Hmm, perhaps cythonizing by hand is your best bet: $ cython carray/carrayExtension.pyx
If you continue having problems, please write to the carray mailing list. Francesc On 12/7/12 5:29 PM, Alvaro Tejero Cantero wrote: > I have now similar dependencies as you, except for Numpy 1.7 beta 2. > > I wish I could help with the carray flavor. > > -- > Running setup.py install for carray > * Found Cython 0.17.2 package installed. > * Found numpy 1.6.2 package installed. > * Found numexpr 2.0.1 package installed. > building 'carray.carrayExtension' extension > C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC > -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 > -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC > compile options: '-Iblosc > -I/home/tejero/Local/Envs/test/lib/python2.7/site-packages/numpy/core/include > -I/usr/include/python2.7 -c' > extra options: '-msse2' > gcc: blosc/blosclz.c > gcc: carray/carrayExtension.c > gcc: error: carray/carrayExtension.c: No such file or directory > gcc: fatal error: no input files > compilation terminated. > gcc: error: carray/carrayExtension.c: No such file or directory > gcc: fatal error: no input files > compilation terminated. > error: Command "gcc -pthread -fno-strict-aliasing -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC > -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 > -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Iblosc > -I/home/tejero/Local/Envs/test/lib/python2.7/site-packages/numpy/core/include > -I/usr/include/python2.7 -c carray/carrayExtension.c -o > build/temp.linux-x86_64-2.7/carray/carrayExtension.o -msse2" failed > with exit status 4 > > > > -รก. > > > > On 7 December 2012 12:47, Francesc Alted <fal...@gmail.com > <mailto:fal...@gmail.com>> wrote: > > On 12/6/12 1:42 PM, Alvaro Tejero Cantero wrote: > > Thank you for the comprehensive round-up. I have some ideas and > > reports below. > > > > What about ctables? The documentation says that it is specificly > > column-access optimized, which is what I need in this scenario > > (sometimes sequential, sometimes random). > > Yes, ctables is optimized for column access. > > > > > Unfortunately I could not get the rootdir parameter for ctables > > __init__ to work in carray 0.4 and pip-installing 0.5 or 0.5.1 leads > > to compilation errors. > > Yep, persistence for carray/ctables objects was added in 0.5. > > > > > This is the ctables-to-disk error: > > > > ct2 = ca.ctable((np.arange(30000000),), names=('range2',), > > rootdir='/tmp/ctable2.ctable') > > > > --------------------------------------------------------------------------- > > TypeError Traceback (most > recent call last) > > > /home/tejero/Dropbox/O/nb/nonridge/<ipython-input-29-255842877a0b> > in<module>() > > ----> 1 ct2= ca.ctable((np.arange(30000000),), > names=('range2',), rootdir='/tmp/ctable2.ctable') > > > > > /home/tejero/Local/Envs/test/lib/python2.7/site-packages/carray/ctable.pyc > in__init__(self, cols, names, **kwargs) > > 158 if column.dtype== np.void: > > 159 raise ValueError, "`cols` > elements cannot be of type void" > > --> 160 column= ca.carray(column, **kwargs) > > 161 elif ratype: > > 162 column= ca.carray(cols[name], **kwargs) > > > > > > /home/tejero/Local/Envs/test/lib/python2.7/site-packages/carray/carrayExtension.so > incarray.carrayExtension.carray.__cinit__ > (carray/carrayExtension.c:3917)() > > > > TypeError: __cinit__() got an unexpected keyword argument 'rootdir' > > > > > > And this is cut from the pip output when trying to upgrade carray. > > > > gcc: carray/carrayExtension.c > > > > gcc: error: carray/carrayExtension.c: No such file or directory > > Hmm, that's strange, because the carrayExtension should have been > cythonized automatically. Here it is part of my install process > with pip: > > Running setup.py install for carray > * Found Cython 0.17.1 package installed. > * Found numpy 1.7.0b2 package installed. > * Found numexpr 2.0.1 package installed. > cythoning carray/carrayExtension.pyx to carray/carrayExtension.c > building 'carray.carrayExtension' extension > C compiler: gcc -fno-strict-aliasing > -I/Users/faltet/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 > -Wall -Wstrict-prototypes > > Hmm, perhaps you need a newer version of Cython? > > > > > > > Two more notes: > > > > * a way was added to check in-disk (compressed) vs in-memory > > (uncompressed) node sizes. I was unable to find the way to use it > > either from the 2.4.0 release notes or from the git issue > > https://github.com/PyTables/PyTables/issues/141#issuecomment-5018763 > > You already found the answer. > > > > > * is/will it be possible to load PyTables carrays as in-memory > carrays > > without decompression? > > Actually, that has been my idea from the very beginning. The > concept of > 'flavor' for the returned objects when reading is already there, so it > should be relatively easy to add a new 'carray' flavor. Maybe you can > contribute this? > > -- > Francesc Alted > > > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add > services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > Pytables-users mailing list > Pytables-users@lists.sourceforge.net > <mailto:Pytables-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/pytables-users > > > > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > > > _______________________________________________ > Pytables-users mailing list > Pytables-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pytables-users -- Francesc Alted ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
