[Debichem-devel] Bug#1113360: openms: FTBFS with CMake 4

roehling at debian.org roehling at debian.org
Mon Sep 1 00:01:53 BST 2025 

Source: openms
Version: 2.6.0+cleaned1-4
Severity: serious
User: cmake at packages.debian.org
Usertags: cmake-4
Tags: ftbfs, forky, sid

Dear maintainer,

During a test rebuild for CMake 4, openms failed to rebuild.

Log Summary:
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[...]
//ADVANCED property for variable: CMAKE_INSTALL_MANDIR
CMAKE_INSTALL_MANDIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_INSTALL_OLDINCLUDEDIR
CMAKE_INSTALL_OLDINCLUDEDIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_INSTALL_SBINDIR
CMAKE_INSTALL_SBINDIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_INSTALL_SHAREDSTATEDIR
CMAKE_INSTALL_SHAREDSTATEDIR-ADVANCED:INTERNAL=1
//Install .so files without execute permission.
CMAKE_INSTALL_SO_NO_EXE:INTERNAL=1
//ADVANCED property for variable: CMAKE_INSTALL_SYSCONFDIR
CMAKE_INSTALL_SYSCONFDIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_LINKER
CMAKE_LINKER-ADVANCED:INTERNAL=1
//Name of CMakeLists files to read
CMAKE_LIST_FILE_NAME:INTERNAL=CMakeLists.txt
//ADVANCED property for variable: CMAKE_MAKE_PROGRAM
CMAKE_MAKE_PROGRAM-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS
CMAKE_MODULE_LINKER_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_DEBUG
CMAKE_MODULE_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL
CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO
CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_NM
CMAKE_NM-ADVANCED:INTERNAL=1
//number of local generators
CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=3
//ADVANCED property for variable: CMAKE_OBJCOPY
CMAKE_OBJCOPY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_OBJDUMP
CMAKE_OBJDUMP-ADVANCED:INTERNAL=1
//Platform information initialized
CMAKE_PLATFORM_INFO_INITIALIZED:INTERNAL=1
//ADVANCED property for variable: CMAKE_RANLIB
CMAKE_RANLIB-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_READELF
CMAKE_READELF-ADVANCED:INTERNAL=1
//Path to CMake installation.
CMAKE_ROOT:INTERNAL=/usr/share/cmake-4.1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_DEBUG
CMAKE_SHARED_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL
CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_RELEASE
CMAKE_SHARED_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO
CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SKIP_INSTALL_RPATH
CMAKE_SKIP_INSTALL_RPATH-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SKIP_RPATH
CMAKE_SKIP_RPATH-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS
CMAKE_STATIC_LINKER_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_DEBUG
CMAKE_STATIC_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL
CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_RELEASE
CMAKE_STATIC_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO
CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STRIP
CMAKE_STRIP-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_TAPI
CMAKE_TAPI-ADVANCED:INTERNAL=1
//uname command
CMAKE_UNAME:INTERNAL=/usr/bin/uname
//ADVANCED property for variable: CMAKE_VERBOSE_MAKEFILE
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//ADVANCED property for variable: COMPRESSIONCOMMAND
COMPRESSIONCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: COVERAGE_COMMAND
COVERAGE_COMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: COVERAGE_EXTRA_FLAGS
COVERAGE_EXTRA_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CTEST_SUBMIT_RETRY_COUNT
CTEST_SUBMIT_RETRY_COUNT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CTEST_SUBMIT_RETRY_DELAY
CTEST_SUBMIT_RETRY_DELAY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_BUILD_ERROR_REPORT_LIMIT
DART_BUILD_ERROR_REPORT_LIMIT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_BUILD_WARNING_REPORT_LIMIT
DART_BUILD_WARNING_REPORT_LIMIT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_ROOT
DART_ROOT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_TESTING_TIMEOUT
DART_TESTING_TIMEOUT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_VERBOSE_BUILD
DART_VERBOSE_BUILD-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DELIVER_CONTINUOUS_EMAIL
DELIVER_CONTINUOUS_EMAIL-ADVANCED:INTERNAL=1
//Details about finding OpenMP
FIND_PACKAGE_MESSAGE_DETAILS_OpenMP:INTERNAL=[TRUE][TRUE][ ][v4.5()]
//Details about finding OpenMP_C
FIND_PACKAGE_MESSAGE_DETAILS_OpenMP_C:INTERNAL=[-fopenmp][/usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so][/usr/lib/aarch64-linux-gnu/libpthread.a][v4.5()]
//Details about finding OpenMP_CXX
FIND_PACKAGE_MESSAGE_DETAILS_OpenMP_CXX:INTERNAL=[-fopenmp][/usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so][/usr/lib/aarch64-linux-gnu/libpthread.a][v4.5()]
//ADVANCED property for variable: GIT_EXECUTABLE
GIT_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: GUNZIPCOMMAND
GUNZIPCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: JAVACOMMAND
JAVACOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: MAKECOMMAND
MAKECOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: MEMORYCHECK_COMMAND
MEMORYCHECK_COMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: MEMORYCHECK_SUPPRESSIONS_FILE
MEMORYCHECK_SUPPRESSIONS_FILE-ADVANCED:INTERNAL=1
//Architecture-bits
OPENMS_64BIT_ARCHITECTURE:INTERNAL=1
//List of paths to be searched when the API documentation is generated
OPENMS_DOCUMENTATION_DIRECTORIES:INTERNAL=
//Result of TRY_COMPILE
OpenMP_COMPILE_RESULT_CXX_fopenmp:INTERNAL=TRUE
//Result of TRY_COMPILE
OpenMP_COMPILE_RESULT_C_fopenmp:INTERNAL=TRUE
//ADVANCED property for variable: OpenMP_CXX_FLAGS
OpenMP_CXX_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OpenMP_CXX_LIB_NAMES
OpenMP_CXX_LIB_NAMES-ADVANCED:INTERNAL=1
//CXX compiler's OpenMP specification date
OpenMP_CXX_SPEC_DATE:INTERNAL=201511
//ADVANCED property for variable: OpenMP_C_FLAGS
OpenMP_C_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OpenMP_C_LIB_NAMES
OpenMP_C_LIB_NAMES-ADVANCED:INTERNAL=1
//C compiler's OpenMP specification date
OpenMP_C_SPEC_DATE:INTERNAL=201511
//Result of TRY_COMPILE
OpenMP_SPECTEST_CXX_:INTERNAL=TRUE
//Result of TRY_COMPILE
OpenMP_SPECTEST_C_:INTERNAL=TRUE
//ADVANCED property for variable: OpenMP_gomp_LIBRARY
OpenMP_gomp_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OpenMP_pthread_LIBRARY
OpenMP_pthread_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: SITE
SITE-ADVANCED:INTERNAL=1
//Test WITH_FPIC
WITH_FPIC:INTERNAL=1
//CMAKE_INSTALL_PREFIX during last run
_GNUInstallDirs_LAST_CMAKE_INSTALL_PREFIX:INTERNAL=/usr
//List of targets that will be exported.
_OPENMS_EXPORT_TARGETS:INTERNAL=

dh_auto_configure: error: cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/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_INSTALL_LIBDIR=lib/aarch64-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/aarch64-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 .. 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 returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-30T11:52:30Z

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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/artifact/2406244/

The most likely cause of build failures is the removed backwards compatibility for
CMake versions earlier than 3.5. You can find additional information in my
debian-devel announcement:

https://lists.debian.org/debian-devel/2025/04/msg00310.html

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/work-request/154350/

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.

Thanks,
Timo

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