[Debian-med-packaging] Bug#1099282: rdp-classifier: FTBFS: src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:28: error: cannot find symbol

[Santiago Vila]

Package: src:rdp-classifier
Version: 2.10.2-7
Severity: serious
Tags: ftbfs trixie sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --with javahelper
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.jar lib/*.jar TEST-*
find test -name '*.class' -delete
rm -f *.list tmp-junit.xml
rm -rf dist
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   jh_clean
Duplicate specification "unlink|u" for option "u"
   dh_clean
 debian/rules binary
dh binary --with javahelper
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
   jh_linkjars
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
jh_build -J rdp_classifier.jar src
jh_build: warning: Java machine does not support --release 7, using --release 8
warning: [options] bootstrap class path not set in conjunction with -source 8
warning: [options] source value 8 is obsolete and will be removed in a future release
warning: [options] target value 8 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:28: error: cannot find symbol
import org.jfree.chart.ChartUtilities;
                      ^
  symbol:   class ChartUtilities
  location: package org.jfree.chart
src/edu/msu/cme/rdp/classifier/train/validation/distance/TaxaSimilarityMain.java:48: error: cannot find symbol
import org.jfree.chart.ChartUtilities;
                      ^
  symbol:   class ChartUtilities
  location: package org.jfree.chart
src/edu/msu/cme/rdp/multicompare/MCSample.java:116: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
            dupCountTable.put(dupSeqList[0], new Integer(dupSeqList.length));
                                             ^
src/edu/msu/cme/rdp/classifier/comparison/Ztable.java:65: warning: [removal] Double(double) in Double has been deprecated and marked for removal
                    zHash.put( initial_value + k, new Double(pvalue));
                                                  ^
src/edu/msu/cme/rdp/classifier/train/validation/crossvalidate/CrossValidateMain.java:98: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal
;            	partialLength = new Integer(line.getOptionValue(LENGTH_SHORT_OPT));
             	                ^
src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:96: error: cannot find symbol
        renderer.setBaseLegendTextFont(lableFont);
                ^
  symbol:   method setBaseLegendTextFont(Font)
  location: variable renderer of type BoxAndWhiskerRenderer
src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:97: error: cannot find symbol
        renderer.setStroke(new BasicStroke( 5.0f ));
                ^
  symbol:   method setStroke(BasicStroke)
  location: variable renderer of type BoxAndWhiskerRenderer
src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:103: error: cannot find symbol
        ChartUtilities.writeScaledChartAsPNG(outStream, boxchart, 800, 1000, 3, 3);
        ^
  symbol:   variable ChartUtilities
  location: class BoxPlotUtils
src/edu/msu/cme/rdp/classifier/train/validation/distance/TaxaSimilarityMain.java:325: error: cannot find symbol
        ((XYPlot) chart.getPlot()).getRenderer().setStroke( new BasicStroke( 2.0f ));
                                                ^
  symbol:   method setStroke(BasicStroke)
  location: interface XYItemRenderer
src/edu/msu/cme/rdp/classifier/train/validation/distance/TaxaSimilarityMain.java:335: error: cannot find symbol
        ChartUtilities.writeScaledChartAsPNG(new PrintStream(new File(outdir, plotTitle + ".linechart.png")), chart, 800, 1000, 3, 3);
        ^
  symbol:   variable ChartUtilities
  location: class TaxaSimilarityMain
src/edu/msu/cme/rdp/classifier/train/TreeFactory.java:100: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                taxidMap.put(new Integer(taxid), tax);
                             ^
src/edu/msu/cme/rdp/classifier/train/TreeFactory.java:104: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                    existCount = new Integer(0);
                                 ^
src/edu/msu/cme/rdp/classifier/train/TreeFactory.java:207: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal
        Taxonomy tax = this.taxidMap.get(new Integer((String) pSeq.getAncestors().get(0)));
                                         ^
src/edu/msu/cme/rdp/classifier/train/TreeFactory.java:214: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
            tax = this.taxidMap.get(new Integer(tax.getParentID()));
                                    ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
7 errors
11 warnings
jh_build: error: find src -name '*.java' -and -type f -print0 | xargs -s 512000 -0 /usr/lib/jvm/default-java/bin/javac -g -cp /usr/share/java/junit.jar:/usr/share/java/commons-cli.jar:/usr/share/java/rdp-alignment.jar:/usr/share/java/rdp-taxonomy-tree.jar:/usr/share/java/jfreechart.jar:debian/_jh_build.rdp_classifier -d debian/_jh_build.rdp_classifier -encoding ISO8859-1 -source 8 -target 8  returned exit code 123
make[1]: *** [debian/rules:13: override_dh_auto_build] Error 255
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202503/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:rdp-classifier, so that this is still
visible in the BTS web page for this package.

Thanks.