Your message dated Sat, 04 Oct 2025 22:20:40 +0000
with message-id <[email protected]>
and subject line Bug#1116910: fixed in sepp 4.5.5+dfsg-2
has caused the Debian Bug report #1116910,
regarding sepp: FTBFS with the nocheck build profile
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.
(NB: If you are a system administrator and have no idea what this
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--
1116910: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1116910
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:sepp
Version: 4.5.5+dfsg-1
Severity: important
Tags: forky sid ftbfs
User: [email protected]
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: sepp
Source-Version: 4.5.5+dfsg-2
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sepp, 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 sepp 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, 05 Oct 2025 00:06:05 +0200
Source: sepp
Architecture: source
Version: 4.5.5+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1116910
Changes:
sepp (4.5.5+dfsg-2) unstable; urgency=medium
.
* Raising Standards version to 4.7.2 (no change)
* Removing the nocheck annotation from the pplacer and hmmer B-D
(Closes: #1116910)
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