[Debichem-devel] Bug#1149284: openms: FTBFS with boost 1.92
Anton Gladky
gladk at debian.org
Tue Sep 29 06:31:51 BST 2026
Package: src:openms
Version: 2.6.0+cleaned1-6
Severity: important
Tags: sid forky ftbfs
User: debian-devel at lists.debian.org
Usertags: boost1.92
Dear Maintainer,
Boost 1.92 will most likely be the default boost version in the
upcoming Debian 14 (forky) release.
openms FTBFS with boost 1.92. Note that the FTBFS may not necessarily be
connected to boost - please check the build log for the actual cause.
boost-defaults pointing to 1.92 is available in experimental, so you can
rebuild your package against it to reproduce the failure and test the fix.
Note: This ticket severity will be increased to RC bug when
boost-defaults is switched to 1.92.
If your package depends on versioned boost packages (e.g. libboost1.90-dev),
please switch to the unversioned (default) ones (e.g. libboost-dev), so the
package follows future boost transitions automatically.
Here is the most probably relevant part of the failing build log:
==================== build log ====================
-- The C compiler identification is GNU 16.2.0
-- The CXX compiler identification is GNU 16.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning (dev) at CMakeLists.txt:73 (include):
Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run
"cmake --help-policy CMP0145" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /usr/share/cmake-4.3/Modules/Dart.cmake:47 (message):
Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run
"cmake --help-policy CMP0145" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:73 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Deprecation Warning at /usr/share/cmake-4.3/Modules/Dart.cmake:56 (cmake_policy):
The OLD behavior for policy CMP0145 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
Call Stack (most recent call first):
CMakeLists.txt:73 (include)
-- Building OpenMS 2.6.0
-- [CMake cannot track Git commits and branching, since Git or the .git folder was not found. ('-D GIT_TRACKING=On')]
-- OpenMP support requested: ON
-- Found OpenMP_C: -fopenmp (found version "5.2")
-- Found OpenMP_CXX: -fopenmp (found version "5.2")
-- Found OpenMP: TRUE (found version "5.2")
-- Architecture: 64 bit
-- Performing Test WITH_FPIC
-- Performing Test WITH_FPIC - Success
-- Compiler checks for conversion: OFF
-- Collection of usage statistics and update notifications enabled.
-- If you don't want this information to be transmitted to our update sever, you can:
-- - Switch the build variable ENABLE_UPDATE_CHECK to OFF to remove the functionality at build time.
-- - Set the environment variable OPENMS_DISABLE_UPDATE_CHECK to disable the functionality at runtime.
CMake Deprecation Warning at src/CMakeLists.txt:35 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at src/openswathalgo/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Warning (dev) at cmake/build_system_macros.cmake:90 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
Call Stack (most recent call first):
src/openswathalgo/CMakeLists.txt:41 (find_boost)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/include (found suitable version "1.92.0", minimum required is "1.48.0")
CMake Deprecation Warning at src/openswathalgo/thirdparty/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at src/openswathalgo/thirdparty/MIToolbox/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Adding library OpenSwathAlgo
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
CMake Warning (dev) at cmake/install_macros.cmake:72 (install):
Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run
"cmake --help-policy CMP0177" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Call Stack (most recent call first):
cmake/add_library_macros.cmake:200 (install_headers)
src/openswathalgo/CMakeLists.txt:58 (openms_add_library)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Adding library OpenSwathAlgo - SUCCESS
CMake Deprecation Warning at src/openms/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at src/openms/thirdparty/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at src/openms/thirdparty/eol-bspline/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at src/openms/thirdparty/evergreen/src/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at src/openms/thirdparty/IsoSpec/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at src/openms/thirdparty/json/CMakeLists.txt:36 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Found XercesC: /usr/lib/x86_64-linux-gnu/libxerces-c.so (found version "3.2.4")
CMake Warning (dev) at cmake/build_system_macros.cmake:90 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
Call Stack (most recent call first):
src/openms/cmake_findExternalLibs.cmake:60 (find_boost)
src/openms/CMakeLists.txt:70 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning at /usr/share/cmake-4.3/Modules/FindBoost.cmake:1459 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-4.3/Modules/FindBoost.cmake:1584 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-4.3/Modules/FindBoost.cmake:2197 (_Boost_MISSING_DEPENDENCIES)
cmake/build_system_macros.cmake:90 (find_package)
src/openms/cmake_findExternalLibs.cmake:60 (find_boost)
src/openms/CMakeLists.txt:70 (include)
CMake Warning at /usr/share/cmake-4.3/Modules/FindBoost.cmake:1459 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-4.3/Modules/FindBoost.cmake:1584 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-4.3/Modules/FindBoost.cmake:2197 (_Boost_MISSING_DEPENDENCIES)
cmake/build_system_macros.cmake:90 (find_package)
src/openms/cmake_findExternalLibs.cmake:60 (find_boost)
src/openms/CMakeLists.txt:70 (include)
CMake Warning at /usr/share/cmake-4.3/Modules/FindBoost.cmake:1459 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-4.3/Modules/FindBoost.cmake:1584 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-4.3/Modules/FindBoost.cmake:2197 (_Boost_MISSING_DEPENDENCIES)
cmake/build_system_macros.cmake:90 (find_package)
src/openms/cmake_findExternalLibs.cmake:60 (find_boost)
src/openms/CMakeLists.txt:70 (include)
CMake Warning at /usr/share/cmake-4.3/Modules/FindBoost.cmake:1459 (message):
New Boost version may have incorrect or missing dependencies and imported
targets
Call Stack (most recent call first):
/usr/share/cmake-4.3/Modules/FindBoost.cmake:1584 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-4.3/Modules/FindBoost.cmake:2197 (_Boost_MISSING_DEPENDENCIES)
cmake/build_system_macros.cmake:90 (find_package)
src/openms/cmake_findExternalLibs.cmake:60 (find_boost)
src/openms/CMakeLists.txt:70 (include)
-- Found Boost: /usr/include (found suitable version "1.92.0", minimum required is "1.48.0") found components: iostreams date_time math_c99 regex
-- Found Boost version 1.92.0
-- Found SEQAN: /build/reproducible-path/openms-2.6.0+cleaned1/debian (found suitable version "1.4.2", minimum required is "1.4.0")
-- Found LIBSVM: /usr/lib/x86_64-linux-gnu/libsvm.so (found suitable version "3.2.4", minimum required is "2.91")
-- Found COIN: /usr/include
-- Found GLPK: /usr/lib/x86_64-linux-gnu/libglpk.so
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8")
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Eigen3 version .. found in /usr/include/eigen3, but at least version 3.3.4 is required
CMake Error at /usr/share/cmake-4.3/Modules/FindPackageHandleStandardArgs.cmake:290 (message):
Could NOT find Eigen3 (missing: EIGEN3_VERSION_OK) (Required is at least
version "3.3.4")
Call Stack (most recent call first):
/usr/share/cmake-4.3/Modules/FindPackageHandleStandardArgs.cmake:654 (_FPHSA_FAILURE_MESSAGE)
cmake/modules/FindEigen3.cmake:76 (find_package_handle_standard_args)
src/openms/cmake_findExternalLibs.cmake:109 (find_package)
src/openms/CMakeLists.txt:70 (include)
-- Configuring incomplete, errors occurred!
cd obj-x86_64-linux-gnu && tail -v -n \+0 CMakeCache.txt
==> CMakeCache.txt <==
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dh_auto_configure: error: cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/x86_64-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DDEBIAN_BUILD=ON -DHAS_XSERVER=OFF -DCMAKE_FIND_LIBRARY_SUFFIXES=.so -DCMAKE_SKIP_RPATH=ON -DCMAKE_INSTALL_PREFIX=/usr -DOPENMS_CONTRIB_LIBS=/usr/lib\;/usr/lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE
=release -DBOOST_USE_STATIC=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_TOPP_TESTING=OFF -DENABLE_CLASS_TESTING=OFF -DENABLE_PIPELINE_TESTING=OFF -DENABLE_TUTORIALS=ON -DSEQAN_INCLUDE_DIR=/build/reproducible-path/openms-2.6.0\+cleaned1/debian -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. returned exit code 1
make[1]: *** [debian/rules:62: override_dh_auto_configure] Error 2
make[1]: Leaving directory '/build/reproducible-path/openms-2.6.0+cleaned1'
make: *** [debian/rules:43: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
==================== end of build log =============
Thanks,
Anton Gladky
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