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fjossinet / RNArtist

With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
https://twitter.com/rnartist_app
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how to add experimental value by loading the SHAPE reactivity file? #4

Closed MingleiYang closed 3 years ago

MingleiYang commented 3 years ago

Hi, Prof. jossinet, I am wondering if there is any way to label the RNA structure color by uploading one file, such as SHAPE experimental data?

fjossinet commented 3 years ago

Hi,

This is on the way. I have initiated this work at the level of the drawing engine of RNArtist (RNArtistCore https://github.com/fjossinet/RNArtistCore). You can see in the README of this project that i produced some examples where data are linked to the 2D and visualised with a colored gradient using the RNArtistCore language. RNArtist has now an editor which allows you to use this language https://twitter.com/rnartist_app/status/1359438446742405121. So technically it should work, but only by using the RNArtistCore language. No graphical controls at now (but this should come soon).

fjossinet commented 3 years ago

Another example here: https://twitter.com/rnartist_app/status/1360291893796610055?s=20

MingleiYang commented 3 years ago

Hi, Prof. jossinet, thank you for your reply.

the RNArtistCore worked but it can not interactively to modify the conformation since my RNA is too long.

so I think may be the second option of ACE editor may be suitable.

However, I checked the new version of RNArtist, I could not see the entrance to use the ACE editor. i think the picture in the https://twitter.com/rnartist_app/status/1359438446742405121 has a sign of ">_", however it doesn't show up in the main screen of the RNArtist. Could you give me some suggestions? thank you very much

My best,

fjossinet commented 3 years ago

Right!. It should be available now with the last commit.

MingleiYang commented 3 years ago

Hi, Prof.Fabrice

Thank you very much fr reply. however, I came across the compilation error as follows,

[INFO] Scanning for projects... [INFO] [INFO] ---------------< io.github.fjossinet.rnartist:rnartist >---------------- [INFO] Building RNArtist 1.0 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ rnartist --- [INFO] Deleting /Users/myang/biosoft/RNArtist/target [INFO] [INFO] --- maven-dependency-plugin:2.8:copy-dependencies (copy-dependencies) @ rnartist --- [INFO] Copying jasypt-1.9.3.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/jasypt-1.9.3.jar [INFO] Copying jcip-annotations-1.0.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/jcip-annotations-1.0.jar [INFO] Copying slf4j-simple-2.0.0-alpha1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/slf4j-simple-2.0.0-alpha1.jar [INFO] Copying ikonli-fontawesome5-pack-12.1.0.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/ikonli-fontawesome5-pack-12.1.0.jar [INFO] Copying podam-7.2.3.RELEASE.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/podam-7.2.3.RELEASE.jar [INFO] Copying ikonli-core-12.1.0.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/ikonli-core-12.1.0.jar [INFO] Copying kotlinx-coroutines-core-1.3.7.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlinx-coroutines-core-1.3.7.jar [INFO] Copying kotlin-reflect-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-reflect-1.4.10.jar [INFO] Copying jdom-2.0.2.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/jdom-2.0.2.jar [INFO] Copying javafx-web-16-ea+6-mac.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-web-16-ea+6-mac.jar [INFO] Copying controlsfx-11.0.3.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/controlsfx-11.0.3.jar [INFO] Copying okio-2.4.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/okio-2.4.1.jar [INFO] Copying objenesis-2.6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/objenesis-2.6.jar [INFO] Copying commons-io-2.6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/commons-io-2.6.jar [INFO] Copying kotlin-scripting-jsr223-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-scripting-jsr223-1.4.10.jar [INFO] Copying javafx-media-16-ea+6-mac.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-media-16-ea+6-mac.jar [INFO] Copying slf4j-api-2.0.0-alpha1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/slf4j-api-2.0.0-alpha1.jar [INFO] Copying javax.annotation-api-1.3.2.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javax.annotation-api-1.3.2.jar [INFO] Copying javafx-base-16-ea+6-mac.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-base-16-ea+6-mac.jar [INFO] Copying javafx-graphics-16-ea+6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-graphics-16-ea+6.jar [INFO] Copying kotlin-daemon-embeddable-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-daemon-embeddable-1.4.10.jar [INFO] Copying kotlin-compiler-embeddable-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-compiler-embeddable-1.4.10.jar [INFO] Copying javafx-media-16-ea+6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-media-16-ea+6.jar [INFO] Copying jackson-core-2.10.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/jackson-core-2.10.1.jar [INFO] Copying kotlin-scripting-compiler-embeddable-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-scripting-compiler-embeddable-1.4.10.jar [INFO] Copying validation-api-1.1.0.Final.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/validation-api-1.1.0.Final.jar [INFO] Copying kotlin-scripting-jvm-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-scripting-jvm-1.4.10.jar [INFO] Copying kotlin-script-runtime-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-script-runtime-1.4.10.jar [INFO] Copying rnartistcore-0.2.5-SNAPSHOT.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/rnartistcore-0.2.5-SNAPSHOT.jar [INFO] Copying javafx-controls-16-ea+6-mac.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-controls-16-ea+6-mac.jar [INFO] Copying javafx-swing-16-ea+6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-swing-16-ea+6.jar [INFO] Copying javafx-web-16-ea+6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-web-16-ea+6.jar [INFO] Copying okhttp-4.3.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/okhttp-4.3.1.jar [INFO] Copying kotlin-stdlib-common-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-stdlib-common-1.4.10.jar [INFO] Copying jackson-databind-2.10.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/jackson-databind-2.10.1.jar [INFO] Copying gson-2.8.6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/gson-2.8.6.jar [INFO] Copying javafx-controls-16-ea+6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-controls-16-ea+6.jar [INFO] Copying swing-worker-1.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/swing-worker-1.1.jar [INFO] Copying javafx-base-16-ea+6.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-base-16-ea+6.jar [INFO] Copying h2-mvstore-1.4.200.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/h2-mvstore-1.4.200.jar [INFO] Copying kotlin-scripting-compiler-impl-embeddable-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-scripting-compiler-impl-embeddable-1.4.10.jar [INFO] Copying ikonli-javafx-12.1.0.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/ikonli-javafx-12.1.0.jar [INFO] Copying commons-lang3-3.8.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/commons-lang3-3.8.1.jar [INFO] Copying kotlin-stdlib-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-stdlib-1.4.10.jar [INFO] Copying javafx-swing-16-ea+6-mac.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-swing-16-ea+6-mac.jar [INFO] Copying nitrite-3.4.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/nitrite-3.4.1.jar [INFO] Copying jackson-annotations-2.10.1.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/jackson-annotations-2.10.1.jar [INFO] Copying javafx-graphics-16-ea+6-mac.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/javafx-graphics-16-ea+6-mac.jar [INFO] Copying kotlin-scripting-common-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-scripting-common-1.4.10.jar [INFO] Copying trove4j-1.0.20181211.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/trove4j-1.0.20181211.jar [INFO] Copying kotlin-scripting-jvm-host-1.4.10.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/kotlin-scripting-jvm-host-1.4.10.jar [INFO] Copying annotations-13.0.jar to /Users/myang/biosoft/RNArtist/target/RNArtist/lib/annotations-13.0.jar [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ rnartist --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 83 resources [INFO] [INFO] --- kotlin-maven-plugin:1.4.10:compile (compile) @ rnartist --- [WARNING] Source root doesn't exist: /Users/myang/biosoft/RNArtist/src/main/java [WARNING] Using experimental Kotlin incremental compilation [INFO] Non-incremental compilation will be performed: No information on previous build [INFO] Kotlin compile iteration: /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/Mediator.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Canvas2D.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/EmbeddedDBGUI.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/ProjectsPanel.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/SelectionShape.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Settings.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/SplashWindow.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/WebBrowser.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/Backend.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/ChimeraDriver.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/EmbeddedDB.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/Utils.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/DrawingLoaded.kt, /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/ExplorerItem.kt [INFO] Exit code: COMPILATION_ERROR [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (131, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (132, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (132, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (133, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (133, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (134, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (143, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (144, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (144, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (145, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (145, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (146, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (157, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (158, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (158, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (159, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (159, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (160, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (181, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (182, 53) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (183, 52) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (183, 75) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (185, 80) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (195, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (196, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (196, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (197, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (197, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (198, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (2101, 53) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (2179, 56) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (5, 42) Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (74, 28) Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (75, 52) Overload resolution ambiguity: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (76, 33) Unresolved reference: junctionsBehaviors [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (121, 33) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (273, 65) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (281, 65) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (799, 19) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (799, 50) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt: (178, 27) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt: (336, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt: (378, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (37, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (65, 36) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (153, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (199, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/EmbeddedDB.kt: (27, 16) Type mismatch: inferred type is SecondaryStructureDrawing? but SecondaryStructureDrawing was expected [INFO] Compiled 19 Kotlin files using incremental compiler [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 21.912 s [INFO] Finished at: 2021-02-25T19:36:51Z [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.jetbrains.kotlin:kotlin-maven-plugin:1.4.10:compile (compile) on project rnartist: Compilation failure: Compilation failure: [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[131,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[132,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[132,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[133,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[133,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[134,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[143,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[144,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[144,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[145,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[145,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[146,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[157,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[158,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[158,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[159,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[159,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[160,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[181,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[182,53] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[183,52] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[183,75] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[185,80] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[195,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[196,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[196,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[197,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[197,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[198,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[2101,53] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[2179,56] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[5,42] Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[74,28] Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[75,52] Overload resolution ambiguity: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[76,33] Unresolved reference: junctionsBehaviors [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[121,33] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[273,65] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[281,65] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[799,19] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[799,50] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt:[178,27] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt:[336,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt:[378,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[37,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[65,36] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[153,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[199,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/EmbeddedDB.kt:[27,16] Type mismatch: inferred type is SecondaryStructureDrawing? but SecondaryStructureDrawing was expected [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/MojoFailureException

thank you very much for your time.

My best

fjossinet commented 3 years ago

Yes sorry, i forgot to deploy the last version of rnartistcore. Should be fine now.

MingleiYang commented 3 years ago

HI, Prof.

thank you for your quick reply.

it seems the problem is still there as follows, I think you may forget to commit the change.

thank you for your time.

My best

[ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (131, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (132, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (132, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (133, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (133, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (134, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (143, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (144, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (144, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (145, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (145, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (146, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (157, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (158, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (158, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (159, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (159, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (160, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (181, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (182, 53) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (183, 52) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (183, 75) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (185, 80) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (195, 43) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (196, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (196, 67) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (197, 48) Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (197, 71) Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (198, 76) Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (2101, 53) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt: (2179, 56) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (5, 42) Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (74, 28) Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (75, 52) Overload resolution ambiguity: public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (76, 33) Unresolved reference: junctionsBehaviors [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (121, 33) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (273, 65) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (281, 65) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (799, 19) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt: (799, 50) Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt: (178, 27) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt: (336, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt: (378, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (37, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (65, 36) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (153, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt: (199, 32) Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/EmbeddedDB.kt: (27, 16) Type mismatch: inferred type is SecondaryStructureDrawing? but SecondaryStructureDrawing was expected [INFO] Compiled 19 Kotlin files using incremental compiler [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 18.829 s [INFO] Finished at: 2021-02-25T22:22:59Z [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.jetbrains.kotlin:kotlin-maven-plugin:1.4.10:compile (compile) on project rnartist: Compilation failure: Compilation failure: [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[131,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[132,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[132,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[133,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[133,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[134,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[143,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[144,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[144,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[145,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[145,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[146,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[157,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[158,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[158,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[159,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[159,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[160,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[181,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[182,53] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[183,52] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[183,75] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[185,80] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[195,43] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[196,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[196,67] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[197,48] Unresolved reference: secondaryStructure [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[197,71] Variable expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[198,76] Type mismatch: inferred type is MouseEvent! but SecondaryStructureDrawing was expected [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[2101,53] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/RNArtist.kt:[2179,56] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[5,42] Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[74,28] Unresolved reference: SecondaryStructureLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[75,52] Overload resolution ambiguity: [ERROR] public inline fun Iterable<TypeVariable(T)>.forEach(action: (TypeVariable(T)) -> Unit): Unit defined in kotlin.collections [ERROR] public inline fun <K, V> Map<out TypeVariable(K), TypeVariable(V)>.forEach(action: (Map.Entry<TypeVariable(K), TypeVariable(V)>) -> Unit): Unit defined in kotlin.collections [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[76,33] Unresolved reference: junctionsBehaviors [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[121,33] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[273,65] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[281,65] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[799,19] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt:[799,50] Unresolved reference: maxBranchLength [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt:[178,27] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt:[336,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt:[378,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[37,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[65,36] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[153,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt:[199,32] Unresolved reference: currentLayout [ERROR] /Users/myang/biosoft/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/EmbeddedDB.kt:[27,16] Type mismatch: inferred type is SecondaryStructureDrawing? but SecondaryStructureDrawing was expected [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/MojoFailureException

fjossinet commented 3 years ago

Mmmh. No problem on my side even with a fresh clone of my own repo. I have given to RNArtistCore a new release number to force the update of this dependency during the RNArtist compilation. May u retry it with mvn clean package ?

MingleiYang commented 3 years ago

Hi, Prof.Fabrice,

I checked this time and it worked beautifully for me.

thank you very much,

My best,

Minglei