blastn2snp error compiling

I want to compile blastn2snp in jvarkit (https://github.com/lindenb/jvarkit/wiki/BlastnToSnp) with below code:

make blastn2snp

but it gave me an error:

compile-samtools:
    [javac] /home/mrb/NGS/Format-tools/jvarkit/htsjdk-1.128/build.xml:244: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 371 source files to /home/mrb/NGS/Format-tools/jvarkit/htsjdk-1.128/classes
    [javac] Compliance level '1.5' is incompatible with source level '1.6'. A compliance level '1.6' or better is required

BUILD FAILED
/home/mrb/NGS/Format-tools/jvarkit/htsjdk-1.128/build.xml:100: The following error occurred while executing this line:
/home/mrb/NGS/Format-tools/jvarkit/htsjdk-1.128/build.xml:244: Compile failed; see the compiler error output for details.

Total time: 0 seconds
make: *** [/home/mrb/NGS/Format-tools/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar] Error 1

I can not understand what is the problem ( Compliance level '1.5' is incompatible with source level '1.6'. A compliance level '1.6' or better is required). Any help greatly appreciated.

Best wishes

blastn2snp blast

• 2,946 views • link

updated 4.1 years ago by Ram

• written 11.3 years ago by Mohammad Reza Bakhtiarizadeh

1 answer

1) please use https://github.com/lindenb/jvarkit/issues to report errors

2) you version of java is just too old. jvarkit requires java 1.7.

• 0 views • link

written 11.3 years ago by Pierre Lindenbaum

Thanks for the help. but my java version is 1.7. You can see:

mrb@linux-kfkz:~/NGS/A-Project/Sheep-RNA-editing/2-Results/EST> java -version
java version "1.7.0_45"
OpenJDK Runtime Environment (IcedTea 2.4.3) (suse-24.9.1-x86_64)
OpenJDK 64-Bit Server VM (build 24.45-b08, mixed mode)

Best

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updated 4.1 years ago by Ram

• written 11.3 years ago by Mohammad Reza Bakhtiarizadeh

Show me the value of ${JAVA_HOME} please

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updated 4.1 years ago by Ram

• written 11.3 years ago by Pierre Lindenbaum

echo $JAVA_HOME
/usr/lib64/jvm/java

Thanks

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updated 4.1 years ago by Ram

• written 11.3 years ago by Mohammad Reza Bakhtiarizadeh

And what's the output of

${JAVA_HOME}/bin/javac -version

please

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updated 4.1 years ago by Ram

• written 11.3 years ago by Pierre Lindenbaum

Thanks so much. I found the problem. The output of ${JAVA_HOME}/bin/java -version is

java version is "1.5.0"

I see the /usr/lib64/jvm/java and got a ls and the results is:

java                        java-1.7.0-openjdk-1.7.0  jre-1.7.0
java-1.5.0                  java-gcj                  jre-1.7.0-openjdk
java-1.5.0-gcj              jre                       jre-gcj
java-1.5.0-gcj-4.8-1.5.0.0  jre-1.5.0                 jre-openjdk
java-1.7.0-openjdk          jre-1.5.0-gcj

How can I handle the problem? which one of these folder has to be JAVA_HOME?

Best

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updated 4.1 years ago by Ram

• written 11.3 years ago by Mohammad Reza Bakhtiarizadeh

nice you found the problem, as far as I can see JAVA_HOME should be the directory containing bin/javac . For now this is a 'simple' admin issue, you should ask stackoverflow.com if there's still a problem.

• 0 views • link

written 11.3 years ago by Pierre Lindenbaum

Really thanks for the help. My problem is fixed and the software is compiled as simple as possible. blastn2snp works great.

Kind regards

• 0 views • link

written 11.3 years ago by Mohammad Reza Bakhtiarizadeh