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0.12.1: ant build error #115

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starsareintherose opened this issue Mar 7, 2023 · 3 comments
Closed

0.12.1: ant build error #115

starsareintherose opened this issue Mar 7, 2023 · 3 comments

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@starsareintherose
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starsareintherose commented Mar 7, 2023 •
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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 starsareintherose mentioned this issue Mar 7, 2023
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@starsareintherose
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if #109 is merged, it should be closed.

@s-andrews
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This is now merged. Are you OK to pull this without a new release since nothing in the released code has changed?

@starsareintherose
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okay, no problem, it works well, just give a patch

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@s-andrews @starsareintherose