Debian Bug report logs - #626362
Fails to build from source if libghemical is recompiled from source

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Package: ghemical; Maintainer for ghemical is Debichem Team <debichem-devel@lists.alioth.debian.org>; Source for ghemical is src:ghemical.

Reported by: Moritz Muehlenhoff <muehlenhoff@univention.de>

Date: Wed, 11 May 2011 10:33:01 UTC

Severity: serious

Tags: squeeze

Found in version ghemical/2.99.2-1

Done: Daniel Leidert <daniel.leidert.spam@gmx.net>

Bug is archived. No further changes may be made.

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Report forwarded to debian-bugs-dist@lists.debian.org, Debichem Team <debichem-devel@lists.alioth.debian.org>:
Bug#626362; Package ghemical. (Wed, 11 May 2011 10:33:05 GMT) Full text and rfc822 format available.

Acknowledgement sent to Moritz Muehlenhoff <muehlenhoff@univention.de>:
New Bug report received and forwarded. Copy sent to Debichem Team <debichem-devel@lists.alioth.debian.org>. (Wed, 11 May 2011 10:33:05 GMT) Full text and rfc822 format available.

Message #5 received at submit@bugs.debian.org (full text, mbox):

From: Moritz Muehlenhoff <muehlenhoff@univention.de>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: Fails to build from source if libghemical is recompiled from source
Date: Wed, 11 May 2011 12:31:42 +0200
Package: ghemical
Version: 2.99.2-1
Severity: serious
Tags: squeeze

Hi Michael/Daniel,

I've tried to rebuild ghemical for Univention Corporate Server, a Debian 
derived distribution based on Debian stable (currently Lenny, our next release 
will be based on Squeeze).

The following was tested against Squeeze, but should equally apply to unstable,
since the versions are the same:

ghemical compiles fine if built against the libghemical binary packages currently
in the archive (i.e. the version uploaded in 2009). However, if libghemical is
rebuild on Squeeze, the build of ghemical fails to build from source:

----
(..)
/usr/lib/../lib/libghemical.so: undefined reference to `sc::MessageGrp::set_default_messagegrp(sc::Ref<sc::MessageGrp> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::VDWShape::VDWShape(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::MolecularEnergy::get_cartesian_gradient()'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::TCHF::TCHF(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::SCMatrixKit::set_default_matrixkit(sc::Ref<sc::SCMatrixKit> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::RefSymmSCMatrix::RefSymmSCMatrix(sc::RefSCDimension const&, sc::Ref<sc::SCMatrixKit
> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::ConnollyShape::ConnollyShape(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::DiscreteConnollyShape::DiscreteConnollyShape(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::SCElementScalarProduct::SCElementScalarProduct()'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::RefBase::reference(sc::RefCount*)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::ShmMessageGrp::ShmMessageGrp(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::UHF::UHF(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `typeinfo for sc::MolecularEnergy'
/usr/lib/../lib/libghemical.so: undefined reference to `typeinfo for sc::OneBodyWavefunction'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::RefSymmSCMatrix::~RefSymmSCMatrix()'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::SCVectordouble::~SCVectordouble()'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::RefCount::unlock_ptr() const'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::BFGSUpdate::BFGSUpdate(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::OSSHF::OSSHF(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::OneBodyWavefunction::orbital_density(sc::SCVector3 const&, int, double*)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::DistSCMatrixKit::DistSCMatrixKit(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::OOGLRender::OOGLRender(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::RenderedMolecularSurface::RenderedMolecularSurface(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::MessageGrp::get_default_messagegrp()'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::KeyVal::exists(char const*)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::Appearance::Appearance(sc::Ref<sc::KeyVal> const&)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::PrefixKeyVal::PrefixKeyVal(sc::Ref<sc::KeyVal> const&, char const*)'
/usr/lib/../lib/libghemical.so: undefined reference to `sc::RenderedBallMolecule::RenderedBallMolecule(sc::Ref<sc::KeyVal> const&)'
collect2: ld returned 1 exit status
make[4]: *** [ghemical] Error 1
make[4]: Leaving directory `/var/build/temp/tmp.JyKUfIlECN/3.0-0-0/ghemical/ghemical-2.99.2/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/var/build/temp/tmp.JyKUfIlECN/3.0-0-0/ghemical/ghemical-2.99.2/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/var/build/temp/tmp.JyKUfIlECN/3.0-0-0/ghemical/ghemical-2.99.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/var/build/temp/tmp.JyKUfIlECN/3.0-0-0/ghemical/ghemical-2.99.2'
make: *** [build-stamp] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
---

I've filed this against ghemical, but the error might just as well be present
in libghemical.

Cheers,
        Moritz




Information forwarded to debian-bugs-dist@lists.debian.org, Debichem Team <debichem-devel@lists.alioth.debian.org>:
Bug#626362; Package ghemical. (Wed, 11 May 2011 17:48:03 GMT) Full text and rfc822 format available.

Acknowledgement sent to Michael Banck <mbanck@debian.org>:
Extra info received and forwarded to list. Copy sent to Debichem Team <debichem-devel@lists.alioth.debian.org>. (Wed, 11 May 2011 17:48:03 GMT) Full text and rfc822 format available.

Message #10 received at 626362@bugs.debian.org (full text, mbox):

From: Michael Banck <mbanck@debian.org>
To: Moritz Muehlenhoff <muehlenhoff@univention.de>, 626362@bugs.debian.org
Subject: Re: [Debichem-devel] Bug#626362: Fails to build from source if libghemical is recompiled from source
Date: Wed, 11 May 2011 19:45:09 +0200
Hi,

On Wed, May 11, 2011 at 12:31:42PM +0200, Moritz Muehlenhoff wrote:
> I've tried to rebuild ghemical for Univention Corporate Server, a Debian 
> derived distribution based on Debian stable (currently Lenny, our next release 
> will be based on Squeeze).

Oh, any particular reason you include ghemical?  Or are you just
rebuilding all the packages anyway?
 
> The following was tested against Squeeze, but should equally apply to unstable,
> since the versions are the same:
> 
> ghemical compiles fine if built against the libghemical binary packages currently
> in the archive (i.e. the version uploaded in 2009). However, if libghemical is
> rebuild on Squeeze, the build of ghemical fails to build from source:
> 
> ----
> (..)
> /usr/lib/../lib/libghemical.so: undefined reference to `sc::MessageGrp::set_default_messagegrp(sc::Ref<sc::MessageGrp> const&)'

Those are from mpqc's libsc7, can you provide the command-line which got
used for linking as well?


Thanks,

Michael




Information forwarded to debian-bugs-dist@lists.debian.org, Debichem Team <debichem-devel@lists.alioth.debian.org>:
Bug#626362; Package ghemical. (Thu, 12 May 2011 13:45:03 GMT) Full text and rfc822 format available.

Acknowledgement sent to Moritz Mühlenhoff <muehlenhoff@univention.de>:
Extra info received and forwarded to list. Copy sent to Debichem Team <debichem-devel@lists.alioth.debian.org>. (Thu, 12 May 2011 13:45:03 GMT) Full text and rfc822 format available.

Message #15 received at 626362@bugs.debian.org (full text, mbox):

From: Moritz Mühlenhoff <muehlenhoff@univention.de>
To: Michael Banck <mbanck@debian.org>
Cc: 626362@bugs.debian.org
Subject: Re: [Debichem-devel] Bug#626362: Fails to build from source if libghemical is recompiled from source
Date: Thu, 12 May 2011 15:31:10 +0200
[Message part 1 (text/plain, inline)]
Hi Michael,

> > I've tried to rebuild ghemical for Univention Corporate Server, a Debian
> > derived distribution based on Debian stable (currently Lenny, our next
> > release will be based on Squeeze).
>
> Oh, any particular reason you include ghemical?  Or are you just
> rebuilding all the packages anyway?

We're rebuilding all of Squeeze/main with the exception of the games section.

(We're differentiating between two sections, one for all the apps covered by 
support (e.g. KDE, Samba, OpenLDAP etc.) and another section, where we build 
all the remaining packages from Squeeze for the convenience of users with 
more specialised needs. ghemical would be in the latter section.)

> Those are from mpqc's libsc7, can you provide the command-line which got
> used for linking as well?

I'm attaching the build logs for mpqc, libghemical and ghemical. There're all 
build without further patches. (The version numbers of the built binaries 
have a distro-specific new tag, though)

Cheers,
Moritz
-- 
Moritz Mühlenhoff                         muehlenhoff@univention.de
Open Source Software Engineer and Consultant
Univention GmbH  Linux for Your Business     fon: +49 421 22 232- 0
Mary-Somerville-Str.1  28359 Bremen          fax: +49 421 22 232-99
http://www.univention.de
[ucs_3.0-0.ghemical.201105061047.log.bz2 (application/x-bzip2, attachment)]
[ucs_3.0-0.libghemical.201105071636.log.bz2 (application/x-bzip2, attachment)]
[ucs_3.0-0.mpqc.201104260927.log.bz2 (application/x-bzip2, attachment)]

Reply sent to Daniel Leidert <daniel.leidert.spam@gmx.net>:
You have taken responsibility. (Sun, 27 Nov 2011 19:33:09 GMT) Full text and rfc822 format available.

Notification sent to Moritz Muehlenhoff <muehlenhoff@univention.de>:
Bug acknowledged by developer. (Sun, 27 Nov 2011 19:33:09 GMT) Full text and rfc822 format available.

Message #20 received at 626362-done@bugs.debian.org (full text, mbox):

From: Daniel Leidert <daniel.leidert.spam@gmx.net>
To: 626362-done@bugs.debian.org, 642664-done@bugs.debian.org
Subject: FTBFS of ghemical
Date: Sun, 27 Nov 2011 20:28:28 +0100
Hi,

We've fixed some issues in mpqc (libsc-dev) and now uploaded the new
versions of ghemical and libghemical. I did not observe any FTBFS in
neither clean CHROOTS nor my worksystem. I'm therefor closing these
reports as I believe, they have been "fixed". Please feel free to reopen
your report of the problem appears again.

Regards, Daniel





Bug archived. Request was from Debbugs Internal Request <owner@bugs.debian.org> to internal_control@bugs.debian.org. (Mon, 26 Dec 2011 07:36:46 GMT) Full text and rfc822 format available.

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