Building Bazel@HEAD results in many Java-related warnings

[fmeum]

Description of the bug:

Running bazel build //src:bazel-dev on current master (e.g. 38bf100) of Bazel itself results in the following warning being emitted for what appears to be almost every Java target:

warning: [options] system modules path not set in conjunction with -source 11

Which category does this issue belong to?

Java Rules

What's the simplest, easiest way to reproduce this bug? Please provide a minimal example if possible.

No response

Which operating system are you running Bazel on?

No response

What is the output of bazel info release?

No response

If bazel info release returns development version or (@non-git), tell us how you built Bazel.

No response

What's the output of git remote get-url origin; git rev-parse master; git rev-parse HEAD ?

No response

Is this a regression? If yes, please try to identify the Bazel commit where the bug was introduced.

No response

Have you found anything relevant by searching the web?

No response

Any other information, logs, or outputs that you want to share?

No response

[fmeum]

CC @cushon

[cushon]

I tried and wasn't able to repro.

I don't see 38bf100, I tested at 2ddacab80af1dca3c04e74809827c47ec4bc8498.

bazel build //src:bazel-dev
bazel-bin/src/bazel-dev build //src:bazel-dev

I don't see warning: [options] system modules path not set ... in the logs.

I tested with openjdk full version "17.0.6+10-LTS" as the local JDK, on a mac.

Am I holding it wrong?

[fmeum]

Sorry for the false alarm, I only see this on #18262, not master. I had the wrong branch checked out. It's still surprising.

[cushon]

Thanks, I can repro with

diff --git a/MODULE.bazel b/MODULE.bazel
index 4068f2e297..a4adc84765 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -24,7 +24,7 @@ bazel_dep(name = "zstd-jni", version = "1.5.2-3.bcr.1")
 bazel_dep(name = "blake3", version = "1.3.3.bcr.1")
 bazel_dep(name = "zlib", version = "1.3")
 bazel_dep(name = "rules_cc", version = "0.0.9")
-bazel_dep(name = "rules_java", version = "6.3.1")
+bazel_dep(name = "rules_java", version = "6.5.1")
 bazel_dep(name = "rules_proto", version = "5.3.0-21.7")
 bazel_dep(name = "rules_jvm_external", version = "5.2")
 bazel_dep(name = "rules_python", version = "0.24.0")
diff --git a/distdir_deps.bzl b/distdir_deps.bzl
index 8c2f8e20c7..593ebc4cca 100644
--- a/distdir_deps.bzl
+++ b/distdir_deps.bzl
@@ -106,9 +106,9 @@ DIST_DEPS = {
             "rules_java_builtin",
             "rules_java_builtin_for_testing",
         ],
-        "archive": "rules_java-6.3.1.tar.gz",
-        "sha256": "117a1227cdaf813a20a1bba78a9f2d8fb30841000c33e2f2d2a640bd224c9282",
-        "urls": ["https://github.com/bazelbuild/rules_java/releases/download/6.3.1/rules_java-6.3.1.tar.gz"],
+        "archive": "rules_java-6.5.1.tar.gz",
+        "sha256": "7b0d9ba216c821ee8697dedc0f9d0a705959ace462a3885fe9ba0347ba950111",
+        "urls": ["https://github.com/bazelbuild/rules_java/releases/download/6.5.1/rules_java-6.5.1.tar.gz"],
         "workspace_file_content": "",
         "used_in": [
             "additional_distfiles",

bazel clean; bazel shutdown; bazel build --toolchain_resolution_debug=bootstrap_runtime_toolchain_type  -s //src/main/java/com/google/devtools/build/lib/cmdline:query_exception_marker_interface
...
warning: [options] system modules path not set in conjunction with -source 11

The issue is that --system is not getting passed to javac:

$ bazel aquery 'mnemonic(Javac, //src/main/java/com/google/devtools/build/lib/cmdline:query_exception_marker_interface)' | grep -A 1 -E 'bootclasspath|system'
...
    --bootclasspath \
    bazel-out/darwin_arm64-fastbuild/bin/external/bazel_tools/tools/jdk/platformclasspath.jar \

I wonder if something is going wrong here: https://github.com/bazelbuild/rules_java/blob/0cdcecb2ee3a1da92f95ba0af036f20fa4179fb5/toolchains/default_java_toolchain.bzl#L246-L249

[benjaminp]

It's unsurprising to see this if host Bazel is <7 as 149cbce was not backported.

[davido]

I can reproduce this problem on Bazel@HEAD (2ddacab), when building with RBE:

  $ bazelisk build --config=remote --remote_instance_name=$PROJECT src:bazel-bin-dev
[...]
warning: [options] system modules path not set in conjunction with -source 11
[...]

[fmeum]

@davido Bazel is currently using a pre-7 Bazel version to build itself, which doesn't have 149cbce.

149cbce has always been missing in the 6.X releases, but this warning is only showing up with a newer rules_java. I am not sure whether 149cbce could break anything if we backport it.

[fmeum]

@bazel-io flag

[fmeum]

This should be fixed by bazelbuild/rules_java#142 + having a rules_java release for Bazel 7+.

[JohnnyMorganz]

Apologies for bringing up an old issue, but this seems most relevant to a problem I am currently facing.

We currently have a Bazel 6.4.0 repository that we recently enabled Bzlmod on. Our java_runtime_version and java_language_version is set to 11. When enabling bzlmod, it caused the JDK version of the compiler to switch from JDK 11 to JDK 17. From what I read based off #19934 (comment), this is expected. The rules_java version for bzlmod on 6.4.0 is 5.5.1.

When we enabled bzlmod, we started getting the same warnings warning: [options] system modules path not set in conjunction with -source 11. But what is more of a problem, is we started to get build failures reference to Record is ambiguous, due to a collision with the class java.lang.Record. This is odd, because that class was only introduced from 16+, but makes sense if the system flag is not being passed to javac.

However, based on this issue, it should be solved by the revert of the platformclasspath commit. But, AIUI this commit was not present for rules_java version 5.5.1 -https://github.com/bazelbuild/rules_java/blob/cc25058f4dcb66d9eaa40f1ccd72a856aa3f6e04/toolchains/default_java_toolchain.bzl#L83. Aquery also shows that bootclasspath is set to bazel-out/k8-fastbuild/bin/external/rules_java~5.5.1/toolchains/platformclasspath.jar. Also, using the temporary workaround in fmeum@6daa568 does not help. So, is there a separate reason why this is happening? (EDIT: see below note)

Here is a minimal repro setup: https://github.com/JohnnyMorganz/bazel-java-system-bug

Command causing failure:

$ USE_BAZEL_VERSION=6.4.0 bazel build //foo

Note that the build is successful when either:
a) disabling bzlmod (removing common --enable_bzlmod)
b) using Bazel 7.0.0+ (USE_BAZEL_VERSION=7.0.0 bazel build //foo), probably because of 149cbce - this is a longer term effort for us so we cannot do this immediately.

I can work around the compilation error by adding explicit imports (which we will need to do anyways if we want to upgrade JDK versions). But, we still get the warning on every java target build.

If this is better served as a new issue, let me know.

EDIT: Diffing the output of aquery before and after bzlmod is enabled produces the below

diff --git a/before_bzlmod b/after_bzlmod
index b5f956f..3b4f908 100644
--- a/before_bzlmod
+++ b/after_bzlmod
@@ -3,13 +3,12 @@ action 'Building foo/libfoo.jar (1 source file)'
   Target: //foo:foo
   Configuration: k8-fastbuild
   Execution platform: @local_config_platform//:host
-  ActionKey: d8678219df820a8bc3a259f6a027e5f2e58ac7cbda6be597aa1150dc5b16dd4e
-  Inputs: [bazel-out/k8-fastbuild/bin/bar/libbar-hjar.jar, bazel-out/k8-fastbuild/bin/bar/libbar-hjar.jdeps, bazel-out/k8-fastbuild/bin/external/bazel_tools/tools/jdk/platformclasspath.jar, external/remote_java_tools/java_tools/JavaBuilder_deploy.jar, external/remotejdk11_linux/bin/jaotc, external/remotejdk11_linux/bin/jar, external/remotejdk11_linux/bin/jarsigner, external/remotejdk11_linux/bin/java, external/remotejdk11_linux/bin/javac, external/remotejdk11_linux/bin/javadoc, external/remotejdk11_linux/bin/javap, external/remotejdk11_linux/bin/jcmd, external/remotejdk11_linux/bin/jconsole, external/remotejdk11_linux/bin/jdb, external/remotejdk11_linux/bin/jdeprscan, external/remotejdk11_linux/bin/jdeps, external/remotejdk11_linux/bin/jfr, external/remotejdk11_linux/bin/jhsdb, external/remotejdk11_linux/bin/jimage, external/remotejdk11_linux/bin/jinfo, external/remotejdk11_linux/bin/jjs, external/remotejdk11_linux/bin/jlink, external/remotejdk11_linux/bin/jmap, external/remotejdk11_linux/bin/jmod, external/remotejdk11_linux/bin/jps, external/remotejdk11_linux/bin/jrunscript, external/remotejdk11_linux/bin/jshell, external/remotejdk11_linux/bin/jstack, external/remotejdk11_linux/bin/jstat, external/remotejdk11_linux/bin/jstatd, external/remotejdk11_linux/bin/keytool, external/remotejdk11_linux/bin/pack200, external/remotejdk11_linux/bin/rmic, external/remotejdk11_linux/bin/rmid, external/remotejdk11_linux/bin/rmiregistry, external/remotejdk11_linux/bin/serialver, external/remotejdk11_linux/bin/unpack200, external/remotejdk11_linux/conf/logging.properties, external/remotejdk11_linux/conf/management/jmxremote.access, external/remotejdk11_linux/conf/management/jmxremote.password.template, external/remotejdk11_linux/conf/management/management.properties, external/remotejdk11_linux/conf/net.properties, external/remotejdk11_linux/conf/security/java.policy, external/remotejdk11_linux/conf/security/java.security, external/remotejdk11_linux/conf/security/policy/README.txt, external/remotejdk11_linux/conf/security/policy/limited/default_US_export.policy, external/remotejdk11_linux/conf/security/policy/limited/default_local.policy, external/remotejdk11_linux/conf/security/policy/limited/exempt_local.policy, external/remotejdk11_linux/conf/security/policy/unlimited/default_US_export.policy, external/remotejdk11_linux/conf/security/policy/unlimited/default_local.policy, external/remotejdk11_linux/conf/sound.properties, external/remotejdk11_linux/include/classfile_constants.h, external/remotejdk11_linux/include/jawt.h, external/remotejdk11_linux/include/jdwpTransport.h, external/remotejdk11_linux/include/jni.h, external/remotejdk11_linux/include/jvmti.h, external/remotejdk11_linux/include/jvmticmlr.h, external/remotejdk11_linux/include/linux/jawt_md.h, external/remotejdk11_linux/include/linux/jni_md.h, external/remotejdk11_linux/lib/classlist, external/remotejdk11_linux/lib/ct.sym, external/remotejdk11_linux/lib/jexec, external/remotejdk11_linux/lib/jfr/default.jfc, external/remotejdk11_linux/lib/jfr/profile.jfc, external/remotejdk11_linux/lib/jli/libjli.so, external/remotejdk11_linux/lib/jrt-fs.jar, external/remotejdk11_linux/lib/jspawnhelper, external/remotejdk11_linux/lib/jvm.cfg, external/remotejdk11_linux/lib/libattach.so, external/remotejdk11_linux/lib/libawt.so, external/remotejdk11_linux/lib/libawt_headless.so, external/remotejdk11_linux/lib/libawt_xawt.so, external/remotejdk11_linux/lib/libdt_socket.so, external/remotejdk11_linux/lib/libextnet.so, external/remotejdk11_linux/lib/libfontmanager.so, external/remotejdk11_linux/lib/libfreetype.so, external/remotejdk11_linux/lib/libinstrument.so, external/remotejdk11_linux/lib/libj2gss.so, external/remotejdk11_linux/lib/libj2pcsc.so, external/remotejdk11_linux/lib/libj2pkcs11.so, external/remotejdk11_linux/lib/libjaas.so, external/remotejdk11_linux/lib/libjava.so, external/remotejdk11_linux/lib/libjavajpeg.so, external/remotejdk11_linux/lib/libjawt.so, external/remotejdk11_linux/lib/libjdwp.so, external/remotejdk11_linux/lib/libjimage.so, external/remotejdk11_linux/lib/libjsig.so, external/remotejdk11_linux/lib/libjsound.so, external/remotejdk11_linux/lib/liblcms.so, external/remotejdk11_linux/lib/libmanagement.so, external/remotejdk11_linux/lib/libmanagement_agent.so, external/remotejdk11_linux/lib/libmanagement_ext.so, external/remotejdk11_linux/lib/libmlib_image.so, external/remotejdk11_linux/lib/libnet.so, external/remotejdk11_linux/lib/libnio.so, external/remotejdk11_linux/lib/libprefs.so, external/remotejdk11_linux/lib/librmi.so, external/remotejdk11_linux/lib/libsaproc.so, external/remotejdk11_linux/lib/libsctp.so, external/remotejdk11_linux/lib/libsplashscreen.so, external/remotejdk11_linux/lib/libsunec.so, external/remotejdk11_linux/lib/libunpack.so, external/remotejdk11_linux/lib/libverify.so, external/remotejdk11_linux/lib/libzip.so, external/remotejdk11_linux/lib/modules, external/remotejdk11_linux/lib/psfont.properties.ja, external/remotejdk11_linux/lib/psfontj2d.properties, external/remotejdk11_linux/lib/security/blocked.certs, external/remotejdk11_linux/lib/security/cacerts, external/remotejdk11_linux/lib/security/default.policy, external/remotejdk11_linux/lib/security/public_suffix_list.dat, external/remotejdk11_linux/lib/server/Xusage.txt, external/remotejdk11_linux/lib/server/libjsig.so, external/remotejdk11_linux/lib/server/libjvm.so, external/remotejdk11_linux/lib/src.zip, external/remotejdk11_linux/lib/tzdb.dat, foo/Foo.java]
+  ActionKey: cd507606ef0653c27a9257406292c1c22aea3e6420d0a3e47715f877cfdd1cda
+  Inputs: [bazel-out/k8-fastbuild/bin/bar/libbar-hjar.jar, bazel-out/k8-fastbuild/bin/bar/libbar-hjar.jdeps, bazel-out/k8-fastbuild/bin/external/rules_java~5.5.1/toolchains/platformclasspath.jar, external/rules_java~5.5.1~toolchains~remote_java_tools/java_tools/JavaBuilder_deploy.jar, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jar, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jarsigner, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/java, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/javac, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/javadoc, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/javap, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jcmd, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jconsole, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jdb, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jdeprscan, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jdeps, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jfr, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jhsdb, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jimage, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jinfo, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jlink, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jmap, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jmod, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jpackage, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jps, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jrunscript, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jshell, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jstack, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jstat, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/jstatd, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/keytool, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/rmiregistry, external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/serialver, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/logging.properties, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/management/jmxremote.access, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/management/jmxremote.password.template, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/management/management.properties, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/net.properties, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/sdp/sdp.conf.template, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/java.policy, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/java.security, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/policy/README.txt, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/policy/limited/default_US_export.policy, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/policy/limited/default_local.policy, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/policy/limited/exempt_local.policy, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/policy/unlimited/default_US_export.policy, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/security/policy/unlimited/default_local.policy, external/rules_java~5.5.1~toolchains~remotejdk17_linux/conf/sound.properties, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/classfile_constants.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/jawt.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/jdwpTransport.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/jni.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/jvmti.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/jvmticmlr.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/linux/jawt_md.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/include/linux/jni_md.h, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/classlist, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/ct.sym, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/jexec, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/jfr/default.jfc, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/jfr/profile.jfc, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/jrt-fs.jar, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/jspawnhelper, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/jvm.cfg, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libattach.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libawt.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libawt_headless.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libawt_xawt.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libdt_socket.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libextnet.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libfontmanager.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libfreetype.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libinstrument.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libj2gss.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libj2pcsc.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libj2pkcs11.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjaas.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjava.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjavajpeg.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjawt.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjdwp.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjimage.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjli.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjsig.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjsound.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libjsvml.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/liblcms.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libmanagement.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libmanagement_agent.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libmanagement_ext.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libmlib_image.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libnet.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libnio.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libprefs.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/librmi.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libsaproc.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libsctp.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libsplashscreen.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libsyslookup.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libverify.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/libzip.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/modules, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/psfont.properties.ja, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/psfontj2d.properties, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/security/blocked.certs, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/security/cacerts, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/security/default.policy, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/security/public_suffix_list.dat, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/server/classes.jsa, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/server/classes_nocoops.jsa, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/server/libjsig.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/server/libjvm.so, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/src.zip, external/rules_java~5.5.1~toolchains~remotejdk17_linux/lib/tzdb.dat, foo/Foo.java]
   Outputs: [bazel-out/k8-fastbuild/bin/foo/libfoo-native-header.jar, bazel-out/k8-fastbuild/bin/foo/libfoo.jar, bazel-out/k8-fastbuild/bin/foo/libfoo.jar_manifest_proto, bazel-out/k8-fastbuild/bin/foo/libfoo.jdeps]
   Environment: [LC_CTYPE=en_US.UTF-8, OSRELEASE=el9, PREVENT_TC_CACHE_POISONING=donotremove]
   ExecutionInfo: {internal-inline-outputs: bazel-out/k8-fastbuild/bin/foo/libfoo.jdeps, supports-multiplex-workers: 1, supports-worker-cancellation: 1, supports-workers: 1}
-  Command Line: (exec external/remotejdk11_linux/bin/java \
-    -XX:-CompactStrings \
+  Command Line: (exec external/rules_java~5.5.1~toolchains~remotejdk17_linux/bin/java \
     '--add-exports=jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED' \
     '--add-exports=jdk.compiler/com.sun.tools.javac.main=ALL-UNNAMED' \
     '--add-exports=jdk.compiler/com.sun.tools.javac.model=ALL-UNNAMED' \
@@ -24,10 +23,9 @@ action 'Building foo/libfoo.jar (1 source file)'
     '--add-opens=java.base/java.nio=ALL-UNNAMED' \
     '--add-opens=java.base/java.lang=ALL-UNNAMED' \
     '-Dsun.io.useCanonCaches=false' \
-    -Xlog:disable \
-    '-Xlog:all=warning:stderr:uptime,level,tags' \
+    -XX:-CompactStrings \
     -jar \
-    external/remote_java_tools/java_tools/JavaBuilder_deploy.jar \
+    external/rules_java~5.5.1~toolchains~remote_java_tools/java_tools/JavaBuilder_deploy.jar \
     --output \
     bazel-out/k8-fastbuild/bin/foo/libfoo.jar \
     --native_header_output \
@@ -38,7 +36,7 @@ action 'Building foo/libfoo.jar (1 source file)'
     --output_deps_proto \
     bazel-out/k8-fastbuild/bin/foo/libfoo.jdeps \
     --bootclasspath \
-    bazel-out/k8-fastbuild/bin/external/bazel_tools/tools/jdk/platformclasspath.jar \
+    bazel-out/k8-fastbuild/bin/external/rules_java~5.5.1/toolchains/platformclasspath.jar \
     --sources \
     foo/Foo.java \
     --javacopts \
@@ -55,7 +53,6 @@ action 'Building foo/libfoo.jar (1 source file)'
     -Xep:EmptyTopLevelDeclaration:OFF \
     -Xep:LenientFormatStringValidation:OFF \
     -Xep:ReturnMissingNullable:OFF \
-    -Xep:UseCorrectAssertInTests:OFF \
     -- \
     --target_label \
     //foo:foo \

And we can see the bootclasspath changed (but it changed from what the reverted commit was trying to do?)
If I try to register a java_toolchain with the old bootclasspath, it doesn't resolve the issue

load("@rules_java//toolchains:default_java_toolchain.bzl", "default_java_toolchain")
default_java_toolchain(
    name = "bazel_java_toolchain",
    bootclasspath = ["@bazel_tools//tools/jdk:platformclasspath"],
    source_version = "11",
    tags = ["manual"],
    target_version = "11",
)

EDIT 2:. According to https://stackoverflow.com/questions/66068153/java-warning-options-system-modules-path-not-set-in-conjunction-with-source, this warning was only introduced in JDK 14+. So it makes sense why this didnt show up pre bzlmod, as that was using JDK 11 runtime for compiler.

However, it was mentioned earlier that

149cbce has always been missing in the 6.X releases, but this warning is only showing up with a newer rules_java

which makes me think that there should be a way to get rid of these warnings. Is that true? I tried upgrading to rules_java 7.0.6 but it still warns. Was this issue solved for pre-Bazel 7?