./gradlew mapuniprot install error

wunalahu2 commented 1 year ago

Verify

Subject of the issue

when I install mapuniprot as the methods described below: http://lindenb.github.io/jvarkit/MapUniProtFeatures.html the error has occured like this : ' FAILURE: Build failed with an exception.

Where: Build file '/home/wunalahu/software/jvarkit/build.gradle' line: 343
What went wrong: Execution failed for mapuniprot com.github.lindenb.jvarkit.tools.misc.MapUniProtFeatures.

Java returned: 255
Try:

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BUILD FAILED in 2s ' and I debug it with the scripts "./gradlew mapuniprot --info > log"and the info written in log is ' [ant:java] [ERROR] The markup in the document preceding the root element must be well-formed. [ant:java] line 1 of https://www.uniprot.org/docs/uniprot.xsd [ant:java] [ant:java] Failed to parse a schema.

Task :mapuniprot FAILED '

I'm wondering if the link 'https://www.uniprot.org/docs/uniprot.xsd' has been deprecated ?

Your environment

my java version: java -version openjdk version "11.0.15" 2022-04-19 javac -version javac 11.0.15

the value of ${JAVA_HOME} JAVA_HOME="/usr/lib/jvm/java-11-openjdk-11.0.15.0.10-3.el8.x86_64/" export PATH=${JAVA_HOME}/bin:${PATH}
which OS centos8

hope reply asap,thank you

lindenb commented 1 year ago

yes, you're right, the doc has moved . I changed it in the dev branch a few days ago: https://github.com/lindenb/jvarkit/commit/c3183aab41ff841e0d43bfab93f0f508426bfb49

lindenb commented 1 year ago

I've just merged dev into master. It should work now.

wunalahu2 commented 1 year ago

I've just merged dev into master. It should work now.

Thank you for your prompt reply.It has been built succesfully. ‘> Task :mapuniprot jar file generated :/home/wunalahu/software/jvarkit/dist/mapuniprot.jar No Test will be executed for mapuniprot

BUILD SUCCESSFUL in 22s’

lindenb / jvarkit