Your message dated Sun, 07 Dec 2025 23:04:29 +0000
with message-id <[email protected]>
and subject line Bug#1099282: fixed in rdp-classifier 2.10.2-8
has caused the Debian Bug report #1099282,
regarding rdp-classifier: FTBFS:
src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:28:
error: cannot find symbol
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1099282: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1099282
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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warning: [options] source value 8 is obsolete and will be removed in a future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warning: [options] target value 8 is obsolete and will be removed in a future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.
--- End Message ---
--- Begin Message ---
Source: rdp-classifier
Source-Version: 2.10.2-8
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
rdp-classifier, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (supplier of updated rdp-classifier package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 07 Dec 2025 23:49:56 +0100
Source: rdp-classifier
Architecture: source
Version: 2.10.2-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1099282
Changes:
rdp-classifier (2.10.2-8) unstable; urgency=medium
.
* Team upload.
* Fixing build failure after API changes in libjfreechart-java
(Closes: #1099282)
* Raising Standards version to 4.7.2 (no change)
* Rewriting d/watch with version 5
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