make command issue - Githubissues

RachelDanie commented 3 years ago

Hello! I see that a number of users have had issues with the make step, but since there have been edits more recently than those threads I wanted to ask about the errors I am getting:ant -f Clustering/build.xml jar Buildfile: /RDPTools/Clustering/build.xml

download-ivy: [get] Getting: http://insecure.repo1.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 :: file = /RDPTools/Clustering/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@metro-pes3307 [ivy:retrieve] confs: [default] [ivy:retrieve] found com.sun.xml.bind#jaxb-impl;2.2.7 in maven [ivy:retrieve] found com.sun.xml.bind#jaxb-core;2.2.7 in maven [ivy:retrieve] found javax.xml.bind#jaxb-api;2.2.7 in maven [ivy:retrieve] found com.sun.istack#istack-commons-runtime;2.16 in maven [ivy:retrieve] found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in maven [ivy:retrieve] found javax.xml.bind#jsr173_api;1.0 in maven [ivy:retrieve] found commons-cli#commons-cli;1.2 in maven [ivy:retrieve] found junit#junit;4.8.2 in maven [ivy:retrieve] found commons-codec#commons-codec;1.8 in maven [ivy:retrieve] found commons-io#commons-io;2.4 in maven [ivy:retrieve] :: resolution report :: resolve 150ms :: artifacts dl 7ms

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

[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering [ivy:retrieve] confs: [default] [ivy:retrieve] 0 artifacts copied, 10 already retrieved (0kB/5ms)

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

deps-jar:

-warn-already-built-jar: [propertyfile] Updating property file: /RDPTools/Clustering/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

download-ivy: [get] Getting: http://insecure.repo1.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 :: file = /RDPTools/AlignmentTools/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@metro-pes3307 [ivy:retrieve] confs: [default] [ivy:retrieve] found commons-lang#commons-lang;2.6 in maven [ivy:retrieve] found commons-cli#commons-cli;1.2 in maven [ivy:retrieve] :: resolution report :: resolve 21ms :: artifacts dl 1ms

|                  |            modules            ||   artifacts   |
|       conf       | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
|      default     |   2   |   0   |   0   |   0   ||   2   |   0   |
---------------------------------------------------------------------

[ivy:retrieve] :: retrieving :: edu.cme.rdp#AlignmentTools [ivy:retrieve] confs: [default] [ivy:retrieve] 0 artifacts copied, 2 already retrieved (0kB/2ms)

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

-check-call-dep:

-maybe-call-dep:

download-ivy: [get] Getting: http://insecure.repo1.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 :: file = /RDPTools/ReadSeq/ivysettings.xml [ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@metro-pes3307 [ivy:retrieve] confs: [default] [ivy:retrieve] found commons-lang#commons-lang;2.6 in maven [ivy:retrieve] found commons-cli#commons-cli;1.2 in maven [ivy:retrieve] found commons-io#commons-io;2.4 in maven [ivy:retrieve] :: resolution report :: resolve 26ms :: artifacts dl 2ms

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

[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq [ivy:retrieve] confs: [default] [ivy:retrieve] 0 artifacts copied, 3 already retrieved (0kB/2ms)

-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: /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: [javac] Compiling 73 source files to /RDPTools/ReadSeq/build/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 5 [javac] error: Source option 5 is no longer supported. Use 6 or later. [javac] error: Target option 1.5 is no longer supported. Use 1.6 or later.

BUILD FAILED /RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line: /RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line: /RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line: /RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line: /RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line: /RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Total time: 1 second Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed make: *** [Clustering/dist/Clustering.jar] Error 1

Here is additional relevant version information:

(Java) openjdk version "11.0.9.1" 2020-11-04 OpenJDK Runtime Environment (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04) OpenJDK 64-Bit Server VM (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04, mixed mode, sharing)

(ant) Apache Ant(TM) version 1.10.5 compiled on March 28 2019

Thank you!

gunturus commented 3 years ago

You need Ant 1.9. that should fix the problem

RachelDanie commented 3 years ago

Thanks Santosh! I was just a little confused about whether the ant version should matter after reading this stackoverflow post that seemed to indicate the java version was more important. Curious if you had thoughts on this before i try to change ant versions. Thanks!

On Thu, Jan 14, 2021 at 6:11 PM Santosh Kumar G notifications@github.com wrote:

You need Ant 1.9. that should fix the problem

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rdpstaff/RDPTools/issues/34#issuecomment-760597717, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETGZCYHJXVH2Y52E47RZG3SZ6P6LANCNFSM4WDK2V4Q .

RachelDanie commented 3 years ago

Sorry link here: https://stackoverflow.com/questions/43354118/installing-multiple-versions-of-ant-on-same-machine

On Thu, Jan 14, 2021 at 10:39 PM Rachel Danielson redanielson@ucdavis.edu wrote:

Thanks Santosh! I was just a little confused about whether the ant version should matter after reading this stackoverflow post that seemed to indicate the java version was more important. Curious if you had thoughts on this before i try to change ant versions. Thanks!

On Thu, Jan 14, 2021 at 6:11 PM Santosh Kumar G notifications@github.com wrote:

You need Ant 1.9. that should fix the problem

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rdpstaff/RDPTools/issues/34#issuecomment-760597717, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETGZCYHJXVH2Y52E47RZG3SZ6P6LANCNFSM4WDK2V4Q .

rdpstaff / RDPTools

make command issue #34