blastn2snp error compiling

Question

[Mohammad Reza Bakhtiarizadeh]

Hi

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

Answer 1

[Pierre Lindenbaum]

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.

[Mohammad Reza Bakhtiarizadeh]

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

[Pierre Lindenbaum]

Show me the value of ${JAVA_HOME} please

[Mohammad Reza Bakhtiarizadeh]

echo $JAVA_HOME
/usr/lib64/jvm/java

Thanks

[Pierre Lindenbaum]

And what's the output of

${JAVA_HOME}/bin/javac -version

please

[Mohammad Reza Bakhtiarizadeh]

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

[Pierre Lindenbaum]

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.

[Mohammad Reza Bakhtiarizadeh]

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

Kind regards