Dear Lawrence,

I'm afraid I'm still having problems, so that doesn't seem to have fixed it. The error looks the same (I've attached the install log)

Tom

On 01/11/16 15:41, T. M. Bendall wrote:

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1
-Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro
-fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
-Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro
-Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat
-Werror=format-security
build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o -lpetsc -o
build/lib.linux-x86_64-2.7/firedrake/hdf5interface.so
-L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib
-Wl,-rpath,/home/tmb15/src/firedrake/lib
    cythoning firedrake/spatialindex.pyx to firedrake/spatialindex.c
    building 'firedrake.spatialindex' extension
    mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security -fPIC
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include
-I/home/tmb15/src/firedrake/include -I/usr/include/python2.7 -c
firedrake/spatialindex.c -o
build/temp.linux-x86_64-2.7/firedrake/spatialindex.o
    In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,
                     from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from firedrake/spatialindex.c:406:
   
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by "
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    In file included from /usr/include/spatialindex/SpatialIndex.h:30:0,
                     from /usr/include/spatialindex/capi/sidx_config.h:56,
                     from /usr/include/spatialindex/capi/sidx_api.h:34,
                     from firedrake/spatialindex.c:409:
    /usr/include/spatialindex/tools/Tools.h:59:20: fatal error:
iostream: No such file or directory
    compilation terminated.
    error: command 'mpicc' failed with exit status 1

This is the problem.  The version of spatialindex shipped with ubuntu
has a broken C API.  We include our own, but you appear to be picking
up the system version.

Does it work if you do "apt-get remove libspatialindex-dev"?

Lawrence

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