Source: libbioparser-dev Version: 3.1.0-1 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20250414 ftbfs-trixie
Hi, During a rebuild of all packages in testing (trixie), your package failed to build on i386. Relevant part (hopefully): > make[1]: Entering directory '/build/reproducible-path/libbioparser-dev-3.1.0' > dh_auto_configure -- -Dbioparser_build_tests=ON > cd obj-i686-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 > -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" > -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu > -Dbioparser_build_tests=ON .. > -- The CXX compiler identification is GNU 14.2.0 > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ - skipped > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found suitable version > "1.3.1", minimum required is "1.2.8") > CMake Warning (dev) at /usr/share/cmake-3.31/Modules/FetchContent.cmake:1953 > (message): > Calling FetchContent_Populate(biosoup) is deprecated, call > FetchContent_MakeAvailable(biosoup) instead. Policy CMP0169 can be set to > OLD to allow FetchContent_Populate(biosoup) to be called directly for now, > but the ability to call it with declared details will be removed completely > in a future version. > Call Stack (most recent call first): > CMakeLists.txt:38 (FetchContent_Populate) > This warning is for project developers. Use -Wno-dev to suppress it. > > CMake Warning at /usr/share/cmake-3.31/Modules/FetchContent.cmake:2111 > (message): > FETCHCONTENT_FULLY_DISCONNECTED is set to true, which requires the source > directory for dependency biosoup to already be populated. This generally > means it must not be set to true the first time CMake is run in a build > directory. The following source directory should already be populated, but > it doesn't exist: > > > /build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu/_deps/biosoup-src > > Policy CMP0170 controls enforcement of this requirement. > Call Stack (most recent call first): > /usr/share/cmake-3.31/Modules/FetchContent.cmake:1978:EVAL:1 > (__FetchContent_Populate) > /usr/share/cmake-3.31/Modules/FetchContent.cmake:1978 (cmake_language) > CMakeLists.txt:38 (FetchContent_Populate) > > > CMake Error at CMakeLists.txt:39 (add_subdirectory): > add_subdirectory given source > > "/build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu/_deps/biosoup-src" > which is not an existing directory. > > > -- Configuring incomplete, errors occurred! > cd obj-i686-linux-gnu && tail -v -n \+0 CMakeCache.txt > ==> CMakeCache.txt <== > # This is the CMakeCache file. > # For build in directory: > /build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu > # It was generated by CMake: /usr/bin/cmake > # You can edit this file to change values found and used by cmake. > # If you do not want to change any of the values, simply exit the editor. > # If you do want to change a value, simply edit, save, and exit the editor. > # The syntax for the file is as follows: > # KEY:TYPE=VALUE > # KEY is the name of a variable in the cache. > # TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!. > # VALUE is the current value for the KEY. > > ######################## > # EXTERNAL cache entries > ######################## > > //Path to a program. > CMAKE_ADDR2LINE:FILEPATH=/usr/bin/addr2line > > //Path to a program. > CMAKE_AR:FILEPATH=/usr/bin/ar > > //Choose the type of build, options are: None Debug Release RelWithDebInfo > // MinSizeRel ... > CMAKE_BUILD_TYPE:STRING=None > > //Enable/Disable color output during build. > CMAKE_COLOR_MAKEFILE:BOOL=ON > > //CXX compiler > CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++ > > //A wrapper around 'ar' adding the appropriate '--plugin' option > // for the GCC compiler > CMAKE_CXX_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-14 > > //A wrapper around 'ranlib' adding the appropriate '--plugin' option > // for the GCC compiler > CMAKE_CXX_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-14 > > //Flags used by the CXX compiler during all build types. > CMAKE_CXX_FLAGS:STRING=-g -O2 > -ffile-prefix-map=/build/reproducible-path/libbioparser-dev-3.1.0=. > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 > > //Flags used by the CXX compiler during DEBUG builds. > CMAKE_CXX_FLAGS_DEBUG:STRING=-g > > //Flags used by the CXX compiler during MINSIZEREL builds. > CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG > > //Flags used by the CXX compiler during NONE builds. > CMAKE_CXX_FLAGS_NONE:STRING= > > //Flags used by the CXX compiler during RELEASE builds. > CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG > > //Flags used by the CXX compiler during RELWITHDEBINFO builds. > 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> > //Flags used by the linker during the creation of modules during > // DEBUG builds. > CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING= > > //Flags used by the linker during the creation of modules during > // MINSIZEREL builds. > CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING= > > //Flags used by the linker during the creation of modules during > // NONE builds. > CMAKE_MODULE_LINKER_FLAGS_NONE:STRING= > > //Flags used by the linker during the creation of modules during > // RELEASE builds. > CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING= > > //Flags used by the linker during the creation of modules during > // RELWITHDEBINFO builds. > CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING= > > //Path to a program. > CMAKE_NM:FILEPATH=/usr/bin/nm > > //Path to a program. > CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy > > //Path to a program. > CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump > > //Value Computed by CMake > CMAKE_PROJECT_DESCRIPTION:STATIC=Bioparser is a c++ header only parsing > library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with > support for zlib compressed files. > > //Value Computed by CMake > CMAKE_PROJECT_HOMEPAGE_URL:STATIC= > > //Value Computed by CMake > CMAKE_PROJECT_NAME:STATIC=bioparser > > //Value Computed by CMake > CMAKE_PROJECT_VERSION:STATIC=3.1.0 > > //Value Computed by CMake > CMAKE_PROJECT_VERSION_MAJOR:STATIC=3 > > //Value Computed by CMake > CMAKE_PROJECT_VERSION_MINOR:STATIC=1 > > //Value Computed by CMake > CMAKE_PROJECT_VERSION_PATCH:STATIC=0 > > //Value Computed by CMake > CMAKE_PROJECT_VERSION_TWEAK:STATIC= > > //Path to a program. > CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib > > //Path to a program. > CMAKE_READELF:FILEPATH=/usr/bin/readelf > > //Flags used by the linker during the creation of shared libraries > // during all build types. > CMAKE_SHARED_LINKER_FLAGS:STRING=-Wl,-z,relro > > //Flags used by the linker during the creation of shared libraries > // during DEBUG builds. > CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING= > > //Flags used by the linker during the creation of shared libraries > // during MINSIZEREL builds. > CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING= > > //Flags used by the linker during the creation of shared libraries > // during NONE builds. > CMAKE_SHARED_LINKER_FLAGS_NONE:STRING= > > //Flags used by the linker during the creation of shared libraries > // during RELEASE builds. > CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING= > > //Flags used by the linker during the creation of shared libraries > // during RELWITHDEBINFO builds. > CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING= > > //No help, variable specified on the command line. > CMAKE_SKIP_INSTALL_ALL_DEPENDENCY:UNINITIALIZED=ON > > //If set, runtime paths are not added when installing shared libraries, > // but are added when building. > CMAKE_SKIP_INSTALL_RPATH:BOOL=NO > > //If set, runtime paths are not added when using shared libraries. > CMAKE_SKIP_RPATH:BOOL=NO > > //Flags used by the linker during the creation of static libraries > // during all build types. > CMAKE_STATIC_LINKER_FLAGS:STRING= > > //Flags used by the linker during the creation of static libraries > // during DEBUG builds. > CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING= > > //Flags used by the linker during the creation of static libraries > // during MINSIZEREL builds. > CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING= > > //Flags used by the linker during the creation of static libraries > // during NONE builds. > CMAKE_STATIC_LINKER_FLAGS_NONE:STRING= > > //Flags used by the linker during the creation of static libraries > // during RELEASE builds. > CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING= > > //Flags used by the linker during the creation of static libraries > // during RELWITHDEBINFO builds. > CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING= > > //Path to a program. > CMAKE_STRIP:FILEPATH=/usr/bin/strip > > //Path to a program. > CMAKE_TAPI:FILEPATH=CMAKE_TAPI-NOTFOUND > > //If this value is on, makefiles will be generated without the > // .SILENT directive, and all commands will be echoed to the console > // during the make. This is useful for debugging only. With Visual > // Studio IDE projects all commands are done without /nologo. > CMAKE_VERBOSE_MAKEFILE:BOOL=ON > > //Directory under which to collect all populated content > FETCHCONTENT_BASE_DIR:PATH=/build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu/_deps > > //Disables all attempts to download or update content and assumes > // source dirs already exist > FETCHCONTENT_FULLY_DISCONNECTED:BOOL=ON > > //Enables QUIET option for all content population > FETCHCONTENT_QUIET:BOOL=ON > > //When not empty, overrides where to find pre-populated content > // for biosoup > FETCHCONTENT_SOURCE_DIR_BIOSOUP:PATH= > > //Enables UPDATE_DISCONNECTED behavior for all content population > FETCHCONTENT_UPDATES_DISCONNECTED:BOOL=OFF > > //The directory containing a CMake configuration file for GTest. > GTest_DIR:PATH=/usr/lib/i386-linux-gnu/cmake/GTest > > //Path to a file. > ZLIB_INCLUDE_DIR:PATH=/usr/include > > //Path to a library. > ZLIB_LIBRARY_DEBUG:FILEPATH=ZLIB_LIBRARY_DEBUG-NOTFOUND > > //Path to a library. > ZLIB_LIBRARY_RELEASE:FILEPATH=/usr/lib/i386-linux-gnu/libz.so > > //Value Computed by CMake > bioparser_BINARY_DIR:STATIC=/build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu > > //Value Computed by CMake > bioparser_IS_TOP_LEVEL:STATIC=ON > > //Value Computed by CMake > bioparser_SOURCE_DIR:STATIC=/build/reproducible-path/libbioparser-dev-3.1.0 > > //Build unit tests > bioparser_build_tests:BOOL=ON > > //Generate install target > bioparser_install:BOOL=ON > > //The directory containing a CMake configuration file for biosoup. > biosoup_DIR:PATH=biosoup_DIR-NOTFOUND > > > ######################## > # INTERNAL cache entries > ######################## > > //ADVANCED property for variable: CMAKE_ADDR2LINE > CMAKE_ADDR2LINE-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: CMAKE_AR > CMAKE_AR-ADVANCED:INTERNAL=1 > //This is the directory where this CMakeCache.txt was created > 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CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_NONE > CMAKE_STATIC_LINKER_FLAGS_NONE-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 > CMAKE_VERBOSE_MAKEFILE-ADVANCED:INTERNAL=1 > //Details about finding ZLIB > FIND_PACKAGE_MESSAGE_DETAILS_ZLIB:INTERNAL=[/usr/lib/i386-linux-gnu/libz.so][/usr/include][c > ][v1.3.1(1.2.8)] > //ADVANCED property for variable: ZLIB_INCLUDE_DIR > ZLIB_INCLUDE_DIR-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: ZLIB_LIBRARY_DEBUG > ZLIB_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: ZLIB_LIBRARY_RELEASE > ZLIB_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 > //linker supports push/pop state > _CMAKE_CXX_LINKER_PUSHPOP_STATE_SUPPORTED:INTERNAL=TRUE > //linker supports push/pop state > _CMAKE_LINKER_PUSHPOP_STATE_SUPPORTED:INTERNAL=TRUE > //CMAKE_INSTALL_PREFIX during last run > _GNUInstallDirs_LAST_CMAKE_INSTALL_PREFIX:INTERNAL=/usr > > dh_auto_configure: error: cd obj-i686-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 > -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" > -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu > -Dbioparser_build_tests=ON .. returned exit code 1 > make[1]: *** [debian/rules:11: override_dh_auto_configure] Error 2 The full build log is available from: http://qa-logs.debian.net/2025/04/14/libbioparser-dev_3.1.0-1_testing-i386.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20250414;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250414&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
