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Error while running phylonco-lphy-examples #521

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CSTE7007 opened this issue Sep 10, 2024 · 3 comments
Closed

Error while running phylonco-lphy-examples #521

CSTE7007 opened this issue Sep 10, 2024 · 3 comments
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@CSTE7007
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CSTE7007 commented Sep 10, 2024 •
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As mentioned here at https://linguaphylo.github.io/extensions/ I tried to use LPhy extension Phylonco and follow the steps of loading example phylonco-lphy-examples.zip as bellow at Loading examples section:

Loading examples

Examples can be found in the releases page of the extension. To load the examples into LPhy Studio:

  1. Go to the releases page of the extension, e.g., Phylonco releases
  2. Download the file with the suffix *-lphy-examples.zip, e.g., phylonco-lphy-examples.zip
  3. Unzip the *-lphy-examples.zip file inside the examples subdirectory of your LPhy installation. Your directory structure should look like this:
    image
  4. Restart LPhy Studio, and these examples will be available through the Menu “File” -> “Example scripts” -> “extensionName”. For the Phylonco extension, this will be available through “File” -> “Example scripts” -> “phylonco”. Loading in the example script gt16CoalErrModel.lphy will display:
    image

Exception and Error

But when I downloaded the phylonco-lphy-examples.zip following directory structure and unziped at mentioned directory. Then while trying to open the example like the image

image

I faced following exception and error as bellow:

Gtk-Message: 13:31:31.447: Failed to load module "canberra-gtk-module"
Registering extension : lphy.base.spi.LPhyBaseImpl
Registering extension : lphy.base.spi.ValueFormatterBaseImpl
Registering extension : lphy.base.spi.SequenceTypeBaseImpl
LPhy standard sequence types : [amino acid, lphy.base.evolution.datatype.Binary@157853da, nucleotide, lphy.base.evolution.datatype.Continuous@71c3b41]
Registering extension : lphystudio.spi.LPhyStudioImpl
Registering extension : lphystudio.spi.ValueFormatterStudioImpl
Registering extension : lphy.core.spi.LPhyCoreImpl
Registering extension : lphy.core.spi.ValueFormatterCoreImpl

GenerativeDistribution : [Bernoulli, Beta, BirthDeath, BirthDeathSampling, BirthDeathSerialSampling, Categorical, Cauchy, Coalescent, Dirichlet, DiscretizeGamma, ErrorModel, Exp, ExpMarkovChain, FossilBirthDeathTree, FullBirthDeath, Gamma, Geometric, InverseGamma, LogNormal, MissingSites, MultispeciesCoalescent, NegativeBinomial, Normal, NormalGamma, PhyloBrownian, PhyloCTMC, PhyloMultivariateBrownian, PhyloOU, Poisson, RandomBooleanArray, RandomComposition, RhoSampleTree, Sequence, SimBDReverse, SimFBDAge, SimFossilsPoisson, SkylineCoalescent, StructuredCoalescent, Uniform, UniformDiscrete, Weibull, WeightedDirichlet, Yule, bSiteRates, sample]
Functions : [aminoAcids, arange, argi, bModelSet, bSiteModel, binaryDataType, binaryRateMatrix, concat2Str, concatArray, copySites, countMigrations, elementsAt, extantTaxa, extantTree, extractTrait, f81, fasta, generalTimeReversible, get, gtr, hammingWeight, hky, ifelse, intersect, invariableSites, jukesCantor, k80, length, lewisMK, localBranchRates, map, migrationMatrix, nchar, newick, ntaxa, nucleotideModel, nucleotides, parseInt, pruneTree, rangeInt, readDelim, readFasta, readNexus, rep, repArray, rmTaxa, select, selectSites, simulate, slice, sort, species, split, standard, sum, sumCols, sumRows, taxa, toDouble, unique, variableSites, wag]
LPhy data types : [Alignment, BModelSet, Boolean, Boolean[], ContinuousCharacterData, Double, Double[], Double[][], FastaAlignment, Integer, Integer[], MetaDataAlignment, NChar, Number, Number[], Number[][], Object, Object[], SequenceType, SimpleAlignment, SiteModel, String, Table, Taxa, TimeTree]
Value formatter for : [Boolean, Double, Integer, SimpleAlignment, String, TimeTree]

ANTLR Tool version 4.13.1 used for code generation does not match the current runtime version 4.11.1
ANTLR Tool version 4.13.1 used for code generation does not match the current runtime version 4.11.1
Set working dir to /home/user/lphy-studio-1.5.0/examples/phylonco

Exception in thread "AWT-EventQueue-0" lphy.core.exception.SimulatorParsingException: Found no implementation for function with name gt16 line 5 character 4
 -> gt16(freq=π,rates=rates)
    ^^^^^^^^^^^^^^^^^^^^^^^^
	at lphy.core@1.5.0/lphy.core.parser.LPhyListenerImpl$LPhyASTVisitor.visitFunction(LPhyListenerImpl.java:920)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$FunctionContext.accept(LPhyParser.java:1431)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitExpression(LPhyBaseVisitor.java:196)
	at lphy.core@1.5.0/lphy.core.parser.LPhyListenerImpl$LPhyASTVisitor.visitExpression(LPhyListenerImpl.java:487)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$ExpressionContext.accept(LPhyParser.java:1763)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visit(AbstractParseTreeVisitor.java:18)
	at lphy.core@1.5.0/lphy.core.parser.LPhyListenerImpl$LPhyASTVisitor.visitDeterm_relation(LPhyListenerImpl.java:245)
	at lphy.core@1.5.0/lphy.core.parser.LPhyListenerImpl$LPhyASTVisitor.visitDeterm_relation(LPhyListenerImpl.java:102)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$Determ_relationContext.accept(LPhyParser.java:889)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitRelation(LPhyBaseVisitor.java:77)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$RelationContext.accept(LPhyParser.java:693)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitRelation_list(LPhyBaseVisitor.java:70)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$Relation_listContext.accept(LPhyParser.java:611)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitRelation_list(LPhyBaseVisitor.java:70)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$Relation_listContext.accept(LPhyParser.java:611)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitRelation_list(LPhyBaseVisitor.java:70)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$Relation_listContext.accept(LPhyParser.java:611)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitRelation_list(LPhyBaseVisitor.java:70)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$Relation_listContext.accept(LPhyParser.java:611)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitRelation_list(LPhyBaseVisitor.java:70)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$Relation_listContext.accept(LPhyParser.java:611)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitModelblock(LPhyBaseVisitor.java:63)
	at lphy.core@1.5.0/lphy.core.parser.LPhyListenerImpl$LPhyASTVisitor.visitModelblock(LPhyListenerImpl.java:118)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$ModelblockContext.accept(LPhyParser.java:533)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitStructured_input(LPhyBaseVisitor.java:28)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$Structured_inputContext.accept(LPhyParser.java:205)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyBaseVisitor.visitInput(LPhyBaseVisitor.java:21)
	at lphy.core@1.5.0/lphy.core.parser.antlr.LPhyParser$InputContext.accept(LPhyParser.java:144)
	at org.antlr.antlr4.runtime@4.11.1/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visit(AbstractParseTreeVisitor.java:18)
	at lphy.core@1.5.0/lphy.core.parser.LPhyParserAction.parse(LPhyParserAction.java:67)
	at lphy.core@1.5.0/lphy.core.parser.LPhyListenerImpl.parse(LPhyListenerImpl.java:53)
	at lphy.core@1.5.0/lphy.core.parser.REPL.parse(REPL.java:97)
	at lphystudio@1.5.0/lphystudio.app.graphicalmodelpanel.GraphicalModelParserDictionary.parse(GraphicalModelParserDictionary.java:20)
	at lphy.core@1.5.0/lphy.core.parser.LPhyParserDictionary.source(LPhyParserDictionary.java:120)
	at lphystudio@1.5.0/lphystudio.app.graphicalmodelpanel.GraphicalModelPanel.source(GraphicalModelPanel.java:242)
	at lphystudio@1.5.0/lphystudio.app.Utils.readFile(Utils.java:128)
	at lphystudio@1.5.0/lphystudio.app.Utils.readFileFromDir(Utils.java:102)
	at lphystudio@1.5.0/lphystudio.app.LinguaPhyloStudio.readFile(LinguaPhyloStudio.java:377)
	at lphystudio@1.5.0/lphystudio.app.LinguaPhyloStudio.lambda$createMenuItemForLPhyScript$18(LinguaPhyloStudio.java:495)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2313)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1028)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1072)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6626)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3389)
	at java.desktop/java.awt.Component.processEvent(Component.java:6391)
	at java.desktop/java.awt.Container.processEvent(Container.java:2266)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5001)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:97)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:746)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:744)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:743)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

My configuration:

lphy-studio-1.5.0
Ubuntu 18.04.6 LTS 64-bit | 8GB RAM
Intel® Core™ i5-3470 CPU @ 3.20GHz × 4
@walterxie
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walterxie commented Sep 13, 2024 •
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@CSTE7007 as I have mentioned in LinguaPhylo/LPhyBeast#152, the current released version of phylonco is not compatible to the current release of lphy 1.5 and lphybeast 1.1.

We are currently working on resolving this issue.

@walterxie walterxie added the duplicate This issue or pull request already exists label Sep 13, 2024
@walterxie
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walterxie commented Sep 13, 2024 •
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duplicate to LinguaPhylo/LPhyBeast#152

@walterxie walterxie mentioned this issue Sep 30, 2024
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@walterxie
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This is solved by new releases, please see my reply in LinguaPhylo/LPhyBeast#152

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