[Debian-med-packaging] Bug#936609: Ported ghmm to Python3 but issues with clapack (Was: Bug#936609: ghmm: Python2 removal in sid/bullseye)

[Andreas Tille]

Control: tags -1 pending, help

Hi,

as you can read below Python2 is EOL.  The Debian Med team has packaged
ghmm for Debian and craftet a Python3 patch which you could use (and
possibly test more deeply than we did).

   https://salsa.debian.org/med-team/ghmm/blob/master/debian/patches/2to3.patch

When trying HMMEd I've got

   ModuleNotFoundError: No module named 'Gato'

but in setup.py I read only a comment:

   #requires   = ['GATO', 'ghmm'],

Could you please clarify whether http://gato.sf.net is really needed
to run ghmm in full functionality?  The other tools (ghmm-cluster,
ghmm-config, probdist, scluster, smix_hmm) are all issuing

   ... is obsolete. If you need it rebuild the GHMM with "GHMM_OBSOLETE".


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 };
      |                                         ^~~~~~~~~~~~~


Do you have any idea how to fix this?  I could just build without lapack
to get ghmm working but I'd consider it a good idea to gain performance
for our users.

Kind regards

      Andreas.


On Fri, Aug 30, 2019 at 07:18:48AM +0000, Matthias Klose wrote:
> Package: src:ghmm
> Version: 0.9~rc3-2
> Severity: normal
> Tags: sid bullseye
> User: debian-python at lists.debian.org
> Usertags: py2removal
> 
> Python2 becomes end-of-live upstream, and Debian aims to remove
> Python2 from the distribution, as discussed in
> https://lists.debian.org/debian-python/2019/07/msg00080.html
> 
> Your package either build-depends, depends on Python2, or uses Python2
> in the autopkg tests.  Please stop using Python2, and fix this issue
> by one of the following actions.
> 
> - Convert your Package to Python3. This is the preferred option.  In
>   case you are providing a Python module foo, please consider dropping
>   the python-foo package, and only build a python3-foo package.  Please
>   don't drop Python2 modules, which still have reverse dependencies,
>   just document them.
>   
>   This is the preferred option.
> 
> - If the package is dead upstream, cannot be converted or maintained
>   in Debian, it should be removed from the distribution.  If the
>   package still has reverse dependencies, raise the severity to
>   "serious" and document the reverse dependencies with the BTS affects
>   command.  If the package has no reverse dependencies, confirm that
>   the package can be removed, reassign this issue to ftp.debian.org,
>   make sure that the bug priority is set to normal and retitle the
>   issue to "RM: PKG -- removal triggered by the Python2 removal".
> 
> - If the package has still many users (popcon >= 300), or is needed to
>   build another package which cannot be removed, document that by
>   adding the "py2keep" user tag (not replacing the py2remove tag),
>   using the debian-python at lists.debian.org user.  Also any
>   dependencies on an unversioned python package (python, python-dev)
>   must not be used, same with the python shebang.  These have to be
>   replaced by python2/python2.7 dependencies and shebang.
> 
>   This is the least preferred option.
> 
> If the conversion or removal needs action on another package first,
> please document the blocking by using the BTS affects command, like
> 
>   affects <bug number of blocking py2removal bug> + src:ghmm
> 
> If there is no py2removal bug for that reverse-dependency, please file
> a bug on this package (similar to this bug report).
> 
> If there are questions, please refer to the wiki page for the removal:
> https://wiki.debian.org/Python/2Removal, or ask for help on IRC
> #debian-python, or the debian-python at lists.debian.org mailing list.
> 
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