Re: [Open-ms-general] Peak1D cannot be used as a template argument

[Antonio T. <ant...@gm...>]

On 05/31/2014 12:44 AM, Hannes Röst wrote:
> Hi Antonio

Hi Hannes.

> 
> Are you using Cython 0.19 or Cython 0.20 ? There is an issue with
> Cython 0.20 which we have fixed in the development version but which
> is probably still present in the 1.11 version:
> https://github.com/OpenMS/OpenMS/commit/32643435f91f18a2c311211a6ac2629f3bafdbb1
> 
> can you try to "rm pyOpenMS/addons/EmgFitter1D.pyx" and see whether
> that helps your situation?

It's related to Cython 0.20.
Patching  pyOpenMS/addons/EmgFitter1D.pyx fixes the problem.

Thanks.
> 
> Hannes
> 
> 
> On 30 May 2014 20:02, Antonio Trande <ant...@gm...> wrote:
> Hi all.
> 
> Another compilation error in OpenMS 1.11.1
> 
> Linking CXX executable bin/QCMerger
> /usr/bin/cmake -E cmake_link_script CMakeFiles/QCMerger.dir/link.txt
> --verbose=1
> /usr/lib64/ccache/c++   -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4
> -grecord-gcc-switches  -m64 -mtune=generic  -fopenmp -DNDEBUG
> -lQtCore -lQtGui
> CMakeFiles/QCMerger.dir/source/APPLICATIONS/UTILS/QCMerger.C.o  -o
> bin/QCMerger -rdynamic lib/libOpenMS.so -lQtOpenGL -lQtSvg -lQtWebKit
> -lQtTest -lQtXml -lQtSql -lQtNetwork lib/libOpenSwathAlgo.so -lgsl
> -lgslcblas -lsvm -lm -lxerces-c -lboost_iostreams -lboost_date_time
> -lboost_math_c99 -lboost_regex -lbz2 -lz -lglpk
> -Wl,-rpath,/home/sagitter/rpmbuild/BUILD/OpenMS-Release1.11.1/lib
> 
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
>         cdef _String _r = self.inst.get().getProductName()
>         py_result = _cast_const_away(<char*>_r.c_str())
>         return py_result
> 
> 
>     def fit1d(libcpp_vector[Peak1D] range_, InterpolationModel model):
>                            ^
> ------------------------------------------------------------
> 
> pyopenms/pyopenms.pyx:3047:28: Python object type 'Peak1D' cannot be
> used as a template argument
> 
> Same compilation environment reported in this mail
> http://sourceforge.net/p/open-ms/mailman/message/32398927/.
> 



-- 
Antonio Trande

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