Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-05 Thread Andreas Tille
Hi Axel,

On Sun, Jul 05, 2015 at 04:03:31AM +0200, Axel Beckert wrote:
 
  [1] 
  https://anonscm.debian.org/cgit/pkg-perl/packages/libgenome-perl.git/commit/?id=205ec3992bde59d9f59870218e68cf9964d60a1a
   
 
 There's one thing in this commit which I consider quite ugly and
 unnecessary: A man page being under
 /usr/lib/debian-med/share/man/man1/gmt.1.gz and then only symlinked to
 /usr/share/man/man1/genome-model-tools.1.gz.
 
 IMHO that's for two reasons: /usr/lib/debian-med/bin/gmt doesn't need
 a man page from a policy point of view, only
 /usr/bin/genome-model-tools does. And then there is a never to be
 found man page under /usr/lib. (A man page under /usr/lib? Come on!
 That's an FHS violation. Or rather was until Debian weakend it for the
 systemd guys.)

Hmmm, from an FHS point of view you are correct.  However, the manpage
is currently found since not only PATH but also MANPATH is prepended so
a user will find the according manpage to the first gmt in the PATH.
 
 So rather than moving the man page from /usr/share/man/man1/gmt.1.gz
 to /usr/lib/debian-med/share/man/man1/gmt.1.gz and then symlinking
 that to /usr/share/man/man1/genome-model-tools.1.gz, I'd just rename
 /usr/share/man/man1/gmt.1.gz to
 /usr/share/man/man1/genome-model-tools.1.gz -- Everything else is IMHO
 unnecessary complexity with horribly non-standard paths.

I agree with the FHS argument.  But if I do not provide a manpage fitting
gmt - the one in /usr/lib/debian-med/bin - a user who calls

man gmt

might under the less probable but possible case the manpage provided by
the gmt package.  What's your suggestion to solve this?  Just using
a better FHS location?
 
 And you would also spare the explicit gzip call and one of the lines
 in debian/dirs.
 
 Additionally there seems trailing whitespace in debian/links, but the
 affected line will be gone anyways if the above is fixed as suggested.

Fixed for the moment - we'll see how this file will be dealt with.
 
 Further there is a change in debian/control which is not mentioned in
 the changelog entry nor seems to be related to the rest of the commit:
 A line Recommends: med-config (= 2.1) has been added. Please add at
 least an according changelog entry for that or remove it again (if it
 was committed accidentially).

It is one part of the change since it supports the PATH change in the
simple way but I now mentioned it explicitly.

Kind regards

  Andreas.

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-05 Thread Sebastiaan Couwenberg
Hi Andreas,

Thanks for your changes to libgenome-perl.

On 07/04/2015 05:26 PM, Andreas Tille wrote:
 I was able to commit[1] a fix for this bug.  I'd like to wait for a
 confirmation of a Perl Group member whether this is OK for a team upload
 or whether this is to less Perl-ish and rather Debian-Med-ish.  I'm
 fine with moving the package to Debian Med or uploading on behalf of the
 perl team - whatever you prefer.
 
 For those who did not followed the discussion see the link below for
 an explanation what was done here.
 
 [1] 
 https://anonscm.debian.org/cgit/pkg-perl/packages/libgenome-perl.git/commit/?id=205ec3992bde59d9f59870218e68cf9964d60a1a
  

I've updated the gmt package in git adding Breaks/Replaces on
libgenome-perl versions preceding the gmt rename ( 0.06-3~).

I'm waiting for feedback from the GMT upstream developers about the gmt
binary and libpsl library renames before uploading the new gmt revision.

Kind Regards,

Bas

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-05 Thread Axel Beckert
Hi Andreas,

Andreas Tille wrote:
  IMHO that's for two reasons: /usr/lib/debian-med/bin/gmt doesn't need
  a man page from a policy point of view, only
  /usr/bin/genome-model-tools does. And then there is a never to be
  found man page under /usr/lib. (A man page under /usr/lib? Come on!
  That's an FHS violation. Or rather was until Debian weakend it for the
  systemd guys.)
 
 Hmmm, from an FHS point of view you are correct.  However, the manpage
 is currently found since not only PATH but also MANPATH is prepended so
 a user will find the according manpage to the first gmt in the PATH.
[...]
  Further there is a change in debian/control which is not mentioned in
  the changelog entry nor seems to be related to the rest of the commit:
  A line Recommends: med-config (= 2.1) has been added. Please add at
  least an according changelog entry for that or remove it again (if it
  was committed accidentially).
 
 It is one part of the change since it supports the PATH change in the
 simple way but I now mentioned it explicitly.

Ok, there indeed seems quite some debian-med magic in this patch of
which I wasn't not aware of. That magic currently sounds rather scary
to me, but this bug report is not the place to discuss this.

So thanks for the fixing the other minor issues I mentioned.

Regards, Axel
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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-05 Thread Andreas Tille
Hi Axel,

On Sun, Jul 05, 2015 at 03:00:06PM +0200, Axel Beckert wrote:
  It is one part of the change since it supports the PATH change in the
  simple way but I now mentioned it explicitly.
 
 Ok, there indeed seems quite some debian-med magic in this patch of
 which I wasn't not aware of.

I admit the MANPATH change is not (yet documented) in the Blends
documentation.

 That magic currently sounds rather scary to me

As long as you do not create ${HOME}/.blends nothing will happen to you
- so I hope this will not scare you to much.

 but this bug report is not the place to discuss this.

Yes, that's true since it is too much hidden.  I would consider
debian-ble...@lists.debian.org the proper place to discuss.  Would you
mind joining there or would you suggest a better place?  Currently the
trick is used only in three packages and it might be better to fix
things soon before we need to change more things later.
 
 So thanks for the fixing the other minor issues I mentioned.

I actually asked to get hints what might be worth fixing - so for sure
I did this.

I think I wait with an upload of the package whether there might be a
chance for a quick consensus about the MANPATH location.  To do so I'll
document the current status and will trigger the discussion either on
debian-blends@l.d.o + Axel in CC or any other place Axel might suggest. 

Kind regards

  Andreas.

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-04 Thread Andreas Tille
Hi again,

I was able to commit[1] a fix for this bug.  I'd like to wait for a
confirmation of a Perl Group member whether this is OK for a team upload
or whether this is to less Perl-ish and rather Debian-Med-ish.  I'm
fine with moving the package to Debian Med or uploading on behalf of the
perl team - whatever you prefer.

For those who did not followed the discussion see the link below for
an explanation what was done here.

Kind regards

   Andreas.

On Sat, Jul 04, 2015 at 04:40:58PM +0200, Andreas Tille wrote:
 Hi Bas,
 
 On Sat, Jul 04, 2015 at 03:02:15PM +0200, Sebastiaan Couwenberg wrote:
 OK, I just documented the way to deal with name space pollution in
 Blends at
 
 http://blends.debian.org/blends/ch06.html#namespace
 
 I hope this might become useful at one day also in other Blends.

[1] 
https://anonscm.debian.org/cgit/pkg-perl/packages/libgenome-perl.git/commit/?id=205ec3992bde59d9f59870218e68cf9964d60a1a
 

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-04 Thread Tim Rühsen
Am Freitag, 3. Juli 2015, 22:11:49 schrieb Sebastiaan Couwenberg:
  * libpsl-dev
  
[...]

Filelist libpsl-dev vs. libgmt-dev:

usr/lib/x86_64-linux-gnu/libpsl.so
 
 The libpsl  gmt packages use different a SONAME. To ensure dependencies
 on the GMT libpsl it's bundled with libgmt in the libgmt5 package.
 
 To resolve the conflict I'm considering renaming the GMT libpsl to
 libgmt-psl.
 
 I've CC'ed the libpsl maintainers, and I would like to ask your opinion
 on this conflict too.

Hi Sebastiaan.

IMO, renaming GMT libpsl to libgmt-psl seems reasonable to me. It is a step 
towards a cleaner library 'namespacing' regarding GMT.

If it comes to renaming the non-GMT file (and/or package), I won't be 
reluctant. You'll have a good reason than.

BTW, I could not CC this mail to Daniel Kahn Gillmor 
d...@40fifthhorseman.net, that's why I took him out of the recipient list.

Regards, Tim

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-04 Thread gregor herrmann
On Sat, 04 Jul 2015 17:26:14 +0200, Andreas Tille wrote:

 I was able to commit[1] a fix for this bug.  I'd like to wait for a
 confirmation of a Perl Group member whether this is OK for a team upload
 or whether this is to less Perl-ish and rather Debian-Med-ish.  I'm
 fine with moving the package to Debian Med or uploading on behalf of the
 perl team - whatever you prefer.

If this is the preferred way to handle the issue in Debian Med I see
no reason not to do it this way.
And according to Uploaders, this package is quite Debian-Med-ish
anyway :)

From my POV, feel free to go ahead with a team upload.
 

Cheers,
gregor

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-04 Thread Andreas Tille
Hi Bas,

On Sat, Jul 04, 2015 at 03:02:15PM +0200, Sebastiaan Couwenberg wrote:
  If you agree to this solution I'll upload it that way.
 
 Yes, please.

OK, I just documented the way to deal with name space pollution in
Blends at

http://blends.debian.org/blends/ch06.html#namespace

I hope this might become useful at one day also in other Blends.
 
 I'm not sure. But I'm a member of the Perl team too, so if you can't
 commit yourself I'm willing to do that too.

I'll try and let you know.

Kind regards

  Andreas. 

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-04 Thread Axel Beckert
Hi,

Andreas Tille wrote:
 I was able to commit[1] a fix for this bug.  I'd like to wait for a
 confirmation of a Perl Group member whether this is OK for a team upload
 or whether this is to less Perl-ish and rather Debian-Med-ish.

Maybe that's partially the case...

 [1] 
 https://anonscm.debian.org/cgit/pkg-perl/packages/libgenome-perl.git/commit/?id=205ec3992bde59d9f59870218e68cf9964d60a1a
  

There's one thing in this commit which I consider quite ugly and
unnecessary: A man page being under
/usr/lib/debian-med/share/man/man1/gmt.1.gz and then only symlinked to
/usr/share/man/man1/genome-model-tools.1.gz.

IMHO that's for two reasons: /usr/lib/debian-med/bin/gmt doesn't need
a man page from a policy point of view, only
/usr/bin/genome-model-tools does. And then there is a never to be
found man page under /usr/lib. (A man page under /usr/lib? Come on!
That's an FHS violation. Or rather was until Debian weakend it for the
systemd guys.)

So rather than moving the man page from /usr/share/man/man1/gmt.1.gz
to /usr/lib/debian-med/share/man/man1/gmt.1.gz and then symlinking
that to /usr/share/man/man1/genome-model-tools.1.gz, I'd just rename
/usr/share/man/man1/gmt.1.gz to
/usr/share/man/man1/genome-model-tools.1.gz -- Everything else is IMHO
unnecessary complexity with horribly non-standard paths.

And you would also spare the explicit gzip call and one of the lines
in debian/dirs.

Additionally there seems trailing whitespace in debian/links, but the
affected line will be gone anyways if the above is fixed as suggested.

Further there is a change in debian/control which is not mentioned in
the changelog entry nor seems to be related to the rest of the commit:
A line Recommends: med-config (= 2.1) has been added. Please add at
least an according changelog entry for that or remove it again (if it
was committed accidentially).

Regards, Axel
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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-04 Thread Sebastiaan Couwenberg
Hi Andreas,

Thansk for the feedback.

On 07/04/2015 02:44 PM, Andreas Tille wrote:
 while I have not dealt with the libgenome-perl package before I think
 your suggestion to hand over /usr/bin/gmt to the gmt package sounds
 reaosnable.  The package has a quite low popcon value and in my naive
 view the main focus is the Perl module and the accompanying scripts
 might (or might not - please correct me if I'm wrong) have a minor
 importance.
 
 So I propose the following solution:
 
1. install the gmt script to
 /usr/lib/debian-med/bin/gmt
2. ln -s /usr/lib/debian-med/bin/gmt /usr/bin/genome-module-tools
3. suggest users of Debian Med to add in front of PATH
 
 The last is provided by med-config (= 2.1).  This is the same solution
 as it is done in plink 1.07-6 which was just uploaded to unstable
 (formerly tested in experimental).  Users are informed about this in
 NEWS.Debian.
 
 If you agree to this solution I'll upload it that way.

Yes, please.

Based on the popcon scores my preference is also to rename the binary in
libgnome-perl. The GMT upstream authors also argue that since they've
been using the name since the 1980s they use has set precedence.

 BTW, has Debian
 Perl team set ACLs to enable me commiting the changes in Git?

I'm not sure. But I'm a member of the Perl team too, so if you can't
commit yourself I'm willing to do that too.

 Kind regards
 
  Andreas.

Kind Regards,

Bas

 On Fri, Jul 03, 2015 at 10:11:49PM +0200, Sebastiaan Couwenberg wrote:
 Control: forwarded -1 https://gmt.soest.hawaii.edu/issues/723

 Hi Andreas,

 Thanks for the comprehensive followup.

 I've uploaded a new revision of gmt to experimental that addresses some
 of the issues.

 On 06/30/2015 02:16 AM, Andreas Beckmann wrote:
 * libgenome-perl

   Filelist libgenome-perl vs. gmt:

   usr/bin/gmt

   Filelist libgenome-perl vs. gmt-common:

   usr/share/man/man1/gmt.1.gz

 This is the most serious conflict to resolve. I've contacted the
 libgenome-perl maintainers [1], but I've not received a reply yet.

 I've put debian-med@ in the CC as they seem the most interested in the
 libgenome-perl package. Please share your opinion on this conflict.

 I've also contacted the GMT upstream developers to raise the issue of
 these conflicts between GMT 5 and other projects. [2]

 [1] https://lists.debian.org/debian-gis/2015/06/msg00119.html
 [2] https://gmt.soest.hawaii.edu/issues/723

 * libpsl-dev

   [...]

   Filelist libpsl-dev vs. libgmt-dev:

   usr/lib/x86_64-linux-gnu/libpsl.so

 The libpsl  gmt packages use different a SONAME. To ensure dependencies
 on the GMT libpsl it's bundled with libgmt in the libgmt5 package.

 To resolve the conflict I'm considering renaming the GMT libpsl to
 libgmt-psl.

 I've CC'ed the libpsl maintainers, and I would like to ask your opinion
 on this conflict too.

 * turnin-ng

   [...]

   Filelist turnin-ng vs. gmt-common:

   usr/share/man/man1/project.1.g

 * pslib-dev

   [...]

   Filelist pslib-dev vs. gmt-common:

   usr/share/man/man3/pslib.3.gz

 These man page issues should be resolved with the Conflicts that were
 added in gmt (5.1.2+dfsg1-1~exp5).

 Kind Regards,

 Bas

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-04 Thread Andreas Tille
Hi Bas,

while I have not dealt with the libgenome-perl package before I think
your suggestion to hand over /usr/bin/gmt to the gmt package sounds
reaosnable.  The package has a quite low popcon value and in my naive
view the main focus is the Perl module and the accompanying scripts
might (or might not - please correct me if I'm wrong) have a minor
importance.

So I propose the following solution:

   1. install the gmt script to
/usr/lib/debian-med/bin/gmt
   2. ln -s /usr/lib/debian-med/bin/gmt /usr/bin/genome-module-tools
   3. suggest users of Debian Med to add in front of PATH

The last is provided by med-config (= 2.1).  This is the same solution
as it is done in plink 1.07-6 which was just uploaded to unstable
(formerly tested in experimental).  Users are informed about this in
NEWS.Debian.

If you agree to this solution I'll upload it that way.  BTW, has Debian
Perl team set ACLs to enable me commiting the changes in Git?

Kind regards

 Andreas.

On Fri, Jul 03, 2015 at 10:11:49PM +0200, Sebastiaan Couwenberg wrote:
 Control: forwarded -1 https://gmt.soest.hawaii.edu/issues/723
 
 Hi Andreas,
 
 Thanks for the comprehensive followup.
 
 I've uploaded a new revision of gmt to experimental that addresses some
 of the issues.
 
 On 06/30/2015 02:16 AM, Andreas Beckmann wrote:
  * libgenome-perl
  
Filelist libgenome-perl vs. gmt:
  
usr/bin/gmt
  
Filelist libgenome-perl vs. gmt-common:
  
usr/share/man/man1/gmt.1.gz
 
 This is the most serious conflict to resolve. I've contacted the
 libgenome-perl maintainers [1], but I've not received a reply yet.
 
 I've put debian-med@ in the CC as they seem the most interested in the
 libgenome-perl package. Please share your opinion on this conflict.
 
 I've also contacted the GMT upstream developers to raise the issue of
 these conflicts between GMT 5 and other projects. [2]
 
 [1] https://lists.debian.org/debian-gis/2015/06/msg00119.html
 [2] https://gmt.soest.hawaii.edu/issues/723
 
  * libpsl-dev
 
[...]
 
Filelist libpsl-dev vs. libgmt-dev:
 
usr/lib/x86_64-linux-gnu/libpsl.so
 
 The libpsl  gmt packages use different a SONAME. To ensure dependencies
 on the GMT libpsl it's bundled with libgmt in the libgmt5 package.
 
 To resolve the conflict I'm considering renaming the GMT libpsl to
 libgmt-psl.
 
 I've CC'ed the libpsl maintainers, and I would like to ask your opinion
 on this conflict too.
 
  * turnin-ng
  
[...]
  
Filelist turnin-ng vs. gmt-common:
  
usr/share/man/man1/project.1.g
  
  * pslib-dev
  
[...]
  
Filelist pslib-dev vs. gmt-common:
  
usr/share/man/man3/pslib.3.gz
 
 These man page issues should be resolved with the Conflicts that were
 added in gmt (5.1.2+dfsg1-1~exp5).
 
 Kind Regards,
 
 Bas
 
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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-07-03 Thread Sebastiaan Couwenberg
Control: forwarded -1 https://gmt.soest.hawaii.edu/issues/723

Hi Andreas,

Thanks for the comprehensive followup.

I've uploaded a new revision of gmt to experimental that addresses some
of the issues.

On 06/30/2015 02:16 AM, Andreas Beckmann wrote:
 * libgenome-perl
 
   Filelist libgenome-perl vs. gmt:
 
   usr/bin/gmt
 
   Filelist libgenome-perl vs. gmt-common:
 
   usr/share/man/man1/gmt.1.gz

This is the most serious conflict to resolve. I've contacted the
libgenome-perl maintainers [1], but I've not received a reply yet.

I've put debian-med@ in the CC as they seem the most interested in the
libgenome-perl package. Please share your opinion on this conflict.

I've also contacted the GMT upstream developers to raise the issue of
these conflicts between GMT 5 and other projects. [2]

[1] https://lists.debian.org/debian-gis/2015/06/msg00119.html
[2] https://gmt.soest.hawaii.edu/issues/723

 * libpsl-dev

   [...]

   Filelist libpsl-dev vs. libgmt-dev:

   usr/lib/x86_64-linux-gnu/libpsl.so

The libpsl  gmt packages use different a SONAME. To ensure dependencies
on the GMT libpsl it's bundled with libgmt in the libgmt5 package.

To resolve the conflict I'm considering renaming the GMT libpsl to
libgmt-psl.

I've CC'ed the libpsl maintainers, and I would like to ask your opinion
on this conflict too.

 * turnin-ng
 
   [...]
 
   Filelist turnin-ng vs. gmt-common:
 
   usr/share/man/man1/project.1.g
 
 * pslib-dev
 
   [...]
 
   Filelist pslib-dev vs. gmt-common:
 
   usr/share/man/man3/pslib.3.gz

These man page issues should be resolved with the Conflicts that were
added in gmt (5.1.2+dfsg1-1~exp5).

Kind Regards,

Bas

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Bug#790524: src:gmt: takes over files from several unrelated packages (was: Re: gmt: libgenome-perl in sid already provides /usr/bin/gmt)

2015-06-29 Thread Andreas Beckmann
Followup-For: Bug #790524
Control: retitle -1 src:gmt: takes over files from several unrelated packages

In addition to libgenome-perl gmt tries to take over files from
several more packages:

* libgenome-perl

  Filelist libgenome-perl vs. gmt:

  usr/bin/gmt

  Filelist libgenome-perl vs. gmt-common:

  usr/share/man/man1/gmt.1.gz

* turnin-ng

  Selecting previously unselected package gmt-common.
  Preparing to unpack .../gmt-common_5.1.2+dfsg1-1~exp4_all.deb ...
  Unpacking gmt-common (5.1.2+dfsg1-1~exp4) ...
  dpkg: error processing archive 
/var/cache/apt/archives/gmt-common_5.1.2+dfsg1-1~exp4_all.deb (--unpack):
   trying to overwrite '/usr/share/man/man1/project.1.gz', which is also in 
package turnin-ng 1.3-1
  Errors were encountered while processing:
   /var/cache/apt/archives/gmt-common_5.1.2+dfsg1-1~exp4_all.deb

  Filelist turnin-ng vs. gmt-common:

  usr/share/man/man1/project.1.g

* pslib-dev

  Selecting previously unselected package gmt-common.
  Preparing to unpack .../gmt-common_5.1.2+dfsg1-1~exp4_all.deb ...
  Unpacking gmt-common (5.1.2+dfsg1-1~exp4) ...
  dpkg: error processing archive 
/var/cache/apt/archives/gmt-common_5.1.2+dfsg1-1~exp4_all.deb (--unpack):
   trying to overwrite '/usr/share/man/man3/pslib.3.gz', which is also in 
package pslib-dev 0.4.5-3+b2
  Errors were encountered while processing:
   /var/cache/apt/archives/gmt-common_5.1.2+dfsg1-1~exp4_all.deb

  Filelist pslib-dev vs. gmt-common:

  usr/share/man/man3/pslib.3.gz

* libpsl-dev

  Selecting previously unselected package libgmt-dev.
  Preparing to unpack .../libgmt-dev_5.1.2+dfsg1-1~exp4_amd64.deb ...
  Unpacking libgmt-dev (5.1.2+dfsg1-1~exp4) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libgmt-dev_5.1.2+dfsg1-1~exp4_amd64.deb (--unpack):
   trying to overwrite '/usr/lib/x86_64-linux-gnu/libpsl.so', which is also in 
package libpsl-dev 0.5.1-1
  Errors were encountered while processing:
   /var/cache/apt/archives/libgmt-dev_5.1.2+dfsg1-1~exp4_amd64.deb

  Filelist libgmt-dev vs. libgmt-dev:

  usr/lib/x86_64-linux-gnu/libpsl.so


Andreas


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