[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 Fri, Oct 21, 2016 at 12:01:26PM +0100, I wrote:
> 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.

This should have been 0351b06^.

> On Thu, Oct 20, 2016 at 10:17:03PM +0200, Sascha Steinbiss wrote:
>> 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.
>> pty_allocate(nonfatal): getpt(): No such file or directory at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24.
>> pty_allocate(nonfatal): openpty(): No such file or directory at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24.
>> pty_allocate(nonfatal): open(/dev/ptmx): Permission denied at /usr/lib/x86_64-linux-gnu/perl5/5.24/IO/Pty.pm line 24.

These messages are just IO-Tty/Tty.xs trying various system-dependent
ways to open a pty, and they all fail.  I think this is a local snafu in
your chroot and they all boil down to open(/dev/ptmx): Permission denied
on your machine.

>> Cannot open a pty at test/test.pl line 551.

I've now further tweaked test/test.pl's pty setup to skip the tests instead
of aborting with this message.  So you may wish to pull this in as a patch
as well as fixing /dev inside your chroot :-)

https://github.com/samtools/samtools/commit/ce4a601a0859bc9ccfcf000dddf0ac77e7d576b3

    John


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