scala sbt scala-3 sbt-native-packager jlink

Fix missing transnitive dependencies with jlink and scala3 `scala.quoted -> scala `

I'm trying to upgrade a scala library to scala3 and cannot seem to figure out how to get the scala3 language to work with jlink. It says I'm missing transitive dependencies on a jlink build. You can see the build failure here.

I can of course add these to the jlinkIgnore settings but that seems to be a poor practice. What are the transitive dependencies at play here that I am missing?

Here is a direct link to a CI failure https://github.com/bitcoin-s/bitcoin-s/actions/runs/15227451712/job/42831225145?pr=5713#step:5:23602

[error] Dependee packages not found in classpath. You can use jlinkIgnoreMissingDependency to silence these.
[error]   org.apache.pekko.http.scaladsl.model -> org.apache.pekko.http.javadsl.model
[error]   org.apache.pekko.stream.serialization -> org.apache.pekko.stream
[error]   scala.quoted -> scala
[error]   scala.quoted.runtime -> scala
[error] stack trace is suppressed; run last appServer / jlinkModules for the full output
[error] (appServer / jlinkModules) Missing package dependencies

Solution

Current reproduction is

git clone https://github.com/Christewart/bitcoin-s-core.git
cd bitcoin-s-core
git checkout 2024-05-11-scala3-crossbuild
git clone https://github.com/bitcoin-s/secp256k1-zkp.git
sbt appServer/universal:packageBin

Your CI fails on sbt appServer/universal:packageBin. Locally it produces the error

[info] Running: jdeps --multi-release 21 -R /media/data/Projects2/bitcoin-s-core/app/server/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/app/server-routes/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/app-commons/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/core/.jvm/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/crypto/.jvm/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/secp256k1jni/target/classes /media/data/Projects2/bitcoin-s-core/db-commons/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/key-manager/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/node/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/async-utils/.jvm/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/chain/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/bitcoind-rpc/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/tor/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/wallet/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/fee-provider/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/dlc-wallet/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/dlc-node/target/scala-3.7.0/classes /media/data/Projects2/bitcoin-s-core/zmq/target/scala-3.7.0/classes /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala3-library_3/3.7.0/scala3-library_3-3.7.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/lihaoyi/upickle_3/4.0.2/upickle_3-4.0.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/ch/qos/logback/logback-classic/1.5.18/logback-classic-1.5.18.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/apache/pekko/pekko-actor_3/1.1.3/pekko-actor_3-1.1.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/apache/pekko/pekko-http_3/1.2.0/pekko-http_3-1.2.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/apache/pekko/pekko-stream_3/1.1.3/pekko-stream_3-1.1.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/apache/pekko/pekko-slf4j_3/1.1.3/pekko-slf4j_3-1.1.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/codehaus/janino/janino/3.1.12/janino-3.1.12.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/code/gson/gson/2.13.1/gson-2.13.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/guava/guava/33.4.8-jre/guava-33.4.8-jre.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/io/dropwizard/metrics/metrics-healthchecks/4.2.30/metrics-healthchecks-4.2.30.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/io/dropwizard/metrics/metrics-jvm/4.2.30/metrics-jvm-4.2.30.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/io/dropwizard/metrics5/metrics-core/5.0.0/metrics-core-5.0.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/net/java/dev/jna/jna/5.17.0/jna-5.17.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/github/waffle/waffle-jna/3.5.1/waffle-jna-3.5.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/osgi/osgi.core/8.0.0/osgi.core-8.0.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/osgi/org.osgi.service.jdbc/1.1.0/org.osgi.service.jdbc-1.1.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/osgi/org.osgi.framework/1.10.0/org.osgi.framework-1.10.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/avalon-framework/avalon-framework/20020627/avalon-framework-20020627.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/logkit/logkit/20020529/logkit-20020529.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/tukaani/xz/1.10/xz-1.10.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/javax/servlet/javax.servlet-api/4.0.1/javax.servlet-api-4.0.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/javax/mail/mail/1.4.7/mail-1.4.7.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/javax/jms/javax.jms-api/2.0.1/javax.jms-api-2.0.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/playframework/play-json_3/3.0.4/play-json_3-3.0.4.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/typesafe/config/1.4.3/config-1.4.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/typesafe/slick/slick_3/3.6.1/slick_3-3.6.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/typesafe/slick/slick-hikaricp_3/3.6.1/slick-hikaricp_3-3.6.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/xerial/sqlite-jdbc/3.49.1.0/sqlite-jdbc-3.49.1.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/lihaoyi/ujson_3/4.0.2/ujson_3-4.0.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/zeromq/jeromq/0.5.4/jeromq-0.5.4.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/lihaoyi/upack_3/4.0.2/upack_3-4.0.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/lihaoyi/upickle-implicits_3/4.0.2/upickle-implicits_3-4.0.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/ch/qos/logback/logback-core/1.5.18/logback-core-1.5.18.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/slf4j/slf4j-api/2.0.17/slf4j-api-2.0.17.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/apache/pekko/pekko-http-core_3/1.2.0/pekko-http-core_3-1.2.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/apache/pekko/pekko-protobuf-v3_3/1.1.3/pekko-protobuf-v3_3-1.1.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/reactivestreams/reactive-streams/1.0.4/reactive-streams-1.0.4.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/typesafe/ssl-config-core_3/0.6.1/ssl-config-core_3-0.6.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/codehaus/janino/commons-compiler/3.1.12/commons-compiler-3.1.12.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/errorprone/error_prone_annotations/2.38.0/error_prone_annotations-2.38.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/guava/failureaccess/1.0.3/failureaccess-1.0.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/jspecify/jspecify/1.0.0/jspecify-1.0.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/j2objc/j2objc-annotations/3.0.0/j2objc-annotations-3.0.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/io/dropwizard/metrics/metrics-core/4.2.30/metrics-core-4.2.30.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/net/java/dev/jna/jna-platform/5.16.0/jna-platform-5.16.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/slf4j/jcl-over-slf4j/2.0.16/jcl-over-slf4j-2.0.16.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/checkerframework/checker-qual/3.48.3/checker-qual-3.48.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/net/bytebuddy/byte-buddy/1.15.11/byte-buddy-1.15.11.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/net/bytebuddy/byte-buddy-agent/1.15.11/byte-buddy-agent-1.15.11.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/osgi/osgi.annotation/8.1.0/osgi.annotation-8.1.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/javax/activation/activation/1.1/activation-1.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/flywaydb/flyway-core/11.8.0/flyway-core-11.8.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/flywaydb/flyway-database-postgresql/11.8.0/flyway-database-postgresql-11.8.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/postgresql/postgresql/42.7.5/postgresql-42.7.5.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/bouncycastle/bcprov-jdk18on/1.80/bcprov-jdk18on-1.80.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scodec/scodec-bits_3/1.2.1/scodec-bits_3-1.2.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/playframework/play-functional_3/3.0.4/play-functional_3-3.0.4.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-core/2.15.2/jackson-core-2.15.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-annotations/2.15.2/jackson-annotations-2.15.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/fasterxml/jackson/datatype/jackson-datatype-jdk8/2.14.3/jackson-datatype-jdk8-2.14.3.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/fasterxml/jackson/datatype/jackson-datatype-jsr310/2.15.2/jackson-datatype-jsr310-2.15.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/fasterxml/jackson/core/jackson-databind/2.15.2/jackson-databind-2.15.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/io/monix/monix-execution_3/3.4.1/monix-execution_3-3.4.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/zaxxer/HikariCP/6.3.0/HikariCP-6.3.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/lihaoyi/upickle-core_3/4.0.2/upickle-core_3-4.0.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/eu/neilalexander/jnacl/1.0.0/jnacl-1.0.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/apache/pekko/pekko-parsing_3/1.2.0/pekko-parsing_3-1.2.0.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/parboiled/parboiled_3/2.5.1/parboiled_3-2.5.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/fasterxml/jackson/dataformat/jackson-dataformat-toml/2.15.2/jackson-dataformat-toml-2.15.2.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/io/monix/monix-internal-jctools_3/3.4.1/monix-internal-jctools_3-3.4.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/io/monix/implicitbox_3/0.3.4/implicitbox_3-0.3.4.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/com/lihaoyi/geny_3/1.1.1/geny_3-1.1.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scijava/native-lib-loader/2.5.0/native-lib-loader-2.5.0.jar
               ^^^^^^^^   <-------------
...
[error] Dependee packages not found in classpath. You can use jlinkIgnoreMissingDependency to silence these.
[error]   org.apache.pekko.http.scaladsl.model -> org.apache.pekko.http.javadsl.model
[error]   org.apache.pekko.stream.serialization -> org.apache.pekko.stream
[error]   scala.quoted -> scala
[error]   scala.quoted.runtime -> scala
[error] stack trace is suppressed; run last appServer / jlinkModules for the full output
[error] (appServer / jlinkModules) Missing package dependencies

[IJ]last appServer / jlinkModules
...
[error] java.lang.RuntimeException: Missing package dependencies
[error]     at scala.sys.package$.error(package.scala:30)
[error]     at com.typesafe.sbt.packager.archetypes.jlink.JlinkPlugin$.$anonfun$projectSettings$9(JlinkPlugin.scala:108)
[error]     at scala.Function1.$anonfun$compose$1(Function1.scala:49)
[error]     at sbt.internal.util.$tilde$greater.$anonfun$$u2219$1(TypeFunctions.scala:63)
[error]     at sbt.std.Transform$$anon$4.work(Transform.scala:69)
[error]     at sbt.Execute.$anonfun$submit$2(Execute.scala:283)
[error]     at sbt.internal.util.ErrorHandling$.wideConvert(ErrorHandling.scala:24)
[error]     at sbt.Execute.work(Execute.scala:292)
[error]     at sbt.Execute.$anonfun$submit$1(Execute.scala:283)
[error]     at sbt.ConcurrentRestrictions$$anon$4.$anonfun$submitValid$1(ConcurrentRestrictions.scala:265)
[error]     at sbt.CompletionService$$anon$2.call(CompletionService.scala:65)
[error]     at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
[error]     at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
[error]     at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
[error]     at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
[error]     at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
[error]     at java.base/java.lang.Thread.run(Thread.java:1583)
[error] (appServer / jlinkModules) Missing package dependencies

Notice the command jdeps ... above.

https://docs.oracle.com/en/java/javase/11/tools/jdeps.html

Simpler reproduction is the following.

For Scala 2:

myscalaproject/src/main/scala/module-info.java

module myscalaproject {
    exports com.example;
}

myscalaproject/src/main/scala/com/example/App.scala

package com.example

object App {
  def main(args: Array[String]): Unit = {
    println("hi")
  }
}

myscalaproject/project/build.properties

sbt.version = 1.11.0

myscalaproject/project/plugins.sbt

addSbtPlugin("com.github.sbt" % "sbt-native-packager" % "1.11.1")

myscalaproject/build.sbt

Global / onChangedBuildSource := ReloadOnSourceChanges

ThisBuild / version := "0.1.0-SNAPSHOT"

ThisBuild / scalaVersion := "2.13.16"

lazy val root = (project in file("."))
  .settings(
    name := "myscalaproject",
    compileOrder := CompileOrder.ScalaThenJava,
    packageOptions += Package.ManifestAttributes(
      "Class-Path" -> "/home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar"
    ),
    Compile / mainClass := Some("com.example.App"),
    //https://stackoverflow.com/questions/21461798/how-to-disable-scaladoc-generation-in-dist-task-in-play-2-2-x-using-project-bui
    Compile / packageDoc / publishArtifact := false,
    packageDoc / publishArtifact := false,
    Compile / doc / sources := Seq.empty
  )
  .enablePlugins(
    JavaAppPackaging,
    JlinkPlugin,
  )

sbt package produces myscalaproject_2.13-0.1.0-SNAPSHOT.jar.

Then jdeps works properly:

jdeps -s -R mydir/myscalaproject_2.13-0.1.0-SNAPSHOT.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar

myscalaproject -> java.base
myscalaproject -> /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar
scala-library-2.13.16.jar -> java.base

But for Scala 3:

myscala3project/src/main/scala/module-info.java

myscala3project/src/main/scala/com/example/App.scala

myscalaproject/project/build.properties

myscala3project/project/plugins.sbt

The same.

myscala3project/build.sbt

Global / onChangedBuildSource := ReloadOnSourceChanges

ThisBuild / version := "0.1.0-SNAPSHOT"

ThisBuild / scalaVersion := "3.7.0"

lazy val root = (project in file("."))
  .settings(
    name := "myscala3project",
    compileOrder := CompileOrder.ScalaThenJava,
    packageOptions += Package.ManifestAttributes(
      "Class-Path" -> Seq(
        "/home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar",
        "/home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala3-library_3/3.7.0/scala3-library_3-3.7.0.jar",
      ).mkString(" ")
    ),
    Compile / mainClass := Some("com.example.App"),
    //https://stackoverflow.com/questions/21461798/how-to-disable-scaladoc-generation-in-dist-task-in-play-2-2-x-using-project-bui
    Compile / packageDoc / publishArtifact := false,
    packageDoc / publishArtifact := false,
    Compile / doc / sources := Seq.empty
  )
  .enablePlugins(
    JavaAppPackaging,
    JlinkPlugin,
  )

jdeps fails:

jdeps -s -R mydir/myscala3project_3-0.1.0-SNAPSHOT.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala3-library_3/3.7.0/scala3-library_3-3.7.0.jar

myscala3project -> java.base
myscala3project -> /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar
myscala3project -> /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala3-library_3/3.7.0/scala3-library_3-3.7.0.jar
scala-library-2.13.16.jar -> java.base
scala3-library_3-3.7.0.jar -> java.base
scala3-library_3-3.7.0.jar -> jdk.unsupported
scala3-library_3-3.7.0.jar -> not found         <------------- !!!
scala3-library_3-3.7.0.jar -> /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar

You will see more details if you remove the summary flag -s

...
scala.quoted          -> scala       scala-library-2.13.16.jar
scala.quoted          -> scala       not found   <------------- ???
...
scala.quoted.runtime  -> scala       scala-library-2.13.16.jar
scala.quoted.runtime  -> scala       not found   <------------- ???
...

It seems there is a bug in jdeps:

A: https://stackoverflow.com/a/75430512/5249621 (Q: jdeps returns "not found")

You can see the actual Path parser checks if the -cp/-classpath argument list contains dir/.* format and not dir/* format as advertised by the docs, examples and the API's javadoc.

// wildcard to parse all JAR files e.g. -classpath dir/*
int i = p.lastIndexOf(".*");

JDK 11 Adoptium JDK 17 Adoptium JDK 21 Adoptium JDK 24 Adoptium JDK 24 Corretto OpenJDK

So if you don't want to patch jdk and jdeps then it seems you should add those lines to jlinkIgnore, indeed.

Update. Actually, the situation is a little more complicated. I patched OpenJDK 25 fixing jdeps. On contrary to .split, .lastIndexOf doesn't support regex. So I replaced

int i = p.lastIndexOf(".*");
if (i > 0) {
   Path dir = Paths.get(p.substring(0, i));
   ...

with

int i = lastIndex(p, ".\\*");
if (i > 0) {
   Path dir = Paths.get(p.substring(0, i));
   ...

private int lastIndex(String str, String regex) {
  String splitted[] = (str + " ").split(regex);
  if (splitted.length == 0 || splitted.length == 1) {
    return -1;
  }
  return str.length() - 1 - splitted[splitted.length - 1].length();
}

https://github.com/DmytroMitin/jdk/commit/9e601728961170940aee1356855f075557bae613

https://stackoverflow.com/a/10619920/5249621 ( Find Last Index Of by Regex in Java )

or just

int i = p.lastIndexOf("*");
if (i > 0) {
   Path dir = Paths.get(p.substring(0, i - 1));
   ...

https://github.com/DmytroMitin/jdk/commit/381ea799460e959eec5a8000d837934fcd29946f

But still jdeps -s -R ... (-s stands for "summary", -R for "recursively" i.e. transitive dependencies) produces not found in some places:

https://github.com/DmytroMitin/so79636833_jdeps_bug_demo/actions/runs/15419307905/job/43389831125

(https://github.com/DmytroMitin/so79636833_jdeps_bug_demo - creating a module via module-info.java seems not significant

https://github.com/DmytroMitin/setup-java

https://github.com/DmytroMitin/jdk25

https://github.com/DmytroMitin/jdk/tree/so79636833_jdeps_bug)

Run JDK 25 jdeps

jdeps -s -R /home/runner/work/so79636833_jdeps_bug_demo/so79636833_jdeps_bug_demo/target/scala-3.7.1/so79636833_jdeps_bug_demo_3-0.1.0-SNAPSHOT.jar /home/runner/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala3-library_3/3.7.1/scala3-library_3-3.7.1.jar /home/runner/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar

scala-library-2.13.16.jar -> java.base
scala3-library_3-3.7.1.jar -> java.base
scala3-library_3-3.7.1.jar -> jdk.unsupported
scala3-library_3-3.7.1.jar -> not found        <------------
scala3-library_3-3.7.1.jar -> /home/runner/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar
so79636833_jdeps_bug_demo_3-0.1.0-SNAPSHOT.jar -> java.base
so79636833_jdeps_bug_demo_3-0.1.0-SNAPSHOT.jar -> /home/runner/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar

I found better flags -v ("verbose" i.e. even more verbose than if just to remove -s) and especially --missing-deps

jdeps --missing-deps  -R target/scala-3.7.1/so79636833_jdeps_bug_demo_3-0.1.0-SNAPSHOT.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala3-library_3/3.7.1/scala3-library_3-3.7.1.jar /home/dmitin/.cache/coursier/v1/https/repo1.maven.org/maven2/org/scala-lang/scala-library/2.13.16/scala-library-2.13.16.jar

scala3-library_3-3.7.1.jar -> not found
  scala.quoted.Quotes$reflectModule$TypeReprModule   -> scala.AnyKind    not found
  scala.quoted.Quotes$reflectModule$TypeTreeModule   -> scala.AnyKind    not found
  scala.quoted.Type                                  -> scala.AnyKind    not found
  scala.quoted.Type$                                 -> scala.AnyKind    not found
  scala.quoted.runtime.QuoteUnpickler                -> scala.AnyKind    not found

So what confuses jdeps in Scala 3 is scala.AnyKind. And this makes sense. In Scala there are types present in sources but not in bytecode, or even some types not present either in sources or bytecode (e.g. ContextFunctionN Can't create an anonymous implementation of ContextFunction1 in Scala 3). But scala.AnyKind is a class present in sources but not in bytecode

https://www.scala-lang.org/api/current/scala/AnyKind.html

https://github.com/scala/scala3/blob/main/library-aux/src/scala/AnyKind.scala

Scala 3. Kind polymorphism and AnyKind type - any code example?

package scala

final abstract class AnyKind

Class.forName("scala.AnyKind") //java.lang.ClassNotFoundException

So the answer to your question

Either this bug is in the jlink tool itself or is something weird about the new scala3 system that didn't exist with scala2

is that it's both a bug in jlink (actually, jdeps) and something specific to Scala 3.

Here is the output of jdeps --missing-deps -R ... for https://github.com/bitcoin-s/bitcoin-s

https://gist.github.com/DmytroMitin/6b6d9338dc8abe38bd15113f1cd0d915