bb execution fails on Gentoo

[edannenberg]

version

1.3.188

platform

Gentoo Linux - amd64

problem

Gentoo supports multiple Java installations, both system-wide and for users. A simple Bash script serves as a wrapper for Java that resolves the path/config of the currently selected Java VM before executing the actual java binary.

$ ls -lah /usr/bin/java
lrwxrwxrwx 1 root root 44 Aug 25  2022 /usr/bin/java -> /usr/libexec/eselect-java/run-java-tool.bash

The run-java-tool.bash script has an internal safe guard for being called directly, it should always be invoked via a symlink.
It looks like Babashka tries to execute Java but resolves the symlink of the java binary before doing so, resulting in the stack trace below.

To confirm this I added some debug output to run-java-tool.bash that outputs the name the wrapper script was invoked as (${0##*/}):

$ java -version
wrapper debug: java <- wrapper was called via symlink
openjdk version "11.0.20.1" 2023-08-24
OpenJDK Runtime Environment Temurin-11.0.20.1+1 (build 11.0.20.1+1)
OpenJDK 64-Bit Server VM Temurin-11.0.20.1+1 (build 11.0.20.1+1, mixed mode)

$ /usr/local/bin/bb --help
wrapper debug: run-java-tool.bash <- wrapper was called directly
* run-java-tool was invoked directly
* run-java-tool should only be used via symlinks to it
Exception in thread "main" clojure.lang.ExceptionInfo:  babashka.process.Process@a0d1a87
	at babashka.process$check.invokeStatic(process.cljc:111)
	at babashka.process$shell.invokeStatic(process.cljc:651)
	at babashka.impl.deps$add_deps$fn__27336.invoke(deps.clj:100)
...

Not resolving the Java binary symlink should fix the issue.

repro

Any execution of the bb command on a Gentoo install:

# /usr/local/bin/bb --help
* run-java-tool was invoked directly
* run-java-tool should only be used via symlinks to it
Exception in thread "main" clojure.lang.ExceptionInfo:  babashka.process.Process@a0d1a87
	at babashka.process$check.invokeStatic(process.cljc:111)
	at babashka.process$shell.invokeStatic(process.cljc:651)
	at babashka.impl.deps$add_deps$fn__27336.invoke(deps.clj:100)
	at borkdude.deps$_main.invokeStatic(deps.clj:1052)
	at borkdude.deps$_main.doInvoke(deps.clj:882)
	at clojure.lang.RestFn.applyTo(RestFn.java:137)
	at clojure.core$apply.invokeStatic(core.clj:667)
	at babashka.impl.deps$add_deps$fn__27343$fn__27344.invoke(deps.clj:106)
	at clojure.lang.AFn.applyToHelper(AFn.java:152)
	at clojure.lang.AFn.applyTo(AFn.java:144)
	at clojure.core$apply.invokeStatic(core.clj:667)
	at clojure.core$with_bindings_STAR_.invokeStatic(core.clj:1990)
	at clojure.core$with_bindings_STAR_.doInvoke(core.clj:1990)
	at clojure.lang.RestFn.invoke(RestFn.java:425)
	at babashka.impl.deps$add_deps$fn__27343.invoke(deps.clj:106)
	at babashka.impl.deps$add_deps.invokeStatic(deps.clj:106)
	at babashka.main$exec$fn__32207.invoke(main.clj:872)
	at clojure.lang.AFn.applyToHelper(AFn.java:152)
	at clojure.lang.AFn.applyTo(AFn.java:144)
	at clojure.core$apply.invokeStatic(core.clj:667)
	at clojure.core$with_bindings_STAR_.invokeStatic(core.clj:1990)
	at clojure.core$with_bindings_STAR_.doInvoke(core.clj:1990)
	at clojure.lang.RestFn.invoke(RestFn.java:425)
	at babashka.main$exec.invokeStatic(main.clj:824)
	at babashka.main$main.invokeStatic(main.clj:1194)
	at babashka.main$main.doInvoke(main.clj:1143)
	at clojure.lang.RestFn.applyTo(RestFn.java:137)
	at clojure.core$apply.invokeStatic(core.clj:667)
	at babashka.main$_main$f__32332__auto____32342.invoke(main.clj:1233)
	at clojure.lang.AFn.run(AFn.java:22)
	at java.base@21.0.1/java.lang.Thread.runWith(Thread.java:1596)
	at java.base@21.0.1/java.lang.Thread.run(Thread.java:1583)
	at org.graalvm.nativeimage.builder/com.oracle.svm.core.thread.PlatformThreads.threadStartRoutine(PlatformThreads.java:832)
	at org.graalvm.nativeimage.builder/com.oracle.svm.core.posix.thread.PosixPlatformThreads.pthreadStartRoutine(PosixPlatformThreads.java:211)
Exception in thread "main" java.lang.NullPointerException
	at clojure.lang.RT.intCast(RT.java:1221)
	at babashka.main$_main.invokeStatic(main.clj:1233)
	at babashka.main$_main.doInvoke(main.clj:1219)
	at clojure.lang.RestFn.applyTo(RestFn.java:137)
	at babashka.main.main(Unknown Source)
	at java.base@21.0.1/java.lang.invoke.LambdaForm$DMH/sa346b79c.invokeStaticInit(LambdaForm$DMH)

[borkdude]

You can work around this for now by setting the JAVA_CMD environment variable

[borkdude]

I guess the symlink is resolved here https://github.com/borkdude/deps.clj/blob/3e5dcdfe7b32e0d358a6f48cd46120596e83f02f/src/borkdude/deps.clj#L281

[borkdude]

I guess many other Clojure tools would fail on this, e.g. tools.build would:

https://github.com/clojure/tools.build/blob/534e07e1d504ab419e3b65c21aac8169fe7170ae/src/main/clojure/clojure/tools/build/tasks/process.clj#L125

[borkdude]

Here is a counter-repro produced by @ingydotnet

$ docker run -it --rm gentoo/stage3 bash
786fba5e0727 / # curl -sSLO https://download.oracle.com/graalvm/21/latest/graalvm-jdk-21_linux-x64_bin.tar.gz
786fba5e0727 / # curl -sSLO https://github.com/babashka/babashka/releases/download/v1.3.188/babashka-1.3.188-linux-amd64.tar.gz
786fba5e0727 / # tar xf graalvm-jdk-21_linux-x64_bin.tar.gz
786fba5e0727 / # tar xf babashka-1.3.188-linux-amd64.tar.gz
786fba5e0727 / # export JAVA_HOME=/graalvm-jdk-21.0.2+13.1 PATH=/:/graalvm-jdk-21.0.2+13.1/bin:$PATH
786fba5e0727 / # bb -Sdeps '{:deps {dev.weavejester/medley {:mvn/version "1.7.0"}}}' -e "(require '[medley.core])"
Clojure tools not yet in expected location: /root/.deps.clj/1.11.1.1435/ClojureTools/clojure-tools-1.11.1.1435.jar
Downloading https://github.com/clojure/brew-install/releases/download/1.11.1.1435/clojure-tools.zip to /root/.deps.clj/1.11.1.1435/ClojureTools/clojure-tools.zip
Unzipping /root/.deps.clj/1.11.1.1435/ClojureTools/clojure-tools.zip ...
Successfully installed clojure tools!
Downloading: org/clojure/clojure/1.11.1/clojure-1.11.1.pom from central
Downloading: org/clojure/core.specs.alpha/0.2.62/core.specs.alpha-0.2.62.pom from central
Downloading: org/clojure/spec.alpha/0.3.218/spec.alpha-0.3.218.pom from central
Downloading: org/clojure/pom.contrib/1.1.0/pom.contrib-1.1.0.pom from central
Downloading: dev/weavejester/medley/1.7.0/medley-1.7.0.pom from clojars
Downloading: org/clojure/core.specs.alpha/0.2.62/core.specs.alpha-0.2.62.jar from central
Downloading: org/clojure/spec.alpha/0.3.218/spec.alpha-0.3.218.jar from central
Downloading: org/clojure/clojure/1.11.1/clojure-1.11.1.jar from central
Downloading: dev/weavejester/medley/1.7.0/medley-1.7.0.jar from clojars

Is it possible to produce a similar repro for your above problem?

[edannenberg]

Thanks for the swift reply! Setting JAVA_CMD worked like a charm.

Setting JAVA_HOME with a manual install like that avoids the issue, the stage3 base image won't even have the java wrapper. Installing a standard Gentoo Java package with emerge -v openjdk-bin should do the trick. If you want to skip all the compiling I also maintain a Gentoo based Clojure image:

$ docker run -it --rm kubler/clojure
$ bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install)
$ bb -Sdeps '{:deps {dev.weavejester/medley {:mvn/version "1.7.0"}}}' -e "(require '[medley.core])"
Clojure tools not yet in expected location: /root/.deps.clj/1.11.1.1435/ClojureTools/clojure-tools-1.11.1.1435.jar
Downloading https://github.com/clojure/brew-install/releases/download/1.11.1.1435/clojure-tools.zip to /root/.deps.clj/1.11.1.1435/ClojureTools/clojure-tools.zip
Unzipping /root/.deps.clj/1.11.1.1435/ClojureTools/clojure-tools.zip ...
Successfully installed clojure tools!
* run-java-tool was invoked directly
* run-java-tool should only be used via symlinks to it
Exception in thread "main" clojure.lang.ExceptionInfo:  babashka.process.Process@8e9e7e77
	at babashka.process$check.invokeStatic(process.cljc:111)
	at babashka.process$shell.invokeStatic(process.cljc:651)
	at babashka.impl.deps$add_deps$fn__27336.invoke(deps.clj:100)

[borkdude]

Closing this since I'm not sure what is a fitting solution here and there is a workaround