Dear Ari,
The line which is failing for you is:
libtool: link: mpicc -dynamiclib -o .libs/libspatialindex.4.dylib -Wl,-force_load,src/spatialindex/.libs/liblibrary.a -Wl,-force_load,src/storagemanager/.libs/libstoragemanager.a -Wl,-force_load,src/rtree/.libs/librtree.a -Wl,-force_load,src/mvrtree/.libs/libmvrtree.a -Wl,-force_load,src/tprtree/.libs/libtprtree.a -Wl,-force_load,src/tools/.libs/libtools.a /usr/local/lib/libstdc++.dylib -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src/.libs -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/libsupc++/.libs -lm -lpthread -install_name /Users/astern/Downloads/firedrake/lib/libspatialindex.4.dylib -compatibility_version 5 -current_version 5.2 -Wl,-single_module
This immediately spews forth the following warnings:
ld: warning: directory not found for option '-L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src'
ld: warning: directory not found for option '-L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src/.libs'
ld: warning: directory not found for option '-L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/libsupc++/.libs'
... and then you get failures to link.
In contrast, the corresponding line from my install log (also on Mojave) is:
libtool: link: mpicc -dynamiclib -o .libs/libspatialindex.4.dylib -Wl,-force_load,src/spatialindex/.libs/liblibrary.a -Wl,-force_load,src/storagemanager/.libs/libstoragemanager.a -Wl,-force_load,src/rtree/.libs/librtree.a -Wl,-force_load,src/mvrtree/.libs/libmvrtree.a -Wl,-force_load,src/tprtree/.libs/libtprtree.a -Wl,-force_load,src/tools/.libs/libtools.a -lstdc++ -lpthread -install_name /Users/dham/src/firedrake-complex/lib/libspatialindex.4.dylib -compatibility_version 5 -current_version 5.2 -Wl,-single_module
libtool: link: mpicc -dynamiclib -o .libs/libspatialindex_c.4.dylib -Wl,-force_load,src/capi/.libs/libsidxc.a ./.libs/libspatialindex.dylib -lstdc++ -lpthread -install_name /Users/dham/src/firedrake-complex/lib/libspatialindex_c.4.dylib -compatibility_version 5 -current_version 5.2 -Wl,-single_module
It therefore appears that the issue is that you have traces in your environment of another libstdc++ which was built in /Users/admin. The build system for libspatialindex is picking this up and failing as a result. It's not immediately obvious to me how your other libstdc++ is leaking into your environment, but that's the think which needs hunting down. Sometimes running "brew doctor" helps in these circumstances as it can find instances where the homebrew versions of things have been overwritten or are otherwise not being used.
Regards,
David
On 31/07/2019, 16:42, "firedrake-bounces(a)imperial.ac.uk on behalf of Stern, Ari" <firedrake-bounces(a)imperial.ac.uk on behalf of stern(a)wustl.edu> wrote:
Hi all,
I've been attempting to install Firedrake using the standard install script, but the installation throws an error when attempting to compile/link libspatialindex. The firedrake-install.log is attached.
A couple pieces of pertinent info:
1. I'm running macOS Mojave 10.14.5 with Homebrew Python 3.
2. Although I have a miniconda installation on my system, I did a "conda deactivate" before running the install script, so nothing from miniconda (except the conda binary itself) is in my path.
Cheers,
Ari