Update all dependencies

Dockerfile

@@ -1,4 +1,4 @@
-FROM  eclipse-temurin:23 AS build
+FROM  eclipse-temurin:25 AS build
 COPY . /home/gradle/src
 USER root
 WORKDIR /home/gradle/src

Ghidra/Debug/Debugger-agent-dbgeng/src/main/py/pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "ghidratrace==11.5",
+    "ghidratrace==12.0",
     "pybag>=2.2.12"
 ]
 

Ghidra/Debug/Debugger-agent-drgn/src/main/py/pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "ghidratrace==11.5",
+    "ghidratrace==12.0",
 ]
 
 [project.urls]

Ghidra/Debug/Debugger-agent-gdb/src/main/py/pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "ghidratrace==11.5",
+    "ghidratrace==12.0",
 ]
 
 [project.urls]

Ghidra/Debug/Debugger-agent-lldb/src/main/py/pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "ghidratrace==11.5",
+    "ghidratrace==12.0",
 ]
 
 [project.urls]

Ghidra/Extensions/MachineLearning/build.gradle

@@ -26,15 +26,15 @@ def protobufVersion = getProperty("ghidra.protobuf.java.version")
 dependencies {
 	api project(':Base')
 
-    api "com.oracle.labs.olcut:olcut-config-protobuf:5.2.0" //{exclude group: "com.google.protobuf", module: "protobuf-java"}
-    api ("com.oracle.labs.olcut:olcut-core:5.2.0") {exclude group: "org.jline"}
-    api "org.tribuo:tribuo-classification-core:4.2.0"
-    api "org.tribuo:tribuo-classification-tree:4.2.0"
-    api "org.tribuo:tribuo-common-tree:4.2.0"
-    api 'org.tribuo:tribuo-core:4.2.0' 
-    api ("org.tribuo:tribuo-data:4.2.0") {exclude group: "com.opencsv"}
-    api "org.tribuo:tribuo-math:4.2.0" 
-    api ("org.tribuo:tribuo-util-onnx:4.2.0") //{exclude group: "com.google.protobuf", module: "protobuf-java"}
+    api "com.oracle.labs.olcut:olcut-config-protobuf:5.3.1" //{exclude group: "com.google.protobuf", module: "protobuf-java"}
+    api ("com.oracle.labs.olcut:olcut-core:5.3.1") {exclude group: "org.jline"}
+    api "org.tribuo:tribuo-classification-core:4.3.2"
+    api "org.tribuo:tribuo-classification-tree:4.3.2"
+    api "org.tribuo:tribuo-common-tree:4.3.2"
+    api 'org.tribuo:tribuo-core:4.3.2' 
+    api ("org.tribuo:tribuo-data:4.3.2") {exclude group: "com.opencsv"}
+    api "org.tribuo:tribuo-math:4.3.2" 
+    api ("org.tribuo:tribuo-util-onnx:4.3.2") //{exclude group: "com.google.protobuf", module: "protobuf-java"}
 
     testImplementation project(path: ':SoftwareModeling', configuration: 'testArtifacts')
     testImplementation "com.google.protobuf:protobuf-java:${protobufVersion}"

Ghidra/Features/BSim/build.gradle

@@ -32,11 +32,11 @@ dependencies {
 	api project(":Decompiler")
 	api project(":CodeCompare")
 
-	api "org.postgresql:postgresql:42.7.6"
-    api "org.apache.commons:commons-dbcp2:2.9.0"
-    api "org.apache.commons:commons-pool2:2.11.1"
-    api "commons-logging:commons-logging:1.2"
-    api "com.h2database:h2:2.2.220"
+	api "org.postgresql:postgresql:42.7.10"
+    api "org.apache.commons:commons-dbcp2:2.14.0"
+    api "org.apache.commons:commons-pool2:2.13.1"
+    api "commons-logging:commons-logging:1.3.5"
+    api "com.h2database:h2:2.4.240"
 }
 
 // Copy postgresql source distro, lshvector plugin source, and make-postgres.sh 

Ghidra/Features/Base/build.gradle

@@ -43,12 +43,12 @@ dependencies {
 
 	api 'org.apache.felix:org.apache.felix.framework:7.0.5'
 	api 'com.github.rotty3000:phidias:0.3.7'
-	api 'biz.aQute.bnd:biz.aQute.bnd.util:7.0.0'
-	api ('biz.aQute.bnd:biz.aQute.bndlib:7.0.0') {exclude group: 'org.osgi'}
+	api 'biz.aQute.bnd:biz.aQute.bnd.util:7.2.1'
+	api ('biz.aQute.bnd:biz.aQute.bndlib:7.2.1') {exclude group: 'org.osgi'}
 	api ('org.osgi:org.osgi.util.promise:1.3.0') {exclude group: 'org.osgi'}
-	api 'org.slf4j:slf4j-api:1.7.25'
+	api 'org.slf4j:slf4j-api:2.0.17'
 
-	runtimeOnly "org.slf4j:slf4j-nop:1.7.25"
+	runtimeOnly "org.slf4j:slf4j-nop:2.0.17"
 
 	// use this if you want slf4j log messages sent to log4j
 	//	runtimeOnly "org.apache.logging.log4j:log4j-slf4j-impl:2.17.1" 
@@ -62,7 +62,7 @@ dependencies {
 	testImplementation project(path: ':SoftwareModeling', configuration: 'testArtifacts')
 	testImplementation project(path: ':DB', configuration: 'testArtifacts')
 
-	javacc 'net.java.dev.javacc:javacc:5.0'
+	javacc 'net.java.dev.javacc:javacc:7.0.13'
 }
 
 

Ghidra/Features/FileFormats/build.gradle

@@ -32,10 +32,10 @@ dependencies {
 
 	// Used by "Android DEX to JAR" file system
 	// dex2jar depends on asm-9.7.1, which is declared in Framework/Emulation
-	api 'de.femtopedia.dex2jar:dex-ir:2.4.24'
-	api 'de.femtopedia.dex2jar:dex-reader:2.4.24'
-	api 'de.femtopedia.dex2jar:dex-reader-api:2.4.24'
-	api 'de.femtopedia.dex2jar:dex-translator:2.4.24'
+	api 'de.femtopedia.dex2jar:dex-ir:2.4.34'
+	api 'de.femtopedia.dex2jar:dex-reader:2.4.34'
+	api 'de.femtopedia.dex2jar:dex-reader-api:2.4.34'
+	api 'de.femtopedia.dex2jar:dex-translator:2.4.34'
 
 	// Used by "Android DEX to SMALI" file system
 	api 'org.smali:baksmali:2.5.2' // requires guava-27.1-android or later

Ghidra/Features/GraphServices/build.gradle

@@ -30,11 +30,11 @@ dependencies {
 	api ("com.github.tomnelson:jungrapht-visualization:1.4") { exclude group: "org.slf4j", module: "slf4j-api" }
 	api ("com.github.tomnelson:jungrapht-layout:1.4") { exclude group: "org.slf4j", module: "slf4j-api" }
 
-	api "org.jgrapht:jgrapht-core:1.5.1"
+	api "org.jgrapht:jgrapht-core:1.5.2"
 
 	// not using jgrapht-io code that depends on antlr, so exclude antlr
-	api ("org.jgrapht:jgrapht-io:1.5.1") { exclude group: "org.antlr", module: "antlr4-runtime" }
+	api ("org.jgrapht:jgrapht-io:1.5.2") { exclude group: "org.antlr", module: "antlr4-runtime" }
 
-	runtimeOnly "org.jheaps:jheaps:0.13"
+	runtimeOnly "org.jheaps:jheaps:0.14"
 }
 

Ghidra/Features/PyGhidra/src/main/py/pyproject.toml

@@ -30,7 +30,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "Jpype1==1.5.2",
+    "Jpype1==1.6.0",
     "packaging"
 ]
 

Ghidra/Framework/Emulation/build.gradle

@@ -27,9 +27,9 @@ dependencies {
 	api project(':Generic')
 	api project(':Utility')
 
-	api 'org.ow2.asm:asm:9.7.1'
-	api 'org.ow2.asm:asm-analysis:9.7.1'
-	api 'org.ow2.asm:asm-commons:9.7.1'
-	api 'org.ow2.asm:asm-tree:9.7.1'
-	api 'org.ow2.asm:asm-util:9.7.1'
+	api 'org.ow2.asm:asm:9.9.1'
+	api 'org.ow2.asm:asm-analysis:9.9.1'
+	api 'org.ow2.asm:asm-commons:9.9.1'
+	api 'org.ow2.asm:asm-tree:9.9.1'
+	api 'org.ow2.asm:asm-util:9.9.1'
 }

Ghidra/Framework/Generic/build.gradle

@@ -26,29 +26,29 @@ eclipse.project.name = 'Framework Generic'
 
 dependencies {
 	api project(':Utility')
-	api ("com.google.guava:guava:32.1.3-jre") {
+	api ("com.google.guava:guava:33.5.0-jre") {
 		exclude group: 'com.google.guava', module: 'listenablefuture'
 		exclude group: 'com.google.errorprone', module: 'error_prone_annotations'
 		exclude group: 'com.google.code.findbugs', module: 'jsr305'
 		exclude group: 'org.checkerframework', module: 'checker-qual'
 	}
-	api "com.google.guava:failureaccess:1.0.1"
+	api "com.google.guava:failureaccess:1.0.3"
 	api "org.jdom:jdom-legacy:1.1.3"
-	api "org.apache.logging.log4j:log4j-api:2.17.1"
-	api "org.apache.logging.log4j:log4j-core:2.17.1"
-	api "org.apache.commons:commons-collections4:4.1"
-	api "org.apache.commons:commons-compress:1.27.1" // requires commons-codec
-	api "commons-codec:commons-codec:1.18.0"
-	api "org.apache.commons:commons-lang3:3.17.0"
-	api "org.apache.commons:commons-text:1.10.0"
-	api "commons-io:commons-io:2.19.0"	
-	api "com.google.code.gson:gson:2.9.0"
-	api "org.bouncycastle:bcpkix-jdk18on:1.80" // requires bcutil and bcprov
-	api "org.bouncycastle:bcprov-jdk18on:1.80"
-	api "org.bouncycastle:bcutil-jdk18on:1.80"
+	api "org.apache.logging.log4j:log4j-api:2.25.3"
+	api "org.apache.logging.log4j:log4j-core:2.25.3"
+	api "org.apache.commons:commons-collections4:4.5.0"
+	api "org.apache.commons:commons-compress:1.28.0" // requires commons-codec
+	api "commons-codec:commons-codec:1.21.0"
+	api "org.apache.commons:commons-lang3:3.20.0"
+	api "org.apache.commons:commons-text:1.15.0"
+	api "commons-io:commons-io:2.21.0"	
+	api "com.google.code.gson:gson:2.13.2"
+	api "org.bouncycastle:bcpkix-jdk18on:1.83" // requires bcutil and bcprov
+	api "org.bouncycastle:bcprov-jdk18on:1.83"
+	api "org.bouncycastle:bcutil-jdk18on:1.83"
 
 	compileOnly "junit:junit:4.13.2"
-	compileOnly "org.hamcrest:hamcrest:2.2"
+	compileOnly "org.hamcrest:hamcrest:3.0"
 
 	constraints {
 		api("com.google.guava:guava") {

Ghidra/Framework/Graph/build.gradle

@@ -34,10 +34,10 @@ dependencies {
 	api "net.sf.jung:jung-graph-impl:2.1.1"
 	api "net.sf.jung:jung-visualization:2.1.1"
 
-	api "org.jgrapht:jgrapht-core:1.5.1"
+	api "org.jgrapht:jgrapht-core:1.5.2"
 
 	// not using jgrapht-io code that depends on antlr, so exclude antlr
-	api ("org.jgrapht:jgrapht-io:1.5.1") { exclude group: "org.antlr", module: "antlr4-runtime" }
+	api ("org.jgrapht:jgrapht-io:1.5.2") { exclude group: "org.antlr", module: "antlr4-runtime" }
 
 	// These have abstract test classes and stubs needed by this module	
 	testImplementation project(path: ':Docking', configuration: 'testArtifacts')

Ghidra/Framework/Gui/build.gradle

@@ -26,7 +26,7 @@ eclipse.project.name = 'Framework Gui'
 
 dependencies {
 	api project(':Generic')
-	api 'com.formdev:flatlaf:3.5.4'
+	api 'com.formdev:flatlaf:3.7'
 
 	compileOnly "junit:junit:4.13.2"
 

Ghidra/Framework/Project/build.gradle

@@ -27,6 +27,6 @@ dependencies {
 	api project(':FileSystem')
 
 	testImplementation project(path: ':Generic', configuration: 'testArtifacts')
-	api "org.tukaani:xz:1.9"
+	api "org.tukaani:xz:1.11"
 }
 

Ghidra/Framework/Pty/build.gradle

@@ -25,8 +25,8 @@ apply plugin: 'eclipse'
 eclipse.project.name = 'Framework Pty'
 
 dependencies {
-	api "net.java.dev.jna:jna:5.14.0"
-	api "net.java.dev.jna:jna-platform:5.14.0"
+	api "net.java.dev.jna:jna:5.18.1"
+	api "net.java.dev.jna:jna-platform:5.18.1"
 	api project(":Docking")
 
 	testImplementation project(":Generic")

Ghidra/Framework/SoftwareModeling/build.gradle

@@ -37,17 +37,17 @@ dependencies {
 
 	api "msv:msv:20050913"
 	api "msv:xsdlib:20050913"
-	api "org.antlr:antlr-runtime:3.5.2"
+	api "org.antlr:antlr-runtime:3.5.3"
 
 	runtimeOnly "msv:relaxngDatatype:20050913"
 	api "msv:isorelax:20050913"	
 
 	// Must specify the specific antlr implementation to use or it will default to trying to find
 	// version 2.7.7 (which we don't have)
-	antlr "org.antlr:antlr:3.5.2"
+	antlr "org.antlr:antlr:3.5.3"
 	// need to add in the antlr dependencies for when we build from flat jar dirs
-	antlr "org.antlr:antlr-runtime:3.5.2"
-	antlr "org.antlr:ST4:4.0.8"
+	antlr "org.antlr:antlr-runtime:3.5.3"
+	antlr "org.antlr:ST4:4.3.4"
 }	
 
 def genSrcDir = 'generated-src/antlr/main'

GhidraBuild/BuildFiles/Doclets/build.gradle

@@ -24,7 +24,7 @@ java {
 }
 
 dependencies {
-	api "com.google.code.gson:gson:2.9.0"
+	api "com.google.code.gson:gson:2.13.2"
 }
 
 rootProject.createJsondocs.dependsOn jar

GhidraBuild/MarkdownSupport/build.gradle

@@ -18,8 +18,8 @@ apply plugin: 'eclipse'
 eclipse.project.name = '_MarkdownSupport'
 
 dependencies {
-	implementation 'org.commonmark:commonmark:0.23.0'
-	implementation 'org.commonmark:commonmark-ext-heading-anchor:0.23.0'
-	implementation 'org.commonmark:commonmark-ext-footnotes:0.23.0'
-	implementation 'org.commonmark:commonmark-ext-gfm-tables:0.23.0'
+	implementation 'org.commonmark:commonmark:0.27.1'
+	implementation 'org.commonmark:commonmark-ext-heading-anchor:0.27.1'
+	implementation 'org.commonmark:commonmark-ext-footnotes:0.27.1'
+	implementation 'org.commonmark:commonmark-ext-gfm-tables:0.27.1'
 }

docker/Dockerfile

@@ -5,7 +5,7 @@
 # a ghidra release using the command 
 # docker build -f docker/Dockerfile -t <image-name>
 ###############################################################
-FROM alpine:3.20 AS base
+FROM alpine:3.23 AS base
 
 LABEL org.opencontainers.image.title="ghidra" \
 	org.opencontainers.image.description="Docker image for Ghidra" \

gradle.properties

@@ -6,4 +6,4 @@ org.gradle.jvmargs=-Xmx2G -Duser.language=en -Duser.country=US
 org.gradle.archives.use-file-system-permissions=true
 
 # Set Ghidra protobuf version
-ghidra.protobuf.java.version=4.31.0
+ghidra.protobuf.java.version=4.33.5

gradle/jacocoProject.gradle

@@ -31,8 +31,8 @@
 apply plugin:'jacoco'
 
 dependencies {
-   jacocoAnt 'org.jacoco:org.jacoco.ant:0.8.11'
-   jacocoAgent 'org.jacoco:org.jacoco.agent:0.8.11'
+   jacocoAnt 'org.jacoco:org.jacoco.ant:0.8.14'
+   jacocoAgent 'org.jacoco:org.jacoco.agent:0.8.14'
 }
 
 // Clean any jacoco files that may have been left behind previously.

gradle/javaProject.gradle

@@ -157,9 +157,9 @@ artifacts {
 	Provide test dependencies here so each build file does not have to.
 */  
 dependencies {
-	integrationTestImplementation "org.hamcrest:hamcrest:2.2"
+	integrationTestImplementation "org.hamcrest:hamcrest:3.0"
 
-	testImplementation "org.hamcrest:hamcrest:2.2"
+	testImplementation "org.hamcrest:hamcrest:3.0"
 
 	testImplementation "junit:junit:4.13.2"
 	pcodeTestImplementation "junit:junit:4.13.2"

gradle/root/jacoco.gradle

@@ -18,8 +18,8 @@ import groovy.io.FileType;
 apply plugin:'jacoco'
 
 dependencies {
-   jacocoAnt 'org.jacoco:org.jacoco.ant:0.8.11'
-   jacocoAgent 'org.jacoco:org.jacoco.agent:0.8.11'
+   jacocoAnt 'org.jacoco:org.jacoco.ant:0.8.14'
+   jacocoAgent 'org.jacoco:org.jacoco.agent:0.8.14'
 }
 
 /*********************************************************************************

gradle/support/fetchDependencies.gradle

@@ -41,7 +41,7 @@ import org.apache.commons.io.filefilter.WildcardFileFilter;
 
 initscript {
 	repositories { mavenCentral() }
-	dependencies { classpath 'commons-io:commons-io:2.11.0' }
+	dependencies { classpath 'commons-io:commons-io:2.21.0' }
 }
 
 ext.NUM_RETRIES = 3 // # of times to try to download a file before failing

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.3.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME