ oscar4-obo ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar:3.3.0:jar (default-jar) @ oscar4-obo ---
[INFO] Building jar: /<<PKGBUILDDIR>>/oscar4-obo/target/oscar4-obo-5.2.0.jar
[INFO]
[INFO] --------------< uk.ac.cam.ch.wwmm.oscar:oscar4-tokenizer >--------------
[INFO] Building oscar4-tokenizer 5.2.0 [5/13]
[INFO] from oscar4-tokeniser/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- enforcer:3.5.0:enforce (enforce-maven) @ oscar4-tokenizer ---
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ oscar4-tokenizer ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ oscar4-tokenizer ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 5 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[INFO] /<<PKGBUILDDIR>>/oscar4-tokeniser/src/main/java/uk/ac/cam/ch/wwmm/oscartokeniser/TokenSequenceSource.java: /<<PKGBUILDDIR>>/oscar4-tokeniser/src/main/java/uk/ac/cam/ch/wwmm/oscartokeniser/TokenSequenceSource.java uses or overrides a deprecated API.
[INFO] /<<PKGBUILDDIR>>/oscar4-tokeniser/src/main/java/uk/ac/cam/ch/wwmm/oscartokeniser/TokenSequenceSource.java: Recompile with -Xlint:deprecation for details.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ oscar4-tokenizer ---
[INFO] Copying 1 resource from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ oscar4-tokenizer ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 5 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
on the class path. A future release of javac may disable annotation processing
unless at least one processor is specified by name (-processor), or a search
path is specified (--processor-path, --processor-module-path), or annotation
processing is enabled explicitly (-proc:only, -proc:full).
Use -Xlint:-options to suppress this message.
Use -proc:none to disable annotation processing.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ oscar4-tokenizer ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar:3.3.0:jar (default-jar) @ oscar4-tokenizer ---
[INFO] Building jar: /<<PKGBUILDDIR>>/oscar4-tokeniser/target/oscar4-tokenizer-5.2.0.jar
[INFO]
[INFO] -----------< uk.ac.cam.ch.wwmm.oscar:oscar4-recogniser-core >-----------
[INFO] Building oscar4-recogniser-core 5.2.0 [6/13]
[INFO] from oscar4-recogniser-core/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for oscar4-parent 5.2.0:
[INFO]
[INFO] oscar4-parent ...................................... SUCCESS [ 0.193 s]
[INFO] oscar4-core ........................................ SUCCESS [ 1.939 s]
[INFO] Chemical Name Dictionaries ......................... SUCCESS [ 0.532 s]
[INFO] oscar4-obo ......................................... SUCCESS [ 0.881 s]
[INFO] oscar4-tokenizer ................................... SUCCESS [ 0.253 s]
[INFO] oscar4-recogniser-core ............................. FAILURE [ 0.013 s]
[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: 3.945 s
[INFO] Finished at: 2025-01-17T16:08:50Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project oscar4-recogniser-core: Could not resolve dependencies for project uk.ac.cam.ch.wwmm.oscar:oscar4-recogniser-core:jar:5.2.0
[ERROR] dependency: dk.brics.automaton:automaton:jar:debian (compile)
[ERROR] Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact dk.brics.automaton:automaton:jar:debian has not been downloaded from it before.
[ERROR] -> [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/DependencyResolutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn <args> -rf :oscar4-recogniser-core
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>>/oscar4-5.2.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/oscar4-5.2.0\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/oscar4-5.2.0\+dfsg/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202501/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:oscar4, so that this is still
visible in the BTS web page for this package.
Thanks.
More information about the Debichem-devel
mailing list