RDPTools
RDPTools copied to clipboard
Published
20 hours ago •
rdpstaff
rdpstaff
make: *** [Clustering/dist/Clustering.jar] Error 1
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!
Hello, I'm having the same issue on a VM Ubuntu18.04 but when I try on my machine (Fedora) it works
According to this issue : https://github.com/rdpstaff/RDPTools/issues/18 I changed jdk11 to jdk8 and it did work! @shimingtan