lindenb
commented
7 months ago Hi, your version of java is just too old. try with java >= 19.
Closed nkneuro closed 7 months ago
lindenb
commented
7 months ago Hi, your version of java is just too old. try with java >= 19.
nkneuro
commented
7 months ago Yes, it worked! Thank you for your comment.
Verify
java -version
java version "11.0.21" 2023-10-17 LTS Java(TM) SE Runtime Environment 18.9 (build 11.0.21+9-LTS-193) Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.21+9-LTS-193, mixed mode)
javac -version javac 11.0.21
Subject of the issue
Describe your issue here.
Failed to compile blastn2snp Task :blastn2snp FAILED FAILURE: Build failed with an exception.
Your environment
version of jvarkit: I believe it is latest (v2023.09.07). Used git-clone to install.
version of java: "11.0.21"
the value of
${JAVA_HOME}echo $JAVA_HOME /Users/nk/jdk-11.0.21.jdk/Contents/Home Also, I set: export PATH=${JAVA_HOME}/bin:$PATHwhich OS macOS ProductVersion: 13.1 BuildVersion: 22C65
Steps to reproduce
Tell us how to reproduce this issue. Please provide an example.
./gradlew blastn2snp
[ant:javac] 100 errors [ant:javac] 12 warnings
Expected behaviour
Tell us what should happen
Actual behaviour
Tell us what happens instead
I want to use blastn2snp and tried to compile it, but failed. I've looked at previous issues, and corrected as much as I could. I don't have much experiences using Java, so it would be helpful if you could look at my issues. The log is attached here.
[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [ant:javac] 1 warning [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/com/sun/xml/bind/jaxb-core/2.2.11/jaxb-api.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-api-2.2.12-b140109.1041.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/txw2-2.2.11.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/istack-commons-runtime-2.21.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/jaxb-api-2.4.0-b180830.0359.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/txw2-2.4.0-b180830.0438.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/istack-commons-runtime-3.0.7.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/stax-ex-1.8.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/FastInfoset-1.2.15.jar": no such file or directory [ant:javac] warning: [path] bad path element "/Users/nk/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/javax.activation-api-1.2.0.jar": no such file or directory [ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java:47: error: cannot access CloserUtil [ant:javac] import htsjdk.samtools.util.CloserUtil; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/CloserUtil.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:68: error: cannot access SAMFileHeader [ant:javac] import htsjdk.samtools.SAMFileHeader; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMFileHeader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:69: error: cannot access SAMFileWriter [ant:javac] import htsjdk.samtools.SAMFileWriter; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMFileWriter.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:70: error: cannot access SAMFileWriterFactory [ant:javac] import htsjdk.samtools.SAMFileWriterFactory; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMFileWriterFactory.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:71: error: cannot access SamRecordFilter [ant:javac] import htsjdk.samtools.filter.SamRecordFilter; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/filter/SamRecordFilter.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:72: error: cannot access AbstractProgressLogger [ant:javac] import htsjdk.samtools.util.AbstractProgressLogger; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/AbstractProgressLogger.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:74: error: cannot access Interval [ant:javac] import htsjdk.samtools.util.Interval; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/Interval.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:75: error: cannot access IntervalTreeMap [ant:javac] import htsjdk.samtools.util.IntervalTreeMap; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/IntervalTreeMap.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:76: error: cannot access ProgressLoggerInterface [ant:javac] import htsjdk.samtools.util.ProgressLoggerInterface; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/ProgressLoggerInterface.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:77: error: cannot access StringUtil [ant:javac] import htsjdk.samtools.util.StringUtil; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/StringUtil.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:78: error: cannot access VariantContext [ant:javac] import htsjdk.variant.variantcontext.VariantContext; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/variantcontext/VariantContext.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:79: error: cannot access VariantContextWriter [ant:javac] import htsjdk.variant.variantcontext.writer.VariantContextWriter; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/variantcontext/writer/VariantContextWriter.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:80: error: cannot access VariantContextWriterBuilder [ant:javac] import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:81: error: cannot access VCFHeader [ant:javac] import htsjdk.variant.vcf.VCFHeader; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFHeader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:82: error: cannot access VCFHeaderLine [ant:javac] import htsjdk.variant.vcf.VCFHeaderLine; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFHeaderLine.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:83: error: cannot access VCFIterator [ant:javac] import htsjdk.variant.vcf.VCFIterator; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFIterator.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:31: error: cannot access SAMSequenceDictionary [ant:javac] import htsjdk.samtools.SAMSequenceDictionary; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMSequenceDictionary.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:919: error: cannot access SamReaderFactory [ant:javac] protected htsjdk.samtools.SamReaderFactory createSamReaderFactory() [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SamReaderFactory.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java:925: error: cannot access SamReader [ant:javac] protected htsjdk.samtools.SamReader openSamReader(final String inputName) [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SamReader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:67: error: cannot access LineIterator [ant:javac] import htsjdk.tribble.readers.LineIterator; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/LineIterator.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:68: error: cannot access LineIteratorImpl [ant:javac] import htsjdk.tribble.readers.LineIteratorImpl; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/LineIteratorImpl.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:69: error: cannot access LineReader [ant:javac] import htsjdk.tribble.readers.LineReader; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/LineReader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:70: error: cannot access SynchronousLineReader [ant:javac] import htsjdk.tribble.readers.SynchronousLineReader; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/SynchronousLineReader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:71: error: cannot access Defaults [ant:javac] import htsjdk.samtools.Defaults; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/Defaults.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:72: error: cannot access SAMException [ant:javac] import htsjdk.samtools.SAMException; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMException.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:73: error: cannot access BlockCompressedInputStream [ant:javac] import htsjdk.samtools.util.BlockCompressedInputStream; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/BlockCompressedInputStream.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:74: error: cannot access BlockCompressedOutputStream [ant:javac] import htsjdk.samtools.util.BlockCompressedOutputStream; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/BlockCompressedOutputStream.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:75: error: cannot access BlockCompressedStreamConstants [ant:javac] import htsjdk.samtools.util.BlockCompressedStreamConstants; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/BlockCompressedStreamConstants.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:77: error: cannot access IOUtil [ant:javac] import htsjdk.samtools.util.IOUtil; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/IOUtil.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:78: error: cannot access RuntimeIOException [ant:javac] import htsjdk.samtools.util.RuntimeIOException; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/RuntimeIOException.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/AcidNucleics.java:29: error: cannot access Allele [ant:javac] import htsjdk.variant.variantcontext.Allele; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/variantcontext/Allele.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/lang/JvarkitException.java:41: error: cannot access Locatable [ant:javac] import htsjdk.samtools.util.Locatable; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/Locatable.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/lang/JvarkitException.java:43: error: cannot access VCFInfoHeaderLine [ant:javac] import htsjdk.variant.vcf.VCFInfoHeaderLine; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFInfoHeaderLine.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/bed/BedLineCodec.java:26: error: cannot access ValidationStringency [ant:javac] import htsjdk.samtools.ValidationStringency; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/ValidationStringency.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/bed/BedLineCodec.java:29: error: cannot access AsciiFeatureCodec [ant:javac] import htsjdk.tribble.AsciiFeatureCodec; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/AsciiFeatureCodec.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/bed/BedLine.java:34: error: cannot access QueryInterval [ant:javac] import htsjdk.samtools.QueryInterval; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/QueryInterval.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/bed/BedLine.java:38: error: cannot access Feature [ant:javac] import htsjdk.tribble.Feature; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/Feature.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SamRecordFilterFactory.java:43: error: cannot access Cigar [ant:javac] import htsjdk.samtools.Cigar; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/Cigar.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SamRecordFilterFactory.java:44: error: cannot access SAMReadGroupRecord [ant:javac] import htsjdk.samtools.SAMReadGroupRecord; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMReadGroupRecord.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SamRecordFilterFactory.java:45: error: cannot access SAMRecord [ant:javac] import htsjdk.samtools.SAMRecord; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMRecord.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:52: error: cannot access SAMSequenceRecord [ant:javac] import htsjdk.samtools.SAMSequenceRecord; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMSequenceRecord.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:54: error: cannot access FileExtensions [ant:javac] import htsjdk.samtools.util.FileExtensions; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/FileExtensions.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:58: error: cannot access FeatureCodec [ant:javac] import htsjdk.tribble.FeatureCodec; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/FeatureCodec.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:65: error: cannot access AbstractVCFCodec [ant:javac] import htsjdk.variant.vcf.AbstractVCFCodec; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/AbstractVCFCodec.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:66: error: cannot access VCF3Codec [ant:javac] import htsjdk.variant.vcf.VCF3Codec; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCF3Codec.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:67: error: cannot access VCFCodec [ant:javac] import htsjdk.variant.vcf.VCFCodec; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFCodec.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:68: error: cannot access VCFConstants [ant:javac] import htsjdk.variant.vcf.VCFConstants; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFConstants.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:69: error: cannot access VCFContigHeaderLine [ant:javac] import htsjdk.variant.vcf.VCFContigHeaderLine; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFContigHeaderLine.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:70: error: cannot access VCFFilterHeaderLine [ant:javac] import htsjdk.variant.vcf.VCFFilterHeaderLine; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFFilterHeaderLine.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:71: error: cannot access VCFFormatHeaderLine [ant:javac] import htsjdk.variant.vcf.VCFFormatHeaderLine; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFFormatHeaderLine.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:74: error: cannot access VCFHeaderLineCount [ant:javac] import htsjdk.variant.vcf.VCFHeaderLineCount; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFHeaderLineCount.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:75: error: cannot access VCFHeaderVersion [ant:javac] import htsjdk.variant.vcf.VCFHeaderVersion; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFHeaderVersion.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/vcf/VCFUtils.java:78: error: cannot access VCFIteratorBuilder [ant:javac] import htsjdk.variant.vcf.VCFIteratorBuilder; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFIteratorBuilder.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:40: error: cannot access PeekableIterator [ant:javac] import htsjdk.samtools.util.PeekableIterator; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/PeekableIterator.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/lang/CharSplitter.java:35: error: cannot access AbstractIterator [ant:javac] import htsjdk.samtools.util.AbstractIterator; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/AbstractIterator.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/samtools/util/SimpleInterval.java:35: error: cannot access CoordMath [ant:javac] import htsjdk.samtools.util.CoordMath; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/CoordMath.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/vcf/BcfIteratorBuilder.java:33: error: cannot access CloseableIterator [ant:javac] import htsjdk.samtools.util.CloseableIterator; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/CloseableIterator.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] Mar 07, 2024 12:52:18 PM com.github.lindenb.jvarkit.annotproc.JVarkitAnnotationProcessor process [ant:javac] INFO: [PROC] process [ant:javac] Mar 07, 2024 12:52:18 PM com.github.lindenb.jvarkit.annotproc.JVarkitAnnotationProcessor copySource [ant:javac] INFO: [PROC] ## Copying src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java -> /Users/nk/jvarkit/tmp/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java [ant:javac] warning: No processor claimed any of these annotations: com.beust.jcommander.Parameter,javax.xml.bind.annotation.XmlRegistry [ant:javac] /Users/nk/jvarkit/tmp/gov/nih/nlm/ncbi/blast/Iteration.java:58: error: cannot access CloserUtil [ant:javac] return iterationIterNum; [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/CloserUtil.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:71: error: cannot access SAMFileHeader [ant:javac] if(this.force_bcf_output) { [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMFileHeader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:72: error: cannot access SAMFileWriter [ant:javac] vcwb.setOutputBCFStream(System.out); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMFileWriter.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:76: error: cannot access SAMFileWriterFactory [ant:javac] vcwb.setOutputVCFStream(System.out); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMFileWriterFactory.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:81: error: cannot access SamRecordFilter [ant:javac] return vcwb.build(); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/filter/SamRecordFilter.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access AbstractProgressLogger [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/AbstractProgressLogger.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access Interval [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/Interval.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access IntervalTreeMap [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/IntervalTreeMap.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access ProgressLoggerInterface [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/ProgressLoggerInterface.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access StringUtil [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/StringUtil.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access VariantContext [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/variantcontext/VariantContext.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access VariantContextWriter [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/variantcontext/writer/VariantContextWriter.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access VariantContextWriterBuilder [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access VCFHeader [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFHeader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access VCFHeaderLine [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFHeaderLine.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/variantcontext/writer/WritingVariantsDelegate.java:84: error: cannot access VCFIterator [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/variant/vcf/VCFIterator.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot access SamReaderFactory [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SamReaderFactory.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot access SamReader [ant:javac] [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SamReader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:72: error: cannot access LineIterator [ant:javac] return peek.peek(); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/LineIterator.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:77: error: cannot access LineIteratorImpl [ant:javac] public static LineIterator of(final InputStream in) { [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/LineIteratorImpl.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:78: error: cannot access LineReader [ant:javac] try { [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/LineReader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:79: error: cannot access SynchronousLineReader [ant:javac] return of(new InputStreamReader(in, "UTF-8")); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/readers/SynchronousLineReader.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:81: error: cannot access Defaults [ant:javac] catch(final IOException err) { [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/Defaults.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:82: error: cannot access SAMException [ant:javac] throw new RuntimeIOException(err); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/SAMException.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:86: error: cannot access BlockCompressedInputStream [ant:javac] public static LineIterator of(final Reader in) { [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/BlockCompressedInputStream.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:87: error: cannot access BlockCompressedOutputStream [ant:javac] return of(new BufferedReader(in)); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/BlockCompressedOutputStream.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:91: error: cannot access BlockCompressedStreamConstants [ant:javac] public static LineIterator of(final BufferedReader in) { [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/BlockCompressedStreamConstants.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:95: error: cannot access IOUtil [ant:javac] public static LineIterator of(final Path path) throws IOException { [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/IOUtil.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/iterator/LineIterators.java:96: error: cannot access RuntimeIOException [ant:javac] final BufferedReader br = IOUtils.openPathForBufferedReading(path); [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/util/RuntimeIOException.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/bed/BedInterval.java:31: error: cannot access QueryInterval [ant:javac] /* interface for 0-Based interval . Not the same as Locatable which is a 1-based interval / [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/samtools/QueryInterval.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/bed/BedInterval.java:37: error: cannot access Feature [ant:javac] /* return 0-based end / [ant:javac] ^ [ant:javac] bad class file: /Users/nk/jvarkit/lib/com/github/samtools/htsjdk/4.0.1/htsjdk-4.0.1.jar(/htsjdk/tribble/Feature.class) [ant:javac] class file has wrong version 61.0, should be 55.0 [ant:javac] Please remove or make sure it appears in the correct subdirectory of the classpath. [ant:javac] Mar 07, 2024 12:52:18 PM com.github.lindenb.jvarkit.annotproc.JVarkitAnnotationProcessor process [ant:javac] INFO: [PROC] process [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:547: error: cannot find symbol [ant:javac] pw.print(mdBuilder); [ant:javac] ^ [ant:javac] symbol: class VCFIterator [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot find symbol [ant:javac] [ant:javac] symbol: class VariantContextWriter [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot find symbol [ant:javac] [ant:javac] symbol: class VCFHeader [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot find symbol [ant:javac] [ant:javac] symbol: class VCFHeader [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot find symbol [ant:javac] [ant:javac] symbol: class VCFIterator [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot find symbol [ant:javac] [ant:javac] symbol: class VariantContextWriter [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/jcommander/CmdUsageBuilder.java:563: error: cannot find symbol [ant:javac] [ant:javac] symbol: class IntervalTreeMap [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/Pedigree.java:823: error: cannot find symbol [ant:javac] [ant:javac] symbol: class Interval [ant:javac] location: class Launcher [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/Pedigree.java:516: error: cannot find symbol [ant:javac] public static Pedigree readPedigree(final VCFHeader header) { [ant:javac] ^ [ant:javac] symbol: class VCFHeader [ant:javac] location: class Pedigree [ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/Pedigree.java:520: error: cannot find symbol [ant:javac] public static Pedigree readPedigree(final Collection metadata) {
[ant:javac] ^
[ant:javac] symbol: class VCFHeaderLine
[ant:javac] location: class Pedigree
[ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/Pedigree.java:524: error: cannot find symbol
[ant:javac] public Set toVCFHeaderLines() {
[ant:javac] ^
[ant:javac] symbol: class VCFHeaderLine
[ant:javac] location: class Pedigree
[ant:javac] /Users/nk/jvarkit/src/main/java/com/github/lindenb/jvarkit/util/Pedigree.java:624: error: cannot find symbol
[ant:javac] public Pedigree parse(final VCFHeader h)
[ant:javac] ^
[ant:javac] symbol: class VCFHeader
[ant:javac] location: class Parser
[ant:javac] 100 errors
[ant:javac] 12 warnings
FAILURE: Build failed with an exception.