Re: More bioperl modules need packaging
On Wed, 20 Nov 2019 at 23:47, Andreas Tille <andreas@an3as.eu> wrote:
> On Wed, Nov 20, 2019 at 11:24:19PM +0000, Carnė Draug wrote:
> > On Wed, 20 Nov 2019 at 17:51, Andreas Tille <andreas@an3as.eu> wrote:
> > > 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?
While ExtUtils::PkgConfig is now available and could find htslib, the
rules file was setting HTSLIB_DIR and so was trying to find it there
(which failed there). By not doing that, Build.PL was continuing down
the methods to find the htslib until it tries ExtUtils::PkgConfig.
I have pushed 8835cdb8c66fadc5ca which fixes that. My build system is
a bit old so I had to reduce the compat version to 11 to test it. I
also changed some others things that you may have different opinion
of.
Best Regards,
David
Reply to: