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rdpstaff / RDPTools

Collection of commonly used RDP Tools for easy building
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Build failed #22

Open DeniRibicic opened 6 years ago

DeniRibicic commented 6 years ago

Hi Folks, I am not able to build rdpTools. I have just followed installation procedure:

  1. git clone https://github.com/rdpstaff/RDPTools.git
  2. cd RDPTools
  3. git submodule init
  4. git submodule update
  5. make

Here the build fails, throwing following error:

BUILD FAILED /home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line: /home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line: /home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line: /home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line: /home/denir/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line: /home/denir/bin/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

Any clues? Deni

gunturus commented 6 years ago

which java are you using

DeniRibicic commented 6 years ago

It's version 9. I actually needed only classifier, and I have installed it through anaconda. So, I am okay now. However, the whole tools installation as specified in your repository still remains a problem.

janpb commented 6 years ago

I just tried to install RDPTools. Replacing ant -f with ant -D"javac.source"=1.6 -D"javac.target"=1.6 in the Makefile seems to compile. However, the installation aborts since it cannot fetch the traindata data.tgz (I guess issue #16). It manages to compile ReadSeq and AlignmentTools. java -jar "ReadSeq/dist/ReadSeq.jar" OK java -jar "AlignmentTools/dist/AlignmentTools.jar" OK

However, despite the following message

     [echo] To run this application from the command line without Ant, try:
     [echo] java -jar "/home/jan/build/RDPTools/TaxonomyTree/dist/TaxonomyTree.jar"

TaxonomyTree.jar fails:

 java -jar "java -jar "TaxonomyTree/dist/TaxonomyTree.jar"AlignmentTools/dist/AlignmentTools.jar"
Error: Unable to access jarfile java -jar TaxonomyTree/dist/TaxonomyTree.jarAlignmentTools/dist/AlignmentTools.jar

Hope this helps.

Setup

Fresh git clone and update of submodules: commit: ee73c1c67d2bb577993b23b9886fa984ca974fb5

System: Ubuntu 17.10

$ unname -a
  Linux 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Java

$ java --version
openjdk 9-Ubuntu
OpenJDK Runtime Environment (build 9-Ubuntu+0-9b181-4)
OpenJDK 64-Bit Server VM (build 9-Ubuntu+0-9b181-4, mixed mode)
mbenucci commented 6 years ago

currently I managed to solve part of the RDPtools error when compiling. @janpb suggestion was massively helpful, however I had to keep the -f option otherwise it couldn't find the build.xml file. My Makefile now looks like this ant -D"javac.source"-1.6 -D"javac.target"=1.6 -f

The Makefile in this way seems to work fine for me, however I encountered another issue further down in the post-jar process of the TaxonomyTree. When downloading the traindata, the build seem to fail, as others already experienced, due to "java.io.EOFException: Unexpected end of ZLIB input stream" (issue #16)

Hope it helps.

System: Ubuntu 16.04 Linux 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Java: openjdk version "9-internal" OpenJDK Runtime Environment (build 9-internal+0-2016-04-14-195246.buildd.src) OpenJDK 64-Bit Server VM (build 9-internal+0-2016-04-14-195246.buildd.src, mixed mode)

rothmi12 commented 5 years ago

I just want to do my part and try to help out the next person who has the issue with the error [Clustering/dist/Clustering.jar] Error 1 while trying to install RDPTools.

Turns out, the version of apache-ant is critical for installation. Successful installation requires apache-ant-1.9.x and will not work with apache-ant-1.10.x

lotrus28 commented 5 years ago

As noted in this issue, installing JDK 7 solves the problem. At least, it has solved mine. That is a bit confusing, as in another issue moving to JDK 8 was recommended.

andrewDSequential commented 2 years ago

Bumping this issue to say that I was using java-11 and had to switch to 8 for install to work on ubuntu

$ update-alternatives --config java There are 2 choices for the alternative java (providing /usr/bin/java).

Selection Path Priority Status

0 /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 auto mode 1 /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 manual mode

$ update-alternatives --config javac There are 2 choices for the alternative javac (providing /usr/bin/javac).

Selection Path Priority Status

0 /usr/lib/jvm/java-11-openjdk-amd64/bin/javac 1111 auto mode 1 /usr/lib/jvm/java-11-openjdk-amd64/bin/javac 1111 manual mode