[Debichem-devel] Bug#1114707: prody: FTBFS with NumPy 2.3

roehling at debian.org roehling at debian.org
Mon Sep 8 20:44:24 BST 2025 

Source: prody
Version: 2.4.1+dfsg-2
Severity: important
User: debian-python at lists.debian.org
Usertags: numpy2.3
Tags: ftbfs, forky, sid

Dear maintainer,

During a test rebuild for NumPy 2.3, prody failed to rebuild.

Log Summary:
-------------------------------------------------------------------------------
[...]
copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb3hsy.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb3mht.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/gnm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pca2k39_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pca2k39_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/commute1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/exanm2nwl_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/anm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/gnm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot_di.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/hit1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/anm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/exanm2nwl_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/mmcif_6zu5.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/mmcif_6yfy.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pca2k39_cov.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/anm1ubi_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/rtb2gb1_project.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/exanm2nwl_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/dcd2k39_truncated.dcd -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/xmlSTI.xml -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.slx -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.sth -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
running build_ext
building 'prody.dynamics.rtbtools' extension
creating build/temp.linux-x86_64-cpython-313/prody/dynamics
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c prody/dynamics/rtbtools.c -o build/temp.linux-x86_64-cpython-313/prody/dynamics/rtbtools.o
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_common.h:380,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:4,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from prody/dynamics/rtbtools.c:9:
prody/dynamics/rtbtools.c: In function ‘dblock_projections2’:
prody/dynamics/rtbtools.c:422:17: error: expected identifier or ‘(’ before ‘__extension__’
  422 |   double **X, **I, **IC, *CM, *W, **A, **ISQT;
      |                 ^
prody/dynamics/rtbtools.c:431:3: error: ‘CM’ undeclared (first use in this function)
  431 |   CM = dvector(1, 3);
      |   ^~
prody/dynamics/rtbtools.c:431:3: note: each undeclared identifier is reported only once for each function it appears in
prody/dynamics/rtbtools.c:432:5: error: lvalue required as left operand of assignment
  432 |   I = dmatrix(1, 3, 1, 3);
      |     ^
prody/dynamics/rtbtools.c:433:3: error: ‘IC’ undeclared (first use in this function); did you mean ‘I’?
  433 |   IC = dmatrix(1, 3, 1, 3);
      |   ^~
      |   I
prody/dynamics/rtbtools.c:434:3: error: ‘W’ undeclared (first use in this function)
  434 |   W = dvector(1, 3);
      |   ^
prody/dynamics/rtbtools.c:435:3: error: ‘A’ undeclared (first use in this function)
  435 |   A = dmatrix(1, 3, 1, 3);
      |   ^
prody/dynamics/rtbtools.c:436:3: error: ‘ISQT’ undeclared (first use in this function)
  436 |   ISQT = dmatrix(1, 3, 1, 3);
      |   ^~~~
prody/dynamics/rtbtools.c:445:28: error: subscripted value is neither array nor pointer nor vector
  445 |       for(i=1; i<=3; i++) I[i][j] = 0.0;
      |                            ^
prody/dynamics/rtbtools.c:481:10: error: subscripted value is neither array nor pointer nor vector
  481 |         I[i][i] += (dd - X[k][i] * X[k][i]);
      |          ^
prody/dynamics/rtbtools.c:484:12: error: subscripted value is neither array nor pointer nor vector
  484 |           I[i][j] -= X[k][i]*X[k][j];
      |            ^
prody/dynamics/rtbtools.c:485:12: error: subscripted value is neither array nor pointer nor vector
  485 |           I[j][i] = I[i][j];
      |            ^
prody/dynamics/rtbtools.c:485:22: error: subscripted value is neither array nor pointer nor vector
  485 |           I[j][i] = I[i][j];
      |                      ^
prody/dynamics/rtbtools.c:493:25: error: subscripted value is neither array nor pointer nor vector
  493 |               IC[i][j]=I[i][j];
      |                         ^
prody/dynamics/rtbtools.c:548:16: error: incompatible type for argument 1 of ‘free_dmatrix’
  548 |   free_dmatrix(I, 1, 3, 1, 3);
      |                ^
      |                |
      |                complex float
prody/dynamics/rtbtools.c:72:28: note: expected ‘double **’ but argument is of type ‘complex float’
   72 | void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch);
      |                   ~~~~~~~~~^
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build 
dh_auto_build: error: pybuild --build -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T05:26:33Z

-------------------------------------------------------------------------------

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/2453550/

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/163650/

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

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