hdf5 1.12.1_0: build failure due to implicit declaration of function 'clock_gettime'

[massonseb]

I cannot upgrade from hdf5 1.12.0_0 to 1.12.1_0 because of a compilation error when building hdf5. There is the error message I get at the end of the main.log file:

:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.1/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_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.1/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_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.1'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.1" && /usr/bin/make -j4 -w all 
:info:build Exit code: 2
:error:build Failed to build hdf5: command execution failed
:debug:build Error code: CHILDSTATUS 90810 2
:debug:build Backtrace: command execution failed
:debug:build     while executing
:debug:build "system {*}$notty {*}$callback {*}$nice $fullcmdstring"
:debug:build     invoked from within
:debug:build "command_exec -callback portprogress::target_progress_callback build"
:debug:build     (procedure "portbuild::build_main" line 8)
:debug:build     invoked from within
:debug:build "$procedure $targetname"
:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_hdf5/hdf5/main.log for details.

[massonseb]

I attached the full main.log file

[eborisch (Eric A. Borisch)]

I don't have an old Mavericks system around to test (and it builds fine with those variants on Catalina), but if you add:

PortGroup legacysupport 1.1

To the top of the Portfile after the other PortGroups, does it work? (You can use sudo port edit hdf5 to go directly to editing the correct Portfile.)

This is failing for lack of the system clock_gettime() and associated CLOCK_MONTONIC, which (according to the man page) was added in Sierra.

[massonseb]

Your fix works perfectly! thank you very much.

[Eric A. Borisch <borisch.eric@…>]

In de53973aea5be460610fd9a8ebc092c3f596c7f7/macports-ports (master):

hdf5: Add legacysupport; reqd. for some variants (​https://github.com/macports/macports-ports/pull/12323)

Fixes #63500