[hdf5] build failure on Linux x86_64 architecture

[drelatgithub]

Package: hdf5[core,szip,zlib]:x64-linux -> 1.12.2#1

Host Environment

• Host: x64-linux
• Compiler: GNU 8.5.0
• vcpkg-tool version: 2022-10-12-b586c2752f75bcc3f6a243749e9a0d94d0d93ccd
  vcpkg-scripts version: 79fa9d8 2022-10-17 (3 hours ago)

To Reproduce

vcpkg install hdf5

Failure logs

-- Downloading https://github.com/HDFGroup/hdf5/archive/hdf5-1_12_2.tar.gz -> HDFGroup-hdf5-hdf5-1_12_2.tar.gz...
-- Extracting source /scratch/zt1/project/██████████/vcpkg/downloads/HDFGroup-hdf5-hdf5-1_12_2.tar.gz
-- Applying patch hdf5_config.patch
-- Applying patch szip.patch
-- Applying patch pkgconfig-requires.patch
-- Applying patch pkgconfig-link-order.patch
-- Using source at /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean
-- Configuring x64-linux-dbg
-- Configuring x64-linux-rel
-- Building x64-linux-dbg
CMake Error at scripts/cmake/vcpkg_execute_build_process.cmake:131 (message):
    Command failed: /scratch/zt1/project/██████████/vcpkg/downloads/tools/cmake-3.24.0-linux/cmake-3.24.0-linux-x86_64/bin/cmake --build . --config Debug --target install -- -v -j129
    Working Directory: /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg
    See logs for more information:
      /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/install-x64-linux-dbg-out.log

Call Stack (most recent call first):
  installed/x64-linux/share/vcpkg-cmake/vcpkg_cmake_build.cmake:74 (vcpkg_execute_build_process)
  installed/x64-linux/share/vcpkg-cmake/vcpkg_cmake_install.cmake:16 (vcpkg_cmake_build)
  ports/hdf5/portfile.cmake:77 (vcpkg_cmake_install)
  scripts/ports.cmake:147 (include)

/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/install-x64-linux-dbg-out.log

[1/345] /usr/bin/cc -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/scratch/zt1/project/██████████/vcpkg/installed/x64-linux/include -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/src -std=c99 -fPIC -Og -ftrapv -fno-common -fmessage-length=0 -g -fPIE -std=gnu99 -MD -MT src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o -MF src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o.d -o src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o -c /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5make_libsettings.c
[2/345] : && /usr/bin/cc -std=c99 -fPIC -Og -ftrapv -fno-common -fmessage-length=0 -g  src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o -o bin/H5make_libsettings  -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/" && :
[3/345] /usr/bin/cc -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/scratch/zt1/project/██████████/vcpkg/installed/x64-linux/include -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/src -std=c99 -fPIC -Og -ftrapv -fno-common -fmessage-length=0 -g -fPIE -std=gnu99 -MD -MT src/CMakeFiles/H5detect.dir/H5detect.c.o -MF src/CMakeFiles/H5detect.dir/H5detect.c.o.d -o src/CMakeFiles/H5detect.dir/H5detect.c.o -c /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5detect.c
[4/345] : && /usr/bin/cc -std=c99 -fPIC -Og -ftrapv -fno-common -fmessage-length=0 -g  src/CMakeFiles/H5detect.dir/H5detect.c.o -o bin/H5detect  -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/" && :
[5/345] cd /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/src && /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/bin/H5make_libsettings H5lib_settings.c && /scratch/zt1/project/██████████/vcpkg/downloads/tools/cmake-3.24.0-linux/cmake-3.24.0-linux-x86_64/bin/cmake -E touch gen_SRCS.stamp2
[6/345] cd /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/src && /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/bin/H5detect H5Tinit.c && /scratch/zt1/project/██████████/vcpkg/downloads/tools/cmake-3.24.0-linux/cmake-3.24.0-linux-x86_64/bin/cmake -E touch gen_SRCS.stamp1



...
Skipped 332 lines
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[135/345] /usr/bin/cc -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/src -isystem /scratch/zt1/project/██████████/vcpkg/installed/x64-linux/include -std=c99 -fPIC -Og -ftrapv -fno-common -fmessage-length=0 -g -fPIC -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wint-to-pointer-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -finline-functions -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wincompatible-pointer-types -Wint-conversion -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wcast-function-type -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -std=gnu99 -MD -MT src/CMakeFiles/hdf5-static.dir/H5FSdbg.c.o -MF src/CMakeFiles/hdf5-static.dir/H5FSdbg.c.o.d -o src/CMakeFiles/hdf5-static.dir/H5FSdbg.c.o -c /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5FSdbg.c
[136/345] /usr/bin/cc -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/src -isystem /scratch/zt1/project/██████████/vcpkg/installed/x64-linux/include -std=c99 -fPIC -Og -ftrapv -fno-common -fmessage-length=0 -g -fPIC -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wint-to-pointer-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -finline-functions -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wincompatible-pointer-types -Wint-conversion -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wcast-function-type -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -std=gnu99 -MD -MT src/CMakeFiles/hdf5-static.dir/H5Dchunk.c.o -MF src/CMakeFiles/hdf5-static.dir/H5Dchunk.c.o.d -o src/CMakeFiles/hdf5-static.dir/H5Dchunk.c.o -c /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c: In function ‘H5D__chunk_io_init’:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:1095:61: warning: cast discards ‘const’ qualifier from pointer target type [-Wcast-qual]
     if ((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0)
                                                             ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:1132:42: warning: cast discards ‘const’ qualifier from pointer target type [-Wcast-qual]
         if (H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) <
                                          ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c: In function ‘H5D__create_chunk_map_single’:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:1570:26: warning: cast discards ‘const’ qualifier from pointer target type [-Wcast-qual]
     chunk_info->mspace = (H5S_t *)fm->mem_space;
                          ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c: In function ‘H5D__create_chunk_file_map_hyper’:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:1853:41: warning: passing argument 1 of ‘H5S_combine_hyperslab’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             if (H5S_combine_hyperslab(fm->file_space, H5S_SELECT_AND, coords, NULL, fm->chunk_dim, NULL,
                                       ~~^~~~~~~~~~~~
In file included from /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Zprivate.h:29,
                 from /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5CXprivate.h:25,
                 from /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:54:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Sprivate.h:278:45: note: expected ‘H5S_t *’ {aka ‘struct H5S_t *’} but argument is of type ‘const H5S_t *’ {aka ‘const struct H5S_t *’}
 H5_DLL herr_t  H5S_combine_hyperslab(H5S_t *old_space, H5S_seloper_t op, const hsize_t start[],
                                      ~~~~~~~^~~~~~~~~
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c: In function ‘H5D__create_chunk_mem_map_hyper’:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:2005:30: warning: cast discards ‘const’ qualifier from pointer target type [-Wcast-qual]
         chunk_info->mspace = (H5S_t *)fm->mem_space;
                              ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c: In function ‘H5D__create_chunk_mem_map_1d’:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:2128:30: warning: cast discards ‘const’ qualifier from pointer target type [-Wcast-qual]
         chunk_info->mspace = (H5S_t *)fm->mem_space;
                              ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c: In function ‘H5D__chunk_allocate’:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:4334:52: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
     H5O_storage_chunk_t *sc                      = &(layout->storage.u.chunk); /* Convenience variable */
                                                    ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:4420:83: warning: cast discards ‘const’ qualifier from pointer target type [-Wcast-qual]
         if (H5D__fill_init(&fb_info, NULL, (H5MM_allocate_t)H5D__chunk_mem_alloc, (void *)pline,
                                                                                   ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:4421:62: warning: cast discards ‘const’ qualifier from pointer target type [-Wcast-qual]
                            (H5MM_free_t)H5D__chunk_mem_free, (void *)pline, &dset->shared->dcpl_cache.fill,
                                                              ^
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c: In function ‘H5D__chunk_copy_cb’:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:6207:75: warning: passing argument 3 of ‘H5O_copy_expand_ref’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             if (H5O_copy_expand_ref(udata->file_src, udata->tid_src, udata->dt_src, buf, nbytes,
                                                                      ~~~~~^~~~~~~~
In file included from /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dprivate.h:25,
                 from /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dpkg.h:30,
                 from /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Dchunk.c:55:
/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5Oprivate.h:997:74: note: expected ‘H5T_t *’ {aka ‘struct H5T_t *’} but argument is of type ‘const H5T_t *’ {aka ‘const struct H5T_t *’}
 H5_DLL herr_t H5O_copy_expand_ref(H5F_t *file_src, hid_t tid_src, H5T_t *dt_src, void *buf_src,
                                                                   ~~~~~~~^~~~~~
[137/345] /usr/bin/cc -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src -I/scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/x64-linux-dbg/src -isystem /scratch/zt1/project/██████████/vcpkg/installed/x64-linux/include -std=c99 -fPIC -Og -ftrapv -fno-common -fmessage-length=0 -g -fPIC -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wint-to-pointer-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -finline-functions -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wincompatible-pointer-types -Wint-conversion -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wcast-function-type -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -std=gnu99 -MD -MT src/CMakeFiles/hdf5-static.dir/H5C.c.o -MF src/CMakeFiles/hdf5-static.dir/H5C.c.o.d -o src/CMakeFiles/hdf5-static.dir/H5C.c.o -c /scratch/zt1/project/██████████/vcpkg/buildtrees/hdf5/src/df5-1_12_2-c0e67ca243.clean/src/H5C.c
ninja: build stopped: subcommand failed.

Additional context

The problem is similar to #24898 but happens on x86_64 architecture. The build fails consistently with fresh vcpkg install.

• CPU arch: x86_64
• CPU name: AMD EPYC 7763 64-Core Processor
• OS: Red Hat Enterprise Linux 8.6 (Ootpa).

[jimwang118]

I did not reproduce this issue locally, it should have been fixed in the latest version, you can try to use the latest version to see if the issue still exists.

[jimwang118]

I could install this port successfully with the latest vcpkg 2023-08-02-6d13efa755f9b5e101712d210199e4139b4c29f6. I will close this issue, please reopen this issue or submit a new issue if you have new problems.