Your message dated Tue, 29 Sep 2026 07:51:04 +0000
with message-id <[email protected]>
and subject line Bug#1146588: fixed in rdkit 202603.4-3
has caused the Debian Bug report #1146588,
regarding rdkit: FTBFS against python 3.15rc1
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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--
1146588: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1146588
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:rdkit
Version: 202603.4-1
User: [email protected]
Usertags: python3.15
Tags: patch, ftbfs, forky, sid
Severity: serious
Hi!
While rebuilding the python related packages against the Python 3.15rc1
version we found that rdkit fails to build from source not only for 3.15
but also for 3.14 [1].
Error: testDistGeomHelpers:
src/catch2/../catch2/internal/catch_output_redirect.hpp:40: void
Catch::OutputRedirect::activate(): Assertion !m_redirectActive &&
"redirect is already active"' failed.
This is because catch2 is not thread safe till release 3.12, but
currently we have 3.7 in Debian, so the tests that depend on thread
safety need workarounds.
It's likely that this only started happening now, due to the new gcc
version.
I applied the fix in the sandbox [2] to be able to build the packages
that depend on rdkit and it has built successfully, please consider
applying the patch to get rdkit to build successfully.
Happy hacking,
[1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4587746/
[2]: https://debusine.debian.net/debian/r-python-python3.15/
--
"Can you imagine what I would do if I could do all I can?" -- Sun Tzu
Saludos /\/\ /\ >< `/
Description: Avoid Catch2 assertions in multithreaded test helper
Catch2 assertion macros are not thread-safe (prior catch2 3.12) and cause
assertion failures in OutputRedirect when invoked concurrently across worker
threads.
Author: Maximiliano Curia <[email protected]>
Forwarded: no
--- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
+++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
@@ -943,17 +943,17 @@ void runblock(const std::vector<std::sha
.useLegacyImplementation = legacyETKDG};
std::vector<int> cids =
DGeomHelpers::EmbedMultipleConfs(*mol, 10, params);
- REQUIRE(cids.size() == 10);
+ TEST_ASSERT(cids.size() == 10);
std::unique_ptr<ForceFields::ForceField> field(
UFF::constructForceField(*mol, 100, cids[0]));
- REQUIRE(field);
+ TEST_ASSERT(field);
field->initialize();
double eng = field->calcEnergy();
if (!feq(eng, energies[i])) {
std::cerr << i << " iter " << j << " " << energies[i] << " != " << eng
<< std::endl;
}
- CHECK(feq(eng, energies[i]));
+ TEST_ASSERT(feq(eng, energies[i]));
}
}
}
Description: Avoid Catch2 assertions in substruct multithreaded test helper
Catch2 assertion macros are not thread-safe and cause assertion failures in
OutputRedirect when invoked concurrently across worker threads.
Author: Maximiliano Curia <[email protected]>
Forwarded: no
--- a/Code/GraphMol/Substruct/testSubstructMatch.cpp
+++ b/Code/GraphMol/Substruct/testSubstructMatch.cpp
@@ -541,7 +541,7 @@ void runblock(const std::vector<std::uni
MatchVectType matchV;
bool found = SubstructMatch(*mol, *query, matchV);
- CHECK(found == hits[i]);
+ TEST_ASSERT(found == hits[i]);
}
}
}
--- End Message ---
--- Begin Message ---
Source: rdkit
Source-Version: 202603.4-3
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
rdkit, 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 rdkit 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: Tue, 29 Sep 2026 03:34:28 -0400
Source: rdkit
Architecture: source
Version: 202603.4-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1146588 1148464
Changes:
rdkit (202603.4-3) unstable; urgency=medium
.
* Build for all supported Python versions (Closes: #1146588, #1148464).
Thanks Maximiliano Curia
* Cleanup debian/rules.
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