[Debian-med-packaging] Bug#1116713: biojava6-live: FTBFS with the nocheck build profile
Santiago Vila
sanvila at debian.org
Tue Sep 30 15:48:22 BST 2025
Package: src:biojava6-live
Version: 6.1.0+dfsg-5
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile
Dear maintainer:
During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:
https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck
(It's a wiki, so you are welcome to contribute)
[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].
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:biojava6-live, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dpkg: warning: --compare-versions used with obsolete relation operator '>'
dh clean --with javahelper
[... snipped ...]
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-alignment ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 53 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[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release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.
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java:[259,108] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java:[261,106] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[INFO] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/demo/DemoAlignProteins.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/demo/DemoAlignProteins.java: Recompile with -Xlint:deprecation for details.
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-alignment ---
[INFO] Copying 11 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-alignment ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 24 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] /<<PKGBUILDDIR>>/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java: Recompile with -Xlint:deprecation for details.
[INFO]
[INFO] --- surefire:2.22.3:test (default-test) @ biojava-alignment ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- jar:3.3.0:jar (default-jar) @ biojava-alignment ---
[INFO] Building jar: /<<PKGBUILDDIR>>/biojava-alignment/target/biojava-alignment-6.1.0.jar
[INFO]
[INFO] --- javadoc:3.10.1:jar (default-cli) @ biojava-alignment ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning: invalid input: '<'
[WARNING] * counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning: @param argument "cutsPerSection" is not a parameter name.
[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning: @param argument "cutsPerSection" is not a parameter name.
[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning: reference not found: Profile
[WARNING] * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:41: warning: @param argument "s1" is not a parameter name.
[WARNING] * @param s1
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:43: warning: @param argument "s2" is not a parameter name.
[WARNING] * @param s2
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java:119: warning: invalid usage of tag {@link #pamDistance(MultipleSequenceAlignment
[WARNING] * method {@link #pamDistance(MultipleSequenceAlignment}). The gapped
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning: invalid input: '<'
[WARNING] * space complexity is a modest (a multiple < 2) increase in time.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning: reference not found: Profile
[WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning: reference not found: Profile
[WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning: reference not found: Profile
[WARNING] * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning: reference not found: Profile
[WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning: reference not found: AlignedSequence
[WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning: @param argument "dbReference" is not a parameter name.
[WARNING] * @param dbReference the string without the initial annotation identifier ( #=GS DR )
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
[WARNING] 58 warnings
[INFO] Building jar: /<<PKGBUILDDIR>>/biojava-alignment/target/biojava-alignment-6.1.0-javadoc.jar
[INFO]
[INFO] -------------------< org.biojava:biojava-structure >--------------------
[INFO] Building biojava-structure 6.1.0 [5/15]
[INFO] from biojava-structure/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.7.1: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.7.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:3.7.1 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 has not been downloaded from it before.
[WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved:
Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
[WARNING] The POM for xmlunit:xmlunit:jar:debian is missing, no dependency information available
[WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Skipping biojava
[INFO] This project has been banned from the build due to previous failures.
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
[INFO] biojava ............................................ SUCCESS [ 0.432 s]
[INFO] biojava-core ....................................... SUCCESS [ 7.141 s]
[INFO] biojava-forester ................................... SUCCESS [ 7.851 s]
[INFO] biojava-alignment .................................. SUCCESS [ 2.570 s]
[INFO] biojava-structure .................................. FAILURE [ 0.039 s]
[INFO] biojava-jcolorbrewer ............................... SKIPPED
[INFO] biojava-structure-gui .............................. SKIPPED
[INFO] biojava-genome ..................................... SKIPPED
[INFO] biojava-modfinder .................................. SKIPPED
[INFO] biojava-ws ......................................... SKIPPED
[INFO] biojava-protein-disorder ........................... SKIPPED
[INFO] biojava-aa-prop .................................... SKIPPED
[INFO] biojava-survival ................................... SKIPPED
[INFO] biojava-ontology ................................... SKIPPED
[INFO] biojava-protein-comparison-tool .................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 18.309 s
[INFO] Finished at: 2025-09-30T11:28:14Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project biojava-structure: Could not resolve dependencies for project org.biojava:biojava-structure:jar:6.1.0
[ERROR] dependency: xmlunit:xmlunit:jar:debian (test)
[ERROR] Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact xmlunit:xmlunit: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 :biojava-structure
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>>/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/<<BUILDDIR>>/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US returned exit code 1
make[1]: *** [debian/rules:38: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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