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

[Hannes R. <han...@gm...>]

Hi Antonio

thank you for reporting this.

@all: this problem does exist in the distributed release source code
version, not in any distributed binary package. I would like to patch
this. Would people generally prefer to have a 1.11.2 OpenMS source
code release (but no binary release) or would a "silent" patch of the
source code files be preferred (otherwise people might get confused to
why there is no 1.11.2 binary download).

Hannes





On 31 May 2014 13:02, Antonio Trande <ant...@gm...> wrote:
> 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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