Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[Sascha Steinbiss]

Hi.

[...]
>> Thanks. This has fixed the problem for me. Is this solution OK for
everyone?
>
> Fine for me

OK, I'll upload later.

Cheers
Sascha

Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[Andreas Tille]

On Sun, Oct 23, 2016 at 04:12:14PM +0200, Sascha Steinbiss wrote:
> > 
> > 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
> 
> Thanks. This has fixed the problem for me. Is this solution OK for everyone?

Fine for me

 Andreas. 

-- 
http://fam-tille.de

Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[Sascha Steinbiss]

Hi all,

thanks John for the detailed explanation and the patches.

>> 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^.

I see. For now I have bundled the correct ax_with_curses.m4 with our source 
package (alongside ax_with_htslib.m4) and use it instead of the one in 
autoconf-archive until this issue gets addressed by you upstream.

>>> 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

Thanks. This has fixed the problem for me. Is this solution OK for everyone?

Cheers
Sascha

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


-- 
 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. 

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)


-- 
 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. 

Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[Andreas Tille]

Hi Sascha,

On Thu, Oct 20, 2016 at 10:17:03PM +0200, Sascha Steinbiss wrote:
> Hi all,
> 
> 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.

May be asking for comments on debian-mentors@l.d.o might make sense.
 
> 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.
> Cannot open a pty at test/test.pl line 551.

Strange as well.

I do not feel really competent here and have no spare time cycles to
have a deeper look in the next week(s).

Kind regards

 Andreas.

-- 
http://fam-tille.de

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

[Chris Lamb]

Sascha Steinbiss wrote:

> I fully agree and that was why I was asking for some extra pair of
> eyeballs before uploading

Excellent. For some reason I read your message as "I'm going to upload
anyway but if someone can take a look that would be nice I guess."

Mea culpa.  :)


Regards,

-- 
  ,''`.
 : :'  : Chris Lamb
 `. `'`  la...@debian.org / chris-lamb.co.uk
   `-

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

[Sascha Steinbiss]

Hi Chris,

>> 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.
> […]
>> I also had to disable a test (test_usage) that otherwise also seems to
>> (mysteriously?) fail
> 
> These two comments make me a little nervous, alas. We should surely work
> out what was — at least roughly! — the issue instead of just patching
> them out, no?

I fully agree and that was why I was asking for some extra pair of eyeballs 
before uploading. Maybe someone from the team can share some insight or maybe a 
better solution, and my patch could simply serve as a pointer.

Cheers
Sascha

Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[Chris Lamb]

Hi Sascha,


> 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.
[…]
> I also had to disable a test (test_usage) that otherwise also seems to
> (mysteriously?) fail

These two comments make me a little nervous, alas. We should surely work
out what was — at least roughly! — the issue instead of just patching
them out, no?


Regards,

-- 
  ,''`.
 : :'  : Chris Lamb
 `. `'`  la...@debian.org / chris-lamb.co.uk
   `-

Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[Sascha Steinbiss]

Hi all,

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.

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

Any comments welcome. Feel free to upload with any modifications if you want.

Cheers
Sascha


> On 16 Oct 2016, at 16:06, Chris Lamb  wrote:
> 
> Source: samtools
> Version: 1.3.1-2
> Severity: serious
> Justification: fails to build from source
> User: reproducible-bui...@lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org
> 
> Dear Maintainer,
> 
> samtools fails to build from source in unstable/amd64:
> 
>  […]
> 
> 
>  
> **
>  ** Starting build
>**
>  
> **
> 
>   Package:  samtools
>   Version:  1.3.1-2
>   Build architecture:   amd64
>   Date: Sun, 16 Oct 2016 16:05:23 +0200
>   Hostname: 80cae65f0728
>   Uname:Linux 80cae65f0728 4.7.0-1-amd64 #1 SMP Debian 
> 4.7.5-1 (2016-09-26) x86_64 GNU/Linux
>   /etc/timezone:Europe/Belgrade
> 
>  
> **
>  ** Installing build dependencies 
>**
>  
> **
> 
>  dh_testdir
>  dh_testroot
>  dh_prep
>  dh_testdir
>  dh_testroot
>  dh_install
>  dh_installdocs
>  dh_installchangelogs
>  dh_compress
>  dh_fixperms
>  dh_installdeb
>  dh_gencontrol
>  dh_md5sums
>  dh_builddeb
>  dpkg-deb: building package 'samtools-build-deps' in 
> '../samtools-build-deps_1.3.1-2_all.deb'.
> 
>  The package has been created.
>  Attention, the package has been created in the current directory,
>  not in ".." as indicated by the message above!
>  Selecting previously unselected package samtools-build-deps.
>  (Reading database ... 23458 files and directories currently installed.)
>  Preparing to unpack samtools-build-deps_1.3.1-2_all.deb ...
>  Unpacking samtools-build-deps (1.3.1-2) ...
>  Reading package lists...
>  Building dependency tree...
>  Reading state information...
>  Correcting dependencies... Done
>  The following additional packages will be installed:
>autoconf-archive bash-completion libhts-dev libhts1 libncurses5-dev
>libtinfo-dev tabix zlib1g-dev
>  Suggested packages:
>ncurses-doc
>  The following NEW packages will be installed:
>autoconf-archive bash-completion libhts-dev libhts1 libncurses5-dev
>libtinfo-dev tabix zlib1g-dev
>  0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
>  1 not fully installed or removed.
>  Need to get 2175 kB of archives.
>  After this operation, 12.3 MB of additional disk space will be used.
>  Get:1 http://httpredir.debian.org/debian sid/main amd64 bash-completion all 
> 1:2.1-4.3 [178 kB]
>  Get:2 http://httpredir.debian.org/debian sid/main amd64 libtinfo-dev amd64 
> 6.0+20160917-1 [77.3 kB]
>  Get:3 http://httpredir.debian.org/debian sid/main amd64 libncurses5-dev 
> amd64 6.0+20160917-1 [173 kB]
>  Get:4 http://httpredir.debian.org/debian sid/main amd64 libhts1 amd64 
> 1.3.1-3 [256 kB]
>  Get:5 http://httpredir.debian.org/debian sid/main amd64 libhts-dev amd64 
> 1.3.1-3 [315 kB]
>  Get:6 http://httpredir.debian.org/debian sid/main amd64 zlib1g-dev amd64 
> 1:1.2.8.dfsg-2+b1 [206 kB]
>  Get:7 http://httpredir.debian.org/debian sid/main amd64 autoconf-archive all 
> 20160916-1 [716 kB]
>  Get:8 http://httpredir.debian.org/debian sid/main amd64 tabix amd64 1.3.1-3 
> [254 kB]
>  Fetched 2175 kB in 0s (3409 kB/s)
>  Selecting previously unselected package bash-completion.
>  (Reading database ... 
> (Reading database ... 5%
> (Reading database ... 10%
> (Reading database ... 15%
> (Reading database ... 20%
> (Reading database ... 25%
> (Reading database ... 30%
> (Reading database ... 35%
> (Reading database ... 40%
> (Reading database ... 45%
> (Reading database ... 50%
> (Reading database ... 55%
> (Reading database ... 60%
> 

Bug#840974: samtools: FTBFS: configure.ac:69: error: macro PKG_CHECK_EXISTS is not defined; is a m4 file missing?

[Chris Lamb]

Source: samtools
Version: 1.3.1-2
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org

Dear Maintainer,

samtools fails to build from source in unstable/amd64:

  […]

  
  
**
  ** Starting build 
  **
  
**
  
   Package:  samtools
   Version:  1.3.1-2
   Build architecture:   amd64
   Date: Sun, 16 Oct 2016 16:05:23 +0200
   Hostname: 80cae65f0728
   Uname:Linux 80cae65f0728 4.7.0-1-amd64 #1 SMP Debian 4.7.5-1 
(2016-09-26) x86_64 GNU/Linux
   /etc/timezone:Europe/Belgrade
  
  
**
  ** Installing build dependencies  
  **
  
**
  
  dh_testdir
  dh_testroot
  dh_prep
  dh_testdir
  dh_testroot
  dh_install
  dh_installdocs
  dh_installchangelogs
  dh_compress
  dh_fixperms
  dh_installdeb
  dh_gencontrol
  dh_md5sums
  dh_builddeb
  dpkg-deb: building package 'samtools-build-deps' in 
'../samtools-build-deps_1.3.1-2_all.deb'.
  
  The package has been created.
  Attention, the package has been created in the current directory,
  not in ".." as indicated by the message above!
  Selecting previously unselected package samtools-build-deps.
  (Reading database ... 23458 files and directories currently installed.)
  Preparing to unpack samtools-build-deps_1.3.1-2_all.deb ...
  Unpacking samtools-build-deps (1.3.1-2) ...
  Reading package lists...
  Building dependency tree...
  Reading state information...
  Correcting dependencies... Done
  The following additional packages will be installed:
autoconf-archive bash-completion libhts-dev libhts1 libncurses5-dev
libtinfo-dev tabix zlib1g-dev
  Suggested packages:
ncurses-doc
  The following NEW packages will be installed:
autoconf-archive bash-completion libhts-dev libhts1 libncurses5-dev
libtinfo-dev tabix zlib1g-dev
  0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
  1 not fully installed or removed.
  Need to get 2175 kB of archives.
  After this operation, 12.3 MB of additional disk space will be used.
  Get:1 http://httpredir.debian.org/debian sid/main amd64 bash-completion all 
1:2.1-4.3 [178 kB]
  Get:2 http://httpredir.debian.org/debian sid/main amd64 libtinfo-dev amd64 
6.0+20160917-1 [77.3 kB]
  Get:3 http://httpredir.debian.org/debian sid/main amd64 libncurses5-dev amd64 
6.0+20160917-1 [173 kB]
  Get:4 http://httpredir.debian.org/debian sid/main amd64 libhts1 amd64 1.3.1-3 
[256 kB]
  Get:5 http://httpredir.debian.org/debian sid/main amd64 libhts-dev amd64 
1.3.1-3 [315 kB]
  Get:6 http://httpredir.debian.org/debian sid/main amd64 zlib1g-dev amd64 
1:1.2.8.dfsg-2+b1 [206 kB]
  Get:7 http://httpredir.debian.org/debian sid/main amd64 autoconf-archive all 
20160916-1 [716 kB]
  Get:8 http://httpredir.debian.org/debian sid/main amd64 tabix amd64 1.3.1-3 
[254 kB]
  Fetched 2175 kB in 0s (3409 kB/s)
  Selecting previously unselected package bash-completion.
  (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 23462 files and directories currently installed.)
  Preparing to unpack .../0-bash-completion_1%3a2.1-4.3_all.deb ...
  Unpacking bash-completion (1:2.1-4.3) ...
  Selecting previously unselected package libtinfo-dev:amd64.
  Preparing to unpack .../1-libtinfo-dev_6.0+20160917-1_amd64.deb ...
  Unpacking libtinfo-dev:amd64 (6.0+20160917-1) ...
  Selecting previously unselected package libncurses5-dev:amd64.
  Preparing to unpack .../2-libncurses5-dev_6.0+20160917-1_amd64.deb ...
  Unpacking libncurses5-dev:amd64 (6.0+20160917-1) ...
  Selecting previously unselected package libhts1:amd64.
  Preparing to unpack .../3-libhts1_1.3.1-3_amd64.deb ...
  Unpacking libhts1:amd64 (1.3.1-3) ...
  Selecting previously unselected package libhts-dev:amd64.
  Preparing to unpack .../4-libhts-dev_1.3.1-3_amd64.deb ...
  Unpacking libhts-dev:amd64 (1.3.1-3) ...
  Selecting previously unselected package zlib1g-dev:amd64.
  Preparing to unpack