[MacPorts] #45157: Dolfin import error
#45157: Dolfin import error -----------------------+-------------------------------- Reporter: mwathen@… | Owner: macports-tickets@… Type: defect | Status: new Priority: High | Milestone: Component: ports | Version: 2.3.1 Keywords: | Port: -----------------------+-------------------------------- Hi, I updated my macport packages and when I now try and import dolfin i get the following error import dolfin --------------------------------------------------------------------------- Exception Traceback (most recent call last) <ipython-input-1-7d9b2153bc0b> in <module>() ----> 1 import dolfin /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/__init__.py in <module>() 2 3 # Special module to handle import issues ----> 4 import dolfin.importhandler 5 6 # Import UFL form language /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/importhandler/__init__.py in <module>() 37 for dep in runtime_dependencies: 38 try: ---> 39 __import__(dep) 40 except ImportError, e: 41 import sys /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/__init__.py in <module>() 16 17 # Import compiler functions ---> 18 from ffc.compiler import compile_form, compile_element 19 20 # Import JIT compiler /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/compiler.py in <module>() 125 126 # FFC modules --> 127 from ffc.analysis import analyze_forms, analyze_elements 128 from ffc.representation import compute_ir 129 from ffc.optimization import optimize_ir /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/analysis.py in <module>() 40 from ffc.log import log, info, begin, end, warning, debug, error, ffc_assert, warning_blue 41 from ffc.utils import all_equal ---> 42 from ffc.quadratureelement import default_quadrature_degree 43 from ffc.utils import all_equal 44 from ffc.tensor import estimate_cost /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/quadratureelement.py in <module>() 25 26 # FIAT modules. ---> 27 from FIAT.functional import PointEvaluation 28 29 # FFC modules. /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/__init__.py in <module>() 9 10 # Import finite element classes ---> 11 from FIAT.finite_element import FiniteElement 12 from FIAT.argyris import Argyris 13 from FIAT.argyris import QuinticArgyris /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/finite_element.py in <module>() 17 18 import numpy ---> 19 from .polynomial_set import PolynomialSet 20 21 class FiniteElement: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/polynomial_set.py in <module>() 27 # an entire set of polynomials) 28 ---> 29 from . import expansions 30 import numpy 31 from .functional import index_iterator /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/expansions.py in <module>() 32 Unable to import the Python Scientific module required by FIAT. 33 Consider installing the package python-scientific. ---> 34 """) 35 36 def xi_triangle( eta ): Exception: Unable to import the Python Scientific module required by FIAT. Consider installing the package python-scientific. I checked that the Python Scientific module is installed ---> Computing dependencies for py-scientific ---> Fetching archive for py-scientific ---> Attempting to fetch py-scientific-2.9.3_0.darwin_13.noarch.tbz2 from http://packages.macports.org/py-scientific ---> Attempting to fetch py- scientific-2.9.3_0.darwin_13.noarch.tbz2.rmd160 from http://packages.macports.org/py-scientific ---> Installing py-scientific @2.9.3_0 ---> Activating py-scientific @2.9.3_0 ---> Cleaning py-scientific ---> Updating database of binaries ---> Scanning binaries for linking errors ---> No broken files found. but I still get the same error.... -- Ticket URL: <https://trac.macports.org/ticket/45157> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------------------- Reporter: mwathen@… | Owner: macports-tickets@… Type: defect | Status: new Priority: High | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: | ------------------------+-------------------------------- Comment (by mwathen@…): Hi, I updated my macport packages and when I now try and import dolfin i get the following error {{{ import dolfin Exception Traceback (most recent call last) <ipython-input-1-7d9b2153bc0b> in <module>() /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/init.py in <module>() 2 3 # Special module to handle import issues 5 6 # Import UFL form language /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/importhandler/init.py in <module>() 37 for dep in runtime_dependencies: 38 try: ---> 39 import(dep) 40 except ImportError, e: 41 import sys /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/init.py in <module>() 16 17 # Import compiler functions ---> 18 from ffc.compiler import compile_form, compile_element 19 20 # Import JIT compiler /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/compiler.py in <module>() 125 126 # FFC modules --> 127 from ffc.analysis import analyze_forms, analyze_elements 128 from ffc.representation import compute_ir 129 from ffc.optimization import optimize_ir /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/analysis.py in <module>() 40 from ffc.log import log, info, begin, end, warning, debug, error, ffc_assert, warning_blue 41 from ffc.utils import all_equal ---> 42 from ffc.quadratureelement import default_quadrature_degree 43 from ffc.utils import all_equal 44 from ffc.tensor import estimate_cost /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/quadratureelement.py in <module>() 25 26 # FIAT modules. ---> 27 from FIAT.functional import PointEvaluation 28 29 # FFC modules. /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/init.py in <module>() 9 10 # Import finite element classes ---> 11 from FIAT.finite_element import FiniteElement 12 from FIAT.argyris import Argyris 13 from FIAT.argyris import QuinticArgyris /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/finite_element.py in <module>() 17 18 import numpy ---> 19 from .polynomial_set import PolynomialSet 20 21 class FiniteElement: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/polynomial_set.py in <module>() 27 # an entire set of polynomials) 28 ---> 29 from . import expansions 30 import numpy 31 from .functional import index_iterator /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/expansions.py in <module>() 32 Unable to import the Python Scientific module required by FIAT. 33 Consider installing the package python-scientific. ---> 34 """) 35 36 def xi_triangle( eta ): Exception: Unable to import the Python Scientific module required by FIAT. Consider installing the package python-scientific. }}} I checked that the Python Scientific module is installed {{{ ---> Computing dependencies for py-scientific ---> Fetching archive for py-scientific ---> Attempting to fetch py-scientific-2.9.3_0.darwin_13.noarch.tbz2 from http://packages.macports.org/py-scientific ---> Attempting to fetch py- scientific-2.9.3_0.darwin_13.noarch.tbz2.rmd160 from http://packages.macports.org/py-scientific ---> Installing py-scientific @2.9.3_0 ---> Activating py-scientific @2.9.3_0 ---> Cleaning py-scientific ---> Updating database of binaries ---> Scanning binaries for linking errors ---> No broken files found. }}} but I still get the same error.... -- Ticket URL: <https://trac.macports.org/ticket/45157#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------- Reporter: mwathen@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: dolfin | ------------------------+-------------------- Changes (by ryandesign@…): * owner: macports-tickets@… => sean@… * priority: High => Normal * port: => dolfin Old description:
Hi,
I updated my macport packages and when I now try and import dolfin i get the following error
import dolfin --------------------------------------------------------------------------- Exception Traceback (most recent call last) <ipython-input-1-7d9b2153bc0b> in <module>() ----> 1 import dolfin
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/__init__.py in <module>() 2 3 # Special module to handle import issues ----> 4 import dolfin.importhandler 5 6 # Import UFL form language
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/importhandler/__init__.py in <module>() 37 for dep in runtime_dependencies: 38 try: ---> 39 __import__(dep) 40 except ImportError, e: 41 import sys
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/__init__.py in <module>() 16 17 # Import compiler functions ---> 18 from ffc.compiler import compile_form, compile_element 19 20 # Import JIT compiler
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/compiler.py in <module>() 125 126 # FFC modules --> 127 from ffc.analysis import analyze_forms, analyze_elements 128 from ffc.representation import compute_ir 129 from ffc.optimization import optimize_ir
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/analysis.py in <module>() 40 from ffc.log import log, info, begin, end, warning, debug, error, ffc_assert, warning_blue 41 from ffc.utils import all_equal ---> 42 from ffc.quadratureelement import default_quadrature_degree 43 from ffc.utils import all_equal 44 from ffc.tensor import estimate_cost
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/quadratureelement.py in <module>() 25 26 # FIAT modules. ---> 27 from FIAT.functional import PointEvaluation 28 29 # FFC modules.
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/__init__.py in <module>() 9 10 # Import finite element classes ---> 11 from FIAT.finite_element import FiniteElement 12 from FIAT.argyris import Argyris 13 from FIAT.argyris import QuinticArgyris
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/finite_element.py in <module>() 17 18 import numpy ---> 19 from .polynomial_set import PolynomialSet 20 21 class FiniteElement:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/polynomial_set.py in <module>() 27 # an entire set of polynomials) 28 ---> 29 from . import expansions 30 import numpy 31 from .functional import index_iterator
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/expansions.py in <module>() 32 Unable to import the Python Scientific module required by FIAT. 33 Consider installing the package python-scientific. ---> 34 """) 35 36 def xi_triangle( eta ):
Exception: Unable to import the Python Scientific module required by FIAT. Consider installing the package python-scientific.
I checked that the Python Scientific module is installed
---> Computing dependencies for py-scientific ---> Fetching archive for py-scientific ---> Attempting to fetch py-scientific-2.9.3_0.darwin_13.noarch.tbz2 from http://packages.macports.org/py-scientific ---> Attempting to fetch py- scientific-2.9.3_0.darwin_13.noarch.tbz2.rmd160 from http://packages.macports.org/py-scientific ---> Installing py-scientific @2.9.3_0 ---> Activating py-scientific @2.9.3_0 ---> Cleaning py-scientific ---> Updating database of binaries ---> Scanning binaries for linking errors ---> No broken files found.
but I still get the same error....
New description: Hi, I updated my macport packages and when I now try and import dolfin i get the following error {{{ import dolfin --------------------------------------------------------------------------- Exception Traceback (most recent call last) <ipython-input-1-7d9b2153bc0b> in <module>() ----> 1 import dolfin /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/__init__.py in <module>() 2 3 # Special module to handle import issues ----> 4 import dolfin.importhandler 5 6 # Import UFL form language /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/importhandler/__init__.py in <module>() 37 for dep in runtime_dependencies: 38 try: ---> 39 __import__(dep) 40 except ImportError, e: 41 import sys /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/__init__.py in <module>() 16 17 # Import compiler functions ---> 18 from ffc.compiler import compile_form, compile_element 19 20 # Import JIT compiler /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/compiler.py in <module>() 125 126 # FFC modules --> 127 from ffc.analysis import analyze_forms, analyze_elements 128 from ffc.representation import compute_ir 129 from ffc.optimization import optimize_ir /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/analysis.py in <module>() 40 from ffc.log import log, info, begin, end, warning, debug, error, ffc_assert, warning_blue 41 from ffc.utils import all_equal ---> 42 from ffc.quadratureelement import default_quadrature_degree 43 from ffc.utils import all_equal 44 from ffc.tensor import estimate_cost /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/quadratureelement.py in <module>() 25 26 # FIAT modules. ---> 27 from FIAT.functional import PointEvaluation 28 29 # FFC modules. /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/__init__.py in <module>() 9 10 # Import finite element classes ---> 11 from FIAT.finite_element import FiniteElement 12 from FIAT.argyris import Argyris 13 from FIAT.argyris import QuinticArgyris /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/finite_element.py in <module>() 17 18 import numpy ---> 19 from .polynomial_set import PolynomialSet 20 21 class FiniteElement: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/polynomial_set.py in <module>() 27 # an entire set of polynomials) 28 ---> 29 from . import expansions 30 import numpy 31 from .functional import index_iterator /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/expansions.py in <module>() 32 Unable to import the Python Scientific module required by FIAT. 33 Consider installing the package python-scientific. ---> 34 """) 35 36 def xi_triangle( eta ): Exception: Unable to import the Python Scientific module required by FIAT. Consider installing the package python-scientific. }}} I checked that the Python Scientific module is installed {{{ ---> Computing dependencies for py-scientific ---> Fetching archive for py-scientific ---> Attempting to fetch py-scientific-2.9.3_0.darwin_13.noarch.tbz2 from http://packages.macports.org/py-scientific ---> Attempting to fetch py- scientific-2.9.3_0.darwin_13.noarch.tbz2.rmd160 from http://packages.macports.org/py-scientific ---> Installing py-scientific @2.9.3_0 ---> Activating py-scientific @2.9.3_0 ---> Cleaning py-scientific ---> Updating database of binaries ---> Scanning binaries for linking errors ---> No broken files found. }}} but I still get the same error.... -- -- Ticket URL: <https://trac.macports.org/ticket/45157#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------- Reporter: mwathen@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: dolfin | ------------------------+-------------------- Comment (by krishnamurthy.vijaykumar@…): I can confirm this. Same problem. Today I tried to reinstall dolfin and and it fails at the configuring stage with the same error. Relevant portion of the main.log file {{{ :info:configure -- Generating SWIG interface. :info:configure -- -------------------------- :info:configure -- :info:configure -- Generating form files in demo, test, bench and dolfin directories. May take some time... :info:configure -- ---------------------------------------------------------------------------------------- :info:configure CMake Error at CMakeLists.txt:825 (message): :info:configure Generation of form files failed: :info:configure :info:configure Traceback (most recent call last): :info:configure :info:configure File "/opt/local/bin/ffc", line 45, in <module> :info:configure from ffc.log import info :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/__init__.py", line 18, in <module> :info:configure from ffc.compiler import compile_form, compile_element :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/compiler.py", line 127, in <module> :info:configure from ffc.analysis import analyze_forms, analyze_elements :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/analysis.py", line 42, in <module> :info:configure from ffc.quadratureelement import default_quadrature_degree :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc/quadratureelement.py", line 27, in <module> :info:configure from FIAT.functional import PointEvaluation :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/__init__.py", line 11, in <module> :info:configure from FIAT.finite_element import FiniteElement :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/finite_element.py", line 19, in <module> :info:configure from .polynomial_set import PolynomialSet :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/polynomial_set.py", line 29, in <module> :info:configure from . import expansions :info:configure File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/FIAT/expansions.py", line 34, in <module> :info:configure """) :info:configure :info:configure Exception: Unable to import the Python Scientific module required by FIAT. :info:configure :info:configure Consider installing the package python-scientific. :info:configure :info:configure :info:configure :info:configure Traceback (most recent call last): :info:configure :info:configure File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.4.0/cmake/scripts /generate-form-files", line 80, in <module> :info:configure raise RuntimeError, "Unable to compile form: %s/%s" % (root, f) :info:configure :info:configure RuntimeError: Unable to compile form: dolfin/ale/Poisson1D.ufl :info:configure :info:configure :info:configure :info:configure -- Configuring incomplete, errors occurred! }}} -- Ticket URL: <https://trac.macports.org/ticket/45157#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------- Reporter: mwathen@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: dolfin | ------------------------+-------------------- Comment (by sean@…): I finally got around to reproducing this. Looking into it now. -- Ticket URL: <https://trac.macports.org/ticket/45157#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------- Reporter: mwathen@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: dolfin | ------------------------+-------------------- Comment (by sean@…): It appears this is a problem with the new [[https://github.com/numpy/numpy/blob/master/doc/release/1.9.0-notes.rst|numpy 1.9]]: * The oldnumeric and numarray modules have been removed. Scientific Python needs this module, so I've created an issue [[https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has- dropped-support-for|here]]. -- Ticket URL: <https://trac.macports.org/ticket/45157#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------- Reporter: mwathen@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: dolfin | ------------------------+-------------------- Comment (by krishnamurthy.vijaykumar@…): Hi Sean, It looks like the dev version of fiat does not have this problem. Would it be possible to make use of this and fix the dolfin port? See here http://fenicsproject.org/pipermail/fenics- support/2014-October/000909.html -Vijay Replying to [comment:7 sean@…]:
It appears this is a problem with the new [[https://github.com/numpy/numpy/blob/master/doc/release/1.9.0-notes.rst|numpy 1.9]]:
* The oldnumeric and numarray modules have been removed.
Scientific Python needs this module, so I've created an issue [[https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has- dropped-support-for|here]].
-- Ticket URL: <https://trac.macports.org/ticket/45157#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------- Reporter: mwathen@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: dolfin | ------------------------+-------------------- Comment (by sean@…): Yeah, looks like that is what I'll have to do. I'm a little busy with work but will try to get around to this later this week. If you feel encouraged to write a patch, please don't hesitate to upload it here :-) -- Ticket URL: <https://trac.macports.org/ticket/45157#comment:10> MacPorts <http://www.macports.org/> Ports system for OS X
#45157: Dolfin import error ------------------------+-------------------- Reporter: mwathen@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Resolution: | Keywords: Port: dolfin | ------------------------+-------------------- Comment (by krishnamurthy.vijaykumar@…): I would be happy to help. But I have never written a patch and don't know how to do that either. If there are some guidelines, let me know and I'll do what I can. -- Ticket URL: <https://trac.macports.org/ticket/45157#comment:11> MacPorts <http://www.macports.org/> Ports system for OS X
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