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rdpstaff / classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
GNU General Public License v2.0
53 stars 32 forks source link

Doesn't build #1

Closed xapple closed 9 years ago

xapple commented 10 years ago

Hi,

I just cloned the repository and typed ant jar as suggested in the README. It didn't build. Here is the error message:

lucass@milou2 share $ git clone https://github.com/rdpstaff/classifier.git
Initialized empty Git repository in /pica/h1/lucass/share/classifier/.git/
remote: Reusing existing pack: 304, done.
remote: Total 304 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (304/304), 839.86 KiB | 629 KiB/s, done.
Resolving deltas: 100% (99/99), done.
lucass@milou2 share $ mv classifier/ rdp_classifier
lucass@milou2 share $ cd rdp_classifier/
lucass@milou2 rdp_classifier (master) $ ant jar
Buildfile: /pica/h1/lucass/share/rdp_classifier/build.xml

download-ivy:
    [mkdir] Created dir: /home/lucass/.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/lucass/.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/lucass/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#classifier;working@milou2.uppmax.uu.se
[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] 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) (403ms)
[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 (400ms)
[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) (474ms)
[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 (430ms)
[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) (455ms)
[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) (514ms)
[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) (429ms)
[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) (353ms)
[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 (403ms)
[ivy:retrieve] :: resolution report :: resolve 6344ms :: artifacts dl 3887ms
        ---------------------------------------------------------------------
        |                  |            modules            ||   artifacts   |
        |       conf       | number| search|dwnlded|evicted|| number|dwnlded|
        ---------------------------------------------------------------------
        |      default     |   3   |   3   |   3   |   0   ||   9   |   9   |
        ---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#classifier
[ivy:retrieve]  confs: [default]
[ivy:retrieve]  9 artifacts copied, 0 already retrieved (2188kB/52ms)

-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-junit:

-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:

deps-jar:
    [mkdir] Created dir: /pica/h1/lucass/share/rdp_classifier/build

-warn-already-built-jar:
[propertyfile] Updating property file: /pica/h1/lucass/share/rdp_classifier/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

BUILD FAILED
/pica/h1/lucass/share/rdp_classifier/nbproject/build-impl.xml:581: The following error occurred while executing this line:
/pica/h1/lucass/share/rdp_classifier/nbproject/build-impl.xml:1074: The following error occurred while executing this line:
java.io.FileNotFoundException: /pica/h1/lucass/share/ReadSeq/build.xml (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:268)
        at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:177)
        at org.apache.tools.ant.ProjectHelper.configureProject(ProjectHelper.java:82)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:393)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        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:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
        at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
        at org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        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:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
        at org.apache.tools.ant.Main.runBuild(Main.java:801)
        at org.apache.tools.ant.Main.startAnt(Main.java:218)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

Total time: 12 seconds
fishjord commented 10 years ago

Classifier depends two other RDP projects (ReadSeq and TaxonomyTree). This repository is primarily intended for developers.

If you would like to build and use the classifier (and other RDP tools), we provide a repository (https://github.com/rdpstaff/RDPTools) that includes all the tools and their build dependencies.