[Debian-med-packaging] Bug#1116910: sepp: FTBFS with the nocheck build profile
Santiago Vila
sanvila at debian.org
Tue Sep 30 15:55:11 BST 2025
Package: src:sepp
Version: 4.5.5+dfsg-1
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile
Dear maintainer:
During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:
https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck
(It's a wiki, so you are welcome to contribute)
[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].
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:sepp, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
I: pybuild base:311: python3.13 setup.py clean
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX license expression:
License :: OSI Approved :: GNU General Public License (GPL)
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
self._finalize_license_expression()
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
rm -f -rf tools/bundled
rm -f -rf tools/merge/build
rm -f sepp.config upp.config
find . -name "*.class" -delete
find . -name "*.jar" -delete
rm -f home.path sepp.egg-info/PKG-INFO sepp.egg-info/SOURCES.txt sepp.egg-info/dependency_links.txt sepp.egg-info/requires.txt sepp.egg-info/top_level.txt
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p tools/bundled/Linux
mkdir -p tools/merge/lib
# Building the jar for sepp.
cd tools/merge && \
CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant
Buildfile: /<<PKGBUILDDIR>>/tools/merge/build.xml
clean:
compile:
[mkdir] Created dir: /<<PKGBUILDDIR>>/tools/merge/classes
[javac] /<<PKGBUILDDIR>>/tools/merge/build.xml:32: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 23 source files to /<<PKGBUILDDIR>>/tools/merge/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Trees.java:32: warning: SunGraphicsEnvironment is internal proprietary API and may be removed in a future release
[javac] import sun.java2d.SunGraphicsEnvironment;
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/algos/lca/SchieberVishkinLCA.java:188: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
[javac] _tnode_idx_lookup.put(n, new Integer(i++));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/io/NewickReader.java:341: warning: [removal] Double(double) in Double has been deprecated and marked for removal
[javac] node.setData(new Double(0));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STITree.java:221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
[javac] return _nodes.get(new Integer(id));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:264: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal
[javac] newRecord.set(locEdgeNum, new Integer(newLab));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:275: warning: [removal] Double(double) in Double has been deprecated and marked for removal
[javac] Double newLWR = new Double(prior * precord.getDouble(2));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:519: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] mainEdgeLen.put(edgeLenMatcher.group(2), new Double(edgeLenMatcher.group(1)));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:616: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] cutoff = new Double(args[i]);
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:656: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] threshold = new Double(args[i]);
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java:177: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal
[javac] pr.set(locEdgeNum, new Integer(newLab));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java:269: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] Double len = new Double(matcher.group(1));
[javac] ^
[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] 15 warnings
jar:
[jar] Building jar: /<<PKGBUILDDIR>>/tools/merge/seppJsonMerger.jar
BUILD SUCCESSFUL
Total time: 1 second
dh_auto_configure
I: pybuild base:311: python3.13 setup.py config
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX license expression:
License :: OSI Approved :: GNU General Public License (GPL)
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
self._finalize_license_expression()
Creating main sepp config file at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/.sepp/main.config and tools at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/.sepp
error: [Errno 2] No such file or directory: '/usr/bin/guppy'
E: pybuild pybuild:389: configure: plugin distutils failed with: exit code=1: python3.13 setup.py config
dh_auto_configure: error: pybuild --configure -i python{version} -p 3.13 returned exit code 13
make[1]: *** [debian/rules:15: override_dh_auto_configure] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
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