Compilation error

[rapodaca]

I'm trying to compile the current master (45bb1a) as per the README (mvn install). The system is MacOS Monterrey (M1).

java --version
openjdk 18.0.2 2022-07-19
OpenJDK Runtime Environment Homebrew (build 18.0.2+0)
OpenJDK 64-Bit Server VM Homebrew (build 18.0.2+0, mixed mode, sharing)

The error message doesn't make it clear how to complete the build without error and I wasn't able to find anything in the README. I did find this, but it's not clear what resolved the issue. I'd prefer to compile the source myself. Thoughts?

[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] cdk                                                                [pom]
[INFO] cdk-base                                                           [pom]
[INFO] cdk-interfaces                                                     [jar]
[INFO] cdk-core                                                           [jar]
[INFO] cdk-standard                                                       [jar]
[INFO] cdk-atomtype                                                       [jar]
[INFO] cdk-valencycheck                                                   [jar]
[INFO] cdk-misc                                                           [pom]
[INFO] cdk-diff                                                           [jar]
[INFO] cdk-test                                                           [jar]
[INFO] cdk-data                                                           [jar]
[INFO] cdk-storage                                                        [pom]
[INFO] cdk-ioformats                                                      [jar]
[INFO] cdk-silent                                                         [jar]
[INFO] cdk-isomorphism                                                    [jar]
[INFO] cdk-datadebug                                                      [jar]
[INFO] cdk-ctab                                                           [jar]
[INFO] cdk-io                                                             [jar]
[INFO] cdk-tool                                                           [pom]
[INFO] cdk-formula                                                        [jar]
[INFO] cdk-dict                                                           [jar]
[INFO] cdk-pdb                                                            [jar]
[INFO] cdk-libiocml                                                       [jar]
[INFO] cdk-smiles                                                         [jar]
[INFO] cdk-extra                                                          [jar]
[INFO] cdk-smarts                                                         [jar]
[INFO] cdk-reaction                                                       [jar]
[INFO] cdk-descriptor                                                     [pom]
[INFO] cdk-fingerprint                                                    [jar]
[INFO] cdk-cip                                                            [jar]
[INFO] cdk-signature                                                      [jar]
[INFO] cdk-charges                                                        [jar]
[INFO] cdk-forcefield                                                     [jar]
[INFO] cdk-sdg                                                            [jar]
[INFO] cdk-builder3dtools                                                 [jar]
[INFO] cdk-builder3d                                                      [jar]
[INFO] cdk-qsar                                                           [jar]
[INFO] cdk-ionpot                                                         [jar]
[INFO] cdk-qsaratomic                                                     [jar]
[INFO] cdk-qsarbond                                                       [jar]
[INFO] cdk-hash                                                           [jar]
[INFO] cdk-fragment                                                       [jar]
[INFO] cdk-model                                                          [jar]
[INFO] cdk-qsarmolecular                                                  [jar]
[INFO] cdk-qsarcml                                                        [jar]
[INFO] cdk-qsarionpot                                                     [jar]
[INFO] cdk-qsarprotein                                                    [jar]
[INFO] cdk-display                                                        [pom]
[INFO] cdk-render                                                         [jar]
[INFO] cdk-renderbasic                                                    [jar]
[INFO] cdk-renderawt                                                      [jar]
[INFO] cdk-renderextra                                                    [jar]
[INFO] cdk-control                                                        [jar]
[INFO] cdk-qm                                                             [jar]
[INFO] cdk-libiomd                                                        [jar]
[INFO] cdk-pdbcml                                                         [jar]
[INFO] cdk-jniinchi-support                                               [jar]
[INFO] cdk-inchi                                                          [jar]
[INFO] cdk-group                                                          [jar]
[INFO] cdk-pcore                                                          [jar]
[INFO] cdk-structgen                                                      [jar]
[INFO] cdk-tautomer                                                       [jar]
[INFO] cdk-legacy                                                         [jar]
[INFO] cdk-app                                                            [pom]
[INFO] cdk-depict                                                         [jar]
[INFO] cdk-iordf                                                          [jar]
[INFO] cdk-bundle                                                         [jar]
[INFO] cdk-annotation                                                     [jar]
[INFO] cdk-test-atomtype                                                  [jar]
[INFO] cdk-log4j                                                          [jar]
[INFO] cdk-test-core                                                      [jar]
[INFO] cdk-test-standard                                                  [jar]
[INFO] cdk-test-valencycheck                                              [jar]
[INFO] cdk-qsarsubstance                                                  [jar]
[INFO] cdk-test-extra                                                     [jar]
[INFO] cdk-slf4j                                                          [jar]
[INFO] 
[INFO] ----------------------< org.openscience.cdk:cdk >-----------------------
[INFO] Building cdk 2.9-SNAPSHOT                                         [1/76]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk ---
[WARNING] Ignoring project type pom - supportedProjectTypes = [jar, bundle]
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk ---
[INFO] Installing /Users/rich/src/java/cdk/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk/2.9-SNAPSHOT/cdk-2.9-SNAPSHOT.pom
[INFO] 
[INFO] --------------------< org.openscience.cdk:cdk-base >--------------------
[INFO] Building cdk-base 2.9-SNAPSHOT                                    [2/76]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-base ---
[WARNING] Ignoring project type pom - supportedProjectTypes = [jar, bundle]
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-base ---
[INFO] Installing /Users/rich/src/java/cdk/base/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-base/2.9-SNAPSHOT/cdk-base-2.9-SNAPSHOT.pom
[INFO] 
[INFO] -----------------< org.openscience.cdk:cdk-interfaces >-----------------
[INFO] Building cdk-interfaces 2.9-SNAPSHOT                              [3/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-interfaces ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/interfaces/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-interfaces ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-interfaces ---
[INFO] Writing manifest: /Users/rich/src/java/cdk/base/interfaces/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-interfaces ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/interfaces/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-interfaces ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-interfaces ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-interfaces ---
[INFO] Building jar: /Users/rich/src/java/cdk/base/interfaces/target/cdk-interfaces-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-interfaces ---
[INFO] Installing /Users/rich/src/java/cdk/base/interfaces/target/cdk-interfaces-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-interfaces/2.9-SNAPSHOT/cdk-interfaces-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/base/interfaces/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-interfaces/2.9-SNAPSHOT/cdk-interfaces-2.9-SNAPSHOT.pom
[INFO] 
[INFO] --------------------< org.openscience.cdk:cdk-core >--------------------
[INFO] Building cdk-core 2.9-SNAPSHOT                                    [4/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 7 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-core ---
[INFO] Writing manifest: /Users/rich/src/java/cdk/base/core/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/core/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-core ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-core ---
[INFO] Building jar: /Users/rich/src/java/cdk/base/core/target/cdk-core-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-core ---
[INFO] Installing /Users/rich/src/java/cdk/base/core/target/cdk-core-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-core/2.9-SNAPSHOT/cdk-core-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/base/core/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-core/2.9-SNAPSHOT/cdk-core-2.9-SNAPSHOT.pom
[INFO] 
[INFO] ------------------< org.openscience.cdk:cdk-standard >------------------
[INFO] Building cdk-standard 2.9-SNAPSHOT                                [5/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-standard ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-standard ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-standard ---
[INFO] Writing manifest: /Users/rich/src/java/cdk/base/standard/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-standard ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/standard/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-standard ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-standard ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-standard ---
[INFO] Building jar: /Users/rich/src/java/cdk/base/standard/target/cdk-standard-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-standard ---
[INFO] Installing /Users/rich/src/java/cdk/base/standard/target/cdk-standard-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-standard/2.9-SNAPSHOT/cdk-standard-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/base/standard/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-standard/2.9-SNAPSHOT/cdk-standard-2.9-SNAPSHOT.pom
[INFO] 
[INFO] ------------------< org.openscience.cdk:cdk-atomtype >------------------
[INFO] Building cdk-atomtype 2.9-SNAPSHOT                                [6/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-atomtype ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 7 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-atomtype ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-atomtype ---
[INFO] Writing manifest: /Users/rich/src/java/cdk/base/atomtype/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-atomtype ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/atomtype/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-atomtype ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-atomtype ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-atomtype ---
[INFO] Building jar: /Users/rich/src/java/cdk/base/atomtype/target/cdk-atomtype-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-atomtype ---
[INFO] Installing /Users/rich/src/java/cdk/base/atomtype/target/cdk-atomtype-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-atomtype/2.9-SNAPSHOT/cdk-atomtype-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/base/atomtype/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-atomtype/2.9-SNAPSHOT/cdk-atomtype-2.9-SNAPSHOT.pom
[INFO] 
[INFO] ----------------< org.openscience.cdk:cdk-valencycheck >----------------
[INFO] Building cdk-valencycheck 2.9-SNAPSHOT                            [7/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-valencycheck ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/valencycheck/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-valencycheck ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-valencycheck ---
[INFO] Writing manifest: /Users/rich/src/java/cdk/base/valencycheck/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-valencycheck ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/valencycheck/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-valencycheck ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.16:test (default-test) @ cdk-valencycheck ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-valencycheck ---
[INFO] Building jar: /Users/rich/src/java/cdk/base/valencycheck/target/cdk-valencycheck-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-valencycheck ---
[INFO] Installing /Users/rich/src/java/cdk/base/valencycheck/target/cdk-valencycheck-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-valencycheck/2.9-SNAPSHOT/cdk-valencycheck-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/base/valencycheck/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-valencycheck/2.9-SNAPSHOT/cdk-valencycheck-2.9-SNAPSHOT.pom
[INFO] 
[INFO] --------------------< org.openscience.cdk:cdk-misc >--------------------
[INFO] Building cdk-misc 2.9-SNAPSHOT                                    [8/76]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-misc ---
[WARNING] Ignoring project type pom - supportedProjectTypes = [jar, bundle]
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-misc ---
[INFO] Installing /Users/rich/src/java/cdk/misc/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-misc/2.9-SNAPSHOT/cdk-misc-2.9-SNAPSHOT.pom
[INFO] 
[INFO] --------------------< org.openscience.cdk:cdk-diff >--------------------
[INFO] Building cdk-diff 2.9-SNAPSHOT                                    [9/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-diff ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/misc/diff/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-diff ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-diff ---
[INFO] Writing manifest: /Users/rich/src/java/cdk/misc/diff/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-diff ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/misc/diff/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-diff ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M7:test (default-test) @ cdk-diff ---
[INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.openscience.cdk.tools.diff.tree.BooleanArrayDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.openscience.cdk.tools.diff.tree.BooleanArrayDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.BondOrderDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.openscience.cdk.tools.diff.tree.BondOrderDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.IntegerDifferenceTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.openscience.cdk.tools.diff.tree.IntegerDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.BooleanDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.openscience.cdk.tools.diff.tree.BooleanDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.AbstractDifferenceTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.openscience.cdk.tools.diff.tree.AbstractDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.Point2dDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.openscience.cdk.tools.diff.tree.Point2dDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.DoubleDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.openscience.cdk.tools.diff.tree.DoubleDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.StringDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.openscience.cdk.tools.diff.tree.StringDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.Point3dDifferenceTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.openscience.cdk.tools.diff.tree.Point3dDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.tree.AbstractDifferenceListTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.openscience.cdk.tools.diff.tree.AbstractDifferenceListTest
[INFO] Running org.openscience.cdk.tools.diff.tree.ChemObjectDifferenceTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.openscience.cdk.tools.diff.tree.ChemObjectDifferenceTest
[INFO] Running org.openscience.cdk.tools.diff.LonePairDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 s - in org.openscience.cdk.tools.diff.LonePairDiffTest
[INFO] Running org.openscience.cdk.tools.diff.ElectronContainerDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.openscience.cdk.tools.diff.ElectronContainerDiffTest
[INFO] Running org.openscience.cdk.tools.diff.AtomContainerDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.openscience.cdk.tools.diff.AtomContainerDiffTest
[INFO] Running org.openscience.cdk.tools.diff.AtomTypeDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.openscience.cdk.tools.diff.AtomTypeDiffTest
[INFO] Running org.openscience.cdk.tools.diff.SingleElectronDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.openscience.cdk.tools.diff.SingleElectronDiffTest
[INFO] Running org.openscience.cdk.tools.diff.AtomDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.openscience.cdk.tools.diff.AtomDiffTest
[INFO] Running org.openscience.cdk.tools.diff.IsotopeDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.openscience.cdk.tools.diff.IsotopeDiffTest
[INFO] Running org.openscience.cdk.tools.diff.BondDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.openscience.cdk.tools.diff.BondDiffTest
[INFO] Running org.openscience.cdk.tools.diff.ChemObjectDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.openscience.cdk.tools.diff.ChemObjectDiffTest
[INFO] Running org.openscience.cdk.tools.diff.ElementDiffTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.openscience.cdk.tools.diff.ElementDiffTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 81, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-diff ---
[INFO] Building jar: /Users/rich/src/java/cdk/misc/diff/target/cdk-diff-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-diff ---
[INFO] Installing /Users/rich/src/java/cdk/misc/diff/target/cdk-diff-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-diff/2.9-SNAPSHOT/cdk-diff-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/misc/diff/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-diff/2.9-SNAPSHOT/cdk-diff-2.9-SNAPSHOT.pom
[INFO] 
[INFO] --------------------< org.openscience.cdk:cdk-test >--------------------
[INFO] Building cdk-test 2.9-SNAPSHOT                                   [10/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-test ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/test/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-test ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-test ---
[WARNING] Manifest org.openscience.cdk:cdk-test:jar:2.9-SNAPSHOT : Unused Export-Package instructions: [org.openscience.*] 
[INFO] Writing manifest: /Users/rich/src/java/cdk/base/test/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-test ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/test/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-test ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M7:test (default-test) @ cdk-test ---
[INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.openscience.cdk.test.CDKTestCase
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.openscience.cdk.test.CDKTestCase
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --- maven-jar-plugin:3.2.2:jar (default-jar) @ cdk-test ---
[INFO] Building jar: /Users/rich/src/java/cdk/base/test/target/cdk-test-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.2:test-jar (default) @ cdk-test ---
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-test ---
[INFO] Installing /Users/rich/src/java/cdk/base/test/target/cdk-test-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-test/2.9-SNAPSHOT/cdk-test-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/base/test/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-test/2.9-SNAPSHOT/cdk-test-2.9-SNAPSHOT.pom
[INFO] Installing /Users/rich/src/java/cdk/base/test/target/cdk-test-2.9-SNAPSHOT-tests.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-test/2.9-SNAPSHOT/cdk-test-2.9-SNAPSHOT-tests.jar
[INFO] 
[INFO] --------------------< org.openscience.cdk:cdk-data >--------------------
[INFO] Building cdk-data 2.9-SNAPSHOT                                   [11/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-data ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/data/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-data ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-data ---
[INFO] Writing manifest: /Users/rich/src/java/cdk/base/data/target/classes/META-INF/MANIFEST.MF
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cdk-data ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/rich/src/java/cdk/base/data/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ cdk-data ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M7:test (default-test) @ cdk-data ---
[INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.openscience.cdk.ReactionSetTest
[INFO] Tests run: 60, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.openscience.cdk.ReactionSetTest
[INFO] Running org.openscience.cdk.ChemObjectTest
[INFO] Tests run: 53, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.openscience.cdk.ChemObjectTest
[INFO] Running org.openscience.cdk.StrandTest
[INFO] Tests run: 201, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.openscience.cdk.StrandTest
[INFO] Running org.openscience.cdk.PseudoAtomTest
[INFO] Tests run: 136, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.openscience.cdk.PseudoAtomTest
[INFO] Running org.openscience.cdk.MonomerTest
[INFO] Tests run: 195, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.openscience.cdk.MonomerTest
[INFO] Running org.openscience.cdk.AtomContainerTest
[INFO] Tests run: 193, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.openscience.cdk.AtomContainerTest
[INFO] Running org.openscience.cdk.SingleElectronTest
[INFO] Tests run: 58, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.openscience.cdk.SingleElectronTest
[INFO] Running org.openscience.cdk.ChemSequenceTest
[INFO] Tests run: 58, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.openscience.cdk.ChemSequenceTest
[INFO] Running org.openscience.cdk.protein.data.PDBStructureTest
[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.openscience.cdk.protein.data.PDBStructureTest
[INFO] Running org.openscience.cdk.protein.data.PDBAtomTest
[INFO] Tests run: 153, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.openscience.cdk.protein.data.PDBAtomTest
[INFO] Running org.openscience.cdk.protein.data.PDBMonomerTest
[INFO] Tests run: 201, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.openscience.cdk.protein.data.PDBMonomerTest
[INFO] Running org.openscience.cdk.protein.data.PDBPolymerTest
[INFO] Tests run: 212, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.openscience.cdk.protein.data.PDBPolymerTest
[INFO] Running org.openscience.cdk.AtomTypeTest
[INFO] Tests run: 112, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.openscience.cdk.AtomTypeTest
[INFO] Running org.openscience.cdk.SubstanceTest
[INFO] Tests run: 78, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 s - in org.openscience.cdk.SubstanceTest
[INFO] Running org.openscience.cdk.ElementTest
[INFO] Tests run: 66, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.openscience.cdk.ElementTest
[INFO] Running org.openscience.cdk.PolymerTest
[INFO] Tests run: 199, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.openscience.cdk.PolymerTest
[INFO] Running org.openscience.cdk.ElectronContainerTest
[INFO] Tests run: 53, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.openscience.cdk.ElectronContainerTest
[INFO] Running org.openscience.cdk.ReactionSchemeTest
[INFO] Tests run: 66, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.openscience.cdk.ReactionSchemeTest
[INFO] Running org.openscience.cdk.CrystalTest
[INFO] Tests run: 204, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.openscience.cdk.CrystalTest
[INFO] Running org.openscience.cdk.RingTest
[INFO] Tests run: 197, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.openscience.cdk.RingTest
[INFO] Running org.openscience.cdk.ChemFileTest
[INFO] Tests run: 58, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.openscience.cdk.ChemFileTest
[INFO] Running org.openscience.cdk.DefaultChemObjectBuilderTest
[INFO] Tests run: 82, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.openscience.cdk.DefaultChemObjectBuilderTest
[INFO] Running org.openscience.cdk.BondTest
[INFO] Tests run: 86, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.openscience.cdk.BondTest
[INFO] Running org.openscience.cdk.ConformerContainerTest
[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.openscience.cdk.ConformerContainerTest
[INFO] Running org.openscience.cdk.FragmentAtomTest
[INFO] Tests run: 136, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.openscience.cdk.FragmentAtomTest
[INFO] Running org.openscience.cdk.AtomContainerSetTest
[INFO] Tests run: 79, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.openscience.cdk.AtomContainerSetTest
[INFO] Running org.openscience.cdk.formula.AdductFormulaTest
[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.openscience.cdk.formula.AdductFormulaTest
[INFO] Running org.openscience.cdk.formula.MolecularFormulaSetTest
[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.openscience.cdk.formula.MolecularFormulaSetTest
[INFO] Running org.openscience.cdk.formula.MolecularFormulaTest
[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.openscience.cdk.formula.MolecularFormulaTest
[INFO] Running org.openscience.cdk.ReactionTest
[INFO] Tests run: 79, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.openscience.cdk.ReactionTest
[INFO] Running org.openscience.cdk.LonePairTest
[INFO] Tests run: 58, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.openscience.cdk.LonePairTest
[INFO] Running org.openscience.cdk.MappingTest
[INFO] Tests run: 54, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.openscience.cdk.MappingTest
[INFO] Running org.openscience.cdk.BioPolymerTest
[INFO] Tests run: 205, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.openscience.cdk.BioPolymerTest
[INFO] Running org.openscience.cdk.AtomTest
[INFO] Tests run: 137, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.openscience.cdk.AtomTest
[INFO] Running org.openscience.cdk.MoleculeTest
[INFO] Tests run: 194, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.openscience.cdk.MoleculeTest
[INFO] Running org.openscience.cdk.AtomContainer2Test
[INFO] Tests run: 194, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.openscience.cdk.AtomContainer2Test
[INFO] Running org.openscience.cdk.event.ChemObjectChangeEventTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.openscience.cdk.event.ChemObjectChangeEventTest
[INFO] Running org.openscience.cdk.AminoAcidTest
[INFO] Tests run: 199, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.openscience.cdk.AminoAcidTest
[INFO] Running org.openscience.cdk.IsotopeTest
[INFO] Tests run: 76, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.openscience.cdk.IsotopeTest
[INFO] Running org.openscience.cdk.ChemModelTest
[INFO] Tests run: 76, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.openscience.cdk.ChemModelTest
[INFO] Running org.openscience.cdk.ChangeEventPropagationTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.openscience.cdk.ChangeEventPropagationTest
[INFO] Running org.openscience.cdk.RingSetTest
[INFO] Tests run: 86, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.openscience.cdk.RingSetTest
[INFO] 
[INFO] Results:
[INFO] 
[INFO] Tests run: 4429, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ cdk-data ---
[INFO] Building jar: /Users/rich/src/java/cdk/base/data/target/cdk-data-2.9-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-data ---
[INFO] Installing /Users/rich/src/java/cdk/base/data/target/cdk-data-2.9-SNAPSHOT.jar to /Users/rich/.m2/repository/org/openscience/cdk/cdk-data/2.9-SNAPSHOT/cdk-data-2.9-SNAPSHOT.jar
[INFO] Installing /Users/rich/src/java/cdk/base/data/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-data/2.9-SNAPSHOT/cdk-data-2.9-SNAPSHOT.pom
[INFO] 
[INFO] ------------------< org.openscience.cdk:cdk-storage >-------------------
[INFO] Building cdk-storage 2.9-SNAPSHOT                                [12/76]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-storage ---
[WARNING] Ignoring project type pom - supportedProjectTypes = [jar, bundle]
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ cdk-storage ---
[INFO] Installing /Users/rich/src/java/cdk/storage/pom.xml to /Users/rich/.m2/repository/org/openscience/cdk/cdk-storage/2.9-SNAPSHOT/cdk-storage-2.9-SNAPSHOT.pom
[INFO] 
[INFO] -----------------< org.openscience.cdk:cdk-ioformats >------------------
[INFO] Building cdk-ioformats 2.9-SNAPSHOT                              [13/76]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cdk-ioformats ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ cdk-ioformats ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 102 source files to /Users/rich/src/java/cdk/storage/ioformats/target/classes
[INFO] 
[INFO] --- maven-bundle-plugin:5.1.8:manifest (bundle-manifest) @ cdk-ioformats ---
[INFO] No MANIFEST.MF file found, generating manifest.
[ERROR] /Users/rich/src/java/cdk/storage/ioformats/target/classes/org/openscience/cdk/io/formats/MDLRXNV2000Format.class
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for cdk 2.9-SNAPSHOT:
[INFO] 
[INFO] cdk ................................................ SUCCESS [  0.313 s]
[INFO] cdk-base ........................................... SUCCESS [  0.006 s]
[INFO] cdk-interfaces ..................................... SUCCESS [  0.600 s]
[INFO] cdk-core ........................................... SUCCESS [  0.177 s]
[INFO] cdk-standard ....................................... SUCCESS [  0.122 s]
[INFO] cdk-atomtype ....................................... SUCCESS [  0.060 s]
[INFO] cdk-valencycheck ................................... SUCCESS [  0.047 s]
[INFO] cdk-misc ........................................... SUCCESS [  0.003 s]
[INFO] cdk-diff ........................................... SUCCESS [  0.992 s]
[INFO] cdk-test ........................................... SUCCESS [  0.377 s]
[INFO] cdk-data ........................................... SUCCESS [  1.559 s]
[INFO] cdk-storage ........................................ SUCCESS [  0.002 s]
[INFO] cdk-ioformats ...................................... FAILURE [  0.525 s]
[INFO] cdk-silent ......................................... SKIPPED
[INFO] cdk-isomorphism .................................... SKIPPED
[INFO] cdk-datadebug ...................................... SKIPPED
[INFO] cdk-ctab ........................................... SKIPPED
[INFO] cdk-io ............................................. SKIPPED
[INFO] cdk-tool ........................................... SKIPPED
[INFO] cdk-formula ........................................ SKIPPED
[INFO] cdk-dict ........................................... SKIPPED
[INFO] cdk-pdb ............................................ SKIPPED
[INFO] cdk-libiocml ....................................... SKIPPED
[INFO] cdk-smiles ......................................... SKIPPED
[INFO] cdk-extra .......................................... SKIPPED
[INFO] cdk-smarts ......................................... SKIPPED
[INFO] cdk-reaction ....................................... SKIPPED
[INFO] cdk-descriptor ..................................... SKIPPED
[INFO] cdk-fingerprint .................................... SKIPPED
[INFO] cdk-cip ............................................ SKIPPED
[INFO] cdk-signature ...................................... SKIPPED
[INFO] cdk-charges ........................................ SKIPPED
[INFO] cdk-forcefield ..................................... SKIPPED
[INFO] cdk-sdg ............................................ SKIPPED
[INFO] cdk-builder3dtools ................................. SKIPPED
[INFO] cdk-builder3d ...................................... SKIPPED
[INFO] cdk-qsar ........................................... SKIPPED
[INFO] cdk-ionpot ......................................... SKIPPED
[INFO] cdk-qsaratomic ..................................... SKIPPED
[INFO] cdk-qsarbond ....................................... SKIPPED
[INFO] cdk-hash ........................................... SKIPPED
[INFO] cdk-fragment ....................................... SKIPPED
[INFO] cdk-model .......................................... SKIPPED
[INFO] cdk-qsarmolecular .................................. SKIPPED
[INFO] cdk-qsarcml ........................................ SKIPPED
[INFO] cdk-qsarionpot ..................................... SKIPPED
[INFO] cdk-qsarprotein .................................... SKIPPED
[INFO] cdk-display ........................................ SKIPPED
[INFO] cdk-render ......................................... SKIPPED
[INFO] cdk-renderbasic .................................... SKIPPED
[INFO] cdk-renderawt ...................................... SKIPPED
[INFO] cdk-renderextra .................................... SKIPPED
[INFO] cdk-control ........................................ SKIPPED
[INFO] cdk-qm ............................................. SKIPPED
[INFO] cdk-libiomd ........................................ SKIPPED
[INFO] cdk-pdbcml ......................................... SKIPPED
[INFO] cdk-jniinchi-support ............................... SKIPPED
[INFO] cdk-inchi .......................................... SKIPPED
[INFO] cdk-group .......................................... SKIPPED
[INFO] cdk-pcore .......................................... SKIPPED
[INFO] cdk-structgen ...................................... SKIPPED
[INFO] cdk-tautomer ....................................... SKIPPED
[INFO] cdk-legacy ......................................... SKIPPED
[INFO] cdk-app ............................................ SKIPPED
[INFO] cdk-depict ......................................... SKIPPED
[INFO] cdk-iordf .......................................... SKIPPED
[INFO] cdk-bundle ......................................... SKIPPED
[INFO] cdk-annotation ..................................... SKIPPED
[INFO] cdk-test-atomtype .................................. SKIPPED
[INFO] cdk-log4j .......................................... SKIPPED
[INFO] cdk-test-core ...................................... SKIPPED
[INFO] cdk-test-standard .................................. SKIPPED
[INFO] cdk-test-valencycheck .............................. SKIPPED
[INFO] cdk-qsarsubstance .................................. SKIPPED
[INFO] cdk-test-extra ..................................... SKIPPED
[INFO] cdk-slf4j .......................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  4.955 s
[INFO] Finished at: 2022-11-29T21:36:21-08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.felix:maven-bundle-plugin:5.1.8:manifest (bundle-manifest) on project cdk-ioformats: Error trying to generate Manifest: /Users/rich/src/java/cdk/storage/ioformats/target/classes/org/openscience/cdk/io/formats/MDLRXNV2000Format.class -> [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 :cdk-ioformats

[egonw]

Thanks, Rich. This is a weird error: Error trying to generate Manifest: /Users/rich/src/java/cdk/storage/ioformats/target/classes/org/openscience/cdk/io/formats/MDLRXNV2000Format.class

[uli-f]

The one thing I cannot find in your description above is the actual maven command you used to build this.

Would you mind adding this to the description. Thanks.

[egonw]

The one thing I cannot find in your description above is the actual maven command you used to build this.

It's in the first line, I think?

[uli-f]

The one thing I cannot find in your description above is the actual maven command you used to build this.

It's in the first line, I think?

Correct! Thanks for pointing this out. Seems it is time for me to call it a day 😄

One more thing though:
Failed to execute goal org.apache.felix:maven-bundle-plugin:5.1.8:manifest (bundle-manifest)

Where does the org.apache.felix:maven-bundle-plugin come from? I cannot find this in any of the pom.xmls of CDK...?

[egonw]

That maven plugin is very new: #934

Yeah, I guess there is something about this module (or even that class specifically) that is not compatible with that plugin. But I find that very unexpected. I'll try to look into this this week. Sorry, it's been too darn busy with the year end approaching :/

[johnmay]

Use Java 17?

[johnmay]

@rapodaca did you have an old build laying around, just tested on:

[john@sentinel:cdk]% java -version
openjdk version "18.0.2.1" 2022-08-18
OpenJDK Runtime Environment (build 18.0.2.1+1-1)
OpenJDK 64-Bit Server VM (build 18.0.2.1+1-1, mixed mode, sharing)
[john@sentinel:cdk]%

And no issues with a "clean install":

$ mvn clean install -q -o -DskipTests  113.83s user 12.62s system 175% cpu 1:12.07 total

I wish this was better advertised by the JDK 18/19 are sort of like public betas and you're better using the LTS Java 8/11/17. Java 17 for example runs the build in only 20s.

[john@sentinel:cdk]% java -version
openjdk version "17.0.1" 2021-10-19
OpenJDK Runtime Environment (build 17.0.1+12-39)
OpenJDK 64-Bit Server VM (build 17.0.1+12-39, mixed mode, sharing)

$ mvn clean install -q -o -DskipTests  58.75s user 4.15s system 296% cpu 21.218 total

[rapodaca]

@johnmay, that worked.

I thought I had freshly cloned the repo before starting, but apparently I had not.

On a fresh clone, calling mvn install using the same commit and system, compilation succeeds and all tests pass.

No need to change JDK or use any other command.

Looking at the timestamps in my first clone, it looks like I may have attempted a build on Nov 11. I could still reproduce the error in that first repo. Using mvn clean then mvn build resolved the problem there as well (which I thought I had tried). 🙃

[johnmay]

Still a little odd as it should just rebuild the parts it needs and even if you changed java versions we compile for java 1.8 so should be ultra compatible.

Thanks for the report though, good to know incase others have similar issues