For the past 96 hours or so, we keep having build failures with Java/Groovy. It seems similar to this issue: https://github.com/travis-ci/travis-ci/issues/10108
We’ve discussed it here: https://gitter.im/nextflow-io/nextflow
This is the .travis.yml:
sudo: required
language: java
jdk: openjdk8
os:
- linux
services:
- docker
before_install:
- export NXF_VER=19.07.0 && curl -fsSL get.nextflow.io | bash
- chmod 777 nextflow
- wget -O test-data.tar.gz --no-check-certificate 'https://docs.google.com/uc?export=download&id=1Jgsj4FEnwhNybaNuovyIdSXG6-iBzAIf'
- tar -xzvf test-data.tar.gz
script:
# Run test script here
- python3 tests/test_runner.py tests/tests.json
It should be using Java8, and downloads this tool based on Groovy: https://www.nextflow.io/
Is there anything going on with other Java libraries or Maven? General build failure errors could be associated with using the wrong version of Java perhaps? https://github.com/nextflow-io/nextflow/issues/677
$ java -Xmx32m -version
openjdk version "1.8.0_141"
OpenJDK Runtime Environment (build 1.8.0_141-8u141-b15-3~14.04-b15)
OpenJDK 64-Bit Server VM (build 25.141-b15, mixed mode)
$ javac -J-Xmx32m -version
javac 9.0.1
45.49s$ export NXF_VER=19.07.0 && curl -fsSL get.nextflow.io | bash
CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:pom:1.7.25
CAPSULE: Downloading dependency org.slf4j:slf4j-parent:pom:1.7.25
CAPSULE: Downloading dependency org.multiverse:multiverse-core:pom:0.7.0
CAPSULE: Downloading dependency org.multiverse:multiverse:pom:0.7.0
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-databind:pom:2.6.7.2
CAPSULE: Downloading dependency com.fasterxml.jackson:jackson-parent:pom:2.6.2
CAPSULE: Downloading dependency com.fasterxml:oss-parent:pom:24
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-batch:pom:1.11.542
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-pom:pom:1.11.542
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb-api:pom:0.10
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb-project:pom:0.10
CAPSULE: Downloading dependency io.airlift:airbase:pom:77
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:pom:2.5.6
CAPSULE: Downloading dependency joda-time:joda-time:pom:2.8.1
CAPSULE: Downloading dependency com.beust:jcommander:pom:1.35
CAPSULE: Downloading dependency org.sonatype.oss:oss-parent:pom:3
CAPSULE: Downloading dependency io.nextflow:nextflow:pom:19.07.0
CAPSULE: Downloading dependency org.jsoup:jsoup:pom:1.11.2
CAPSULE: Downloading dependency ch.grengine:grengine:pom:1.3.0
CAPSULE: Downloading dependency jline:jline:pom:2.9
CAPSULE: Downloading dependency org.sonatype.oss:oss-parent:pom:7
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb:pom:0.10
CAPSULE: Downloading dependency javax.mail:mail:pom:1.4.7
CAPSULE: Downloading dependency com.sun.mail:all:pom:1.4.7
CAPSULE: Downloading dependency net.java:jvnet-parent:pom:1
CAPSULE: Downloading dependency org.slf4j:jul-to-slf4j:pom:1.7.25
CAPSULE: Downloading dependency org.apache.httpcomponents:httpcore:pom:4.4.9
CAPSULE: Downloading dependency org.apache.httpcomponents:httpcomponents-core:pom:4.4.9
CAPSULE: Downloading dependency org.apache.httpcomponents:httpcomponents-parent:pom:9
CAPSULE: Downloading dependency org.apache:apache:pom:18
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-core:pom:2.6.7
CAPSULE: Downloading dependency ch.qos.logback:logback-classic:pom:1.1.11
CAPSULE: Downloading dependency ch.qos.logback:logback-parent:pom:1.1.11
CAPSULE: Downloading dependency org.codehaus.gpars:gpars:pom:1.2.1
CAPSULE: Downloading dependency com.esotericsoftware.kryo:kryo:pom:2.24.0
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-ec2:pom:1.11.542
CAPSULE: Downloading dependency io.nextflow:nf-commons:pom:19.07.0
CAPSULE: Downloading dependency org.apache.ivy:ivy:pom:2.3.0
CAPSULE: Downloading dependency org.apache:apache:pom:7
CAPSULE: Downloading dependency com.googlecode.javaewah:JavaEWAH:pom:1.1.6
CAPSULE: Downloading dependency org.sonatype.oss:oss-parent:pom:5
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:pom:2.5.6
CAPSULE: Downloading dependency javax.activation:activation:pom:1.1.1
CAPSULE: Downloading dependency com.jcraft:jsch:pom:0.1.54
CAPSULE: Downloading dependency org.sonatype.oss:oss-parent:pom:6
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:pom:2.5.6
CAPSULE: Downloading dependency com.jcraft:jzlib:pom:1.1.1
CAPSULE: Downloading dependency io.nextflow:nxf-s3fs:pom:1.0.6
CAPSULE: Downloading dependency org.codehaus.jsr166-mirror:jsr166y:pom:1.7.0
CAPSULE: Downloading dependency org.slf4j:slf4j-api:pom:1.7.25
CAPSULE: Downloading dependency org.apache.httpcomponents:httpclient:pom:4.5.5
CAPSULE: Downloading dependency org.apache.httpcomponents:httpcomponents-client:pom:4.5.5
CAPSULE: Downloading dependency org.apache.httpcomponents:httpcomponents-parent:pom:10
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-s3:pom:1.11.542
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-kms:pom:1.11.542
CAPSULE: Downloading dependency ch.qos.logback:logback-core:pom:1.1.11
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-iam:pom:1.11.542
CAPSULE: Downloading dependency com.fasterxml.jackson.dataformat:jackson-dataformat-cbor:pom:2.6.7
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-core:pom:1.11.542
CAPSULE: Downloading dependency commons-lang:commons-lang:pom:2.6
CAPSULE: Downloading dependency org.apache.commons:commons-parent:pom:17
CAPSULE: Downloading dependency software.amazon.ion:ion-java:pom:1.0.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:pom:2.5.6
CAPSULE: Downloading dependency org.objenesis:objenesis:pom:2.1
CAPSULE: Downloading dependency org.objenesis:objenesis-parent:pom:2.1
CAPSULE: Transfer failed: capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact org.objenesis:objenesis-parent:pom:2.1 from/to central (https://repo1.maven.org/maven2/): connect timed out (for stack trace, run with -Dcapsule.log=verbose)
CAPSULE: Downloading dependency org.yaml:snakeyaml:pom:1.18
CAPSULE: Transfer failed: capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact org.yaml:snakeyaml:pom:1.18 from/to central (https://repo1.maven.org/maven2/): connect timed out (for stack trace, run with -Dcapsule.log=verbose)
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:pom:2.5.6
CAPSULE: Transfer failed: capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact org.codehaus.groovy:groovy-xml:pom:2.5.6 from/to central (https://repo1.maven.org/maven2/): connect timed out (for stack trace, run with -Dcapsule.log=verbose)
CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:pom:1.7.25
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:pom:19.07.0
CAPSULE: Downloading dependency com.google.guava:guava:pom:21.0
CAPSULE: Downloading dependency com.google.guava:guava-parent:pom:21.0
CAPSULE: Downloading dependency com.amazonaws:jmespath-java:pom:1.11.542
CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit:pom:5.2.1.201812262042-r
CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit-parent:pom:5.2.1.201812262042-r
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-annotations:pom:2.6.0
CAPSULE: Downloading dependency com.fasterxml.jackson:jackson-parent:pom:2.6.1
CAPSULE: Downloading dependency com.fasterxml:oss-parent:pom:23
CAPSULE: Downloading dependency commons-codec:commons-codec:pom:1.10
CAPSULE: Downloading dependency org.apache.commons:commons-parent:pom:35
CAPSULE: Downloading dependency org.apache:apache:pom:15
CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.multiverse:multiverse-core:jar:0.7.0
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.2
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-batch:jar:1.11.542
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb-api:jar:0.10
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:2.5.6
CAPSULE: Downloading dependency joda-time:joda-time:jar:2.8.1
CAPSULE: Downloading dependency com.beust:jcommander:jar:1.35
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:19.07.0
CAPSULE: Downloading dependency org.jsoup:jsoup:jar:1.11.2
CAPSULE: Downloading dependency ch.grengine:grengine:jar:1.3.0
CAPSULE: Downloading dependency jline:jline:jar:2.9
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb:jar:0.10
CAPSULE: Downloading dependency javax.mail:mail:jar:1.4.7
CAPSULE: Downloading dependency org.slf4j:jul-to-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.apache.httpcomponents:httpcore:jar:4.4.9
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-core:jar:2.6.7
CAPSULE: Downloading dependency ch.qos.logback:logback-classic:jar:1.1.11
CAPSULE: Downloading dependency org.codehaus.gpars:gpars:jar:1.2.1
CAPSULE: Downloading dependency com.esotericsoftware.kryo:kryo:jar:2.24.0
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-ec2:jar:1.11.542
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:19.07.0
CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.3.0
CAPSULE: Downloading dependency com.googlecode.javaewah:JavaEWAH:jar:1.1.6
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:2.5.6
CAPSULE: Downloading dependency javax.activation:activation:jar:1.1.1
CAPSULE: Downloading dependency com.jcraft:jsch:jar:0.1.54
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:2.5.6
CAPSULE: Downloading dependency com.jcraft:jzlib:jar:1.1.1
CAPSULE: Downloading dependency io.nextflow:nxf-s3fs:jar:1.0.6
CAPSULE: Downloading dependency org.codehaus.jsr166-mirror:jsr166y:jar:1.7.0
CAPSULE: Downloading dependency org.slf4j:slf4j-api:jar:1.7.25
CAPSULE: Downloading dependency org.apache.httpcomponents:httpclient:jar:4.5.5
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-s3:jar:1.11.542
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-kms:jar:1.11.542
CAPSULE: Downloading dependency ch.qos.logback:logback-core:jar:1.1.11
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-iam:jar:1.11.542
CAPSULE: Downloading dependency com.fasterxml.jackson.dataformat:jackson-dataformat-cbor:jar:2.6.7
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-core:jar:1.11.542
CAPSULE: Downloading dependency commons-lang:commons-lang:jar:2.6
CAPSULE: Downloading dependency software.amazon.ion:ion-java:jar:1.0.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:2.5.6
CAPSULE: Downloading dependency org.objenesis:objenesis:jar:2.1
CAPSULE: Downloading dependency org.yaml:snakeyaml:jar:1.18
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:2.5.6
CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:19.07.0
CAPSULE: Downloading dependency com.google.guava:guava:jar:21.0
CAPSULE: Downloading dependency com.amazonaws:jmespath-java:jar:1.11.542
CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit:jar:5.2.1.201812262042-r
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0
CAPSULE: Downloading dependency commons-codec:commons-codec:jar:1.10
CAPSULE EXCEPTION: Error resolving dependencies. while processing attribute Allow-Snapshots: false (for stack trace, run with -Dcapsule.log=verbose)
Unable to initialize nextflow environment
The command "export NXF_VER=19.07.0 && curl -fsSL get.nextflow.io | bash" failed and exited with 1 during .
Your build has been stopped.