Can't use custom Gem (Bad file descriptor)

[Poundex]

Hello,

I am trying to use a custom Gem but running the prepare JAR task is failing with a strange error:
extconf failed Bad file descriptor - /bin/sh

I can install the Gem successfully with the external Gem command.

Full output:

16:00:07: Executing 'clean asciidoctorGemsJar'...

> Task :clean

> Task :asciidoctorGemsPrepare
2024-01-08T16:00:10.276Z [/127.0.0.1:59950 to /127.0.0.1:38421 workers] WARN FilenoUtil : Native subprocess control requires open access to the JDK IO subsystem
Pass '--add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED' to enable.

Successfully installed concurrent-ruby-1.2.2
Successfully installed i18n-1.14.1
Successfully installed ruby-enum-0.9.0
Building native extensions. This could take a while...
ERROR:  Error installing /home/pounder/.gradle/caches/modules-2/files-2.1/rubygems/mathematical/1.6.18/7ca3dcf196407c547dae654654e86f892cb8c493/mathematical-1.6.18.gem:
	ERROR: Failed to build gem native extension.

    current directory: /home/pounder/workspace/3p/d2l-java/build/.asciidoctorGems/gems/mathematical-1.6.18/ext/mathematical
/home/pounder/.sdkman/candidates/java/20-tem/bin/java -cp :/home/pounder/.gradle/caches/modules-2/files-2.1/org.jruby/jruby-complete/9.3.8.0/8e11191265ab501930125081d8c21a3f55f1b8cd/jruby-complete-9.3.8.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.asciidoctor/asciidoctor-gradle-jvm-epub/4.0.0/c110459834da386d1e28e6c1873abd0be03a0774/asciidoctor-gradle-jvm-epub-4.0.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.asciidoctor/asciidoctor-gradle-jvm-gems/4.0.0/68c1a36d9828b76e4d4fdf09cc75c9ac62c3a121/asciidoctor-gradle-jvm-gems-4.0.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.asciidoctor/asciidoctor-gradle-jvm/4.0.0/d7559f3bd9fe8eef8521f0e31d67bf7c77a4bbab/asciidoctor-gradle-jvm-4.0.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.asciidoctor/asciidoctor-gradle-base/4.0.0/ebbc22fed8a8f152b954edd9410318e9f06bca5a/asciidoctor-gradle-base-4.0.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle.jruby/jrubygradle-resolver/1.0.0/f3fb67db407e21634deb742f1db00d4bd3ba7a06/jrubygradle-resolver-1.0.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant-herd/2.2.2/e5b7a0b126a5ea4cda4ef2cd1d2b93ebcbeb23f2/grolifant-herd-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant80/2.2.2/5f5b27c6c7d5cae6fb2d49b9f46da00dfe0b7d6d/grolifant80-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant70/2.2.2/299a226fd304d2755bde366b871771ddf7d85472/grolifant70-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant60/2.2.2/af90d5d87e7efeb5eea059c379d9e92395d44790/grolifant60-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant50/2.2.2/97f53ac70dd4314b0c711cca0646e09ac2e5798c/grolifant50-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant40-legacy-api/2.2.2/53fd44ecfb638e3223a1b167e5ab8bfb0307f59d/grolifant40-legacy-api-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant40/2.2.2/ebbe374a81d61f38f092c7817149f18d80911f3f/grolifant40-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant-core/2.2.2/891b3262afae6a8a2eae6ed94aad37c01a6336cf/grolifant-core-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.ysb33r.gradle/grolifant-rawhide/2.2.2/749af56246ef16d40fedef7a43ad6899f27ae99c/grolifant-rawhide-2.2.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.asciidoctor/asciidoctorj-api/2.5.7/37ea651d5f1ba2ad3d1c09eb2356b17f35c15bb5/asciidoctorj-api-2.5.7.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.tukaani/xz/1.6/5b6f921f1810bdf90e25471968f741f87168b64/xz-1.6.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.github.http-builder-ng/http-builder-ng-okhttp/1.0.3/f5a767dc67c1e60daba8cd974007aeef06068fbd/http-builder-ng-okhttp-1.0.3.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.ratpack/ratpack-core/1.6.1/5d6041a76c83769f09164d485609c30e26d2a958/ratpack-core-1.6.1.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.codehaus.groovy/groovy-nio/3.0.13/bfdc9d5c9ca5dc1efb0f9543dd732b7c20647fcd/groovy-nio-3.0.13.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.github.http-builder-ng/http-builder-ng-core/1.0.3/ad2b181931a4c451f8f456c7b5eaffc9fda8fee6/http-builder-ng-core-1.0.3.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.burgstaller/okhttp-digest/1.10/ab01486e496bb761888197b3c5c179f49b79d668/okhttp-digest-1.10.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.squareup.okhttp3/okhttp/3.5.0/4b0bb6bfbecbdd42b97ff400af342bfe7f32bc83/okhttp-3.5.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.ratpack/ratpack-exec/1.6.1/76566346af31fc2df3a30828d02ab4a76218d25e/ratpack-exec-1.6.1.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-codec-http/4.1.32.Final/b9218adba7353ad5a75fcb639e4755d64bd6ddf/netty-codec-http-4.1.32.Final.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-handler/4.1.32.Final/b4e3fa13f219df14a9455cc2111f133374428be0/netty-handler-4.1.32.Final.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.sun.activation/javax.activation/1.2.0/bf744c1e2776ed1de3c55c8dac1057ec331ef744/javax.activation-1.2.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.github.ben-manes.caffeine/caffeine/2.6.2/c8fd8817f9d2b2ced82f8968e0dd943aab557de0/caffeine-2.6.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.javassist/javassist/3.22.0-GA/3e83394258ae2089be7219b971ec21a8288528ad/javassist-3.22.0-GA.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.datatype/jackson-datatype-guava/2.9.8/b7f7819800f8ebe51a03dd951636f6dbc6245ce6/jackson-datatype-guava-2.9.8.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.datatype/jackson-datatype-jdk8/2.9.8/bcd02aa9195390e23747ed40bf76be869ad3a2fb/jackson-datatype-jdk8-2.9.8.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.datatype/jackson-datatype-jsr310/2.9.8/28ad1bced632ba338e51c825a652f6e11a8e6eac/jackson-datatype-jsr310-2.9.8.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-databind/2.9.8/11283f21cc480aa86c4df7a0a3243ec508372ed2/jackson-databind-2.9.8.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.dataformat/jackson-dataformat-yaml/2.9.8/a1c807329eb0c75976aeb5961a506b3516ffeae3/jackson-dataformat-yaml-2.9.8.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.yaml/snakeyaml/1.23/ec62d74fe50689c28c0ff5b35d3aebcaa8b5be68/snakeyaml-1.23.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.codehaus.groovy/groovy/3.0.13/7652b22000c2cebbfdcfdf530a64e41baa518cb/groovy-3.0.13.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.apache.commons/commons-collections4/4.4/62ebe7544cb7164d87e0637a2a6a2bdc981395e8/commons-collections4-4.4.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/xml-resolver/xml-resolver/1.2/3d0f97750b3a03e0971831566067754ba4bfd68c/xml-resolver-1.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.ratpack/ratpack-base/1.6.1/2fd3ffd5fa3bd0e5aed91814cf7e9a8c5b6d56db/ratpack-base-1.6.1.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-api/1.7.25/da76ca59f6a57ee3102f8f9bd9cee742973efa8a/slf4j-api-1.7.25.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.squareup.okio/okio/1.11.0/840897fcd7223a8143f1d9b6f69714e7be34fd50/okio-1.11.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-transport-native-epoll/4.1.32.Final/9261e2930ab30681230a1192878dc2d17525350d/netty-transport-native-epoll-4.1.32.Final-linux-x86_64.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-codec/4.1.32.Final/8f32bd79c5a16f014a4372ed979dc62b39ede33a/netty-codec-4.1.32.Final.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-transport-native-unix-common/4.1.32.Final/3d2aea6a2873b0a6503645dc296bc0ce6d01a25a/netty-transport-native-unix-common-4.1.32.Final.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-transport/4.1.32.Final/d5e5a8ff9c2bc7d91ddccc536a5aca1a4355bd8b/netty-transport-4.1.32.Final.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-buffer/4.1.32.Final/46ede57693788181b2cafddc3a5967ed2f621c8/netty-buffer-4.1.32.Final.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/org.reactivestreams/reactive-streams/1.0.2/323964c36556eb0e6209f65c1cef72b53b461ab8/reactive-streams-1.0.2.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-annotations/2.9.0/7c10d545325e3a6e72e06381afe469fd40eb701/jackson-annotations-2.9.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.fasterxml.jackson.core/jackson-core/2.9.8/f5a654e4675769c716e5b387830d19b501ca191/jackson-core-2.9.8.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/com.google.guava/guava/21.0/3a3d111be1be1b745edfa7d91678a12d7ed38709/guava-21.0.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-resolver/4.1.32.Final/3e0114715cb125a12db8d982b2208e552a91256d/netty-resolver-4.1.32.Final.jar:/home/pounder/.gradle/caches/modules-2/files-2.1/io.netty/netty-common/4.1.32.Final/e95de4f762606f492328e180c8ad5438565a5e3b/netty-common-4.1.32.Final.jar org.jruby.Main -I uri:classloader:/META-INF/jruby.home/lib/ruby/stdlib -r ./siteconf20240108-496572-1j6nzcv.rb extconf.rb
extconf failedBad file descriptor - /bin/sh

Gem files will remain installed in /home/pounder/workspace/3p/d2l-java/build/.asciidoctorGems/gems/mathematical-1.6.18 for inspection.
Results logged to /home/pounder/workspace/3p/d2l-java/build/.asciidoctorGems/extensions/universal-java-20/2.6.0/mathematical-1.6.18/gem_make.out
Successfully installed asciimath-2.0.5
Successfully installed asciidoctor-2.0.20
Successfully installed asciidoctor-mathematical-0.3.5
6 gems installed

> Task :asciidoctorGemsJar

BUILD SUCCESSFUL in 11s
3 actionable tasks: 3 executed
16:00:18: Execution finished 'clean asciidoctorGemsJar'.

Even though the task succeeds, there are errors and the subsequent tasks do not work:

16:05:27: Executing 'asciidoctorEpub'...


> Task :asciidoctorEpub FAILED
1 actionable task: 1 executed
2024-01-08T16:05:28.204Z [WorkerExecutor Queue] WARN FilenoUtil : Native subprocess control requires open access to the JDK IO subsystem
Pass '--add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED' to enable.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':asciidoctorEpub'.
> A failure occurred while executing org.ysb33r.grolifant.internal.v6.jvm.worker.InternalWorkerAppExecutor
   > org.jruby.exceptions.LoadError: (LoadError) no such file to load -- asciidoctor-mathematical

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --info or --debug option to get more log output.
> Run with --scan to get full insights.
> Get more help at https://help.gradle.org.

BUILD FAILED in 1s
16:05:29: Execution finished 'asciidoctorEpub'.

I tried a --no-build-cache workaround from another issue which looked like it might be similar/related, but this had no effect.

Full build.gradle:

plugins {
	id("org.asciidoctor.jvm.convert") version "4.0.0"
	id("org.asciidoctor.jvm.epub") version "4.0.0"
	id("org.asciidoctor.jvm.gems") version "4.0.0"
}

repositories {
	mavenCentral()
	ruby {
		gems()
	}
}

dependencies {
	asciidoctorGems 'rubygems:asciidoctor-mathematical:0.3.5'
}

asciidoctorj {
	requires 'asciidoctor-mathematical'
}

asciidoctor {
	baseDirFollowsSourceFile()
	outputDir = "${project.buildDir}/docs/public"
}

asciidoctorEpub {
	baseDirFollowsSourceFile()
	ebookFormats("EPUB3")
	// TODO: Need to download/inline all images as this doesn't happen automatically :(
//	resources {
//		from('src/docs/asciidoc/images') {
//			include '*.png'
//		}
//		into './images'
//	}
}

assemble.dependsOn(asciidoctor, asciidoctorEpub)

Diag info:

------------------------------------------------------------
Gradle 8.5
------------------------------------------------------------

Build time:   2023-11-29 14:08:57 UTC
Revision:     28aca86a7180baa17117e0e5ba01d8ea9feca598

Kotlin:       1.9.20
Groovy:       3.0.17
Ant:          Apache Ant(TM) version 1.10.13 compiled on January 4 2023
JVM:          21 (Eclipse Adoptium 21+35-LTS)
OS:           Linux 6.6.10-arch1-1 amd64

Thank you

[ysb33r]

2024-01-08T16:05:28.204Z [WorkerExecutor Queue] WARN FilenoUtil : Native subprocess control requires open access to the JDK IO subsystem
Pass '--add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED' to enable.

This is probably a JDK21-related issue. Unfortunately with asciidoctorGemsPrepare there is no public method to access the fork options at present.

> A failure occurred while executing org.ysb33r.grolifant.internal.v6.jvm.worker.InternalWorkerAppExecutor
   > org.jruby.exceptions.LoadError: (LoadError) no such file to load -- asciidoctor-mathematical

With the new asciidoctorj engine, it is not always necessary to supply a requires statement and doing so can cause issues.
Try removing the asciidoctorj.requires entry and see if it runs.
It it does not, I'll craft a test with asciidoctor-mathematical to see if I can reproduce the issue.

[diguage]

I met a similar problem: it could not download gem. I submitted to #684 (comment)