I used the neo4j-rdkit plugin in (neo4j desktop) windows environment without any issue. However, I tried the the same for the neo4j-rdkit plugin within the neo4j docker image but with no success. I have found here another related post but unfortunately it doesn't solve my issue. Other neo4j plugins such as APOC, GDS, etc. worked fine with me.
Here the detailed error:
`docker run --user="$(id -u):$(id -g)" --publish=7474:7474 --publish=7687:7687 -e NEO4J_dbms_security_procedures_unrestricted=apoc.,gds.,n10s.,rdkit. -e NEO4J_rdkit_index_sanitize=true --volume=$HOME/data/neo4j/data:/var/lib/neo4j/data --volume=$HOME/data/neo4j/logs:/var/lib/neo4j/logs --volume=$HOME/data/neo4j/plugins:/var/lib/neo4j/plugins --volume=$HOME/data/neo4j/import:/var/lib/neo4j/import --name neo4j neo4j
2022-02-07 17:13:52.340+0000 INFO Starting...
2022-02-07 17:13:52.753+0000 INFO This instance is ServerId{f2bc4375} (f2bc4375-4ffd-45e6-ab0a-9b108d516b64)
2022-02-07 17:13:54.369+0000 INFO ======== Neo4j 4.4.3 ========
2022-02-07 17:13:54.722+0000 INFO Loading libraries from JAR
2022-02-07 17:13:54.839+0000 INFO trying to load native library /tmp/rdkit-153718487753989773/libGraphMolWrap.so
2022-02-07 17:13:54.854+0000 ERROR Failed to start Neo4j on 0.0.0.0:7474.
java.lang.RuntimeException: Error starting Neo4j database server at /data/databases
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:228) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.build(DatabaseManagementServiceFactory.java:181) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.CommunityBootstrapper.createNeo(CommunityBootstrapper.java:36) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:142) [neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:95) [neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:34) [neo4j-4.4.3.jar:4.4.3]
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.rdkit.neo4j.bin.LibraryLoaderLifecycle@6094de13' failed to initialize. Please see the attached cause exception "/tmp/rdkit-153718487753989773/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:424) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.extension.AbstractExtensions.init(AbstractExtensions.java:77) ~[neo4j-kernel-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:101) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.3.jar:4.4.3]
... 5 more
Caused by: java.lang.UnsatisfiedLinkError: /tmp/rdkit-153718487753989773/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load0(Native Method) ~[?:?]
at java.lang.ClassLoader$NativeLibrary.load(ClassLoader.java:2442) ~[?:?]
at java.lang.ClassLoader$NativeLibrary.loadLibrary(ClassLoader.java:2498) ~[?:?]
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:2694) ~[?:?]
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:2627) ~[?:?]
at java.lang.Runtime.load0(Runtime.java:768) ~[?:?]
at java.lang.System.load(System.java:1837) ~[?:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.lambda$loadNativeLibraries$0(LibraryLoaderLifecycle.java:75) ~[rdkit-index-1.2.0-4.2.jar:?]
at java.util.ArrayList.forEach(ArrayList.java:1541) ~[?:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.loadNativeLibraries(LibraryLoaderLifecycle.java:73) ~[rdkit-index-1.2.0-4.2.jar:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.init(LibraryLoaderLifecycle.java:55) ~[rdkit-index-1.2.0-4.2.jar:?]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.extension.AbstractExtensions.init(AbstractExtensions.java:77) ~[neo4j-kernel-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:101) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.3.jar:4.4.3]`
I used the neo4j-rdkit plugin in (neo4j desktop) windows environment without any issue. However, I tried the the same for the neo4j-rdkit plugin within the neo4j docker image but with no success. I have found here another related post but unfortunately it doesn't solve my issue. Other neo4j plugins such as APOC, GDS, etc. worked fine with me.
Here the detailed error:
`docker run --user="$(id -u):$(id -g)" --publish=7474:7474 --publish=7687:7687 -e NEO4J_dbms_security_procedures_unrestricted=apoc.,gds.,n10s.,rdkit. -e NEO4J_rdkit_index_sanitize=true --volume=$HOME/data/neo4j/data:/var/lib/neo4j/data --volume=$HOME/data/neo4j/logs:/var/lib/neo4j/logs --volume=$HOME/data/neo4j/plugins:/var/lib/neo4j/plugins --volume=$HOME/data/neo4j/import:/var/lib/neo4j/import --name neo4j neo4j
2022-02-07 17:13:52.340+0000 INFO Starting...
2022-02-07 17:13:52.753+0000 INFO This instance is ServerId{f2bc4375} (f2bc4375-4ffd-45e6-ab0a-9b108d516b64)
2022-02-07 17:13:54.369+0000 INFO ======== Neo4j 4.4.3 ========
2022-02-07 17:13:54.722+0000 INFO Loading libraries from JAR
2022-02-07 17:13:54.839+0000 INFO trying to load native library /tmp/rdkit-153718487753989773/libGraphMolWrap.so
2022-02-07 17:13:54.854+0000 ERROR Failed to start Neo4j on 0.0.0.0:7474.
java.lang.RuntimeException: Error starting Neo4j database server at /data/databases
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:228) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.build(DatabaseManagementServiceFactory.java:181) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.CommunityBootstrapper.createNeo(CommunityBootstrapper.java:36) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:142) [neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:95) [neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:34) [neo4j-4.4.3.jar:4.4.3]
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.rdkit.neo4j.bin.LibraryLoaderLifecycle@6094de13' failed to initialize. Please see the attached cause exception "/tmp/rdkit-153718487753989773/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:424) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.extension.AbstractExtensions.init(AbstractExtensions.java:77) ~[neo4j-kernel-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:101) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.3.jar:4.4.3]
... 5 more
Caused by: java.lang.UnsatisfiedLinkError: /tmp/rdkit-153718487753989773/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load0(Native Method) ~[?:?]
at java.lang.ClassLoader$NativeLibrary.load(ClassLoader.java:2442) ~[?:?]
at java.lang.ClassLoader$NativeLibrary.loadLibrary(ClassLoader.java:2498) ~[?:?]
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:2694) ~[?:?]
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:2627) ~[?:?]
at java.lang.Runtime.load0(Runtime.java:768) ~[?:?]
at java.lang.System.load(System.java:1837) ~[?:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.lambda$loadNativeLibraries$0(LibraryLoaderLifecycle.java:75) ~[rdkit-index-1.2.0-4.2.jar:?]
at java.util.ArrayList.forEach(ArrayList.java:1541) ~[?:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.loadNativeLibraries(LibraryLoaderLifecycle.java:73) ~[rdkit-index-1.2.0-4.2.jar:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.init(LibraryLoaderLifecycle.java:55) ~[rdkit-index-1.2.0-4.2.jar:?]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.extension.AbstractExtensions.init(AbstractExtensions.java:77) ~[neo4j-kernel-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:101) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.3.jar:4.4.3]`