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rdpstaff / classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
GNU General Public License v2.0
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Problems with make file #15

Closed nbetrapa closed 8 years ago

nbetrapa commented 8 years ago

I have been trying to make the RDPtools, however I keep running into make issues. I am following the instructions on the README file, I am making using super user prevligies (SU). Below is the output. Kindly help me figure this out.

ant -f Clustering/build.xml jar Buildfile: /opt/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: /root/.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:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@mbac.gmu.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] :: resolution report :: resolve 253ms :: artifacts dl 21ms

|                  |            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/10ms)

-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: /opt/RDPTools/Clustering/build/built-jar.properties

deps-jar:

-warn-already-built-jar: [propertyfile] Updating property file: /opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@mbac.gmu.edu [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 31ms :: artifacts dl 4ms

|                  |            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/3ms)

-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: /opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@mbac.gmu.edu [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 39ms :: artifacts dl 6ms

|                  |            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/3ms)

-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: /opt/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:

-post-compile:

compile:

-pre-jar:

-post-jar:

jar: [echo] To run this application from the command line without Ant, try: [echo] java -jar "/opt/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 "/opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#SeqFilters;working@mbac.gmu.edu [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 jfree#jfreechart;1.0.13 in public [ivy:retrieve] found jfree#jcommon;1.0.16 in public [ivy:retrieve] :: resolution report :: resolve 46ms :: artifacts dl 6ms

|                  |            modules            ||   artifacts   |
|       conf       | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
|      default     |   4   |   0   |   0   |   0   ||   10  |   0   |
---------------------------------------------------------------------

[ivy:retrieve] :: retrieving :: edu.cme.rdp#SeqFilters [ivy:retrieve] confs: [default] [ivy:retrieve] 0 artifacts copied, 10 already retrieved (0kB/3ms)

-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: /opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ProbeMatch;working@mbac.gmu.edu [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 junit#junit;4.8.2 in public [ivy:retrieve] :: resolution report :: resolve 32ms :: artifacts dl 5ms

|                  |            modules            ||   artifacts   |
|       conf       | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
|      default     |   3   |   0   |   0   |   0   ||   9   |   0   |
---------------------------------------------------------------------

[ivy:retrieve] :: retrieving :: edu.cme.rdp#ProbeMatch [ivy:retrieve] confs: [default] [ivy:retrieve] 0 artifacts copied, 9 already retrieved (0kB/3ms)

-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: 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: /opt/RDPTools/Clustering/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

-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 "/opt/RDPTools/ProbeMatch/dist/ProbeMatch.jar"

-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 "/opt/RDPTools/SeqFilters/dist/SeqFilters.jar"

-check-call-dep:

-maybe-call-dep:

-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: [javac] Compiling 72 source files to /opt/RDPTools/Clustering/build/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/pyro/cluster/ClusterReplay.java:26: error: cannot find symbol [javac] import edu.msu.cme.rdp.taxatree.Taxon; [javac] ^ [javac] symbol: class Taxon [javac] location: package edu.msu.cme.rdp.taxatree [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/pyro/cluster/ClusterReplay.java:27: error: cannot find symbol [javac] import edu.msu.cme.rdp.taxatree.TaxonHolder; [javac] ^ [javac] symbol: class TaxonHolder [javac] location: package edu.msu.cme.rdp.taxatree [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:22: error: package edu.msu.cme.rdp.taxatree.utils does not exist [javac] import edu.msu.cme.rdp.taxatree.utils.NewickPrintVisitor; [javac] ^ [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:23: error: package edu.msu.cme.rdp.taxatree.utils.NewickPrintVisitor does not exist [javac] import edu.msu.cme.rdp.taxatree.utils.NewickPrintVisitor.NewickDistanceFactory; [javac] ^ [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:50: error: cannot find symbol [javac] TaxonHolder lastMerged = null; [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:53: error: cannot find symbol [javac] Map<Integer, TaxonHolder> taxonMap = new HashMap(); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:60: error: cannot find symbol [javac] TaxonHolder holder; [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:60: error: cannot find symbol [javac] TaxonHolder holder; [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:64: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, seqids.get(0), "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:64: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, seqids.get(0), "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:66: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:66: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:70: error: cannot find symbol [javac] TaxonHolder th = new TaxonHolder(new Taxon(id, seqid, "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:70: error: cannot find symbol [javac] TaxonHolder th = new TaxonHolder(new Taxon(id, seqid, "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:70: error: cannot find symbol [javac] TaxonHolder th = new TaxonHolder(new Taxon(id, seqid, "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:84: error: cannot find symbol [javac] TaxonHolder holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:84: error: cannot find symbol [javac] TaxonHolder holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:84: error: cannot find symbol [javac] TaxonHolder holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:106: error: cannot find symbol [javac] NewickPrintVisitor visitor = new NewickPrintVisitor(newickTreeOut, false, new NewickDistanceFactory() { [javac] ^ [javac] symbol: class NewickPrintVisitor [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:106: error: cannot find symbol [javac] NewickPrintVisitor visitor = new NewickPrintVisitor(newickTreeOut, false, new NewickDistanceFactory() { [javac] ^ [javac] symbol: class NewickPrintVisitor [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:106: error: cannot find symbol [javac] NewickPrintVisitor visitor = new NewickPrintVisitor(newickTreeOut, false, new NewickDistanceFactory() { [javac] ^ [javac] symbol: class NewickDistanceFactory [javac] location: class TreeBuilder [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 21 errors [javac] 1 warning

BUILD FAILED /opt/RDPTools/Clustering/nbproject/build-impl.xml:955: The following error occurred while executing this line: /opt/RDPTools/Clustering/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Total time: 4 seconds make: *\ [Clustering/dist/Clustering.jar] Error 1

chaibenl commented 8 years ago

nbetrapa,

Have you installed apache ant? Looks like all the errors can be traced back to it.

Benli Chai RDP Staff

On Sun, May 1, 2016 at 4:44 PM, nbetrapa notifications@github.com wrote:

I have been trying to make the RDPtools, however I keep running into make issues. I am following the instructions on the README file, I am making using super user prevligies (SU). Below is the output. Kindly help me figure this out.

ant -f Clustering/build.xml jar Buildfile: /opt/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: /root/.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:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering; working@mbac.gmu.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] :: resolution report :: resolve 253ms :: artifacts dl 21ms

| | 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/10ms)

-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: /opt/RDPTools/Clustering/build/built-jar.properties

deps-jar:

-warn-already-built-jar: [propertyfile] Updating property file: /opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools; working@mbac.gmu.edu [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 31ms :: artifacts dl 4ms

| | 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/3ms)

-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: /opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq; working@mbac.gmu.edu [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 39ms :: artifacts dl 6ms

| | 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/3ms)

-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: /opt/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:

-post-compile:

compile:

-pre-jar:

-post-jar:

jar: [echo] To run this application from the command line without Ant, try: [echo] java -jar "/opt/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 "/opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#SeqFilters; working@mbac.gmu.edu [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 jfree#jfreechart;1.0.13 in public [ivy:retrieve] found jfree#jcommon;1.0.16 in public

[ivy:retrieve] :: resolution report :: resolve 46ms :: artifacts dl 6ms

| | modules || artifacts |

| conf | number| search|dwnlded|evicted|| number|dwnlded|

| default | 4 | 0 | 0 | 0 || 10 | 0 |

[ivy:retrieve] :: retrieving :: edu.cme.rdp#SeqFilters [ivy:retrieve] confs: [default] [ivy:retrieve] 0 artifacts copied, 10 already retrieved (0kB/3ms)

-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: /opt/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: /root/.ant/lib/ivy.jar [get] Not modified - so not downloaded

init-ivy:

resolve: [ivy:retrieve] :: loading settings :: url = jar:file:/root/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ProbeMatch; working@mbac.gmu.edu [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 junit#junit;4.8.2 in public

[ivy:retrieve] :: resolution report :: resolve 32ms :: artifacts dl 5ms

| | modules || artifacts |

| conf | number| search|dwnlded|evicted|| number|dwnlded|

| default | 3 | 0 | 0 | 0 || 9 | 0 |

[ivy:retrieve] :: retrieving :: edu.cme.rdp#ProbeMatch [ivy:retrieve] confs: [default] [ivy:retrieve] 0 artifacts copied, 9 already retrieved (0kB/3ms)

-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: 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: /opt/RDPTools/Clustering/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

-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 "/opt/RDPTools/ProbeMatch/dist/ProbeMatch.jar"

-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 "/opt/RDPTools/SeqFilters/dist/SeqFilters.jar"

-check-call-dep:

-maybe-call-dep:

-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: [javac] Compiling 72 source files to /opt/RDPTools/Clustering/build/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/pyro/cluster/ClusterReplay.java:26: error: cannot find symbol [javac] import edu.msu.cme.rdp.taxatree.Taxon; [javac] ^ [javac] symbol: class Taxon [javac] location: package edu.msu.cme.rdp.taxatree [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/pyro/cluster/ClusterReplay.java:27: error: cannot find symbol [javac] import edu.msu.cme.rdp.taxatree.TaxonHolder; [javac] ^ [javac] symbol: class TaxonHolder [javac] location: package edu.msu.cme.rdp.taxatree [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:22: error: package edu.msu.cme.rdp.taxatree.utils does not exist [javac] import edu.msu.cme.rdp.taxatree.utils.NewickPrintVisitor; [javac] ^ [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:23: error: package edu.msu.cme.rdp.taxatree.utils.NewickPrintVisitor does not exist [javac] import edu.msu.cme.rdp.taxatree.utils.NewickPrintVisitor.NewickDistanceFactory; [javac] ^ [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:50: error: cannot find symbol [javac] TaxonHolder lastMerged = null; [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:53: error: cannot find symbol [javac] Map taxonMap = new HashMap(); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:60: error: cannot find symbol [javac] TaxonHolder holder; [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:60: error: cannot find symbol [javac] TaxonHolder holder; [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:64: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, seqids.get(0), "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:64: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, seqids.get(0), "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:66: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:66: error: cannot find symbol [javac] holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:70: error: cannot find symbol [javac] TaxonHolder th = new TaxonHolder(new Taxon(id, seqid, "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:70: error: cannot find symbol [javac] TaxonHolder th = new TaxonHolder(new Taxon(id, seqid, "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:70: error: cannot find symbol [javac] TaxonHolder th = new TaxonHolder(new Taxon(id, seqid, "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:84: error: cannot find symbol [javac] TaxonHolder holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:84: error: cannot find symbol [javac] TaxonHolder holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class TaxonHolder [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:84: error: cannot find symbol [javac] TaxonHolder holder = new TaxonHolder(new Taxon(taxid++, "", "")); [javac] ^ [javac] symbol: class Taxon [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:106: error: cannot find symbol [javac] NewickPrintVisitor visitor = new NewickPrintVisitor(newickTreeOut, false, new NewickDistanceFactory() { [javac] ^ [javac] symbol: class NewickPrintVisitor [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:106: error: cannot find symbol [javac] NewickPrintVisitor visitor = new NewickPrintVisitor(newickTreeOut, false, new NewickDistanceFactory() { [javac] ^ [javac] symbol: class NewickPrintVisitor [javac] location: class TreeBuilder [javac] /opt/RDPTools/Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java:106: error: cannot find symbol [javac] NewickPrintVisitor visitor = new NewickPrintVisitor(newickTreeOut, false, new NewickDistanceFactory() { [javac] ^ [javac] symbol: class NewickDistanceFactory [javac] location: class TreeBuilder [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 21 errors [javac] 1 warning

BUILD FAILED /opt/RDPTools/Clustering/nbproject/build-impl.xml:955: The following error occurred while executing this line: /opt/RDPTools/Clustering/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Total time: 4 seconds make: *\ [Clustering/dist/Clustering.jar] Error 1

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nbetrapa commented 8 years ago

Hello Benli,

I do have apache installed.

Here is the output when i type ant -version,

ant -version Apache Ant(TM) version 1.9.4 compiled on April 29 2014

rdpstaffmsu commented 8 years ago

Hi, nbetrapa,

I couldn't replicate the errors you encountered. This tool does not require root installation. A wild guess is that root installation may cause some conflicts at the system level. Try the entire clone process as a regular user.

Benli

On Sun, May 1, 2016 at 6:01 PM, nbetrapa notifications@github.com wrote:

Hello Benli,

I do have apache installed.

Here is the output when i type ant -version,

ant -version Apache Ant(TM) version 1.9.4 compiled on April 29 2014

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RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

nbetrapa commented 8 years ago

Hello Benli,

I really appreciate the follow up and help provided. I tried the entire clone process as a regular user, however the install still fails.

I was wondering if this had to do anything with the following error while git update

github.com[0: 192.30.252.128]: errno=Connection timed out fatal: unable to connect a socket (Connection timed out) Clone of 'git://github.com/rdpstaff/TaxonomyTree' into submodule path 'TaxonomyTree' failed

Also, the only reason I am installing RDPTools is to be able to get access to the RDP Classifier 11 jar executable file. Kindly help me on this.

rdpstaffmsu commented 8 years ago

Ok, it is a "better" error - only the time out setting is involved. Would you run the following command prior to the procedure?:

“git config --global url."https://".insteadOf git://”

Please let me know how it works for you.

Benli

On Tue, May 3, 2016 at 1:01 PM, nbetrapa notifications@github.com wrote:

Hello Benli,

I really appreciate the follow up and help provided. I tried the entire clone process as a regular user, however the install still fails.

I was wondering if this had to do anything with the following error while git update

github.com[0: 192.30.252.128]: errno=Connection timed out fatal: unable to connect a socket (Connection timed out) Clone of 'git://github.com/rdpstaff/TaxonomyTree' into submodule path 'TaxonomyTree' failed

Also, the only reason I am installing RDPTools is to be able to get access to the RDP Classifier 11 jar executable file. Kindly help me on this.

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/rdpstaff/classifier/issues/15#issuecomment-216596149

RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

nbetrapa commented 8 years ago

Hello Benli,

Thank you for the assistance, I followed your advice and was able to clone everything. However, the recent error message I received is with respect to the classifier which is the most important build I am looking for. Below is the error:

BUILD SUCCESSFUL Total time: 2 seconds make: *\ No rule to make target classifier/nbproject/build-impl.xml', needed byclassifier/dist/classifier.jar'. Stop.

I hope this is the last error I would face. I am really grateful for all the help you are providing.

nbetrapa commented 8 years ago

Hello Benli,

Kindly ignore the previous comment. After the error I got above, I ran the line,

git submodule update

That pulled all the remaining modules and was able to successfully install RDP tools.

Thank you for all the help!