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`launch_nextflow` does not handle properly the spaces in java path

Open asl opened this issue 3 years ago • 0 comments

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)

asl avatar Sep 16 '22 12:09 asl