include/except.h error

[sebastian-luna-valero]

Hello,

I get the following error when cythoning Python code in a conda environment:

cythoning CGAT/Components/Components.pyx to CGAT/Components/Components.cpp
building 'CGAT.Components' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/CGAT
creating build/temp.linux-x86_64-3.6/CGAT/Components
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/ifs/mirror/jenkins/PipelineRegressionTests/conda-install/envs/jenkins-env/include/python3.6m -c CGAT/Components/Components.cpp -o build/temp.linux-x86_64-3.6/CGAT/Components/Components.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
In file included from /ifs/mirror/jenkins/PipelineRegressionTests/conda-install/envs/jenkins-env/include/assert.h:5:0,
                 from /ifs/mirror/jenkins/PipelineRegressionTests/conda-install/envs/jenkins-env/include/python3.6m/Python.h:48,
                 from CGAT/Components/Components.cpp:4:
/ifs/mirror/jenkins/PipelineRegressionTests/conda-install/envs/jenkins-env/include/except.h:15:32: error: conflicting declaration 'typedef struct Except_Frame_T* Except_Frame_T'
 typedef struct Except_Frame_T *Except_Frame_T;
                                ^
/ifs/mirror/jenkins/PipelineRegressionTests/conda-install/envs/jenkins-env/include/except.h:15:16: error: 'struct Except_Frame_T' has a previous declaration as 'struct Except_Frame_T'
 typedef struct Except_Frame_T *Except_Frame_T;
                ^
/ifs/mirror/jenkins/PipelineRegressionTests/conda-install/envs/jenkins-env/include/except.h:17:18: error: field 'prev' has incomplete type
   Except_Frame_T prev;
                  ^
error: command 'gcc' failed with exit status 1

After googling [1,2], it looks like the problem is a broken include/except.h file. Could you please confirm?

Best regards,
Sebastian

[1] isovic/graphmap#77
[2] https://groups.google.com/forum/#!topic/bedtools-discuss/CURWF19qBuA

[sebastian-luna-valero]

It turned out to be an issue with gmap=2017.05.08 from bioconda.

Sorry for the noise.