Build error for the library "hdf5"

[news24lor]

I was updating all my installed software and updating the library "hdf5" from version 1.14.1-2 to version 1.14.2 I had several compilation errors and the library did not update. This library is important because it is linked to GDAL and consequently also to QGIS3 and many other software.

The compilation error is this:

:info:build libtool: compile:  /usr/bin/clang -DHAVE_CONFIG_H -I. -I../fortran/src -I/opt/local/lib/libaec/include -DNDEBUG -UH5_DEBUG_API -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64/src/H5FDsubfiling -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3 -pipe -Os -arch arm64 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MT H5Ztrans.lo -MD -MP -MF .deps/H5Ztrans.Tpo -c H5Ztrans.c  -fno-common -DPIC -o .libs/H5Ztrans.o
:info:build libtool: compile:  /usr/bin/clang -DHAVE_CONFIG_H -I. -I../fortran/src -I/opt/local/lib/libaec/include -DNDEBUG -UH5_DEBUG_API -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64/src/H5FDsubfiling -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3 -pipe -Os -arch arm64 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MT H5Zszip.lo -MD -MP -MF .deps/H5Zszip.Tpo -c H5Zszip.c -o H5Zszip.o >/dev/null 2>&1
:info:build libtool: link: /usr/bin/clang -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3 -pipe -Os -arch arm64 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-commons -Wl,use_dylibs -Wl,-headerpad_max_install_names -Wl,-rpath -Wl,/opt/local/lib/libgcc -arch arm64 -Wl,-syslibroot -Wl,/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -o H5detect H5detect.o  -L/opt/local/lib/libaec/lib -L/opt/local/lib -lsz -lz -ldl -lm
:info:build libtool: link: /usr/bin/clang -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3 -pipe -Os -arch arm64 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-commons -Wl,use_dylibs -Wl,-headerpad_max_install_names -Wl,-rpath -Wl,/opt/local/lib/libgcc -arch arm64 -Wl,-syslibroot -Wl,/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -o H5make_libsettings H5make_libsettings.o  -L/opt/local/lib/libaec/lib -L/opt/local/lib -lsz -lz -ldl -lm
:info:build ld: unknown options: -commons 
:info:build ld: unknown options: -commons 
:info:build clang: error: linker command failed with exit code 1 (use -v to see invocation)
:info:build clang: error: linker command failed with exit code 1 (use -v to see invocation)
:info:build make[2]: *** [H5make_libsettings] Error 1
:info:build make[2]: *** Waiting for unfinished jobs....
:info:build make[2]: *** [H5detect] Error 1
:info:build libtool: compile:  /usr/bin/clang -DHAVE_CONFIG_H -I. -I../fortran/src -I/opt/local/lib/libaec/include -DNDEBUG -UH5_DEBUG_API -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64/src/H5FDsubfiling -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3 -pipe -Os -arch arm64 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MT H5Zscaleoffset.lo -MD -MP -MF .deps/H5Zscaleoffset.Tpo -c H5Zscaleoffset.c -o H5Zscaleoffset.o >/dev/null 2>&1
:info:build libtool: compile:  /usr/bin/clang -DHAVE_CONFIG_H -I. -I../fortran/src -I/opt/local/lib/libaec/include -DNDEBUG -UH5_DEBUG_API -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64/src/H5FDsubfiling -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3 -pipe -Os -arch arm64 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MT H5Ztrans.lo -MD -MP -MF .deps/H5Ztrans.Tpo -c H5Ztrans.c -o H5Ztrans.o >/dev/null 2>&1
:info:build libtool: compile:  /usr/bin/clang -DHAVE_CONFIG_H -I. -I../fortran/src -I/opt/local/lib/libaec/include -DNDEBUG -UH5_DEBUG_API -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64/src/H5FDsubfiling -I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3 -pipe -Os -arch arm64 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MT H5Tconv.lo -MD -MP -MF .deps/H5Tconv.Tpo -c H5Tconv.c -o H5Tconv.o >/dev/null 2>&1
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64/src'
:info:build make[1]: *** [all] Error 2
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64/src'
:info:build make: *** [all-recursive] Error 1
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.2-arm64" && /usr/bin/make -j10 -w all 
:info:build Exit code: 2
:error:build Failed to build hdf5: command execution failed
:debug:build Error code: NONE
:debug:build Backtrace: command execution failed
:debug:build     while executing
:debug:build "$procedure $targetname"
:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/main.log for details.

[jmroot (Joshua Root)]

#68194

[Dave-Allured (Dave Allured)]

@news24lor, please see the discussion in #68194 about ensuring that you do not have mismatched versions of Xcode and Command Line Tools.

[news24lor]

Hi

I have last "Xcode 15" and Command Line Tools updated with macOS Ventura 13.5.2.

My Mac has an Apple Silicon M2Pro Processor.

The problem is with "hdf5" 1.14.2. There was no problem with "hdf5" 1.14.1.

[Dave-Allured (Dave Allured)]

Okay. Your original error message is the same as for #68194. It looks like there may be a common cause. Please post a complete main.log file on that ticket. Use attach, do not paste lengthy output in-line. Let's continue the conversation on that ticket. This ticket is closed as a duplicate.