> On 2 Nov 2018, at 17:53, Matthew Knepley <knepley@gmail.com> wrote:
> ...

> Successfully cloned repository libspatialindex
> Checking out branch master
> Successfully checked out branch master
> Traceback (most recent call last):
>   File "../bin/firedrake-update", line 1207, in <module>
>     build_and_install_libspatialindex()
>   File "../bin/firedrake-update", line 808, in build_and_install_libspatialindex
>     check_call(["./autogen.sh"])
>   File "../bin/firedrake-update", line 435, in check_call
>     log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode())
>   File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 336, in check_output
>     **kwargs).stdout
>   File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 418, in run
>     output=stdout, stderr=stderr)
> subprocess.CalledProcessError: Command '['./autogen.sh']' returned non-zero exit status 1.
>
>
> Update log saved in firedrake-update.log
>
> Here is the log.
>
> Ah ha! You need autotools, but do not check up front :) We get farther

When you first ran "firedrake-install" you said --no-package-manager, so we assumed that you had all the things we need.


> (firedrake)  127:/PETSc3/fem$ export PATH=${PATH}:${HOME}/MacSoftware/bin
> (firedrake) :/PETSc3/fem$ which libtoolize
> /Users/knepley/MacSoftware/bin/libtoolize
> (firedrake) :/PETSc3/fem$ firedrake-update --honour-pythonpath
> Running /PETSc3/fem/firedrake/bin/firedrake-update --honour-pythonpath
> Updating the git repository for firedrake
> Creating firedrake-update script.
> Running ../bin/firedrake-update --no-update-script --honour-pythonpath
> Xcode and homebrew installation disabled. Proceeding on the rash assumption that packaged dependencies are in place.
> Finding dependencies of PyOP2
>
> Finding dependencies of firedrake
>
> Updating the git repository for petsc4py
> Updating the git repository for COFFEE
> Updating the git repository for ufl
> Updating the git repository for fiat
> Updating the git repository for FInAT
> Updating the git repository for tsfc
> Updating the git repository for PyOP2
> Updating the git repository for firedrake
> Installing pip dependencies for COFFEE
> Installing pip dependencies for ufl
> No dependencies found. Skipping.
> Installing pip dependencies for fiat
> No dependencies found. Skipping.
> Installing pip dependencies for FInAT
> Installing pip dependencies for tsfc
> Installing pip dependencies for PyOP2
> Installing pip dependencies for firedrake
> Installing h5py
> Updating the git repository for h5py
> No need to rebuild h5py
> Installing libspatialindex
> Updating the git repository for libspatialindex
> No need to rebuild libspatialindex
> Cleaning COFFEE
> Installing COFFEE/
> Cleaning ufl
> Installing ufl/
> Cleaning fiat
> Installing fiat/
> Cleaning FInAT
> Installing FInAT/
> Cleaning tsfc
> Installing tsfc/
> Cleaning PyOP2
> Traceback (most recent call last):
>   File "../bin/firedrake-update", line 1216, in <module>
>     clean(p)
>   File "../bin/firedrake-update", line 633, in clean
>     check_call(["python", "setup.py", "clean"])
>   File "../bin/firedrake-update", line 435, in check_call
>     log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode())
>   File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 336, in check_output
>     **kwargs).stdout
>   File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 418, in run
>     output=stdout, stderr=stderr)
> subprocess.CalledProcessError: Command '['python', 'setup.py', 'clean']' returned non-zero exit status 1.
>
>
> Update log saved in firedrake-update.log
> 
> Here is the log.
>
> I see. My petsc4py is not visible in this venv. WIll fix that.
>
We should have installed petsc4py, but obviously didn't and then the firedrake-update has some logic to not rebuild it.

Just "pip install -U --no-deps firedrake/src/petsc4py"

Lawrence