For info, I faced same issue on biojava3-live (bug #712359
<http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=712359>).
DefaultFontMapper in libitext5-java moved to com.itextpdf.awt

To fix it :

-import com.itextpdf.text.pdf.DefaultFontMapper;
+import com.itextpdf.awt.DefaultFontMapper;

Olivier


 compile:
    [javac] /«PKGBUILDDIR»/build.xml:39: warning: 'includeantruntime' was not 
set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 115 source files to /«PKGBUILDDIR»/build
    [javac] /«PKGBUILDDIR»/src/figtree/application/FigTreeFrame.java:5: cannot 
find symbol
    [javac] symbol  : class DefaultFontMapper
    [javac] location: package com.itextpdf.text.pdf
    [javac] import com.itextpdf.text.pdf.DefaultFontMapper;
    [javac]                             ^
    [javac] /«PKGBUILDDIR»/src/figtree/application/FigTreeFrame.java:1105: 
cannot find symbol
    [javac] symbol  : class DefaultFontMapper
    [javac] location: class figtree.application.FigTreeFrame
    [javac]                 Graphics2D g2d = 
tp.createGraphics((float)bounds.getWidth(), (float)bounds.getHeight(), new 
DefaultFontMapper());
    [javac]                                                                     
                                        ^
    [javac] Note: /«PKGBUILDDIR»/src/figtree/application/FigTreePDF.java uses 
or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: 
/«PKGBUILDDIR»/src/figtree/treeviewer/painters/LabelPainterController.java uses 
unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 2 errors

BUILD FAILED
/«PKGBUILDDIR»/build.xml:39: Compile failed; see the compiler error output for 
details.

Total time: 8 seconds
dh_auto_build: ant returned exit code 1
make: *** [binary] Error 2

> The full build log is available from:
>    
> http://aws-logs.debian.net/ftbfs-logs/2013/06/20/figtree_1.3.1-2_unstable.log
>
> A list of current common problems and possible solutions is available at 
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
>
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
>
> _______________________________________________
> Debian-med-packaging mailing list
> [email protected]
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

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