Your message dated Sat, 11 Oct 2025 13:19:26 +0000
with message-id <[email protected]>
and subject line Bug#1114720: fixed in scikit-fmm 2025.06.23-1
has caused the Debian Bug report #1114720,
regarding scikit-fmm: FTBFS with NumPy 2.3
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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--
1114720: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114720
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: scikit-fmm
Version: 2024.09.16-1
Severity: important
User: [email protected]
Usertags: numpy2.3
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for NumPy 2.3, scikit-fmm failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
Found pkg-config: NO
Run-time dependency python found: YES 3.13
Build targets in project: 2
skfmm 2024.09.16
User defined options
Native files :
/build/reproducible-path/scikit-fmm-2024.09.16/.mesonpy-3jw2p2vt/meson-python-native-file.ini
b_ndebug : if-release
b_vscrt : md
buildtype : release
libdir : lib/x86_64-linux-gnu
localstatedir: /var
prefix : /usr
sysconfdir : /etc
wrap_mode : nodownload
Found ninja-1.12.1 at /usr/bin/ninja
meson-python: warning: Extra keys present in "project": 'url'
+ /usr/bin/ninja --verbose
[1/10] c++ -Icfmm.cpython-313-x86_64-linux-gnu.so.p -I. -I.. -I../skfmm
-I../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -fvisibility=hidden -fvisibility-inlines-hidden
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/scikit-fmm-2024.09.16=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-MD -MQ cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_fmm.cpp.o -MF
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_fmm.cpp.o.d -o
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_fmm.cpp.o -c ../skfmm/fmm.cpp
FAILED: cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_fmm.cpp.o
c++ -Icfmm.cpython-313-x86_64-linux-gnu.so.p -I. -I.. -I../skfmm
-I../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -fvisibility=hidden -fvisibility-inlines-hidden
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/scikit-fmm-2024.09.16=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-MD -MQ cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_fmm.cpp.o -MF
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_fmm.cpp.o.d -o
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_fmm.cpp.o -c ../skfmm/fmm.cpp
In file included from
../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
from
../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h:237,
from ../skfmm/fmm.cpp:6:
../skfmm/fmm.cpp: In function ‘PyObject* distance_method(PyObject*, PyObject*)’:
../skfmm/fmm.cpp:116:46: error: ‘NPY_IN_ARRAY’ was not declared in this scope
116 | 10, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:96:28:
note: in definition of macro ‘PyArray_FROMANY’
96 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
[2/10] c++ -Icfmm.cpython-313-x86_64-linux-gnu.so.p -I. -I.. -I../skfmm
-I../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -fvisibility=hidden -fvisibility-inlines-hidden
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/scikit-fmm-2024.09.16=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-MD -MQ cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_heap.cpp.o -MF
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_heap.cpp.o.d -o
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_heap.cpp.o -c ../skfmm/heap.cpp
[3/10] c++ -Icfmm.cpython-313-x86_64-linux-gnu.so.p -I. -I.. -I../skfmm
-I../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -fvisibility=hidden -fvisibility-inlines-hidden
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/scikit-fmm-2024.09.16=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-MD -MQ cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_travel_time_marcher.cpp.o
-MF cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_travel_time_marcher.cpp.o.d -o
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_travel_time_marcher.cpp.o -c
../skfmm/travel_time_marcher.cpp
../skfmm/travel_time_marcher.cpp: In member function ‘virtual double
travelTimeMarcher::updatePointOrderTwo(int, std::set<int>)’:
../skfmm/travel_time_marcher.cpp:87:25: warning: comparison of integer
expressions of different signedness: ‘std::set<int>::size_type’ {aka ‘long
unsigned int’} and ‘int’ [-Wsign-compare]
87 | if(avoid_dim.size() == dim_) return
std::numeric_limits<double>::infinity(); //end of the recursion, use inf so
that it is discarded selecting the minimum
| ~~~~~~~~~~~~~~~~~^~~~~~~
[4/10] c++ -Icfmm.cpython-313-x86_64-linux-gnu.so.p -I. -I.. -I../skfmm
-I../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -fvisibility=hidden -fvisibility-inlines-hidden
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/scikit-fmm-2024.09.16=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-MD -MQ
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_extension_velocity_marcher.cpp.o
-MF
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_extension_velocity_marcher.cpp.o.d
-o
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_extension_velocity_marcher.cpp.o
-c ../skfmm/extension_velocity_marcher.cpp
[5/10] c++ -Icfmm.cpython-313-x86_64-linux-gnu.so.p -I. -I.. -I../skfmm
-I../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -fvisibility=hidden -fvisibility-inlines-hidden
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/scikit-fmm-2024.09.16=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-MD -MQ cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_base_marcher.cpp.o -MF
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_base_marcher.cpp.o.d -o
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_base_marcher.cpp.o -c
../skfmm/base_marcher.cpp
In file included from ../skfmm/base_marcher.cpp:6:
In member function ‘int baseMarcher::_getN(int, int, int, int)’,
inlined from ‘void baseMarcher::solve()’ at
../skfmm/base_marcher.cpp:201:33:
../skfmm/base_marcher.h:77:25: warning: ‘coord’ may be used uninitialized
[-Wmaybe-uninitialized]
77 | int newc = coord[dim]+dir;
| ~~~~~~~~~^
../skfmm/base_marcher.h: In member function ‘void baseMarcher::solve()’:
../skfmm/base_marcher.h:75:9: note: ‘coord’ declared here
75 | int coord[MaximumDimension];
| ^~~~~
[6/10] c++ -Icfmm.cpython-313-x86_64-linux-gnu.so.p -I. -I.. -I../skfmm
-I../../../../usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -fvisibility=hidden -fvisibility-inlines-hidden
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/scikit-fmm-2024.09.16=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-MD -MQ cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_distance_marcher.cpp.o -MF
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_distance_marcher.cpp.o.d -o
cfmm.cpython-313-x86_64-linux-gnu.so.p/skfmm_distance_marcher.cpp.o -c
../skfmm/distance_marcher.cpp
ninja: build stopped: subcommand failed.
ERROR Backend subprocess exited when trying to invoke build_wheel
E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1:
python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir
/build/reproducible-path/scikit-fmm-2024.09.16/.pybuild/cpython3_3.13_scikit-fmm
--config-setting compile-args=--verbose --config-setting
setup-args=--wrap-mode=nodownload --config-setting setup-args=--prefix=/usr
--config-setting setup-args=--sysconfdir=/etc --config-setting
setup-args=--localstatedir=/var --config-setting
setup-args=--libdir=lib/x86_64-linux-gnu
dh_auto_build: error: pybuild --build -i python{version} -p 3.13 returned exit
code 13
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T11:12:04Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/debian/developers-roehling.numpy/artifact/2456787/
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/debian/developers-roehling.numpy/work-request/164095/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Cheers
Timo
--- End Message ---
--- Begin Message ---
Source: scikit-fmm
Source-Version: 2025.06.23-1
Done: Bdale Garbee <[email protected]>
We believe that the bug you reported is fixed in the latest version of
scikit-fmm, 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.
Bdale Garbee <[email protected]> (supplier of updated scikit-fmm 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: Sat, 11 Oct 2025 06:52:11 -0600
Source: scikit-fmm
Architecture: source
Version: 2025.06.23-1
Distribution: unstable
Urgency: medium
Maintainer: Bdale Garbee <[email protected]>
Changed-By: Bdale Garbee <[email protected]>
Closes: 1114720
Changes:
scikit-fmm (2025.06.23-1) unstable; urgency=medium
.
* new upstream version, fix for deprecated NumPy API and Python 3.11,
closes: #1114720
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