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[hdf5] Build error on x64-linux looking for libz.a #42436

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Barugon opened this issue Nov 29, 2024 · 5 comments
Open

[hdf5] Build error on x64-linux looking for libz.a #42436

Barugon opened this issue Nov 29, 2024 · 5 comments
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@Mengna-Li
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category:port-bug The issue is with a library, which is something the port should already support

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@Barugon
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Barugon commented Nov 29, 2024 •
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Package: hdf5[core,cpp,szip,zlib]:[email protected]#3

Host Environment

  • Host: x64-linux
  • Compiler: GNU 14.2.1
  • vcpkg-tool version: 2024-11-12-eb492805e92a2c14a230f5c3deb3e89f6771c321
    vcpkg-scripts version: cd124b8 2024-11-29 (20 hours ago)

To Reproduce

vcpkg install gdal:x64-linux

Failure logs

-- Using cached HDFGroup-hdf5-hdf5_1.14.4.3.tar.gz.
-- Cleaning sources at /home/barugon/Downloads/vcpkg/buildtrees/hdf5/src/5_1.14.4.3-7f241d6199.clean. Use --editable to skip cleaning for the packages you specify.
-- Extracting source /home/barugon/Downloads/vcpkg/downloads/HDFGroup-hdf5-hdf5_1.14.4.3.tar.gz
-- Applying patch hdf5_config.patch
-- Applying patch add-_Float16-type-on-aarch64.patch
-- Applying patch pkgconfig-requires.patch
-- Using source at /home/barugon/Downloads/vcpkg/buildtrees/hdf5/src/5_1.14.4.3-7f241d6199.clean
-- Configuring x64-linux-dbg
CMake Error at scripts/cmake/vcpkg_execute_required_process.cmake:127 (message):
    Command failed: /usr/bin/cmake /home/barugon/Downloads/vcpkg/buildtrees/hdf5/src/5_1.14.4.3-7f241d6199.clean -G Ninja -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=/home/barugon/Downloads/vcpkg/packages/hdf5_x64-linux/debug -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DHDF5_ENABLE_PARALLEL=OFF -DHDF5_BUILD_TOOLS=OFF -DHDF5_BUILD_HL_GIF_TOOLS=OFF -DHDF5_BUILD_CPP_LIB=ON -DHDF5_ENABLE_SZIP_SUPPORT=ON -DHDF5_ENABLE_SZIP_ENCODING=ON -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DHDF5_BUILD_FORTRAN=OFF -DHDF5_ENABLE_THREADSAFE=OFF -DHDF5_BUILD_UTILS=OFF -DHDF5_ENABLE_MAP_API=OFF -DUSE_LIBAEC_STATIC=ON -DBUILD_TESTING=OFF -DHDF5_BUILD_EXAMPLES=OFF -DHDF5_INSTALL_DATA_DIR=share/hdf5/data -DHDF5_INSTALL_CMAKE_DIR=share/hdf5 -DHDF_PACKAGE_NAMESPACE:STRING=hdf5:: -DHDF5_MSVC_NAMING_CONVENTION=OFF -DALLOW_UNSUPPORTED=OFF -DCMAKE_MAKE_PROGRAM=/home/barugon/Downloads/vcpkg/downloads/tools/ninja/1.10.2-linux/ninja -DCMAKE_SYSTEM_NAME=Linux -DBUILD_SHARED_LIBS=OFF -DVCPKG_CHAINLOAD_TOOLCHAIN_FILE=/home/barugon/Downloads/vcpkg/scripts/toolchains/linux.cmake -DVCPKG_TARGET_TRIPLET=x64-linux -DVCPKG_SET_CHARSET_FLAG=ON -DVCPKG_PLATFORM_TOOLSET=external -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_SKIP=TRUE -DCMAKE_VERBOSE_MAKEFILE=ON -DVCPKG_APPLOCAL_DEPS=OFF -DCMAKE_TOOLCHAIN_FILE=/home/barugon/Downloads/vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_ERROR_ON_ABSOLUTE_INSTALL_DESTINATION=ON -DVCPKG_CXX_FLAGS= -DVCPKG_CXX_FLAGS_RELEASE= -DVCPKG_CXX_FLAGS_DEBUG= -DVCPKG_C_FLAGS= -DVCPKG_C_FLAGS_RELEASE= -DVCPKG_C_FLAGS_DEBUG= -DVCPKG_CRT_LINKAGE=dynamic -DVCPKG_LINKER_FLAGS= -DVCPKG_LINKER_FLAGS_RELEASE= -DVCPKG_LINKER_FLAGS_DEBUG= -DVCPKG_TARGET_ARCHITECTURE=x64 -DCMAKE_INSTALL_LIBDIR:STRING=lib -DCMAKE_INSTALL_BINDIR:STRING=bin -D_VCPKG_ROOT_DIR=/home/barugon/Downloads/vcpkg -D_VCPKG_INSTALLED_DIR=/home/barugon/Downloads/vcpkg/installed -DVCPKG_MANIFEST_INSTALL=OFF
    Working Directory: /home/barugon/Downloads/vcpkg/buildtrees/hdf5/x64-linux-dbg
    Error code: 1
    See logs for more information:
      /home/barugon/Downloads/vcpkg/buildtrees/hdf5/config-x64-linux-dbg-CMakeCache.txt.log
      /home/barugon/Downloads/vcpkg/buildtrees/hdf5/config-x64-linux-dbg-CMakeConfigureLog.yaml.log
      /home/barugon/Downloads/vcpkg/buildtrees/hdf5/config-x64-linux-dbg-out.log
      /home/barugon/Downloads/vcpkg/buildtrees/hdf5/config-x64-linux-dbg-err.log

Call Stack (most recent call first):
  installed/x64-linux/share/vcpkg-cmake/vcpkg_cmake_configure.cmake:287 (vcpkg_execute_required_process)
  ports/hdf5/portfile.cmake:63 (vcpkg_cmake_configure)
  scripts/ports.cmake:196 (include)
/home/barugon/Downloads/vcpkg/buildtrees/hdf5/config-x64-linux-dbg-err.log 
CMake Error at /usr/lib64/cmake/ZLIB/ZLIB.cmake:81 (message):
  The imported target "ZLIB::zlibstatic" references the file

     "/usr/lib64/libz.a"

  but this file does not exist.  Possible reasons include:

  * The file was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and contained

     "/usr/lib64/cmake/ZLIB/ZLIB.cmake"

  but not all the files it references.

Call Stack (most recent call first):
  /usr/lib64/cmake/ZLIB/zlib-config.cmake:44 (include)
  /home/barugon/Downloads/vcpkg/installed/x64-linux/share/zlib/vcpkg-cmake-wrapper.cmake:12 (_find_package)
  /home/barugon/Downloads/vcpkg/scripts/buildsystems/vcpkg.cmake:813 (include)
  CMakeFilters.cmake:73 (find_package)
  CMakeLists.txt:873 (include)
/home/barugon/Downloads/vcpkg/buildtrees/hdf5/config-x64-linux-dbg-out.log 
-- The C compiler identification is GNU 14.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Final: share/hdf5/data
-- Looking for include file sys/file.h
-- Looking for include file sys/file.h - found
-- Looking for include files sys/file.h, sys/ioctl.h
-- Looking for include files sys/file.h, sys/ioctl.h - found
-- Looking for 3 include files sys/file.h, ..., sys/resource.h
-- Looking for 3 include files sys/file.h, ..., sys/resource.h - found
-- Looking for 4 include files sys/file.h, ..., sys/socket.h
-- Looking for 4 include files sys/file.h, ..., sys/socket.h - found
-- Looking for 5 include files sys/file.h, ..., sys/stat.h
-- Looking for 5 include files sys/file.h, ..., sys/stat.h - found
-- Looking for 6 include files sys/file.h, ..., sys/time.h
-- Looking for 6 include files sys/file.h, ..., sys/time.h - found
-- Looking for 7 include files sys/file.h, ..., sys/types.h
-- Looking for 7 include files sys/file.h, ..., sys/types.h - found
-- Looking for 8 include files sys/file.h, ..., features.h
-- Looking for 8 include files sys/file.h, ..., features.h - found
-- Looking for 9 include files sys/file.h, ..., dirent.h
-- Looking for 9 include files sys/file.h, ..., dirent.h - found
-- Looking for 10 include files sys/file.h, ..., unistd.h
-- Looking for 10 include files sys/file.h, ..., unistd.h - found
-- Looking for 11 include files sys/file.h, ..., pwd.h
-- Looking for 11 include files sys/file.h, ..., pwd.h - found
-- Looking for 12 include files sys/file.h, ..., pthread.h
-- Looking for 12 include files sys/file.h, ..., pthread.h - found
-- Looking for 13 include files sys/file.h, ..., dlfcn.h
-- Looking for 13 include files sys/file.h, ..., dlfcn.h - found
-- Looking for 14 include files sys/file.h, ..., netinet/in.h
-- Looking for 14 include files sys/file.h, ..., netinet/in.h - found
-- Looking for 15 include files sys/file.h, ..., netdb.h
-- Looking for 15 include files sys/file.h, ..., netdb.h - found
-- Looking for 16 include files sys/file.h, ..., arpa/inet.h
-- Looking for 16 include files sys/file.h, ..., arpa/inet.h - found
-- Looking for include file quadmath.h
-- Looking for include file quadmath.h - found
-- Looking for ceil in m;
-- Looking for ceil in m; - found
-- Looking for dlopen in dl;m
-- Looking for dlopen in dl;m - found
-- Looking for WSAStartup in ws2_32;m;dl
-- Looking for WSAStartup in ws2_32;m;dl - not found
-- Looking for gethostbyname in wsock32;m;dl
-- Looking for gethostbyname in wsock32;m;dl - not found
-- Looking for gethostname in ucb;m;dl
-- Looking for gethostname in ucb;m;dl - not found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of char
-- Check size of char - done
-- Check size of short
-- Check size of short - done
-- Check size of int
-- Check size of int - done
-- Check size of unsigned
-- Check size of unsigned - done
-- Check size of long
-- Check size of long - done
-- Check size of long long
-- Check size of long long - done
-- Check size of float
-- Check size of float - done
-- Check size of double
-- Check size of double - done
-- Check size of long double
-- Check size of long double - done
-- Check size of int8_t
-- Check size of int8_t - done
-- Check size of uint8_t
-- Check size of uint8_t - done
-- Check size of int_least8_t
-- Check size of int_least8_t - done
-- Check size of uint_least8_t
-- Check size of uint_least8_t - done
-- Check size of int_fast8_t
-- Check size of int_fast8_t - done
-- Check size of uint_fast8_t
-- Check size of uint_fast8_t - done
-- Check size of int16_t
-- Check size of int16_t - done
-- Check size of uint16_t
-- Check size of uint16_t - done
-- Check size of int_least16_t
-- Check size of int_least16_t - done
-- Check size of uint_least16_t
-- Check size of uint_least16_t - done
-- Check size of int_fast16_t
-- Check size of int_fast16_t - done
-- Check size of uint_fast16_t
-- Check size of uint_fast16_t - done
-- Check size of int32_t
-- Check size of int32_t - done
-- Check size of uint32_t
-- Check size of uint32_t - done
-- Check size of int_least32_t
-- Check size of int_least32_t - done
-- Check size of uint_least32_t
-- Check size of uint_least32_t - done
-- Check size of int_fast32_t
-- Check size of int_fast32_t - done
-- Check size of uint_fast32_t
-- Check size of uint_fast32_t - done
-- Check size of int64_t
-- Check size of int64_t - done
-- Check size of uint64_t
-- Check size of uint64_t - done
-- Check size of int_least64_t
-- Check size of int_least64_t - done
-- Check size of uint_least64_t
-- Check size of uint_least64_t - done
-- Check size of int_fast64_t
-- Check size of int_fast64_t - done
-- Check size of uint_fast64_t
-- Check size of uint_fast64_t - done
-- Check size of size_t
-- Check size of size_t - done
-- Check size of ssize_t
-- Check size of ssize_t - done
-- Check size of ptrdiff_t
-- Check size of ptrdiff_t - done
-- Check size of off_t
-- Check size of off_t - done
-- Check size of time_t
-- Check size of time_t - done
-- Check size of _Bool
-- Check size of _Bool - done
-- Looking for CLOCK_MONOTONIC
-- Looking for CLOCK_MONOTONIC - not found
-- Performing Test H5_HAVE_TM_GMTOFF
-- Performing Test H5_HAVE_TM_GMTOFF - Success
-- Performing Test H5_HAVE___TM_GMTOFF
-- Performing Test H5_HAVE___TM_GMTOFF - Failed
-- Performing Test H5_HAVE_STRUCT_TIMEZONE
-- Performing Test H5_HAVE_STRUCT_TIMEZONE - Failed
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Performing Test H5_HAVE_STAT_ST_BLOCKS
-- Performing Test H5_HAVE_STAT_ST_BLOCKS - Success
-- Looking for ioctl
-- Looking for ioctl - found
-- Performing Test H5_HAVE_STRUCT_VIDEOCONFIG
-- Performing Test H5_HAVE_STRUCT_VIDEOCONFIG - Failed
-- Performing Test H5_HAVE_STRUCT_TEXT_INFO
-- Performing Test H5_HAVE_STRUCT_TEXT_INFO - Failed
-- Looking for _getvideoconfig
-- Looking for _getvideoconfig - not found
-- Looking for gettextinfo
-- Looking for gettextinfo - not found
-- Looking for _scrsize
-- Looking for _scrsize - not found
-- Looking for GetConsoleScreenBufferInfo
-- Looking for GetConsoleScreenBufferInfo - not found
-- Looking for TIOCGWINSZ
-- Looking for TIOCGWINSZ - found
-- Looking for TIOCGETD
-- Looking for TIOCGETD - found
-- Looking for alarm
-- Looking for alarm - found
-- Looking for fcntl
-- Looking for fcntl - found
-- Looking for flock
-- Looking for flock - found
-- Looking for fork
-- Looking for fork - found
-- Looking for gethostname
-- Looking for gethostname - found
-- Looking for getrusage
-- Looking for getrusage - found
-- Looking for pread
-- Looking for pread - found
-- Looking for pwrite
-- Looking for pwrite - found
-- Looking for rand_r
-- Looking for rand_r - found
-- Looking for random
-- Looking for random - found
-- Looking for strcasestr
-- Looking for strcasestr - found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for symlink
-- Looking for symlink - found
-- Looking for tmpfile
-- Looking for tmpfile - found
-- Looking for asprintf
-- Looking for asprintf - found
-- Looking for vasprintf
-- Looking for vasprintf - found
-- Looking for waitpid
-- Looking for waitpid - found
-- Looking for sigsetjmp
-- Looking for sigsetjmp - found
-- Looking for clock_gettime
-- Looking for clock_gettime - found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for clock_gettime in posix4
-- Looking for clock_gettime in posix4 - not found
-- Check size of CLOCK_MONOTONIC_COARSE
-- Check size of CLOCK_MONOTONIC_COARSE - done
-- Checking if _Float16 support is available
-- Check size of _Float16
-- Check size of _Float16 - done
-- Looking for FLT16_EPSILON
-- Looking for FLT16_EPSILON - found
-- Looking for FLT16_MIN
-- Looking for FLT16_MIN - found
-- Looking for FLT16_MAX
-- Looking for FLT16_MAX - found
-- Looking for FLT16_MIN_10_EXP
-- Looking for FLT16_MIN_10_EXP - found
-- Looking for FLT16_MAX_10_EXP
-- Looking for FLT16_MAX_10_EXP - found
-- Looking for FLT16_MANT_DIG
-- Looking for FLT16_MANT_DIG - found
-- Looking for fabsf16
-- Looking for fabsf16 - not found
-- Found Perl: /usr/bin/perl (found version "5.40.0")
-- ....All Warnings are enabled
-- Configuring incomplete, errors occurred!
/home/barugon/Downloads/vcpkg/buildtrees/hdf5/config-x64-linux-dbg-CMakeCache.txt.log 
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//No help, variable specified on the command line.
HDF5_BUILD_FORTRAN:UNINITIALIZED=OFF

//Build Test Generators
HDF5_BUILD_GENERATORS:BOOL=OFF

//No help, variable specified on the command line.
HDF5_BUILD_HL_GIF_TOOLS:UNINITIALIZED=OFF

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HDF5_BUILD_STATIC_TOOLS:BOOL=ON

//No help, variable specified on the command line.
HDF5_BUILD_TOOLS:UNINITIALIZED=OFF

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HDF5_BUILD_UTILS:UNINITIALIZED=OFF

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HDF5_DISABLE_COMPILER_WARNINGS:BOOL=OFF

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//enable the use of Clang tools
HDF5_ENABLE_ANALYZER_TOOLS:BOOL=OFF

//Determines whether NDEBUG is defined to control assertions (OFF
// NO YES)
HDF5_ENABLE_ASSERTS:STRING=OFF

//Enable the function stack tracing (for developer debugging).
HDF5_ENABLE_CODESTACK:BOOL=OFF

//Enable code coverage for Libraries and Programs
HDF5_ENABLE_COVERAGE:BOOL=OFF

//Turn on extra debug output in all packages
HDF5_ENABLE_DEBUG_APIS:BOOL=OFF

//Enable deprecated public API symbols
HDF5_ENABLE_DEPRECATED_SYMBOLS:BOOL=ON

//Enable HDF5 developer group warnings
HDF5_ENABLE_DEV_WARNINGS:BOOL=OFF

//Build the Direct I/O Virtual File Driver
HDF5_ENABLE_DIRECT_VFD:BOOL=OFF

//Embed library info into executables
HDF5_ENABLE_EMBEDDED_LIBINFO:BOOL=ON

//format source files
HDF5_ENABLE_FORMATTERS:BOOL=OFF

//Enable HDFS
HDF5_ENABLE_HDFS:BOOL=OFF

//Instrument The library
HDF5_ENABLE_INSTRUMENT:BOOL=OFF

//No help, variable specified on the command line.
HDF5_ENABLE_MAP_API:UNINITIALIZED=OFF

//Build the Mirror Virtual File Driver
HDF5_ENABLE_MIRROR_VFD:BOOL=OFF

//Enable support for non-standard programming language features
HDF5_ENABLE_NONSTANDARD_FEATURES:BOOL=ON

//Enable support for _Float16 C datatype
HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16:BOOL=ON

//Enable optimization flags/settings independently from the build
// mode
HDF5_ENABLE_OPTIMIZATION:BOOL=OFF

//Enable parallel build (requires MPI)
HDF5_ENABLE_PARALLEL:BOOL=OFF

//Use pread/pwrite in sec2/log/core VFDs in place of read/write
// (when available)
HDF5_ENABLE_PREADWRITE:BOOL=ON

//Enable profiling flags independently from the build mode.
HDF5_ENABLE_PROFILING:BOOL=OFF

//Build the ROS3 Virtual File Driver
HDF5_ENABLE_ROS3_VFD:BOOL=OFF

//execute the Clang sanitizer
HDF5_ENABLE_SANITIZERS:BOOL=OFF

//Build Parallel HDF5 Subfiling VFD
HDF5_ENABLE_SUBFILING_VFD:BOOL=OFF

//Add debug symbols to the library independent of the build mode
// and optimization level (OFF NO YES)
HDF5_ENABLE_SYMBOLS:STRING=OFF

//No help, variable specified on the command line.
HDF5_ENABLE_SZIP_ENCODING:UNINITIALIZED=ON

//No help, variable specified on the command line.
HDF5_ENABLE_SZIP_SUPPORT:UNINITIALIZED=ON

//No help, variable specified on the command line.
HDF5_ENABLE_THREADSAFE:UNINITIALIZED=OFF

//Enable API tracing capability
HDF5_ENABLE_TRACE:BOOL=OFF

//Indicate that a memory checker is used
HDF5_ENABLE_USING_MEMCHECKER:BOOL=OFF

//Interpret some warnings as errors
HDF5_ENABLE_WARNINGS_AS_ERRORS:BOOL=OFF

//Enable Zlib Filters
HDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON

//Use prefix for custom library naming.
HDF5_EXTERNAL_LIB_PREFIX:STRING=

//Ignore file locks when disabled on file system
HDF5_IGNORE_DISABLED_FILE_LOCKS:BOOL=ON

//No help, variable specified on the command line.
...
Skipped 134 lines
...
// target directory for executables. Requires CMake 3.14.
X_VCPKG_APPLOCAL_DEPS_INSTALL:BOOL=OFF

//(experimental) Add USES_TERMINAL to VCPKG_APPLOCAL_DEPS to force
// serialization.
X_VCPKG_APPLOCAL_DEPS_SERIALIZED:BOOL=OFF

//The directory containing a CMake configuration file for ZLIB.
ZLIB_DIR:PATH=/usr/lib64/cmake/ZLIB

//Path to a file.
ZLIB_INCLUDE_DIR:PATH=/home/barugon/Downloads/vcpkg/installed/x64-linux/include

//Path to a library.
ZLIB_LIBRARY_DEBUG:FILEPATH=/home/barugon/Downloads/vcpkg/installed/x64-linux/debug/lib/libz.a

//Path to a library.
ZLIB_LIBRARY_RELEASE:FILEPATH=/home/barugon/Downloads/vcpkg/installed/x64-linux/lib/libz.a

//Use External Library Building for ZLIB
ZLIB_USE_EXTERNAL:BOOL=OFF

//The directory which contains the installed libraries for each
// triplet
_VCPKG_INSTALLED_DIR:PATH=/home/barugon/Downloads/vcpkg/installed

//No help, variable specified on the command line.
_VCPKG_ROOT_DIR:UNINITIALIZED=/home/barugon/Downloads/vcpkg


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//Result of TRY_COMPILE
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//Details about finding Perl
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//Other test 
H5_DEV_T_IS_SCALAR:INTERNAL=1
//Checking IF the cpu is power9 and cannot correctly converting
// long double values
H5_DISABLE_SOME_LDOUBLE_CONV:INTERNAL=
//Result of TRY_COMPILE
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//Have include sys/file.h;sys/ioctl.h;sys/resource.h;sys/socket.h;sys/stat.h;sys/time.h;sys/types.h;features.h;dirent.h
H5_HAVE_DIRENT_H:INTERNAL=1
//Have include sys/file.h;sys/ioctl.h;sys/resource.h;sys/socket.h;sys/stat.h;sys/time.h;sys/types.h;features.h;dirent.h;unistd.h;pwd.h;pthread.h;dlfcn.h
H5_HAVE_DLFCN_H:INTERNAL=1
//Have function fabsf16
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//Have function fcntl
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//Have include sys/file.h;sys/ioctl.h;sys/resource.h;sys/socket.h;sys/stat.h;sys/time.h;sys/types.h;features.h
H5_HAVE_FEATURES_H:INTERNAL=1
//Have function flock
H5_HAVE_FLOCK:INTERNAL=1
//Have function fork
H5_HAVE_FORK:INTERNAL=1
//Have function GetConsoleScreenBufferInfo
H5_HAVE_GETCONSOLESCREENBUFFERINFO:INTERNAL=
//Have function gethostname
H5_HAVE_GETHOSTNAME:INTERNAL=1
//Have function getrusage
H5_HAVE_GETRUSAGE:INTERNAL=1
//Have function gettextinfo
H5_HAVE_GETTEXTINFO:INTERNAL=
//Have function gettimeofday
H5_HAVE_GETTIMEOFDAY:INTERNAL=1
//Have function ioctl
H5_HAVE_IOCTL:INTERNAL=1
//Have library dl;m
H5_HAVE_LIBDL:INTERNAL=1
//Have library m;
H5_HAVE_LIBM:INTERNAL=1
//Have library ucb;m;dl
H5_HAVE_LIBUCB:INTERNAL=
//Have library ws2_32;m;dl
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//Have library wsock32;m;dl
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//Have symbol sigsetjmp
H5_HAVE_MACRO_SIGSETJMP:INTERNAL=1
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H5_HAVE_NETINET_IN_H:INTERNAL=1
//Have function pread
H5_HAVE_PREAD:INTERNAL=1
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//Have function random
H5_HAVE_RANDOM:INTERNAL=1
//Have function rand_r
H5_HAVE_RAND_R:INTERNAL=1
//Other test 
H5_HAVE_SOCKLEN_T:INTERNAL=1
//Test H5_HAVE_STAT_ST_BLOCKS
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//Have function strcasestr
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//Other test 
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//Test H5_HAVE_STRUCT_VIDEOCONFIG
H5_HAVE_STRUCT_VIDEOCONFIG:INTERNAL=
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H5_HAVE_SYMLINK:INTERNAL=1
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H5_HAVE_SYS_FILE_H:INTERNAL=1
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H5_HAVE_SYS_TYPES_H:INTERNAL=1
//Other test 
H5_HAVE_TIMEZONE:INTERNAL=1
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H5_HAVE_TIOCGETD:INTERNAL=1
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H5_HAVE_TIOCGWINSZ:INTERNAL=1
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H5_HAVE_TM_GMTOFF:INTERNAL=1
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//Have function vasprintf
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H5_LDOUBLE_TO_FLOAT16_CORRECT:INTERNAL=1
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//Checking if correctly converting long double to _Float16 values
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//Result of try_run()
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//Checking IF correctly converting long double to (unsigned) long
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H5_LDOUBLE_TO_LLONG_ACCURATE:INTERNAL=1
//Result of TRY_COMPILE
H5_LDOUBLE_TO_LLONG_ACCURATE_COMPILE:INTERNAL=TRUE
//Result of try_run()
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//Checking IF your system converts long double to (unsigned) long
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H5_LDOUBLE_TO_LONG_SPECIAL:INTERNAL=
//Result of TRY_COMPILE
H5_LDOUBLE_TO_LONG_SPECIAL_COMPILE:INTERNAL=TRUE
//Result of try_run()
H5_LDOUBLE_TO_LONG_SPECIAL_RUN:INTERNAL=1
//Checking IF correctly converting (unsigned) long long to long
// double values
H5_LLONG_TO_LDOUBLE_CORRECT:INTERNAL=1
//Result of TRY_COMPILE
H5_LLONG_TO_LDOUBLE_CORRECT_COMPILE:INTERNAL=TRUE
//Result of try_run()
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//Checking IF your system can convert (unsigned) long to long double
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H5_LONG_TO_LDOUBLE_SPECIAL:INTERNAL=
//Result of TRY_COMPILE
H5_LONG_TO_LDOUBLE_SPECIAL_COMPILE:INTERNAL=TRUE
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H5_SIZEOF_CHAR:INTERNAL=1
//CHECK_TYPE_SIZE: sizeof(double)
H5_SIZEOF_DOUBLE:INTERNAL=8
//CHECK_TYPE_SIZE: sizeof(float)
H5_SIZEOF_FLOAT:INTERNAL=4
//CHECK_TYPE_SIZE: sizeof(int)
H5_SIZEOF_INT:INTERNAL=4
//CHECK_TYPE_SIZE: sizeof(int16_t)
H5_SIZEOF_INT16_T:INTERNAL=2
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H5_SIZEOF_INT32_T:INTERNAL=4
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H5_SIZEOF_INT64_T:INTERNAL=8
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H5_SIZEOF_INT8_T:INTERNAL=1
//CHECK_TYPE_SIZE: sizeof(int_fast16_t)
H5_SIZEOF_INT_FAST16_T:INTERNAL=8
//CHECK_TYPE_SIZE: sizeof(int_fast32_t)
H5_SIZEOF_INT_FAST32_T:INTERNAL=8
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H5_SIZEOF_INT_FAST64_T:INTERNAL=8
//CHECK_TYPE_SIZE: sizeof(int_fast8_t)
H5_SIZEOF_INT_FAST8_T:INTERNAL=1
//CHECK_TYPE_SIZE: sizeof(int_least16_t)
H5_SIZEOF_INT_LEAST16_T:INTERNAL=2
//CHECK_TYPE_SIZE: sizeof(int_least32_t)
H5_SIZEOF_INT_LEAST32_T:INTERNAL=4
//CHECK_TYPE_SIZE: sizeof(int_least64_t)
H5_SIZEOF_INT_LEAST64_T:INTERNAL=8
//CHECK_TYPE_SIZE: sizeof(int_least8_t)
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        Change Dir: '/home/barugon/Downloads/vcpkg/buildtrees/hdf5/x64-linux-dbg/CMakeFiles/CMakeTmp'
        
        Run Build Command(s): /home/barugon/Downloads/vcpkg/downloads/tools/ninja/1.10.2-linux/ninja -v cmTC_91fb4
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  -
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      - "config/cmake/ConfigureChecks.cmake:982 (CHECK_FUNCTION_EXISTS)"
      - "CMakeLists.txt:457 (include)"
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    buildResult:
      variable: "H5_HAVE_FABSF16"
      cached: true
      stdout: |
        Change Dir: '/home/barugon/Downloads/vcpkg/buildtrees/hdf5/x64-linux-dbg/CMakeFiles/CMakeScratch/TryCompile-Dg1V1X'
        
        Run Build Command(s): /home/barugon/Downloads/vcpkg/downloads/tools/ninja/1.10.2-linux/ninja -v cmTC_4e418
        [1/2] /usr/bin/gcc -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -D__STDC_WANT_IEC_60559_TYPES_EXT__  -fPIC -DCHECK_FUNCTION_EXISTS=fabsf16 -o CMakeFiles/cmTC_4e418.dir/CheckFunctionExists.c.o -c /home/barugon/Downloads/vcpkg/buildtrees/hdf5/x64-linux-dbg/CMakeFiles/CMakeScratch/TryCompile-Dg1V1X/CheckFunctionExists.c
        <command-line>: warning: conflicting types for built-in function ‘fabsf16’; expected ‘_Float16(_Float16)’ [-Wbuiltin-declaration-mismatch]
        /home/barugon/Downloads/vcpkg/buildtrees/hdf5/x64-linux-dbg/CMakeFiles/CMakeScratch/TryCompile-Dg1V1X/CheckFunctionExists.c:7:3: note: in expansion of macro ‘CHECK_FUNCTION_EXISTS’
            7 |   CHECK_FUNCTION_EXISTS(void);
              |   ^~~~~~~~~~~~~~~~~~~~~
        /home/barugon/Downloads/vcpkg/buildtrees/hdf5/x64-linux-dbg/CMakeFiles/CMakeScratch/TryCompile-Dg1V1X/CheckFunctionExists.c:1:1: note: ‘fabsf16’ is declared in header ‘<math.h>’
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        FAILED: cmTC_4e418 
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        >>> referenced by CheckFunctionExists.c
        >>>               CMakeFiles/cmTC_4e418.dir/CheckFunctionExists.c.o:(main)
        collect2: error: ld returned 1 exit status
        ninja: build stopped: subcommand failed.
        
      exitCode: 1
...
@Barugon
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Barugon commented Nov 29, 2024 •
edited
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It appears that it's looking for /usr/lib64/libz.a when it should be looking for vcpkg/installed/x64-linux/lib/libz.a or vcpkg/packages/zlib_x64-linux/lib/libz.a?

zlib-devel is installed on my system but it doesn't appear to include the static library.

@dg0yt
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dg0yt commented Nov 30, 2024

I guess /usr/lib64/cmake/ZLIB/zlib-config.cmake is from Fedora zlib-ng package. It bypasses vcpkg's wrapping of find_package(ZLIB).
Here, config mode is enabled by the NAMES keyword, in a first find_package attempt
https://github.com/HDFGroup/hdf5/blob/57948148dbcb275c9a39212eebc62e071b11a00d/CMakeFilters.cmake#L73
This line would need to be patched out.

@dg0yt
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dg0yt commented Nov 30, 2024 •
edited
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zlib-devel is installed on my system but it doesn't appear to include the static library.

I think the cmake config is from zlib-ng-devel. The static lib is in zlib-ng-compat-static. IMO this is a Fedora packaging bug because it affects all use of the CMake config. (IDK, but it broke my Fedora packaging on openSUSE Build Service.)

But vcpkg port hdf5 must use vcpkg zlib.

@Barugon
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Barugon commented Dec 2, 2024

I guess /usr/lib64/cmake/ZLIB/zlib-config.cmake is from Fedora zlib-ng package. It bypasses vcpkg's wrapping of find_package(ZLIB). Here, config mode is enabled by the NAMES keyword, in a first find_package attempt https://github.com/HDFGroup/hdf5/blob/57948148dbcb275c9a39212eebc62e071b11a00d/CMakeFilters.cmake#L73 This line would need to be patched out.

Thanks, this got me past the issue. Should I make a PR with the change?

@Mengna-Li Mengna-Li added the category:port-bug The issue is with a library, which is something the port should already support label Dec 2, 2024
@dg0yt
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dg0yt commented Dec 2, 2024

Should I make a PR with the change?

This would be welcome. At least you can test the Fedora side.

@jimwang118 jimwang118 mentioned this issue Dec 10, 2024
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[hdf5] Fix link library error jimwang118/vcpkg
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@dg0yt @Barugon @Mengna-Li