[gentoo-science] openbabel-2.0.2 does not build with gcc-4.3.2

[gentoo-science] openbabel-2.0.2 does not build with gcc-4.3.2

[Valmor de Almeida]

Hello,

Apparently openbabel does not build. Is this a header file problem?

-> gcc --version
gcc (Gentoo 4.3.2-r3 p1.6, pie-10.1.5) 4.3.2
Copyright (C) 2008 Free Software Foundation, Inc.

[snip]

../../src/data.h:113: error: 'strncpy' was not declared in this scope
make[3]: *** [vector3.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [matrix3x3.lo] Error 1
make[3]: Leaving directory
`/var/tmp/portage/sci-chemistry/openbabel-2.0.2/work/openbabel-2.0.2/src/math'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/var/tmp/portage/sci-chemistry/openbabel-2.0.2/work/openbabel-2.0.2/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/var/tmp/portage/sci-chemistry/openbabel-2.0.2/work/openbabel-2.0.2/src'
make: *** [all-recursive] Error 1
 *
 * ERROR: sci-chemistry/openbabel-2.0.2 failed.
 * Call stack:
 *               ebuild.sh, line   48:  Called src_compile
 *             environment, line   90:  Called _eapi0_src_compile
 *               ebuild.sh, line  591:  Called _eapi2_src_compile
 *               ebuild.sh, line  625:  Called die
 * The specific snippet of code:
 *              emake || die "emake failed"
 *  The die message:
 *   emake failed
 *
 * If you need support, post the topmost build error, and the call stack
if relevant.
 * A complete build log is located at
'/var/tmp/portage/sci-chemistry/openbabel-2.0.2/temp/build.log'.
 * The ebuild environment file is located at
'/var/tmp/portage/sci-chemistry/openbabel-2.0.2/temp/environment'.


Thanks for any help.

--
Valmor

Re: [gentoo-science] openbabel-2.0.2 does not build with gcc-4.3.2

[Mathias Weigt]

Valmor de Almeida schrieb:
> Hello,
> 
> Apparently openbabel does not build. Is this a header file problem?
> 
> -> gcc --version
> gcc (Gentoo 4.3.2-r3 p1.6, pie-10.1.5) 4.3.2
> Copyright (C) 2008 Free Software Foundation, Inc.
> 
> [snip]
> 
> ../../src/data.h:113: error: 'strncpy' was not declared in this scope
> make[3]: *** [vector3.lo] Error 1
> make[3]: *** Waiting for unfinished jobs....
> make[3]: *** [matrix3x3.lo] Error 1
> make[3]: Leaving directory
> `/var/tmp/portage/sci-chemistry/openbabel-2.0.2/work/openbabel-2.0.2/src/math'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory
> `/var/tmp/portage/sci-chemistry/openbabel-2.0.2/work/openbabel-2.0.2/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory
> `/var/tmp/portage/sci-chemistry/openbabel-2.0.2/work/openbabel-2.0.2/src'
> make: *** [all-recursive] Error 1

> Thanks for any help.
> 
> --
> Valmor
> 

have a look at Bugzilla:
http://bugs.gentoo.org/show_bug.cgi?id=262081

There you can find a patch for this old version of openbabel...

-- 
Mathias Weigt

Institute of Pharmaceutical Chemistry
University of Bonn

An der Immenburg 4
53121 Bonn
Germany

Phone: +49/228/73-5240

Re: [gentoo-science] openbabel-2.0.2 does not build with gcc-4.3.2

[Valmor de Almeida]

Mathias Weigt wrote:

>>
> 
> have a look at Bugzilla:
> http://bugs.gentoo.org/show_bug.cgi?id=262081
> 
> There you can find a patch for this old version of openbabel...
> 

Thanks for the info. I emerged

=sci-chemistry/openbabel-2.2.1 ~x86

and it compiled without problems; let's see what happens next...

Re: [gentoo-science] openbabel-2.0.2 does not build with gcc-4.3.2

[Marcus D. Hanwell]

On Wednesday 13 May 2009 12:23:20 Valmor de Almeida wrote:
> Mathias Weigt wrote:
> > have a look at Bugzilla:
> > http://bugs.gentoo.org/show_bug.cgi?id=262081
> >
> > There you can find a patch for this old version of openbabel...
>
> Thanks for the info. I emerged
>
> =sci-chemistry/openbabel-2.2.1 ~x86
>
> and it compiled without problems; let's see what happens next...

I have been cleaning up Open Babel, and hope to get a new version 
stabilized soon. It will likely be 2.2.1 as that has been in portage for 
longer than a month. I will mark it stable on amd64, and see about 
getting the same done on other architectures.

Thanks,

Marcus