rdpstaffmsu
commented
7 years ago Would you re-run the entire process starting from "git clone"? Our server had some issue in the past day or two and some files might not be accessible. Let me know if that works this time. Thank you.
Benli Chai RDP Staff
On Sun, Mar 5, 2017 at 5:28 PM, gadarjat notifications@github.com wrote:
I'm trying to install RDPTools on a linux system (RHEL 7.3). When I run:
sudo git submodule init sudo git submodule update sudo make
I get an error:
ant -f Clustering/build.xml jar make: ant: Command not found make: *** [Clustering/dist/Clustering.jar] Error 127
Despite the "ant: Command not found" my system does recognize ant (and it's in the path); ant just seems to want a good build.xml file.
$ ant Buildfile: build.xml does not exist! Build failed
When I run ant using the RDP build.xml file I get a long output, below, which includes this error:
$ ant -f Clustering/build.xml jar [...] BUILD FAILED /usr/local/src/RDPTools/Clustering/build.xml:104: impossible to ivy retrieve: java.lang.RuntimeException: problem during retrieve of edu.cme.rdp#clustering: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory) $ ant -f Clustering/build.xml jar [...]
Full output:
$ ant -f Clustering/build.xml jar Buildfile: /usr/local/src/RDPTools/Clustering/build.xml
download-ivy: [mkdir] Created dir: /home/gadarjat/.ant/lib [get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar [get] To: /home/gadarjat/.ant/lib/ivy.jar
init-ivy:
resolve: [ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ :: [ivy:retrieve] :: loading settings :: url = jar:file:/home/gadarjat/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@carabid.espm.berkeley.edu [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] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7-javadoc.jar ... [ivy:retrieve] .............................................................................................................................................................................................................................................................. (1449kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar(javadoc) (142ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.jar ... [ivy:retrieve] .................................................................................................................................................. (898kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar (58ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7-sources.jar ... [ivy:retrieve] ......................................................................................................................................................................... (1109kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar(source) (77ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2.jar ... [ivy:retrieve] .. (40kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar (19ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2-sources.jar ... [ivy:retrieve] .... (47kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar(source) (19ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2-javadoc.jar ... [ivy:retrieve] ............................ (209kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar(javadoc) (25ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-sources.jar ... [ivy:retrieve] ...................... (143kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar(source) (22ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-javadoc.jar ... [ivy:retrieve] ........................................................... (387kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar(javadoc) (29ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.jar ... [ivy:retrieve] ............................... (231kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8-sources.jar ... [ivy:retrieve] .......................................... (271kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar(source) (25ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8-javadoc.jar ... [ivy:retrieve] ...................................................... (389kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar(javadoc) (27ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8.jar ... [ivy:retrieve] .................................... (257kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4-sources.jar ... [ivy:retrieve] ............................... (240kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar(source) (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.jar ... [ivy:retrieve] ............................ (180kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar (31ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4-javadoc.jar ... [ivy:retrieve] ..................................................................................................... (707kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar(javadoc) (38ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-core/2.2.7/jaxb-core-2.2.7.jar ... [ivy:retrieve] ......................... (216kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-core;2.2.7!jaxb-core.jar (22ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/fastinfoset/FastInfoset/1.2.12/FastInfoset-1.2.12.jar ... [ivy:retrieve] ....................................... (286kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.xml.fastinfoset#FastInfoset;1.2.12!FastInfoset.jar (24ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/xml/bind/jaxb-api/2.2.7/jaxb-api-2.2.7.jar ... [ivy:retrieve] ............. (97kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] javax.xml.bind#jaxb-api;2.2.7!jaxb-api.jar (20ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/istack/istack-commons-runtime/2.16/istack-commons-runtime-2.16.jar ... [ivy:retrieve] .. (22kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] com.sun.istack#istack-commons-runtime;2.16!istack-commons-runtime.jar (19ms) [ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/xml/bind/jsr173_api/1.0/jsr173_api-1.0.jar ... [ivy:retrieve] ...... (48kB) [ivy:retrieve] .. (0kB) [ivy:retrieve] [SUCCESSFUL ] javax.xml.bind#jsr173_api;1.0!jsr173_api.jar (19ms) [ivy:retrieve] :: resolution report :: resolve 1488ms :: artifacts dl 699ms
| | modules || artifacts | | conf | number| search|dwnlded|evicted|| number|dwnlded| --------------------------------------------------------------------- | default | 10 | 10 | 10 | 0 || 20 | 20 | ---------------------------------------------------------------------[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering [ivy:retrieve] confs: [default]
BUILD FAILED /usr/local/src/RDPTools/Clustering/build.xml:104: impossible to ivy retrieve: java.lang.RuntimeException: problem during retrieve of edu.cme.rdp#clustering: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory) at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:206) at org.apache.ivy.Ivy.retrieve(Ivy.java:540) at org.apache.ivy.ant.IvyRetrieve.doExecute(IvyRetrieve.java:59) at org.apache.ivy.ant.IvyTask.execute(IvyTask.java:277) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) 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:348) at org.apache.tools.ant.Target.execute(Target.java:435) at org.apache.tools.ant.Target.performTasks(Target.java:456) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405) at org.apache.tools.ant.Project.executeTarget(Project.java:1376) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) at org.apache.tools.ant.Project.executeTargets(Project.java:1260) 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:113) Caused by: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.
(FileOutputStream.java:213) at java.io.FileOutputStream. (FileOutputStream.java:162) at org.apache.ivy.util.FileUtil.copy(FileUtil.java:147) at org.apache.ivy.util.FileUtil.copy(FileUtil.java:122) at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:140) ... 20 more Total time: 3 seconds
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amansgill
gunturus
najouamghazli
caijian89
andersonnb6
I'm trying to install RDPTools on a linux system (RHEL 7.3). When I run:
I get an error:
Despite the "ant: Command not found" my system does recognize ant (and it's in the path); ant just seems to want a good build.xml file.
When I run ant using the command in the initial error output, I get a long output, below, which includes this error:
Full output: