Your message dated Fri, 28 Nov 2025 12:05:07 +0000
with message-id <[email protected]>
and subject line Bug#1114707: fixed in prody 2.6.1+dfsg-1
has caused the Debian Bug report #1114707,
regarding prody: 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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--
1114707: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114707
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: prody
Version: 2.4.1+dfsg-2
Severity: important
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: prody
Source-Version: 2.6.1+dfsg-1
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
prody, 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.
Andrius Merkys <[email protected]> (supplier of updated prody 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: Fri, 28 Nov 2025 06:44:43 -0500
Source: prody
Architecture: source
Version: 2.6.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1058454 1071807 1114707
Changes:
prody (2.6.1+dfsg-1) unstable; urgency=medium
.
* New upstream version 2.6.1+dfsg (Closes: #1058454, #1071807, #1114707)
* Adjust debian/watch to mangle numbered release candidates.
* Exclude prody/proteins/hpbmodule/hpb_Python* with prebuilt shared
libraries.
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Files:
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prody_2.6.1+dfsg-1.debian.tar.xz
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