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SAXParseException when building backlocate #11

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sargant opened this issue Aug 15, 2014 · 3 comments
Closed

SAXParseException when building backlocate #11

sargant opened this issue Aug 15, 2014 · 3 comments

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@sargant
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sargant commented Aug 15, 2014

Can run all the steps under "Download & Install" on the Compilation page fine, but when I try to compile backlocate with ant backlocate, I get the following error:

Buildfile: /scratch/ukapd/jvarkit/jvarkit/build.xml

backlocate:

BUILD FAILED
/scratch/ukapd/jvarkit/jvarkit/build.xml:1854: The following error occurred while executing this line:
/scratch/ukapd/jvarkit/jvarkit/build.xml:198: The following error occurred while executing this line:
/scratch/ukapd/jvarkit/jvarkit/build.xml:8: java.util.InvalidPropertiesFormatException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
    at java.util.XMLUtils.load(XMLUtils.java:76)
    at java.util.Properties.loadFromXML(Properties.java:868)
    ....(trim)....

ant -version is Apache Ant(TM) version 1.9.2 compiled on July 8 2013

The first few lines of build.xml are:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE project SYSTEM "build.dtd">
<project name="jvarkit" default="all" basedir=".">
<property file="build.properties"/>
<property name="http.proxy" value="localhost:80"/>
<property name="generated.dir" value="src/main/generated-sources/java"/>
<property name="test.output" value="tests"/>
<property file="${htsjdk.home}/htsjdk.version.property.xml"/>

<!--define htsjdk.home if is not defined in the file "build.properties" -->
<property name="htsjdk.home" value="htsjdk"/>
...

The content of ./htsjdk/htsjdk.version.property.xml is:

#htsjdk version
#Fri, 15 Aug 2014 11:02:22 +0100

htsjdk-version=1.117

build.properties is entirely commented out

@lindenb
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lindenb commented Aug 15, 2014

Hum... I'll be away from my code for some times. But it looks like htsjdk produced a non-XML file while it is named "*.xml". Can you please try to rename "./htsjdk/htsjdk.version.property.xml" to``"./htsjdk/htsjdk.version.properties" (and in the jvarkit/build.xml file too)

@sargant
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sargant commented Aug 15, 2014

That does work, thanks.

@nmb85
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nmb85 commented Sep 6, 2014

Yes, that solved it for me, too; thanks!

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