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launch_nextflow does not handle properly the spaces in java path #3214

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asl opened this issue Sep 16, 2022 · 2 comments
Closed

launch_nextflow does not handle properly the spaces in java path #3214

asl opened this issue Sep 16, 2022 · 2 comments
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@asl
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asl commented Sep 16, 2022

Bug report

Expected behavior and actual behavior

Cannot run nextflow CLI

Steps to reproduce the problem

Just run nextflow CLI script

Program output

We are having:

/opt/homebrew/bin/nextflow: line 177: /Library/Internet: No such file or directory
/opt/homebrew/bin/nextflow: line 177: exec: /Library/Internet: cannot execute: No such file or directory

apparently the code in launch_nextflow does not handle properly spaces. For the record, here is the contents of ${launcher[@]}:

"/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java" "-XX:+TieredCompilation" "-XX:TieredStopAtLevel=1" "-Djava.io.tmpdir=/var/folders/jm/hc1mgp813kb_9x8z1kdwvqjc0000gn/T/" "-Djava.library.path=/Users/asl/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java" "-Dfile.encoding=UTF-8" "-Dcapsule.app=nextflow_21.04.1" "-Djava.awt.headless=true" "-Dcapsule.jar=/Users/asl/.nextflow/framework/21.04.1/nextflow-21.04.1-one.jar" "-classpath" "/Users/asl/.nextflow/framework/21.04.1/nextflow-21.04.1-one.jar:/Users/asl/.nextflow/capsule/deps/io/nextflow/nextflow/21.04.1/nextflow-21.04.1.jar:/Users/asl/.nextflow/capsule/deps/org/apache/ivy/ivy/2.3.0/ivy-2.3.0.jar:/Users/asl/.nextflow/capsule/deps/io/nextflow/nf-httpfs/21.04.1/nf-httpfs-21.04.1.jar:/Users/asl/.nextflow/capsule/deps/io/nextflow/nf-commons/21.04.1/nf-commons-21.04.1.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-nio/3.0.7/groovy-nio-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-templates/3.0.7/groovy-templates-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-xml/3.0.7/groovy-xml-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-json/3.0.7/groovy-json-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy/3.0.7/groovy-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/jul-to-slf4j/1.7.25/jul-to-slf4j-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/log4j-over-slf4j/1.7.25/log4j-over-slf4j-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/ch/qos/logback/logback-classic/1.1.11/logback-classic-1.1.11.jar:/Users/asl/.nextflow/capsule/deps/ch/qos/logback/logback-core/1.1.11/logback-core-1.1.11.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.jar:/Users/asl/.nextflow/capsule/deps/ch/grengine/grengine/1.3.0/grengine-1.3.0.jar:/Users/asl/.nextflow/capsule/deps/commons-lang/commons-lang/2.6/commons-lang-2.6.jar:/Users/asl/.nextflow/capsule/deps/org/pf4j/pf4j-update/2.3.0/pf4j-update-2.3.0.jar:/Users/asl/.nextflow/capsule/deps/commons-codec/commons-codec/1.10/commons-codec-1.10.jar:/Users/asl/.nextflow/capsule/deps/com/beust/jcommander/1.35/jcommander-1.35.jar:/Users/asl/.nextflow/capsule/deps/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar:/Users/asl/.nextflow/capsule/deps/org/iq80/leveldb/leveldb/0.12/leveldb-0.12.jar:/Users/asl/.nextflow/capsule/deps/org/eclipse/jgit/org.eclipse.jgit/5.2.1.201812262042-r/org.eclipse.jgit-5.2.1.201812262042-r.jar:/Users/asl/.nextflow/capsule/deps/javax/mail/mail/1.4.7/mail-1.4.7.jar:/Users/asl/.nextflow/capsule/deps/javax/activation/activation/1.1.1/activation-1.1.1.jar:/Users/asl/.nextflow/capsule/deps/org/yaml/snakeyaml/1.18/snakeyaml-1.18.jar:/Users/asl/.nextflow/capsule/deps/org/jsoup/jsoup/1.11.2/jsoup-1.11.2.jar:/Users/asl/.nextflow/capsule/deps/jline/jline/2.9/jline-2.9.jar:/Users/asl/.nextflow/capsule/deps/org/pf4j/pf4j/3.4.1/pf4j-3.4.1.jar:/Users/asl/.nextflow/capsule/deps/com/google/guava/guava/24.1.1-jre/guava-24.1.1-jre.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/org/multiverse/multiverse-core/0.7.0/multiverse-core-0.7.0.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/jsr166-mirror/jsr166y/1.7.0/jsr166y-1.7.0.jar:/Users/asl/.nextflow/capsule/deps/org/objenesis/objenesis/2.1/objenesis-2.1.jar:/Users/asl/.nextflow/capsule/deps/org/iq80/leveldb/leveldb-api/0.12/leveldb-api-0.12.jar:/Users/asl/.nextflow/capsule/deps/com/jcraft/jsch/0.1.54/jsch-0.1.54.jar:/Users/asl/.nextflow/capsule/deps/com/jcraft/jzlib/1.1.1/jzlib-1.1.1.jar:/Users/asl/.nextflow/capsule/deps/com/googlecode/javaewah/JavaEWAH/1.1.6/JavaEWAH-1.1.6.jar:/Users/asl/.nextflow/capsule/deps/com/github/zafarkhaja/java-semver/0.9.0/java-semver-0.9.0.jar:/Users/asl/.nextflow/capsule/deps/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar:/Users/asl/.nextflow/capsule/deps/org/checkerframework/checker-compat-qual/2.0.0/checker-compat-qual-2.0.0.jar:/Users/asl/.nextflow/capsule/deps/com/google/errorprone/error_prone_annotations/2.1.3/error_prone_annotations-2.1.3.jar:/Users/asl/.nextflow/capsule/deps/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14.jar:/Users/asl/.nextflow/capsule/deps/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar" "nextflow.cli.Launcher"

Environment

  • Nextflow version: [?]
  • Java version: 1.8.0_261
  • Operating system: macOS
  • Bash version: (use the command $SHELL --version):
GNU bash, version 3.2.57(1)-release (arm64-apple-darwin21)
Copyright (C) 2007 Free Software Foundation, Inc.

(note that $SHELL reports current shell which might be not bash)

@stale
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stale bot commented Mar 18, 2023

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the stale label Mar 18, 2023
@stale stale bot closed this as completed Jun 10, 2023
@pditommaso pditommaso reopened this Jun 12, 2023
@pditommaso pditommaso removed the stale label Jun 12, 2023
@pditommaso
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Solved via #2951

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