[Debian-med-packaging] Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[John Marshall]

On Thu, Oct 20, 2016 at 10:17:03PM +0200, Sascha Steinbiss wrote:
> I have pushed a fix (9aac9cb) to Git, solving the FTBFS. Before doing
> an upload I would be very happy if an Autotools-savvy person could
> take another closer look because admittedly I am not really sure about
> the cause of the problem.

The problem is that the autoconf-archive maintainers accepted this
incredibly misguided patch (and its predecessor):

http://git.savannah.gnu.org/cgit/autoconf-archive.git/commit/?id=6dc6cc55a1f3248c8bc39b0abcd5aeb4a3e34a06
http://git.savannah.gnu.org/cgit/autoconf-archive.git/commit/?id=0351b066631215b4fdc3c672a8ef90b233687655

This pointlessly changed the variables set by AX_WITH_CURSES, and pretty
much changes it to believe in an infallible pkg-config -- which IMHO is
the opposite of what autoconf macros are there for.  (And other distros'
broken .pc files have demonstrated pkg-config's fallibility in the past!)

This is what will finally push samtools to carry its own autoconf macros
in an m4 directory instead of having the git repository build require
macros from autoconf-archive.  (If you build from release tarballs you
don't experience this problem.  I wish distro packagers would build from
our release tarballs.)

So the real solution here is to revert your autoconf-archive to 6dc6cc5^
and use that unborked ax_with_curses.m4, which will in future be bundled
with samtools.

> I also had to disable a test (test_usage) that otherwise also seems to
> (mysteriously?) fail in my building chroot, resulting in:
> 
> pty_allocate(nonfatal): posix_openpt(): Permission denied at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24.

Interesting.  No idea what's going on here, but we have made these tests
deactivatable in the past for the benefit of Debian's build systems (see
https://github.com/samtools/samtools/issues/300) and can further tweak
this if needed.

    John  (upstream)


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