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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.