Your message dated Thu, 02 Oct 2025 15:34:34 +0000
with message-id <[email protected]>
and subject line Bug#1116713: fixed in biojava6-live 6.1.0+dfsg-6
has caused the Debian Bug report #1116713,
regarding biojava6-live: FTBFS with the nocheck build profile
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.)
--
1116713: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1116713
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:biojava6-live
Version: 6.1.0+dfsg-5
Severity: important
Tags: forky sid ftbfs
User: [email protected]
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: biojava6-live
Source-Version: 6.1.0+dfsg-6
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
biojava6-live, 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 biojava6-live 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: Thu, 02 Oct 2025 17:05:05 +0200
Source: biojava6-live
Architecture: source
Version: 6.1.0+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1116713
Changes:
biojava6-live (6.1.0+dfsg-6) unstable; urgency=medium
.
* Raising Standards version to 4.7.2 (no change)
* Updating d/watch to monitor 6.x versions
* Rmeoving nocheck annotation for the B-D xmlunit(Closes: #1116713)
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