Install RDPTools-make erro

[liu-zihui]

I'm also seeing this error on Linux .....
(base) [zihuiliu@bogon RDPTools]$ make
ant -f classifier/build.xml jar
Buildfile: /home/zihuiliu/software/RDPTools/classifier/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/zihuiliu/.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/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#classifier;working@localhost
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] found jfree#jfreechart;1.0.13 in public
[ivy:retrieve] found jfree#jcommon;1.0.16 in public
[ivy:retrieve] :: resolution report :: resolve 87ms :: artifacts dl 8ms

| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|

| default | 5 | 0 | 0 | 0 || 13 | 0 |

[ivy:retrieve] :: retrieving :: edu.cme.rdp#classifier
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 13 already retrieved (0kB/4ms)
-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/zihuiliu/software/RDPTools/classifier/build/built-jar.properties
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/zihuiliu/software/RDPTools/classifier/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/zihuiliu/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@localhost
[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 16ms :: 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/zihuiliu/software/RDPTools/classifier/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/zihuiliu/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@localhost
[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 19ms :: 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/zihuiliu/software/RDPTools/classifier/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:
-post-compile:
compile:
-pre-jar:
-post-jar:
jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/zihuiliu/software/RDPTools/ReadSeq/dist/ReadSeq.jar"
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/zihuiliu/software/RDPTools/AlignmentTools/dist/AlignmentTools.jar"
-check-call-dep:
-maybe-call-dep:
-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/zihuiliu/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#RDPTaxonomyTree;working@localhost
[ivy:retrieve] confs: [default]
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] :: resolution report :: resolve 7ms :: artifacts dl 1ms

| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|

| default | 1 | 0 | 0 | 0 || 3 | 0 |

[ivy:retrieve] :: retrieving :: edu.cme.rdp#RDPTaxonomyTree
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 3 already retrieved (0kB/0ms)
-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:
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:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-debug
-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/zihuiliu/software/RDPTools/classifier/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/zihuiliu/software/RDPTools/TaxonomyTree/dist/TaxonomyTree.jar"
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: /home/zihuiliu/software/RDPTools/classifier/build/classes/data.tgz
[get] Not modified - so not downloaded
[untar] Expanding: /home/zihuiliu/software/RDPTools/classifier/build/classes/data.tgz into /home/zihuiliu/software/RDPTools/classifier/build/classes
BUILD FAILED
/home/zihuiliu/software/RDPTools/classifier/build.xml:51: Error while expanding /home/zihuiliu/software/RDPTools/classifier/build/classes/data.tgz
java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117)
at org.apache.tools.tar.TarBuffer.readBlock(TarBuffer.java:253)
at org.apache.tools.tar.TarBuffer.readRecord(TarBuffer.java:220)
at org.apache.tools.tar.TarInputStream.read(TarInputStream.java:603)
at java.io.FilterInputStream.read(FilterInputStream.java:107)
at org.apache.tools.ant.taskdefs.Expand.extractFile(Expand.java:368)
at org.apache.tools.ant.taskdefs.Untar.expandStream(Untar.java:160)
at org.apache.tools.ant.taskdefs.Untar.expandFile(Untar.java:106)
at org.apache.tools.ant.taskdefs.Expand.execute(Expand.java:152)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:352)
at org.apache.tools.ant.Target.execute(Target.java:437)
at org.apache.tools.ant.Target.performTasks(Target.java:458)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1406)
at org.apache.tools.ant.Project.executeTarget(Project.java:1377)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1261)
at org.apache.tools.ant.Main.runBuild(Main.java:857)
at org.apache.tools.ant.Main.startAnt(Main.java:236)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:287)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)
Total time: 3 seconds
make: *** [classifier/dist/classifier.jar] 错误 1
(base) [zihuiliu@bogon RDPTools]$

######################################################################################################

(base) [zihuiliu@bogon RDPTools]$ java -version
openjdk version "1.8.0_212"
OpenJDK Runtime Environment (build 1.8.0_212-b04)
OpenJDK 64-Bit Server VM (build 25.212-b04, mixed mode)
(base) [zihuiliu@bogon RDPTools]$ javac -version
javac 1.8.0_212
(base) [zihuiliu@bogon RDPTools]$ ant -v
Apache Ant(TM) version 1.9.14 compiled on March 12 2019
Trying the default build file: build.xml
Buildfile: build.xml does not exist!
Build failed
(base) [zihuiliu@bogon RDPTools]$ lsb_release -a
LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.5 (Final)
Release: 6.5
Codename: Final
(base) [zihuiliu@bogon RDPTools]$