0.12.1: ant build error
starsareintherose opened this issue · 3 comments
starsareintherose commented
full log is here
Buildfile: /build/fastqc/src/FastQC-0.12.1/build.xml
build-subprojects:
init:
[mkdir] Created dir: /build/fastqc/src/FastQC-0.12.1/bin
[copy] Copying 59 files to /build/fastqc/src/FastQC-0.12.1/bin
build-project:
[echo] FastQC: /build/fastqc/src/FastQC-0.12.1/build.xml
[javac] Compiling 138 source files to /build/fastqc/src/FastQC-0.12.1/bin
[javac] warning: [options] system modules path not set in conjunction with -source 11
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:28: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.CigarElement;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:29: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.CigarOperator;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:30: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.SAMFormatException;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:31: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.SAMRecord;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:32: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.SamInputResource;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:33: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.SamReader;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:34: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.SamReaderFactory;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:35: error: package htsjdk.samtools does not exist
[javac] import htsjdk.samtools.ValidationStringency;
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:50: error: cannot find symbol
[javac] private SamReader br;
[javac] ^
[javac] symbol: class SamReader
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:53: error: cannot find symbol
[javac] Iterator<SAMRecord> it;
[javac] ^
[javac] symbol: class SAMRecord
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/org/apache/commons/math3/util/MathUtils.java:57: warning: [removal] Double(double) in Double has been deprecated and marked for removal
[javac] return new Double(value).hashCode();
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/org/apache/commons/math3/util/ResizableDoubleArray.java:915: warning: [removal] Float(float) in Float has been deprecated and marked for removal
[javac] hashData[0] = new Float(expansionFactor).hashCode();
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/org/apache/commons/math3/util/ResizableDoubleArray.java:916: warning: [removal] Float(float) in Float has been deprecated and marked for removal
[javac] hashData[1] = new Float(contractionCriteria).hashCode();
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:64: error: cannot find symbol
[javac] br = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(SamInputResource.of(fis));
[javac] ^
[javac] symbol: variable ValidationStringency
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:64: error: cannot find symbol
[javac] br = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(SamInputResource.of(fis));
[javac] ^
[javac] symbol: variable SamReaderFactory
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:64: error: cannot find symbol
[javac] br = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(SamInputResource.of(fis));
[javac] ^
[javac] symbol: variable SamInputResource
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:103: error: cannot find symbol
[javac] SAMRecord record;
[javac] ^
[javac] symbol: class SAMRecord
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:122: error: cannot find symbol
[javac] catch (SAMFormatException sfe) {
[javac] ^
[javac] symbol: class SAMFormatException
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:139: error: package SamReader does not exist
[javac] if (br.type() != SamReader.Type.SAM_TYPE) {
[javac] ^
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:153: error: cannot find symbol
[javac] List<CigarElement> elements = record.getCigar().getCigarElements();
[javac] ^
[javac] symbol: class CigarElement
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:156: error: cannot find symbol
[javac] if (elements.get(elements.size()-1).getOperator().equals(CigarOperator.S)) {
[javac] ^
[javac] symbol: variable CigarOperator
[javac] location: class BAMFile
[javac] /build/fastqc/src/FastQC-0.12.1/uk/ac/babraham/FastQC/Sequence/BAMFile.java:164: error: cannot find symbol
[javac] if (elements.get(0).getOperator().equals(CigarOperator.S)) {
[javac] ^
[javac] symbol: variable CigarOperator
[javac] location: class BAMFile
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 19 errors
[javac] 4 warnings
BUILD FAILED
/build/fastqc/src/FastQC-0.12.1/build.xml:35: Compile failed; see the compiler error output for details.
Total time: 1 second
Could you update the build.xml file ?
starsareintherose commented
if #109 is merged, it should be closed.
s-andrews commented
This is now merged. Are you OK to pull this without a new release since nothing in the released code has changed?
starsareintherose commented
okay, no problem, it works well, just give a patch