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rdpstaff / RDPTools

Collection of commonly used RDP Tools for easy building
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make: *** [Clustering/dist/Clustering.jar] Error 1 #28

Open shimingtan opened 5 years ago

shimingtan commented 5 years ago

Dear All,

I am trying to download the RDP tools, and am facing the following error:

(base) tanshiming@S620100019205:~/tools/RDPTools$ make
ant -f Clustering/build.xml jar
Buildfile: /home/tanshiming/tools/RDPTools/Clustering/build.xml

download-ivy:
      [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
      [get] To: /home/tanshiming/.ant/lib/ivy.jar
      [get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/home/tanshiming/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@S620100019205
[ivy:retrieve]  confs: [default]
[ivy:retrieve]  found com.sun.xml.bind#jaxb-impl;2.2.7 in public
[ivy:retrieve]  found com.sun.xml.bind#jaxb-core;2.2.7 in public
[ivy:retrieve]  found javax.xml.bind#jaxb-api;2.2.7 in public
[ivy:retrieve]  found com.sun.istack#istack-commons-runtime;2.16 in public
[ivy:retrieve]  found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in public
[ivy:retrieve]  found javax.xml.bind#jsr173_api;1.0 in public
[ivy:retrieve]  found commons-cli#commons-cli;1.2 in public
[ivy:retrieve]  found junit#junit;4.8.2 in public
[ivy:retrieve]  found commons-codec#commons-codec;1.8 in public
[ivy:retrieve]  found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 197ms :: artifacts dl 13ms
    ---------------------------------------------------------------------
    |                  |            modules            ||   artifacts   |
    |       conf       | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    |      default     |   10  |   0   |   0   |   0   ||   20  |   0   |
    ---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering
[ivy:retrieve]  confs: [default]
[ivy:retrieve]  0 artifacts copied, 20 already retrieved (0kB/5ms)

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:

-init-macrodef-javac:

-init-macrodef-test-impl:

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:

-init-macrodef-debug:

-init-macrodef-java:

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:
   [delete] Deleting: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties

deps-jar:

-warn-already-built-jar:
[propertyfile] Updating property file: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

download-ivy:
      [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
      [get] To: /home/tanshiming/.ant/lib/ivy.jar
      [get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/tanshiming/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@S620100019205
[ivy:retrieve]  confs: [default]
[ivy:retrieve]  found commons-lang#commons-lang;2.6 in public
[ivy:retrieve]  found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] :: resolution report :: resolve 21ms :: artifacts dl 2ms
    ---------------------------------------------------------------------
    |                  |            modules            ||   artifacts   |
    |       conf       | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    |      default     |   2   |   0   |   0   |   0   ||   6   |   0   |
    ---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#AlignmentTools
[ivy:retrieve]  confs: [default]
[ivy:retrieve]  0 artifacts copied, 6 already retrieved (0kB/1ms)

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac

-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend

-init-macrodef-test-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart

-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug

-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:

deps-jar:

-warn-already-built-jar:
[propertyfile] Updating property file: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

download-ivy:
      [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
      [get] To: /home/tanshiming/.ant/lib/ivy.jar
      [get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/tanshiming/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@S620100019205
[ivy:retrieve]  confs: [default]
[ivy:retrieve]  found commons-lang#commons-lang;2.6 in public
[ivy:retrieve]  found commons-cli#commons-cli;1.2 in public
[ivy:retrieve]  found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 21ms :: artifacts dl 3ms
    ---------------------------------------------------------------------
    |                  |            modules            ||   artifacts   |
    |       conf       | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    |      default     |   3   |   0   |   0   |   0   ||   9   |   0   |
    ---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq
[ivy:retrieve]  confs: [default]
[ivy:retrieve]  0 artifacts copied, 9 already retrieved (0kB/1ms)

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac

-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend

-init-macrodef-test-impl:

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart

-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug

-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:

deps-jar:

-warn-already-built-jar:
[propertyfile] Updating property file: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties

-check-automatic-build:

-clean-after-automatic-build:

-verify-automatic-build:

-pre-pre-compile:

-pre-compile:

-copy-persistence-xml:

-compile-depend:

-do-compile:
    [javac] Compiling 73 source files to /home/tanshiming/tools/RDPTools/ReadSeq/build/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 5
    [javac] error: Source option 5 is no longer supported. Use 7 or later.
    [javac] error: Target option 5 is no longer supported. Use 7 or later.

BUILD FAILED
/home/tanshiming/tools/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Total time: 2 seconds
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 1

Will appreciate any advice I can get.

Thank You!

cjuigne commented 4 years ago

Hello, I'm having the same issue on a VM Ubuntu18.04 but when I try on my machine (Fedora) it works

cjuigne commented 4 years ago

According to this issue : https://github.com/rdpstaff/RDPTools/issues/18 I changed jdk11 to jdk8 and it did work! @shimingtan