September 2015 - macports-tickets - lists.macosforge.org

[MacPorts] #48168: openmpi Update to 1.8.6
by MacPorts 09 Sep '15

09 Sep '15

#48168: openmpi Update to 1.8.6 -------------------------------------+-------------------------------- Reporter: hans.ekkehard.plesser@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: openmpi -------------------------------------+-------------------------------- The attached patch - updates openmpi to version 1.8.6 - adds 5.1 to the list of gcc versions It is my first attempt at updating a portfile, I hope it will be useful. -- Ticket URL: <https://trac.macports.org/ticket/48168> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48768: julia: use llvm-3.6 or -3.7
by MacPorts 09 Sep '15

09 Sep '15

#48768: julia: use llvm-3.6 or -3.7 --------------------------+-------------------- Reporter: ryandesign@… | Owner: sean@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: julia --------------------------+-------------------- julia currently uses llvm-3.5. Could this please be changed to use a newer stable version of llvm, such as llvm-3.6 or (after #48759 is resolved) llvm-3.7? julia also defaults to the gcc49 variant, but gcc5 is the latest stable version; perhaps gcc5 could be used by default as well. -- Ticket URL: <https://trac.macports.org/ticket/48768> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48604: Dolfin install fails
by MacPorts 09 Sep '15

09 Sep '15

#48604: Dolfin install fails -----------------------------+-------------------------------- Reporter: eld.khattatov@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: dolfin -----------------------------+-------------------------------- Hello, When trying to install dolfin I am getting the following error message: {{{ ---> Computing dependencies for dolfin ---> Configuring dolfin Error: org.macports.configure for port dolfin returned: configure failure: command execution failed Please see the log file for port dolfin for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port dolfin failed }}} I have already installed py-ffc, py-fiat, py-instant and py-ufl of version 1.5.0, although there were two warnings during the installation of these: {{{ Warning: Error parsing file /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ffc_time_ext/time_elements_ext.so: Error opening or reading file Warning: Error parsing file /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/ufc/_ufc.so: Error opening or reading file }}} The log file "main.log" is also attached, the error there is "ImportError: No module named ufc", however on the "ufc" port page it is written that it is no longer needed as it was included in ffc. Could you please recommend me the way of solving this issue? Thank you. -- Ticket URL: <https://trac.macports.org/ticket/48604> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48235: Cannot upgrade to slepc, possible mismatch b/w petsc and slepc
by MacPorts 09 Sep '15

09 Sep '15

#48235: Cannot upgrade to slepc, possible mismatch b/w petsc and slepc ------------------------+-------------------------------- Reporter: cpraveen@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: slepc ------------------------+-------------------------------- Hi I upgrade to petsc 3.5.3_2 but slepc latest version is showing as 3.5.3_1 I am not able to upgrade slepc. I have attached log file. -- Ticket URL: <https://trac.macports.org/ticket/48235> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48169: openmpi @1.7.5 enforces flat namespace, causing problems with some applications
by MacPorts 09 Sep '15

09 Sep '15

#48169: openmpi @1.7.5 enforces flat namespace, causing problems with some applications -------------------------------------+-------------------------------- Reporter: hans.ekkehard.plesser@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: openmpi -------------------------------------+-------------------------------- Per [118768], `configure.args` were extended to enforce a flat namespace when building OpenMPI. This was necessary to solve #42667 and #39826. Unfortunately, this causes problems for other applications which rely on two-level namespaces, e.g. when combining a C++ application using MPI with a Python interface. These problems disappear when [118768] is reversed. Since flat namespaces apparently are needed in some cases, and two-level namespaces in others, I think the openmpi port should have a variant that allows users to choose between flat and two-level namespaces. Unfortunately, the openmpi Portfile looks too intimidating for me to try to add such a variant. Since Apple deprecates flat namespaces ([https://developer.apple.com/library/mac/documentation/Porting/Conceptual/Po… Apple Developer Docs]) and many ports recently seem to have been transitioning to two-level namespaces, I would suggest to make two-level namespaces (i.e., pre-[11768] behavior) the default. -- Ticket URL: <https://trac.macports.org/ticket/48169> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48072: dolfin @1.5.0_2 command "import dolfin" fails in python
by MacPorts 09 Sep '15

09 Sep '15

#48072: dolfin @1.5.0_2 command "import dolfin" fails in python ------------------------+-------------------------------- Reporter: hgonzale@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: dolfin ------------------------+-------------------------------- Running the following command: {{{ % python -c "import dolfin" }}} generates the following error: {{{ Traceback (most recent call last): File "<string>", line 1, in <module> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/__init__.py", line 16, in <module> from . import cpp File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/cpp/__init__.py", line 42, in <module> exec("from . import %s" % module_name) File "<string>", line 1, in <module> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/cpp/common.py", line 132, in <module> __pythonversion__ = "%d.%d.%d"%(tuple(map(int, [tmp[2], tmp[4], tmp[6]]))) ValueError: invalid literal for int() with base 10: 'a' }}} I'm using python version 2.7.10, installed using Macports. -- Ticket URL: <https://trac.macports.org/ticket/48072> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48053: mpi-doc: supported_archs noarch
by MacPorts 09 Sep '15

09 Sep '15

#48053: mpi-doc: supported_archs noarch --------------------------+--------------------- Reporter: ryandesign@… | Owner: sean@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.99 Keywords: | Port: mpi-doc --------------------------+--------------------- mpi-doc does not appear to install any architecture-specific files, so it should indicate this by using "supported_archs noarch". -- Ticket URL: <https://trac.macports.org/ticket/48053> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #47935: py34-scipy doesn't include weave
by MacPorts 09 Sep '15

09 Sep '15

#47935: py34-scipy doesn't include weave ------------------------+-------------------------------- Reporter: macports@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: py34-scipy ------------------------+-------------------------------- I've got both py27-scipy and py34-scipy installed, and weave is missing from the latter. {{{ py27-scipy @0.15.1_0+gfortran (active) py34-scipy @0.15.1_0+gfortran (active) }}} I have: {{{ /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/weave/ }}} but not {{{ /opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4 /site-packages/scipy/weave/ }}} I can't see any indication from the package info or variants that there's any way to configure it differently to include/exclude weave, and the scipy docs seem to suggest any installation of scipy will include weave, so not sure why this would be the case. py34-scipy seems to be installed pre-built from binaries (?), so wondering if its an issue with the build, or a technical problem with weave being pre-built? (i.e. does it need to be built locally?) -- Ticket URL: <https://trac.macports.org/ticket/47935> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48701: julia @0.3.11 fails building using MacPorts clang
by MacPorts 09 Sep '15

09 Sep '15

#48701: julia @0.3.11 fails building using MacPorts clang ------------------------+-------------------------------- Reporter: braumann@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: julia ------------------------+-------------------------------- As I had noticed that clang version 3.0 (tags/Apple/clang-211.10.1) shipped with Xcode 4.2 is not capable to build julia (it stops after a while complaining about a missing cholmod.h) I came up with the idea to use a newer MacPorts clang, e.g. 3.5: {{{ sudo port -d install julia configure.compiler=macports-clang-3.5 }}} In fact, during configuring the main component are being set {{{CC=/opt/local/bin/clang-mp-3.5 CXX=/opt/local/bin/clang++-mp-3.5 FC=/opt/local/bin/gfortran-mp-4.9}}} However, julia then expects a non-existing variant of ar: /opt/local/bin/clang-ar: No such file or directory Instead, julia should take /opt/local/bin/llvm-ar-mp-3.5 (which in turn is a shell script pointing to /opt/local/libexec/llvm-3.5/bin/llvm-ar). Since I have no idea how to work around this problem on the Portfile level, my first attempt was to make a copy of the llvm-ar-mp-3.5 shell script under the name clang-ar. To my surprise this did not work, it complained about an unknown switch -ru. So I gave up this without doing research on the switch variants of ar. So my last resort was to symlink a clang-ar to /usr/bin/ar - the latter is from Xcode (I suppose), inside /opt/local/bin I called {{{$ sudo ln -s /usr/bin/ar clang-ar}}}. This hack worked, and also is "valid" for other clang versions, e.g. 3.4 or 3.6! However, my experiment ended with a fatal error: {{{ ... In file included from codegen.cpp:35: In file included from /opt/local/libexec/llvm-3.5/include/llvm/ExecutionEngine/ExecutionEngine.h:19: In file included from /opt/local/libexec/llvm-3.5/include/llvm/ADT/SmallVector.h:17: /opt/local/libexec/llvm-3.5/include/llvm/ADT/iterator_range.h:37:29: error: no member named 'move' in namespace 'std' : begin_iterator(std::move(begin_iterator)), ~~~~~^ /opt/local/libexec/llvm-3.5/include/llvm/ADT/iterator_range.h:38:27: error: no member named 'move' in namespace 'std' end_iterator(std::move(end_iterator)) {} ~~~~~^ /opt/local/libexec/llvm-3.5/include/llvm/ADT/iterator_range.h:49:33: error: no member named 'move' in namespace 'std' return iterator_range<T>(std::move(x), std::move(y)); ~~~~~^ /opt/local/libexec/llvm-3.5/include/llvm/ADT/iterator_range.h:49:47: error: no member named 'move' in namespace 'std' return iterator_range<T>(std::move(x), std::move(y)); ~~~~~^ In file included from codegen.cpp:35: In file included from /opt/local/libexec/llvm-3.5/include/llvm/ExecutionEngine/ExecutionEngine.h:19: In file included from /opt/local/libexec/llvm-3.5/include/llvm/ADT/SmallVector.h:20: /opt/local/libexec/llvm-3.5/include/llvm/Support/MathExtras.h:21:10: fatal error: 'type_traits' file not found #include <type_traits> ^ 5 errors generated. ... }}} Any ideas? -- Ticket URL: <https://trac.macports.org/ticket/48701> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48432: import error common
by MacPorts 09 Sep '15

09 Sep '15

#48432: import error common ------------------------------+-------------------------------- Reporter: gideon.simpson@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: dolfin ------------------------------+-------------------------------- I recently cleaned up and updated my macports installation, and I'm getting the following error on dolfin: {{{ Python 2.7.10 (default, May 25 2015, 13:06:17) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import dolfin Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/__init__.py", line 16, in <module> from . import cpp File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/dolfin/cpp/__init__.py", line 42, in <module> exec("from . import %s" % module_name) File "<string>", line 1, in <module> ImportError: cannot import name common }}} -- Ticket URL: <https://trac.macports.org/ticket/48432> MacPorts <https://www.macports.org/> Ports system for OS X

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