Your message dated Sun, 14 Sep 2025 09:55:46 +0200
with message-id <[email protected]>
and subject line Bug#1114722: Removed package(s) from unstable
has caused the Debian Bug report #1114722,
regarding symfit: FTBFS with NumPy 2.3
to be marked as done.
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--
1114722: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114722
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: symfit
Version: 0.5.6-3
Severity: important
User: [email protected]
Usertags: numpy2.3
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for NumPy 2.3, symfit failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
warn("IPython parent '{0}' is not a writable location,"
reading sources... [ 19%] examples/ex_ODEModel
reading sources... [ 22%] examples/ex_bivariate_likelihood
/usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent
'../..' is not a writable location, using a temp directory.
warn("IPython parent '{0}' is not a writable location,"
reading sources... [ 26%] examples/ex_fourier_series
reading sources... [ 30%] examples/ex_interactive_guesses_ODE
reading sources... [ 33%] examples/ex_interactive_guesses_nD
reading sources... [ 37%] examples/ex_interactive_guesses_vector_2D
reading sources... [ 41%] examples/ex_mexican_hat
/usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent
'../..' is not a writable location, using a temp directory.
warn("IPython parent '{0}' is not a writable location,"
reading sources... [ 44%] examples/ex_multidataset_likelihood
reading sources... [ 48%] examples/ex_ode_system
/usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent
'../..' is not a writable location, using a temp directory.
warn("IPython parent '{0}' is not a writable location,"
Notebook error!
Versions
========
* Platform: linux; (Linux-6.1.0-38-amd64-x86_64-with-glibc2.41)
* Python version: 3.13.7 (CPython)
* Sphinx version: 8.2.3
* Docutils version: 0.21.2
* Jinja2 version: 3.1.6
* Pygments version: 2.18.0
Last Messages
=============
reading sources... [ 41%]
examples/ex_mexican_hat
reading sources... [ 44%]
examples/ex_multidataset_likelihood
reading sources... [ 48%]
examples/ex_ode_system
Loaded Extensions
=================
* sphinx.ext.mathjax (8.2.3)
* alabaster (0.7.16)
* sphinx.ext.autodoc.preserve_defaults (8.2.3)
* sphinx.ext.autodoc.type_comment (8.2.3)
* sphinx.ext.autodoc.typehints (8.2.3)
* sphinx.ext.autodoc (8.2.3)
* sphinx.ext.viewcode (8.2.3)
* sphinx.ext.intersphinx (8.2.3)
* nbsphinx (0.9.5)
Traceback
=========
File "/usr/lib/python3/dist-packages/nbsphinx/__init__.py", line 641, in
parse
raise NotebookError('\n'.join(lines))
nbsphinx.NotebookError: CellExecutionError in examples/ex_ode_system.ipynb:
------------------
k1_f.min, k1_f.max = 0, 1
k1_r.min, k1_r.max = 0, 1
k2_f.min, k2_f.max = 0, 1
k2_r.min, k2_r.max = 0, 1
fit = Fit(model, t=tdata, MM=data[MM], F=data[F],
FMMF=None, FMM=None,
sigma_F=sigma_data, sigma_MM=sigma_data)
fit_result = fit.execute()
print(fit_result)
------------------
[0;31m---------------------------------------------------------------------------[0m
[0;31mAttributeError[0m Traceback (most recent
call last)
Cell [0;32mIn[4], line 9[0m
[1;32m 4[0m k2_r[38;5;241m.[39mmin, k2_r[38;5;241m.[39mmax
[38;5;241m=[39m [38;5;241m0[39m, [38;5;241m1[39m
[1;32m 6[0m fit [38;5;241m=[39m Fit(model,
t[38;5;241m=[39mtdata, MM[38;5;241m=[39mdata[MM], F[38;5;241m=[39mdata[F],
[1;32m 7[0m
FMMF[38;5;241m=[39m[38;5;28;01mNone[39;00m,
FMM[38;5;241m=[39m[38;5;28;01mNone[39;00m,
[1;32m 8[0m sigma_F[38;5;241m=[39msigma_data,
sigma_MM[38;5;241m=[39msigma_data)
[0;32m----> 9[0m fit_result [38;5;241m=[39m
[43mfit[49m[38;5;241;43m.[39;49m[43mexecute[49m[43m([49m[43m)[49m
[1;32m 10[0m [38;5;28mprint[39m(fit_result)
File
[0;32m/build/reproducible-path/symfit-0.5.6/symfit/core/fit.py:574[0m, in
[0;36mFit.execute[0;34m(self, **minimize_options)[0m
[1;32m 566[0m [38;5;250m[39m[38;5;124;03m"""[39;00m
[1;32m 567[0m [38;5;124;03mExecute the fit.[39;00m
[1;32m 568[0m
[0;32m (...)[0m
[1;32m 571[0m [38;5;124;03m:return: FitResults instance[39;00m
[1;32m 572[0m [38;5;124;03m"""[39;00m
[1;32m 573[0m minimizer_ans [38;5;241m=[39m
[38;5;28mself[39m[38;5;241m.[39mminimizer[38;5;241m.[39mexecute([38;5;241m*[39m[38;5;241m*[39mminimize_options)
[0;32m--> 574[0m minimizer_ans[38;5;241m.[39mcovariance_matrix
[38;5;241m=[39m
[38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43mcovariance_matrix[49m[43m([49m
[1;32m 575[0m [43m
[49m[38;5;28;43mdict[39;49m[43m([49m[38;5;28;43mzip[39;49m[43m([49m[38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43mmodel[49m[38;5;241;43m.[39;49m[43mparams[49m[43m,[49m[43m
[49m[43mminimizer_ans[49m[38;5;241;43m.[39;49m[43m_popt[49m[43m)[49m[43m)[49m
[1;32m 576[0m [43m[49m[43m)[49m
[1;32m 577[0m [38;5;66;03m# Overwrite the DummyModel with the current
model[39;00m
[1;32m 578[0m minimizer_ans[38;5;241m.[39mmodel [38;5;241m=[39m
[38;5;28mself[39m[38;5;241m.[39mmodel
File
[0;32m/build/reproducible-path/symfit-0.5.6/symfit/core/fit.py:301[0m, in
[0;36mHasCovarianceMatrix.covariance_matrix[0;34m(self, best_fit_params)[0m
[1;32m 292[0m [38;5;250m [39m[38;5;124;03m"""[39;00m
[1;32m 293[0m [38;5;124;03m Class which impersonates ``base``,
but which returns zeros[39;00m
[1;32m 294[0m [38;5;124;03m for the models Hessian. This will
effectively result in the[39;00m
[1;32m 295[0m [38;5;124;03m calculation of the approximate
Hessian by calculating[39;00m
[1;32m 296[0m [38;5;124;03m outer(J.T, J) when calling
``base.eval_hessian``.[39;00m
[1;32m 297[0m [38;5;124;03m """[39;00m
[1;32m 299[0m objective [38;5;241m=[39m
HessApproximation([38;5;28mself[39m[38;5;241m.[39mobjective[38;5;241m.[39mmodel,
[1;32m 300[0m
[38;5;28mself[39m[38;5;241m.[39mobjective[38;5;241m.[39mdata)
[0;32m--> 301[0m cov_matrix [38;5;241m=[39m
[38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_covariance_matrix[49m[43m([49m[43mbest_fit_params[49m[43m,[49m
[1;32m 302[0m [43m
[49m[43mobjective[49m[38;5;241;43m=[39;49m[43mobjective[49m[43m)[49m
[1;32m 304[0m [38;5;28;01mreturn[39;00m cov_matrix
File
[0;32m/build/reproducible-path/symfit-0.5.6/symfit/core/fit.py:256[0m, in
[0;36mHasCovarianceMatrix._covariance_matrix[0;34m(self, best_fit_params,
objective)[0m
[1;32m 254[0m rss [38;5;241m=[39m [38;5;241m2[39m
[38;5;241m*[39m
objective([38;5;241m*[39m[38;5;241m*[39mkey2str(best_fit_params))
[1;32m 255[0m [38;5;66;03m# Degrees of freedom[39;00m
[0;32m--> 256[0m raw_dof [38;5;241m=[39m
np[38;5;241m.[39msum([[43mnp[49m[38;5;241;43m.[39;49m[43mproduct[49m(shape)
[38;5;28;01mfor[39;00m shape [38;5;129;01min[39;00m
[38;5;28mself[39m[38;5;241m.[39mdata_shapes[[38;5;241m1[39m]])
[1;32m 257[0m dof [38;5;241m=[39m raw_dof [38;5;241m-[39m
[38;5;28mlen[39m([38;5;28mself[39m[38;5;241m.[39mmodel[38;5;241m.[39mparams)
[1;32m 258[0m [38;5;28;01mif[39;00m
[38;5;28mself[39m[38;5;241m.[39mabsolute_sigma:
[1;32m 259[0m [38;5;66;03m# When interpreting as measurement
error, we do not rescale.[39;00m
File [0;32m/usr/lib/python3/dist-packages/numpy/__init__.py:795[0m, in
[0;36m__getattr__[0;34m(attr)[0m
[1;32m 792[0m [38;5;28;01mimport[39;00m
[38;5;21;01mnumpy[39;00m[38;5;21;01m.[39;00m[38;5;21;01mchar[39;00m
[38;5;28;01mas[39;00m [38;5;21;01mchar[39;00m
[1;32m 793[0m [38;5;28;01mreturn[39;00m
char[38;5;241m.[39mchararray
[0;32m--> 795[0m [38;5;28;01mraise[39;00m
[38;5;167;01mAttributeError[39;00m([38;5;124mf[39m[38;5;124m"[39m[38;5;124mmodule
[39m[38;5;132;01m{[39;00m[38;5;18m__name__[39m[38;5;132;01m!r}[39;00m[38;5;124m
has no attribute
[39m[38;5;132;01m{[39;00mattr[38;5;132;01m!r}[39;00m[38;5;124m"[39m)
[0;31mAttributeError[0m: module 'numpy' has no attribute 'product'
You can ignore this error by setting the following in conf.py:
nbsphinx_allow_errors = True
The full traceback has been saved in:
/tmp/sphinx-err-hds5bofy.log
To report this error to the developers, please open an issue at
<https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message
can be provided next time.
make[1]: *** [debian/rules:8: override_dh_auto_build] Error 2
make[1]: Leaving directory '/build/reproducible-path/symfit-0.5.6'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T12:14:15Z
-------------------------------------------------------------------------------
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/2457210/
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/164154/
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 ---
Version: 0.5.6-3+rm
Dear submitter,
as the package symfit has just been removed from the Debian archive
unstable we hereby close the associated bug reports. We are sorry
that we couldn't deal with your issue properly.
For details on the removal, please see https://bugs.debian.org/1113919
The version of this package that was in Debian prior to this removal
can still be found using https://snapshot.debian.org/.
Please note that the changes have been done on the master archive and
will not propagate to any mirrors until the next dinstall run at the
earliest.
This message was generated automatically; if you believe that there is
a problem with it please contact the archive administrators by mailing
[email protected].
Debian distribution maintenance software
pp.
Paul Tagliamonte (the ftpmaster behind the curtain)
--- End Message ---
