[Debichem-devel] Bug#1117731: rdkit FTBFS on riscv64: The following tests FAILED: 149 - distGeomHelpersCatch (Timeout)

[Adrian Bunk]

Source: rdkit
Version: 202503.6-1
Severity: serious
Tags: ftbfs patch
X-Debbugs-Cc: debian-riscv at lists.debian.org
User: debian-riscv at lists.debian.org
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.
-------------- next part --------------
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