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sanger-pathogens / Artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
http://sanger-pathogens.github.io/Artemis
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I try to build, but exec fail #344

Open starsareintherose opened 1 year ago

starsareintherose commented 1 year ago

OS: Arch Linux

version: 18.2.0

tested under: java11 20

Build command: 

  mvn validate
  mvn package

act

+ QUIET=no
+ SOURCE=act
+ '[' -h act ']'
+++ dirname act
++ cd -P .
++ pwd
+ APPLICATION_HOME=/usr/share/artemis
+ [[ '' != '' ]]
+ APPLICATION_PROPERTIES='-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX '
+ test 0 '!=' 0
+ JAR_NAME=act.jar
+ JAR_FILE_DEFAULT=/usr/share/artemis/target/jars/act.jar
+ JAR_FILE_INSTALLED=/usr/share/artemis/dist/act.jar
+ ARTEMIS_CP=/usr/share/artemis:/usr/share/artemis/target/jars/act.jar:/usr/share/artemis/dist/act.jar
+ [[ '' = '' ]]
++ which java
+ JAVA=/usr/bin/java
+ add_proxy_properties
+ [[ http://127.0.0.1:1087/ = '' ]]
+ [[ http://127.0.0.1:1087/ = '' ]]
+ [[ http://127.0.0.1:1087/ != '' ]]
++ echo http://127.0.0.1:1087/
++ sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'
+ APPLICATION_PROPERTIES='-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  -DproxySet=true  -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/'
+ [[ '' = '' ]]
+ FLAGS='-mx2g -ms100m -noverify'
+ FLAGS='-mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED'
++ uname
+ PLATTMP=Linux
+ [[ Linux = \D\a\r\w\i\n ]]
+ [[ no = no ]]
+ echo 'Starting ACT with arguments: -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  -DproxySet=true  -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/ '
Starting ACT with arguments: -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  -DproxySet=true  -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/ 
+ /usr/bin/java -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX -DproxySet=true -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/ -cp /usr/share/artemis:/usr/share/artemis/target/jars/act.jar:/usr/share/artemis/dist/act.jar uk.ac.sanger.artemis.components.ActMain
Exception in thread "main" java.lang.ExceptionInInitializerError
    at uk.ac.sanger.artemis.components.FileViewer.<init>(FileViewer.java:156)
    at uk.ac.sanger.artemis.components.FileViewer.<init>(FileViewer.java:122)
    at uk.ac.sanger.artemis.components.FileViewer.<init>(FileViewer.java:115)
    at uk.ac.sanger.artemis.components.LogViewer$1.<init>(LogViewer.java:92)
    at uk.ac.sanger.artemis.components.LogViewer.maybeMakeViewer(LogViewer.java:91)
    at uk.ac.sanger.artemis.components.LogViewer.log(LogViewer.java:61)
    at uk.ac.sanger.artemis.components.Splash.initLogger(Splash.java:252)
    at uk.ac.sanger.artemis.components.Splash.<init>(Splash.java:147)
    at uk.ac.sanger.artemis.components.Splash.<init>(Splash.java:173)
    at uk.ac.sanger.artemis.components.ActMain.<init>(ActMain.java:71)
    at uk.ac.sanger.artemis.components.ActMain.main(ActMain.java:421)
Caused by: java.lang.NullPointerException: inStream parameter is null
    at java.base/java.util.Objects.requireNonNull(Objects.java:246)
    at java.base/java.util.Properties.load(Properties.java:406)
    at uk.ac.sanger.artemis.Options.readQualifierInfo(Options.java:1401)
    at uk.ac.sanger.artemis.Options.makeEntryInformation(Options.java:1309)
    at uk.ac.sanger.artemis.Options.<clinit>(Options.java:1500)
    ... 11 more
+ result=1
+ exit 1

art

+ QUIET=no
+ SOURCE=art
+ '[' -h art ']'
+++ dirname art
++ cd -P .
++ pwd
+ APPLICATION_HOME=/usr/share/artemis
+ [[ '' != '' ]]
+ APPLICATION_PROPERTIES='-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX '
+ test 0 '!=' 0
+ JAR_NAME=artemis.jar
+ JAR_FILE_DEFAULT=/usr/share/artemis/target/jars/artemis.jar
+ JAR_FILE_INSTALLED=/usr/share/artemis/dist/artemis.jar
+ ARTEMIS_CP=/usr/share/artemis:/usr/share/artemis/target/jars/artemis.jar:/usr/share/artemis/dist/artemis.jar
+ [[ '' = '' ]]
++ which java
+ JAVA=/usr/bin/java
+ add_proxy_properties
+ [[ http://127.0.0.1:1087/ = '' ]]
+ [[ http://127.0.0.1:1087/ = '' ]]
+ [[ http://127.0.0.1:1087/ != '' ]]
++ echo http://127.0.0.1:1087/
++ sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'
+ APPLICATION_PROPERTIES='-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  -DproxySet=true  -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/'
+ [[ '' = '' ]]
+ FLAGS='-mx2g -ms100m -noverify'
+ FLAGS='-mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED'
++ uname
+ PLATTMP=Linux
+ [[ Linux = \D\a\r\w\i\n ]]
+ [[ no = \n\o ]]
+ echo 'Starting Artemis with arguments: -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  -DproxySet=true  -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/ '
Starting Artemis with arguments: -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  -DproxySet=true  -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/ 
+ /usr/bin/java -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX -DproxySet=true -Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=1087/ -cp /usr/share/artemis:/usr/share/artemis/target/jars/artemis.jar:/usr/share/artemis/dist/artemis.jar uk.ac.sanger.artemis.components.ArtemisMain
Exception in thread "AWT-EventQueue-0" java.lang.ExceptionInInitializerError
    at uk.ac.sanger.artemis.components.FileViewer.<init>(FileViewer.java:156)
    at uk.ac.sanger.artemis.components.FileViewer.<init>(FileViewer.java:122)
    at uk.ac.sanger.artemis.components.FileViewer.<init>(FileViewer.java:115)
    at uk.ac.sanger.artemis.components.LogViewer$1.<init>(LogViewer.java:92)
    at uk.ac.sanger.artemis.components.LogViewer.maybeMakeViewer(LogViewer.java:91)
    at uk.ac.sanger.artemis.components.LogViewer.log(LogViewer.java:61)
    at uk.ac.sanger.artemis.components.Splash.initLogger(Splash.java:252)
    at uk.ac.sanger.artemis.components.Splash.<init>(Splash.java:147)
    at uk.ac.sanger.artemis.components.Splash.<init>(Splash.java:173)
    at uk.ac.sanger.artemis.components.ArtemisMain.<init>(ArtemisMain.java:78)
    at uk.ac.sanger.artemis.components.ArtemisMain$10.run(ArtemisMain.java:793)
    at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
    at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
    at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
    at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Caused by: java.lang.NullPointerException: inStream parameter is null
    at java.base/java.util.Objects.requireNonNull(Objects.java:246)
    at java.base/java.util.Properties.load(Properties.java:406)
    at uk.ac.sanger.artemis.Options.readQualifierInfo(Options.java:1401)
    at uk.ac.sanger.artemis.Options.makeEntryInformation(Options.java:1309)
    at uk.ac.sanger.artemis.Options.<clinit>(Options.java:1500)
    ... 24 more
+ result=0
+ exit 0