[Debian-med-packaging] Bug#936609: Advent calendar bug squashing issue (Was: Bug#936609: cblas / gsl hint needed (Was: Bug#936609: Ported ghmm to Python3 but issues with clapack))

[Andreas Tille]

Hi folks,

this issue is something for our advent calendar.  Anybody with cblas
knowledge?

Kind regards

       Andreas.

On Mon, Jan 27, 2020 at 10:55:25AM +0100, Andreas Tille wrote:
> Hi again,
> 
> with my last mail I wanted to express:  Hmmmm, to stupid to turn
> this hint into real code.  Any more detailed hint / patch would be
> really welcome.
> 
> Kind regards
> 
>       Andreas.
> 
> On Mon, Jan 06, 2020 at 12:56:17PM +0100, Andreas Tille wrote:
> > Hi Mo,
> > 
> > On Sun, Jan 05, 2020 at 08:19:07AM +0000, Mo Zhou wrote:
> > > GSL provides a set of CBLAS API/ABI, delivered with shared object
> > > "libgslcblas.so" and header "gsl_cblas.h".  That subset becomes
> > > redundant once you include the headers of any standard/compatible
> > > (C)BLAS library. That's what the compilation error means.
> > 
> > Seems you want to tell me to not include gsl_cblas.h header.  However,
> > the code has no hit for
> > 
> >    grep -R gsl_cblas
> > 
> > so the header is not included explicitly.  So while your hint explains
> > the error I need to admit I have no idea yet, how to fix it.
> >  
> > > Make sure that the code only use one CBLAS implementation. In the
> > > context of debian, I'd recommend you use the CBLAS ABI from libblas-dev,
> > > and avoid linking against -lcblas. Link against -lblas instead.
> > 
> > OK, once I'm at the linking step I might come back to this hint.
> > 
> > Kind regards
> > 
> >       Andreas.
> >  
> > > On Sun, Jan 05, 2020 at 07:55:05AM +0100, Andreas Tille wrote:
> > > > Control: tags -1 help
> > > > 
> > > > Hi,
> > > > 
> > > > I was asking upstream about this issue[1] and an issue about gsl usage
> > > > is suspected.  Any hint how this can be fixed?
> > > > 
> > > > > Finally I have a question about building with lapack.  I get:
> > > > > 
> > > > > ...
> > > > > libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-fdebug-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong -      Wformat -Werror=format-security -I/usr/include -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c  -fPIC -DPIC -o .libs/rng.o
> > > > > In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,
> > > > >                  from matrixop.c:48:
> > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:9: error: nested redefinition of 'enum CBLAS_ORDER'
> > > > >     5 |    enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };
> > > > >       |         ^~~~~~~~~~~
> > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:9: error: redeclaration of 'enum CBLAS_ORDER'
> > > > > In file included from /usr/include/gsl/gsl_blas_types.h:28,
> > > > >                  from /usr/include/gsl/gsl_blas.h:29,
> > > > >                  from /usr/include/gsl/gsl_linalg.h:30,
> > > > >                  from matrixop.c:44:
> > > > > /usr/include/gsl/gsl_cblas.h:46:6: note: originally defined here
> > > > >    46 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
> > > > >       |      ^~~~~~~~~~~
> > > > > In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,
> > > > >                  from matrixop.c:48:
> > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:22: error: redeclaration of enumerator 'CblasRowMajor'
> > > > >     5 |    enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };
> > > > >       |                      ^~~~~~~~~~~~~
> > > > > In file included from /usr/include/gsl/gsl_blas_types.h:28,
> > > > >                  from /usr/include/gsl/gsl_blas.h:29,
> > > > >                  from /usr/include/gsl/gsl_linalg.h:30,
> > > > >                  from matrixop.c:44:
> > > > > /usr/include/gsl/gsl_cblas.h:46:19: note: previous definition of 'CblasRowMajor' was here
> > > > >    46 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
> > > > >       |                   ^~~~~~~~~~~~~
> > > > > In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,
> > > > >                  from matrixop.c:48:
> > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:41: error: redeclaration of enumerator 'CblasColMajor'
> > > > >     5 |    enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };
> > > > >       |                                         ^~~~~~~~~~~~~
> > > > > 
> > > > > 
> > > > 
> > > > Kind regards
> > > > 
> > > >      Andreas.
> > > > 
> > > > 
> > > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=936609#19
> > > > 
> > > > -- 
> > > > http://fam-tille.de
> > > > 
> > > 
> > 
> > -- 
> > http://fam-tille.de
> > 
> > 
> 
> -- 
> http://fam-tille.de
> 
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