Help needed to detect lib via pkg-config (Was: More bioperl modules need packaging)
Hi,
On Thu, Nov 21, 2019 at 12:47:26AM +0100, Andreas Tille wrote:
> Hi Carnë,
>
> On Wed, Nov 20, 2019 at 11:24:19PM +0000, Carnë Draug wrote:
> > > when beeing here at BioHackathon I had some discussion about packaging
> > > ensembl libs. I'm not really sure what might be a good package to start
> > > but I picked libensembl-bio-db-hts-perl[1]. You see that I prefixed the
> > > upstream name by libensembl and postfixed by -perl as per Perl modules
> > > policy. Feel free to comment on that naming scheme.
> >
> > This is not a BioPerl package/distribution. While it is on the Bio::
> > namespace, it is not authored or maintained by the BioPerl project.
>
> Yes. That's that's why I had the (may be questionable) idea to use the
> ensembl prefix to make this clear.
I now renamed the package and the Git archive according to your suggestion
to libbio-db-hts-perl[1]
> > About the package name, policy states that the package name should
> > match the main module name. In this case, the main module is
> > Bio::DB::HTS so the package should be named libbio-db-hts-perl.
>
> OK, fine for me to drop ensembl again.
Done.
> > > Unfortunately I was not able to tell the configure step where to find
> > > htslib. I'd assume it should be detected automatically but since it
> > > is not I tried the following three methods - all with no success:
> > > [...]
> > > 6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
> > > 7. common library locations: /usr /usr/local, /usr/share, /opt/local
> > >
> > > If none of the above succeeds but htslib is registered with pkg-config, the script
> > > will try using pkg-config paths (via ExtUtils::PkgConfig) without checking if header
> > > and library files exist.
> > >
> > >
> > > Any hint how to fix this?
> >
> > I have never used or installed this distribution. However, looking at
> > d/control the libextutils-pkgconfig-perl package does not appear on
> > build-depends. This seems to be required to find htslib automatically
> > (with pkg-config).
> >
> > That's my guess.
>
> Hmmm,
>
> $ git diff
> diff --git a/debian/control b/debian/control
> index e3d3a7a..794e917 100644
> --- a/debian/control
> +++ b/debian/control
> @@ -6,6 +6,7 @@ Uploaders: Andreas Tille <tille@debian.org>
> Testsuite: autopkgtest-pkg-perl
> Build-Depends: debhelper-compat (= 12),
> libmodule-build-perl,
> + libextutils-pkgconfig-perl,
> libhts-dev
> Build-Depends-Indep: perl,
> libbio-perl-perl,
>
>
> does not change anything. :-(
Any other ideas how to make sure libhts will be found?
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/libbio-db-hts-perl
--
http://fam-tille.de
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