With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
Home Page: https://twitter.com/rnartist_app
License: Other
My name is Fabrice Jossinet. I'm biologist, bioinformatician & assistant professor at the University of Strasbourg, France.
I'm creating visual tools to explore and study 2D and 3D architectures of RNA molecules.
Languages used: Java, Kotlin, JavaFX, Python.
Some screenshots of my current highly active project RNArtist:
Hello,
While following the instructions to install, I came across this compile error:
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 19 source files to /home/patrick/tools/RNArtist/RNArtist/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:00 min
[INFO] Finished at: 2021-01-04T11:52:19+01:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (java-compile) on project rnartist: Fatal error compiling: error: release version 15 not supported -> [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
The installed version of java is:
$ java --version
openjdk 11.0.9.1 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04)
OpenJDK 64-Bit Server VM (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04, mixed mode, sharing)
The maven version is:
$ mvn -version
Apache Maven 3.6.0
Maven home: /usr/share/maven
Java version: 11.0.9.1, vendor: Ubuntu, runtime: /usr/lib/jvm/java-11-openjdk-amd64
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "5.4.0-52-generic", arch: "amd64", family: "unix"
Hi,
I am trying to install RNArtist on Ubuntu 20.04 with following jdk version:
openjdk version "11.0.18" 2023-01-17
OpenJDK Runtime Environment (build 11.0.18+10-post-Ubuntu-0ubuntu120.04.1)
OpenJDK 64-Bit Server VM (build 11.0.18+10-post-Ubuntu-0ubuntu120.04.1, mixed mode, sharing)
As mentioned, I have changed the java.version in pom.xml to 11.0.18.
mvn clean package works successfully with the following build success:
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 38.109 s
[INFO] Finished at: 2023-03-08T20:41:11+05:30
[INFO] ------------------------------------------------------------------------
But, the next exec command fails with a build failure. The log is as follows:
ARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/usr/share/maven/lib/guice.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for io.github.fjossinet.rnartist:rnartist:jar:1.0
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.codehaus.mojo:exec-maven-plugin @ line 314, column 21
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ---------------< io.github.fjossinet.rnartist:rnartist >----------------
[INFO] Building RNArtist 1.0
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- exec-maven-plugin:3.0.0:exec (default-cli) @ rnartist ---
Error occurred during initialization of boot layer
java.lang.module.FindException: Error reading module: /home/dolly/Documents/RNArtist/target/RNArtist/lib/javafx-base-20-ea+2-linux.jar
Caused by: java.lang.module.InvalidModuleDescriptorException: Unsupported major.minor version 61.0
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
at org.apache.commons.exec.DefaultExecutor.executeInternal (DefaultExecutor.java:404)
at org.apache.commons.exec.DefaultExecutor.execute (DefaultExecutor.java:166)
at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:982)
at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:929)
at org.codehaus.mojo.exec.ExecMojo.execute (ExecMojo.java:457)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:566)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.753 s
[INFO] Finished at: 2023-03-08T20:41:18+05:30
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:3.0.0:exec (default-cli) on project rnartist: Command execution failed.: Process exited with an error: 1 (Exit value: 1) -> [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
Can you kindly help sort this error out, please?
Awaiting for your kind response.
Hi,
I would like to save all my setting in RNArtists in json format.
However, when I loaded the JSON format next time, it came errors, the stacktrace was:
java.lang.IllegalArgumentException: No enum constant io.github.fjossinet.rnartist.core.model.ConnectorId.
at java.base/java.lang.Enum.valueOf(Enum.java:273)
at [email protected]/io.github.fjossinet.rnartist.core.model.ConnectorId.valueOf(Drawings.kt)
at [email protected]/io.github.fjossinet.rnartist.core.model.io.ParsersKt.parseProject$lambda-19(parsers.kt:312)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)
at [email protected]/io.github.fjossinet.rnartist.core.model.io.ParsersKt.parseProject(parsers.kt:313)
at [email protected]/io.github.fjossinet.rnartist.core.model.io.ParsersKt.parseJSON(parsers.kt:292)
at [email protected]/io.github.fjossinet.rnartist.RNArtist$1$loadData$1.call(RNArtist.kt:110)
at [email protected]/io.github.fjossinet.rnartist.RNArtist$1$loadData$1.call(RNArtist.kt:104)
at javafx.graphics/javafx.concurrent.Task$TaskCallable.call(Task.java:1426)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.lang.Thread.run(Thread.java:832)
Could you please give some suggestions?
My best,
Hi,
it seems like not function of saving into a svg figure in the new version of app.
my best,
Hi, fjossinet,
I think the function which colors the nucleotides between values only showed the two values in the variables of "value". and "to".
The value between these two variables didnot show the intermediate color. Basically, there are only two colors shown in the plot.
Could you give some suggestion please?
My best,
Hi,
when i tried to load the previous project, the error happened,
kotlin.UninitializedPropertyAccessException: lateinit property connectedJunction has not been initialized
at [email protected]/io.github.fjossinet.rnartist.core.model.JunctionDrawing.update(Drawings.kt:2567)
at [email protected]/io.github.fjossinet.rnartist.core.model.JunctionDrawing.setCurrentLayout(Drawings.kt:2221)
at [email protected]/io.github.fjossinet.rnartist.core.io.ParsersKt.parseProject(parsers.kt:431)
at [email protected]/io.github.fjossinet.rnartist.core.io.ParsersKt.parseJSON(parsers.kt:412)
at [email protected]/io.github.fjossinet.rnartist.io.EmbeddedDB.getProject(EmbeddedDB.kt:28)
at [email protected]/io.github.fjossinet.rnartist.gui.ProjectsPanel$ProjectCell$2$loadData$1.call(ProjectsPanel.kt:218)
at [email protected]/io.github.fjossinet.rnartist.gui.ProjectsPanel$ProjectCell$2$loadData$1.call(ProjectsPanel.kt:215)
at javafx.graphics/javafx.concurrent.Task$TaskCallable.call(Task.java:1426)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.lang.Thread.run(Thread.java:833)
and I also noticed that at the console, the error information of this showed up:
[INFO] --- exec-maven-plugin:3.0.0:exec (default-cli) @ rnartist ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Thank you very much,
My best,
We just istalled RNArtist on a MacOS (Apache Maven 3.9.1, OpenJDK 20.0.1 2023-04-18) and it seemed to work fine but any time we try to open one of the sample files, we get the same error message (independent of file format). It also seems the user interface is missing some elements compared to the screenshots in the documentation.
I attached a two screenshots, one of the error message and one of the UI.
Hi,
Thank you for your great efforts for generating this software.
recently I found there are some issue about the software,
for example,
bit130
gcagcaggaagcacuaugggcgcagcgucaaugacgcugacgguacaggccagacaauuauugucugauauagugcAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAAGAAUccuggcugu
(((((((((.((((((((..(((((((((...))))))).))........((((((.....)))))).)))))))).((((((((......(((((...(((....))...)..)))))))))))))........(((((((((........))))))))).....)))).)))))
showing this result:
1, there are "X"
2, the red bond was ignored by RNArist.
Btw, when the RNAstructure is more than 600nt. the software cannot save the figure which can show the charactors of the nucleotides. It can only show the skelton of the structure. is there any way to show the big RNA structure with the nucleotide able to be shown?
My best,
Thank you
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?
Hey!
This software runs on my laptop (Ubuntu 20.04), and fails to start up when I try to run it on our workstation (CentOS 7). Tried it on two independent workstations.
This is the error I get when I run mvn clean package:
Plenty download success...
[WARNING] Using experimental Kotlin incremental compilation
[INFO] Non-incremental compilation will be performed: NO_BUILD_HISTORY
[INFO] Kotlin compile iteration: /path/to/RNArtist/src/main/kotlin/RNArtist.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/Mediator.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Canvas2D.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnar
tist/gui/EmbeddedDBGUI.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Explorer.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnob.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/JunctionKnobFX.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/ProjectsPanel.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/SelectionShape.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Settings.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/SplashWindow.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/WebBrowser.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/Button.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/ColorPicker.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/HBox.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/ScriptEditor.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/TextField.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/TypeChooser.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/ChimeraDriver.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/ChimeraXDriver.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/EmbeddedDB.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/io/Utils.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/DrawingLoaded.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/ExplorerItem.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/BpseqKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/BracketNotationKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ClosedCurly.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ColorField.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ColorKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/CtKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/DSLElement.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/DSLKeyword.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/DSLParameter.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/DataKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/FileField.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/FloatField.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/HideKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/IntegerField.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/JunctionKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/LayoutKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/LineKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/LocationKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/NewLine.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/OpenedCurly.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/Operator.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/OptionalDSLKeyword.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/OptionalDSLParameter.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ParameterField.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/RNArtistKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/RfamKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ScriptTab.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/SecondaryStructureKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/SequenceBnParameter.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ShowKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/StockholmKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/StringValueWithQuotes.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/StringWithQuotes.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/StringWithoutQuotes.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ThemeKw.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/TypeField.kt, /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/model/editor/ViennaKw.kt
[INFO] Exit code: COMPILATION_ERROR
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (17, 8) Unresolved reference: netscape
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt: (118, 20) Unresolved reference: JSObject
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/ScriptEditor.kt: (100, 45) Function invocation 'isEmpty(...)' expected
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/ScriptEditor.kt: (100, 45) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch:
public inline fun <T> Array<out TypeVariable(T)>.isEmpty(): Boolean defined in kotlin.collections
public inline fun BooleanArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ByteArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharSequence.isEmpty(): Boolean defined in kotlin.text
public inline fun DoubleArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun FloatArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun IntArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun LongArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ShortArray.isEmpty(): Boolean defined in kotlin.collections
[INFO] Compiled 62 Kotlin files using incremental compiler
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 6:31.775s
[INFO] Finished at: Thu Dec 23 16:00:40 IST 2021
[INFO] Final Memory: 182M/516M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.jetbrains.kotlin:kotlin-maven-plugin:1.6.0:compile (compile) on project rnartist: Compilation failure: Compilation failure:
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[17,8] Unresolved reference: netscape
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/Editor.kt:[118,20] Unresolved reference: JSObject
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/ScriptEditor.kt:[100,45] Function invocation 'isEmpty(...)' expected
[ERROR] /path/to/RNArtist/src/main/kotlin/io/github/fjossinet/rnartist/gui/editor/ScriptEditor.kt:[100,45] Unresolved reference. None of the following candidates is applicable because of receiver type mismatch:
[ERROR] public inline fun <T> Array<out TypeVariable(T)>.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun BooleanArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun ByteArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun CharArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun CharSequence.isEmpty(): Boolean defined in kotlin.text
[ERROR] public inline fun DoubleArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun FloatArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun IntArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun LongArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] public inline fun ShortArray.isEmpty(): Boolean defined in kotlin.collections
[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
And when I anyway proceed to run mvn exec:exec, it spits out an error quoted below:
Unrecognized option: --module-path
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:982)
at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:929)
at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:457)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:414)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:357)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 12.549s
[INFO] Finished at: Thu Dec 23 16:02:01 IST 2021
[INFO] Final Memory: 14M/293M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:3.0.0:exec (default-cli) on project rnartist: Command execution failed. Process exited with an error: 1 (Exit value: 1) -> [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
More information
lsb_release -a
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.9.2009 (Core)
Release: 7.9.2009
Codename: Core
uname -r
3.10.0-1160.45.1.el7.x86_64
java -version
openjdk version "1.8.0_312"
OpenJDK Runtime Environment (build 1.8.0_312-b07)
OpenJDK 64-Bit Server VM (build 25.312-b07, mixed mode)
Hi, Fjossinet,
I noticed that when the RNA structure is long, the saved svg cannot be labelled with the nucleotide. The numbers of the position are only shown when you zoom in the structure.
Could you give some suggestion?
My best,
I tried to run it on my Mac and got the following error:
Error: Unable to access jarfile lib/rnartist-1.0.jar
Please let me know how I can fix this problem?
hi, i tried to compile the RNArtist following the instruction, but I came across this error,
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 19 source files to /home/parallels/biosoft/RNArtist/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 26.677 s
[INFO] Finished at: 2021-01-01T12:02:14Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (java-compile) on project rnartist: Fatal error compiling: error: release version 15 not supported -> [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
it seems I used Java 15, however, when I checked the version issue by using mvn -version, I am using java 11,
Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f)
Maven home: /opt/maven
Java version: 11.0.9.1, vendor: Red Hat, Inc., runtime: /usr/lib/jvm/java-11-openjdk-11.0.9.11-2.el7_9.x86_64
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "3.10.0-862.11.6.el7.x86_64", arch: "amd64", family: "unix"
could you give me some suggestions about what may happen?
thank you very much!!
Hello,
I am trying to launch the RNArtist in Ubuntu 18 and I am getting the following error message:
(openjdk 11.0.14 2022-01-18)
I googled the problem but could't find a solution, any idea how can I solve this.
Thanks for your help.
Best,
Amir
$ ./launch_rnartist_for_Linux.sh
Error occurred during initialization of boot layer
java.lang.module.FindException: Module javafx.controls not found
Hi,
I am wondering whether it is possible that the SVG file can include the order information of the sequence. Currently, the SVG file includes the coordination, however, the order information (from 5' end to 3' end) was not included.
another question, how to parse the JSON file output and become an image file?
My best
I want to get the visualization of RNA PDB file in 2D format. But when I want to install RNArtist in my computer with windows system. I downloaded the RNArtist github master and installed the mvn.
When I run the commond 'mvn clean package', I got the mistakes.
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\DrawingsLoadedPanel.kt: (166, 45) Cannot access 'url': it is private in 'Image'
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (281, 16) Unresolved reference: tabSize
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (384, 25) Function invocation 'isEmpty(...)' expected
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (384, 25) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch:
public inline fun Array<out TypeVariable(T)>.isEmpty(): Boolean defined in kotlin.collections
public inline fun BooleanArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ByteArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharSequence.isEmpty(): Boolean defined in kotlin.text
public inline fun DoubleArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun FloatArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun IntArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun LongArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ShortArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (436, 45) Function invocation 'isEmpty(...)' expected
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (436, 45) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch:
public inline fun Array<out TypeVariable(T)>.isEmpty(): Boolean defined in kotlin.collections
public inline fun BooleanArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ByteArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharSequence.isEmpty(): Boolean defined in kotlin.text
public inline fun DoubleArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun FloatArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun IntArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun LongArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ShortArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (469, 62) Function invocation 'isEmpty(...)' expected
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (469, 62) Unresolved reference. None of the following candidates is applicable because of receiver type mismatch:
public inline fun Array<out TypeVariable(T)>.isEmpty(): Boolean defined in kotlin.collections
public inline fun BooleanArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ByteArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun CharSequence.isEmpty(): Boolean defined in kotlin.text
public inline fun DoubleArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun FloatArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun IntArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun LongArray.isEmpty(): Boolean defined in kotlin.collections
public inline fun ShortArray.isEmpty(): Boolean defined in kotlin.collections
[ERROR] F:\01-Molmap\code\Assemble\RNArtist-master\src\main\kotlin\io\github\fjossinet\rnartist\gui\editor\ScriptEditor.kt: (474, 59) Function invocation 'isEmpty(...)' expected
Is there anyone to help me?
My java version:
java version "1.8.0_333"
Java(TM) SE Runtime Environment (build 1.8.0_333-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.333-b02, mixed mode)
My mvn version:
java version "1.8.0_333"
Java(TM) SE Runtime Environment (build 1.8.0_333-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.333-b02, mixed mode)
Hello RNArtist,
Love the visualization and looking forward to following this package as it grows.
Can you slow down the zoom in/out feature? if im not careful I can completely lose the molecule bc of how fast it zooms, haha.
Another question, are you planning on integrating the ability to visualize base pairing probability files?
Thanks,
Austin Herbert
Hi, fjossinet,
The command-line (Editor) seems cannot render the RNA structure in this new version.
when I click the run the editor butter, the error shows:
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
javax.script.ScriptException: ERROR Unable to initialize repl compiler:
DEBUG Using JVM IR backend
ERROR java.lang.ExceptionInInitializerError: java.lang.ExceptionInInitializerError: java.lang.IllegalStateException: Unable to initialize repl compiler:
DEBUG Using JVM IR backend
ERROR java.lang.ExceptionInInitializerError: java.lang.ExceptionInInitializerError
at [email protected]/org.jetbrains.kotlin.cli.common.repl.KotlinJsr223JvmScriptEngineBase.asJsr223EvalResult(KotlinJsr223JvmScriptEngineBase.kt:104)
at [email protected]/org.jetbrains.kotlin.cli.common.repl.KotlinJsr223JvmScriptEngineBase.compileAndEval(KotlinJsr223JvmScriptEngineBase.kt:63)
at [email protected]/kotlin.script.experimental.jvmhost.jsr223.KotlinJsr223ScriptEngineImpl.compileAndEval(KotlinJsr223ScriptEngineImpl.kt:94)
at [email protected]/org.jetbrains.kotlin.cli.common.repl.KotlinJsr223JvmScriptEngineBase.eval(KotlinJsr223JvmScriptEngineBase.kt:31)
at java.scripting/javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at [email protected]/io.github.fjossinet.rnartist.io.github.fjossinet.rnartist.gui.Editor.lambda-4$lambda-3(Editor.kt:52)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:391)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
My best,
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
Django
The Web framework for perfectionists with deadlines.
Laravel
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft
Open source projects and samples from Microsoft.
Google
Google ❤️ Open Source for everyone.
Alibaba
Alibaba Open Source for everyone
D3
Data-Driven Documents codes.
Tencent
China tencent open source team.