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rdpstaff / RDPTools

Collection of commonly used RDP Tools for easy building
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Install RDPTools-make erro #27

Open liu-zihui opened 5 years ago

liu-zihui commented 5 years ago

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]$

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(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]$