Your message dated Tue, 21 Oct 2025 10:34:47 +0000
with message-id <[email protected]>
and subject line Bug#1117731: fixed in rdkit 202503.6-3
has caused the Debian Bug report #1117731,
regarding rdkit FTBFS on riscv64: The following tests FAILED: 149 -
distGeomHelpersCatch (Timeout)
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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--
1117731: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1117731
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: rdkit
Version: 202503.6-1
Severity: serious
Tags: ftbfs patch
X-Debbugs-Cc: [email protected]
User: [email protected]
Usertags: riscv64
https://buildd.debian.org/status/logs.php?pkg=rdkit&arch=riscv64
...
The following tests FAILED:
149 - distGeomHelpersCatch (Timeout)
Errors while running CTest
make[2]: *** [Makefile:94: test] Error 8
The attached patch raises the timeout from 25 minutes to 2 hours,
and also reverts previous test disabling due to timeouts.
Build dependency on the soon in unstable CMake 4 for --timeout=7200,
I gave up trying to find a way of passing --timeout 7200 to ctest.
diff -Nru rdkit-202503.6/debian/control rdkit-202503.6/debian/control
--- rdkit-202503.6/debian/control 2025-10-07 10:44:06.000000000 +0300
+++ rdkit-202503.6/debian/control 2025-10-07 10:44:06.000000000 +0300
@@ -9,7 +9,7 @@
architecture-is-little-endian,
bison,
catch2,
- cmake,
+ cmake (>= 4.1.2-1),
debhelper-compat (= 13),
dh-python,
doxygen,
diff -Nru rdkit-202503.6/debian/control.in rdkit-202503.6/debian/control.in
--- rdkit-202503.6/debian/control.in 2025-10-07 10:44:06.000000000 +0300
+++ rdkit-202503.6/debian/control.in 2025-10-07 10:44:06.000000000 +0300
@@ -9,7 +9,7 @@
architecture-is-little-endian,
bison,
catch2,
- cmake,
+ cmake (>= 4.1.2-1),
debhelper-compat (= 13),
dh-python,
doxygen,
diff -Nru rdkit-202503.6/debian/patches/disable_riscv64_timeout_tests.patch
rdkit-202503.6/debian/patches/disable_riscv64_timeout_tests.patch
--- rdkit-202503.6/debian/patches/disable_riscv64_timeout_tests.patch
2025-10-07 10:44:06.000000000 +0300
+++ rdkit-202503.6/debian/patches/disable_riscv64_timeout_tests.patch
1970-01-01 02:00:00.000000000 +0200
@@ -1,37 +0,0 @@
---- a/Code/GraphMol/SynthonSpaceSearch/CMakeLists.txt
-+++ b/Code/GraphMol/SynthonSpaceSearch/CMakeLists.txt
-@@ -13,8 +13,9 @@
-
- rdkit_catch_test(testSynthonSpaceSubstructureSearch
substructure_search_catch_tests.cpp
- LINK_LIBRARIES SubstructMatch SubstructLibrary SynthonSpaceSearch)
--rdkit_catch_test(testSynthonSpaceFingerprintSearch
fingerprint_search_catch_tests.cpp
-- LINK_LIBRARIES SubstructMatch SubstructLibrary SynthonSpaceSearch)
-+# Disabled by Debian due to timeouts on riscv64
-+# rdkit_catch_test(testSynthonSpaceFingerprintSearch
fingerprint_search_catch_tests.cpp
-+# LINK_LIBRARIES SubstructMatch SubstructLibrary SynthonSpaceSearch)
- rdkit_catch_test(testSynthonSpaceRascalSearch rascal_search_catch_tests.cpp
- LINK_LIBRARIES SubstructMatch SubstructLibrary SynthonSpaceSearch)
-
---- a/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeLists.txt
-+++ b/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeLists.txt
-@@ -5,4 +5,5 @@
- DEST Chem
- LINK_LIBRARIES SynthonSpaceSearch)
-
--add_pytest(pySynthonSpaceSearch
${CMAKE_CURRENT_SOURCE_DIR}/testSynthonSpaceSearch.py)
-+# Disabled by Debian due to timeouts on riscv64
-+# add_pytest(pySynthonSpaceSearch
${CMAKE_CURRENT_SOURCE_DIR}/testSynthonSpaceSearch.py)
---- a/Code/GraphMol/CMakeLists.txt
-+++ b/Code/GraphMol/CMakeLists.txt
-@@ -129,8 +129,9 @@
- add_subdirectory(MolInteractionFields)
-
-
--rdkit_test(graphmolTest1 test1.cpp LINK_LIBRARIES FileParsers SmilesParse
GraphMol
-- SubstructMatch ForceFieldHelpers ForceField)
-+# Disabled by Debian due to timeouts on riscv64
-+# rdkit_test(graphmolTest1 test1.cpp LINK_LIBRARIES FileParsers SmilesParse
GraphMol
-+# SubstructMatch ForceFieldHelpers ForceField)
-
- rdkit_test(graphmolcpTest cptest.cpp LINK_LIBRARIES SmilesParse GraphMol)
-
diff -Nru rdkit-202503.6/debian/patches/series
rdkit-202503.6/debian/patches/series
--- rdkit-202503.6/debian/patches/series 2025-10-07 10:44:06.000000000
+0300
+++ rdkit-202503.6/debian/patches/series 2025-10-07 10:44:06.000000000
+0300
@@ -9,5 +9,4 @@
fix_inchi_linking.patch
disable_inchi_test.patch
disable_python_test.patch
-disable_riscv64_timeout_tests.patch
better_enums.patch
diff -Nru rdkit-202503.6/debian/rules rdkit-202503.6/debian/rules
--- rdkit-202503.6/debian/rules 2025-10-07 10:44:06.000000000 +0300
+++ rdkit-202503.6/debian/rules 2025-10-07 10:44:06.000000000 +0300
@@ -40,7 +40,8 @@
-DRDK_BUILD_PGSQL=ON \
-DRDK_PGSQL_STATIC=OFF \
-DPostgreSQL_CONFIG=/usr/bin/pg_config \
-
-DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/18/server"
+
-DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/18/server" \
+ -DCMAKE_CTEST_ARGUMENTS=--timeout=7200
include /usr/share/postgresql-common/pgxs_debian_control.mk
--- End Message ---
--- Begin Message ---
Source: rdkit
Source-Version: 202503.6-3
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, 21 Oct 2025 06:00:34 -0400
Source: rdkit
Architecture: source
Version: 202503.6-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1117731
Changes:
rdkit (202503.6-3) unstable; urgency=medium
.
* Increase ctest timeout to 7200 (Closes: #1117731). Thanks Adrian Bunk.
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