Open DeniRibicic opened 6 years ago
which java are you using
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.
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.
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)
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)
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
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.
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).
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).
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
Hi Folks, I am not able to build rdpTools. I have just followed installation procedure:
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