I'll make these changes to the sources as well so that users are not bitten by these numpy bugs in the future. The bug workarounds are not invasive or damaging, so this should be no issue.
Cheers, Edward On 19 October 2012 21:29, Jack Howarth <[email protected]> wrote: > On Fri, Oct 19, 2012 at 05:27:25PM +0200, Edward d'Auvergne wrote: >> Hi, >> >> This is now another problem which I haven't encountered because none >> of my test systems (Mac OS X 10.6 and 10.7, MS Windows 2000 and 7, and >> GNU/Linux (with Python 2.3, 2.4, 2.5, 2.6, 2.7, 3.1, 3.2, and 3.3)) >> have the Scientific Python module installed anymore. I'll have to >> play with this on the weekend. This new issue is the VMD interfacing >> via Scientific Python. I would suggest changing the Scientific Python >> VMD section from the dep_check.py file. I.e. on line 160 from: >> >> "except ImportError:" >> >> to: >> >> "except:" >> >> as a work around. I might have to report this as a numpy bug - from >> all the reports I can now clearly see that that is where the broken >> code is - but also have relax work around it. I hope you don't see >> any other problems. >> >> Cheers, >> >> Edward > > Edward, > Thanks, that additional change was sufficient, with the other two patches, > to allow relax 2.1.2 to build > under fink. I'll just add those to the relax-py.patch for now and use the > existing relax 2.1.2 tarball. > Jack > >> >> >> >> >> On 19 October 2012 17:13, Jack Howarth <[email protected]> wrote: >> > On Fri, Oct 19, 2012 at 04:54:21PM +0200, Edward d'Auvergne wrote: >> >> Hi Jack, >> >> >> >> I noticed this one too late. It is a very, very strange error! The >> >> problem is scipy: it's a bit of a wild mix of crazy code which tends >> >> to do a lot of weird low level things to Python. In this case, I >> >> traced the problem back to a change which only affected the import of >> >> the ctypes Python module. I really don't know how slightly changing a >> >> ctypes import statement would trigger a bug in scipy - that is >> >> bizarre. I fixed it after branching relax 2.1.2 at: >> >> >> >> http://article.gmane.org/gmane.science.nmr.relax.scm/15667 >> >> http://article.gmane.org/gmane.science.nmr.relax.scm/15668 >> >> >> >> There are two options, the change at r17912 >> >> (http://article.gmane.org/gmane.science.nmr.relax.scm/15668) should be >> >> sufficient and could be ported to the 2.1.2 code. Or I could release >> >> 2.1.3 with just this change and only release the source tar.bz2 file >> >> for fink. Which option is easiest for you? >> >> >> >> Cheers, >> >> >> >> Edward >> > >> > Edward, >> > Neither http://article.gmane.org/gmane.science.nmr.relax.scm/15668 or >> > it in combination with >> > http://article.gmane.org/gmane.science.nmr.relax.scm/15667 >> > appear to be sufficient to eliminate the error here... >> > >> > /sw/bin/python2.7 /sw/bin/scons >> > scons: Reading SConscript files ... >> > AttributeError: 'builtin_function_or_method' object has no attribute >> > 'dispatch': >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/SConstruct", >> > line 37: >> > from scons.distrib import package, gpg_sign >> > File >> > "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/scons/distrib.py", line >> > 32: >> > from version import version >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/version.py", >> > line 26: >> > import dep_check >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/dep_check.py", >> > line 157: >> > from Scientific.Visualization import VMD # This requires Numeric to >> > be installed (at least in Scientific 2.7.8). >> > File "/sw/lib/python2.7/site-packages/Scientific/Visualization/VMD.py", >> > line 40: >> > from Scientific.Geometry import Transformation, Vector, ex, ey, ez >> > File "/sw/lib/python2.7/site-packages/Scientific/Geometry/__init__.py", >> > line 25: >> > import Scientific_vector >> > File "Scientific_vector.pyx", line 13: >> > None >> > File "/sw/lib/python2.7/site-packages/Scientific/N.py", line 15: >> > from numpy.oldnumeric import * >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/__init__.py", >> > line 14: >> > from compat import * >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py", line >> > 106: >> > class Unpickler(pickle.Unpickler): >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py", line >> > 110: >> > dispatch = copy.copy(pickle.Unpickler.dispatch) >> > >> > Jack >> >> >> >> >> >> >> >> On 19 October 2012 16:00, Jack Howarth <[email protected]> wrote: >> >> > Edward, >> >> > While trying to update the current fink relax-py packaging to the >> >> > new 2.1.2 release. >> >> > I ran into a build failure of the form... >> >> > >> >> > /sw/bin/python2.7 /sw/bin/scons >> >> > scons: Reading SConscript files ... >> >> > AttributeError: 'builtin_function_or_method' object has no attribute >> >> > 'dispatch': >> >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/SConstruct", >> >> > line 37: >> >> > from scons.distrib import package, gpg_sign >> >> > File >> >> > "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/scons/distrib.py", >> >> > line 32: >> >> > from version import version >> >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/version.py", >> >> > line 26: >> >> > import dep_check >> >> > File >> >> > "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/dep_check.py", line >> >> > 143: >> >> > import scipy >> >> > File "/sw/lib/python2.7/site-packages/scipy/__init__.py", line 85: >> >> > from numpy import oldnumeric >> >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/__init__.py", >> >> > line 14: >> >> > from compat import * >> >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py", >> >> > line 106: >> >> > class Unpickler(pickle.Unpickler): >> >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py", >> >> > line 110: >> >> > dispatch = copy.copy(pickle.Unpickler.dispatch) >> >> > >> >> > This failure didn't occur with the relax 2.1.0 or 2.1.1 releases. >> >> > Interestingly this >> >> > error looks like the one described in the thread... >> >> > >> >> > http://scons.tigris.org/ds/viewMessage.do?dsForumId=1272&dsMessageId=2695657 >> >> > >> >> > Jack _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
