Hi again, any more hints how we finally can build ghmm?
Kind regards Andreas. On Sat, Dec 05, 2020 at 04:52:14PM +0100, Andreas Tille wrote: > Hi Dirk, > > thanks for the hint but simply using gsl as is was done in this package > and now it does not build any more. However, maybe I misunderstood you > hint. > > Kind regards > > Andreas. > > On Sat, Dec 05, 2020 at 08:32:33AM -0600, Dirk Eddelbuettel wrote: > > > > On 5 December 2020 at 12:09, Andreas Tille wrote: > > | this issue is something for our advent calendar. Anybody with cblas > > | knowledge? > > > > I am the GNU GSL maintainer, and I at one point also worked a lot with the > > Atlas and other LAPACK/BLAS packages. I think Mo may be wrong here: I did > > the > > same approach of "oh we can just skip GSL's cblas". I think that is > > wrong. The way the C interface of the GNU GSL works appears to be require > > GSL > > + GSL CBLAS. That is what every package I know using GSL does -- even though > > that "looks weird and redundant". > > > > >From a quick look at http://ghmm.org it also looks like GLS is purely > > optional and for RNGs only -- just like my RcppZiggurat (upstream) package > > does which just relies on my RcppGSL (upstream) package which just export > > `gsl-config --libs`, and has for years. > > > > So I'd give the GSL defaults here a try. > > > > (That said Mo knows a lot more than I do about BLAS, but I've watched a lot > > of GSL build too over the decades I looked after that package.) > > > > Dirk > > > > > > | 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 > > | > > > | > _______________________________________________ > > | > Debian-med-packaging mailing list > > | > debian-med-packag...@alioth-lists.debian.net > > | > > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging > > | > > | -- > > | http://fam-tille.de > > | > > > > -- > > https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > > > > > > -- > http://fam-tille.de > > -- http://fam-tille.de