Bug#890400: Soname bump + symbols file in Git - please verify: Bug#890400: physamp: autopkgtest failure

[Andreas Tille]

Dear Julien,

On Thu, Feb 15, 2018 at 07:51:03PM +0100, Julien Yann Dutheil wrote:
> 
> Thanks a lot for the proposal. I would like to fix that one upstream to, so
> I will probably upload a new version.

This is why I did not yet uploaded.

> More generally, we'e thinking of some ways to improve things upstream,
> because a minor version update should not lead to an interface break in my
> opinion...

We definitely share the same opinion here. ;-)

Kind regards

   Andreas.

-- 
http://fam-tille.de

Bug#890400: Soname bump + symbols file in Git - please verify: Bug#890400: physamp: autopkgtest failure

[Julien Yann Dutheil]

Dear Andreas,

Thanks a lot for the proposal. I would like to fix that one upstream to, so
I will probably upload a new version.
More generally, we'e thinking of some ways to improve things upstream,
because a minor version update should not lead to an interface break in my
opinion...

Best,

Julien.

On Thu, Feb 15, 2018 at 4:00 PM, Andreas Tille  wrote:

> Control: tags -1 pending
>
> Hi Julien,
>
> I've commited a *proposal* in Git.  I did not uploaded yet since I have
> no idea whether you as upstream would prefer a different solution to
> solve this issue.
>
> In any case I also added a symbols file.  If we had this before it would
> have ringed a bell for the symbols change.
>
> Please let me know what you think.
>
> Kind regards
>
>Andreas.
>
> --
> http://fam-tille.de
>



-- 
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 986

§ Max Planck Institute for Evolutionary Biology
Molecular Systems Evolution
Department of Evolutionary Genetics
Plön -- GERMANY

§ Institute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE

Bug#890400: Soname bump + symbols file in Git - please verify: Bug#890400: physamp: autopkgtest failure

[Andreas Tille]

Control: tags -1 pending

Hi Julien,

I've commited a *proposal* in Git.  I did not uploaded yet since I have
no idea whether you as upstream would prefer a different solution to
solve this issue.

In any case I also added a symbols file.  If we had this before it would
have ringed a bell for the symbols change.

Please let me know what you think.

Kind regards

   Andreas.

-- 
http://fam-tille.de

Processed: Soname bump + symbols file in Git - please verify: Bug#890400: physamp: autopkgtest failure

[Debian Bug Tracking System]

Processing control commands:

> tags -1 pending
Bug #890400 [libbpp-core3] libbpp-core3: ABI change without soname chenge
Bug #890405 [libbpp-core3] libbpp-core3: ABI change without soname chenge
Added tag(s) pending.
Added tag(s) pending.

-- 
890400: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890400
890405: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890405
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Bug#890400: physamp: autopkgtest failure

[Adrian Bunk]

Control: reassign -1 libbpp-core3 2.3.2-1
Control: reassign 890405 libbpp-core3 2.3.2-1
Control: forcemerge -1 890405
Control: retitle -1 libbpp-core3: ABI change without soname chenge
Control: affects -1 src:physamp src:maffilter

On Wed, Feb 14, 2018 at 04:08:10PM +0100, Julien Yann Dutheil wrote:
> Will do, also for maffilter.
> 
> J.
> 
> On 14 Feb 2018 13:15, "Andreas Tille"  wrote:
> 
> > Hi Graham,
> >
> > I guess Julien Dutheil will care for a patch.
> >
> > Kind regards
> >
> >Andreas.
> >
> > On Wed, Feb 14, 2018 at 02:00:18PM +0200, Graham Inggs wrote:
> > > Source: physamp
> > > Version: 1.0.3-1
> > > Severity: serious
> > > User: ubuntu-de...@lists.ubuntu.com
> > > Usertags: origin-ubuntu bionic autopkgtest
> > >
> > > Hi Maintainer
> > >
> > > Since the upload of libbpp-core 2.3.2-1, physamp's autopkgtests have been
> > > failing [1] with the following error:
> > >
> > > autopkgtest [03:46:54]: test run-unit-test: [---
> > > bppalnoptim: symbol lookup error: bppalnoptim: undefined symbol: _
> > ZN3bpp16ApplicationTools18getDoubleParameterERKNSt7__
> > cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt3mapIS6_S6_
> > St4lessIS6_ESaISt4pairIS7_S6_EEEdS8_bi
>...

Note that there is nothing in maffilter or physamp that needs fixing,[1]
the bug is that the libbpp-core3 ABI changed without changing the soname:

src/Bpp/App/ApplicationTools.h:
 static double getDoubleParameter(
   const std::string& parameterName,
-  std::map& params,
+  const std::map& params,
   double defaultValue,
   const std::string& suffix = "",
   bool suffixIsOptional = true,

And a few other functions with similar changes.

In C++ this is an ABI change.

cu
Adrian

[1] a no-change rebuild would make them work again,
but that wouldn't fix the actual problem

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

Processed: Re: Bug#890400: physamp: autopkgtest failure

[Debian Bug Tracking System]

Processing control commands:

> reassign -1 libbpp-core3 2.3.2-1
Bug #890400 [src:physamp] physamp: autopkgtest failure
Bug reassigned from package 'src:physamp' to 'libbpp-core3'.
No longer marked as found in versions physamp/1.0.3-1.
Ignoring request to alter fixed versions of bug #890400 to the same values 
previously set
Bug #890400 [libbpp-core3] physamp: autopkgtest failure
Marked as found in versions libbpp-core/2.3.2-1.
> reassign 890405 libbpp-core3 2.3.2-1
Bug #890405 [maffilter] maffilter: undefined symbol
Bug reassigned from package 'maffilter' to 'libbpp-core3'.
No longer marked as found in versions maffilter/1.2.1+dfsg-1.
Ignoring request to alter fixed versions of bug #890405 to the same values 
previously set
Bug #890405 [libbpp-core3] maffilter: undefined symbol
Marked as found in versions libbpp-core/2.3.2-1.
> forcemerge -1 890405
Bug #890400 [libbpp-core3] physamp: autopkgtest failure
Bug #890405 [libbpp-core3] maffilter: undefined symbol
Merged 890400 890405
> retitle -1 libbpp-core3: ABI change without soname chenge
Bug #890400 [libbpp-core3] physamp: autopkgtest failure
Bug #890405 [libbpp-core3] maffilter: undefined symbol
Changed Bug title to 'libbpp-core3: ABI change without soname chenge' from 
'physamp: autopkgtest failure'.
Changed Bug title to 'libbpp-core3: ABI change without soname chenge' from 
'maffilter: undefined symbol'.
> affects -1 src:physamp src:maffilter
Bug #890400 [libbpp-core3] libbpp-core3: ABI change without soname chenge
Bug #890405 [libbpp-core3] libbpp-core3: ABI change without soname chenge
Added indication that 890400 affects src:physamp and src:maffilter
Added indication that 890405 affects src:physamp and src:maffilter

-- 
890400: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890400
890405: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890405
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Bug#890400: physamp: autopkgtest failure

[Julien Yann Dutheil]

Will do, also for maffilter.

J.

On 14 Feb 2018 13:15, "Andreas Tille"  wrote:

> Hi Graham,
>
> I guess Julien Dutheil will care for a patch.
>
> Kind regards
>
>Andreas.
>
> On Wed, Feb 14, 2018 at 02:00:18PM +0200, Graham Inggs wrote:
> > Source: physamp
> > Version: 1.0.3-1
> > Severity: serious
> > User: ubuntu-de...@lists.ubuntu.com
> > Usertags: origin-ubuntu bionic autopkgtest
> >
> > Hi Maintainer
> >
> > Since the upload of libbpp-core 2.3.2-1, physamp's autopkgtests have been
> > failing [1] with the following error:
> >
> > autopkgtest [03:46:54]: test run-unit-test: [---
> > bppalnoptim: symbol lookup error: bppalnoptim: undefined symbol: _
> ZN3bpp16ApplicationTools18getDoubleParameterERKNSt7__
> cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt3mapIS6_S6_
> St4lessIS6_ESaISt4pairIS7_S6_EEEdS8_bi
> > autopkgtest [03:46:55]: test run-unit-test: ---]
> > autopkgtest [03:46:55]: test run-unit-test:  - - - - - - - - - - results
> - -
> > - - - - - - - -
> > run-unit-testFAIL non-zero exit status 127
> >
> >
> > It looks like a symbol was dropped and a transition is needed.
> >
> > Regards
> > Graham
> >
> >
> > [1] https://ci.debian.net/packages/p/physamp/unstable/amd64/
> >
> > ___
> > Debian-med-packaging mailing list
> > debian-med-packag...@lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/
> debian-med-packaging
> >
>
> --
> http://fam-tille.de
>

Bug#890400: physamp: autopkgtest failure

[Andreas Tille]

Hi Graham,

I guess Julien Dutheil will care for a patch.

Kind regards

   Andreas.

On Wed, Feb 14, 2018 at 02:00:18PM +0200, Graham Inggs wrote:
> Source: physamp
> Version: 1.0.3-1
> Severity: serious
> User: ubuntu-de...@lists.ubuntu.com
> Usertags: origin-ubuntu bionic autopkgtest
> 
> Hi Maintainer
> 
> Since the upload of libbpp-core 2.3.2-1, physamp's autopkgtests have been
> failing [1] with the following error:
> 
> autopkgtest [03:46:54]: test run-unit-test: [---
> bppalnoptim: symbol lookup error: bppalnoptim: undefined symbol: 
> _ZN3bpp16ApplicationTools18getDoubleParameterERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt3mapIS6_S6_St4lessIS6_ESaISt4pairIS7_S6_EEEdS8_bi
> autopkgtest [03:46:55]: test run-unit-test: ---]
> autopkgtest [03:46:55]: test run-unit-test:  - - - - - - - - - - results - -
> - - - - - - - -
> run-unit-testFAIL non-zero exit status 127
> 
> 
> It looks like a symbol was dropped and a transition is needed.
> 
> Regards
> Graham
> 
> 
> [1] https://ci.debian.net/packages/p/physamp/unstable/amd64/
> 
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 

-- 
http://fam-tille.de

Bug#890400: physamp: autopkgtest failure

[Graham Inggs]

Source: physamp
Version: 1.0.3-1
Severity: serious
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu bionic autopkgtest

Hi Maintainer

Since the upload of libbpp-core 2.3.2-1, physamp's autopkgtests have 
been failing [1] with the following error:


autopkgtest [03:46:54]: test run-unit-test: [---
bppalnoptim: symbol lookup error: bppalnoptim: undefined symbol: 
_ZN3bpp16ApplicationTools18getDoubleParameterERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt3mapIS6_S6_St4lessIS6_ESaISt4pairIS7_S6_EEEdS8_bi

autopkgtest [03:46:55]: test run-unit-test: ---]
autopkgtest [03:46:55]: test run-unit-test:  - - - - - - - - - - results 
- - - - - - - - - -

run-unit-testFAIL non-zero exit status 127


It looks like a symbol was dropped and a transition is needed.

Regards
Graham


[1] https://ci.debian.net/packages/p/physamp/unstable/amd64/