esmf @8.5.0: ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libnetcdff.7.dylib'

[ekinakoglu (Ekin Akoglu)]

esmf cannot be installed due to build error on macOS Sonoma; therefore, ncarg installation also fails. The offending part in the main.log is as follows:

:info:build ld: warning: duplicate -rpath '/opt/local/lib' ignored
:info:build ld: warning: duplicate -rpath '/opt/local/lib' ignored
:info:build ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libnetcdff.7.dylib'
:info:build clang: error: linker command failed with exit code 1 (use -v to see invocation)
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0'
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0'
:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0'
:info:build cd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/src/Infrastructure/Trace/preload ;\
:info:build 	/Library/Developer/CommandLineTools/usr/bin/make tracelib_static
:info:build make[2]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/src/Infrastructure/Trace/preload'
:info:build ar cr /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/lib/libO/Darwin.gfortranclang.64.mpiuni.default/libesmftrace_static.a wrappers_io.o wrappers_mpi.o wrappers.o
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/src/Infrastructure/Trace/preload'
:info:build cd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/src/Infrastructure/Trace/preload ;\
:info:build 	/Library/Developer/CommandLineTools/usr/bin/make tracelib_preload
:info:build make[2]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/src/Infrastructure/Trace/preload'
:info:build /usr/bin/clang++ -install_name /opt/local/lib/libesmftrace_preload.dylib -dynamiclib -o /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/lib/libO/Darwin.gfortranclang.64.mpiuni.default/libesmftrace_preload.dylib preload.o preload_io.o preload_mpi.o wrappers.o wrappers_io.o wrappers_mpi.o -pthread -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/lib/libO/Darwin.gfortranclang.64.mpiuni.default -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib/gcc13/gcc/arm64-apple-darwin23/13.2.0/../../../ -Wl,-rpath,/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0/lib/libO/Darwin.gfortranclang.64.mpiuni.default -Wl,-rpath,/opt/local/lib -Wl,-rpath,/opt/local/lib -Wl,-rpath,/opt/local/lib -Wl,-rpath,/opt/local/lib/gcc13/gcc/arm64-apple-darwin23/13.2.0/../../../ -lgfortran -lvecLibFort -lnetcdff -lnetcdf -lxerces-c -lyaml-cpp -lesmf
:info:build ld: warning: duplicate -rpath '/opt/local/lib' ignored
:info:build ld: warning: duplicate -rpath '/opt/local/lib' ignored
:info:build ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libnetcdff.7.dylib'
:info:build clang: error: linker command failed with exit code 1 (use -v to see invocation)
:info:build make[2]: *** [tracelib_preload] Error 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_esmf/esmf/work/esmf-8.5.0/src/Infrastructure/Trace/preload'
:info:build make[1]: *** [build_tracelibs] 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_esmf/esmf/work/esmf-8.5.0'
:info:build make: *** [lib] Error 2
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_esmf/esmf/work/esmf-8.5.0" && /usr/bin/make -j12 -w lib 
:info:build Exit code: 2
:error:build Failed to build esmf: command execution failed
:debug:build Error code: CHILDSTATUS 26957 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_macports_release_tarballs_ports_science_esmf/esmf/main.log for details.

[ryandesign (Ryan Carsten Schmidt)]

Presumably a duplicate of #68239.

[kencu (Ken)]

There is something wrong with the way the compilers PG works out the gcc version. I noticed it before and added some debugging code to the function, but it shows up here again in the build and is possibly related to why it is failing:

:debug:main Running callback compilers::add_gcc_rpath_support
:debug:main compilers PG: GCC version reports being UNKNOWN to MacPorts
:debug:main compilers PG: RPATH added to ldflags as GCC version is UNKNOWN
:debug:main Finished running callback compilers::add_gcc_rpath_support

[cjones051073 (Chris Jones)]

The LC_RPATH message is just a warning, so I doubt is the underlying issue here. More likely this is just Xcode 15.0 again.

[ryandesign (Ryan Carsten Schmidt)]

Replying to cjones051073:

The LC_RPATH message is just a warning, so I doubt is the underlying issue here. More likely this is just Xcode 15.0 again.

The LC_RPATH message does not include the word "warning". Yes, this is a new problem in Xcode 15+.

[Dave-Allured (Dave Allured)]

Please look closely. There are TWO DIFFERENT LC_RPATH messages coming from the v15 linker, and they mean two completely different things. In the current context, one is a harmless warning, the other is a fatal error. Taken directly from the quoted log file above:

:info:build ld: warning: duplicate -rpath '/opt/local/lib' ignored

This one is only a warning. This is complaining about options specified on the CURRENT linker command line. For example, see line 16 in the above log file quote.

:info:build ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libnetcdff.7.dylib'

This is the real error. This is complaining about the contents of a PREVIOUSLY BUILT FILE, namely /opt/local/lib/libnetcdff.7.dylib. This problem can be solved by building libnetcdff without duplicate LC_RPATH's, thereby making it compatible with Xcode 15.

[kencu (Ken)]

there are likely to be hundreds of libraries built over the past year or two by macports that have duplicate rpath entries in them.

once the cause for that has been removed (we know what it is) they will all need to be rebuilt

for now MacPorts is instead dreaming Apple will remove that duplicate rpath test from their new linker

dreams are nice.

[Dave-Allured (Dave Allured)]

Pull request in progress: ​https://github.com/macports/macports-ports/pull/22672

[Dave-Allured (Dave Allured)]

Closed ​https://github.com/macports/macports-ports/pull/22672 without merging.

Superseded by: ​https://github.com/macports/macports-ports/commit/1c0c4cb3f024edf05c0298866500acb5314140a9

This issue is resolved. Please port upgrade and rebuild your ESMF. Someone please close this ticket. Thanks.

[Dave-Allured (Dave Allured)]

Before rebuilding ESMF, please ensure that your ports netcdf and netcdf-fortran are both up to date. Both contained duplicate LC_RPATH's which broke later builds. Both are now resolved.

See ​https://github.com/macports/macports-ports/pull/21835 for netcdf-fortran, which was the source of this particular ESMF issue.