Your message dated Wed, 26 Aug 2009 11:32:16 +0000
with message-id <[email protected]>
and subject line Bug#543059: fixed in gromacs 4.0.5-4
has caused the Debian Bug report #543059,
regarding gromacs: FTBFS: /usr/bin/install: will not overwrite just-created
`/build/user-gromacs_4.0.5-3-amd64-USJwHp/gromacs-4.0.5/debian/gromacs/usr/include/gromacs/gmx_parallel_3dfft.h'
with `../../../include/gmx_parallel_3dfft.h'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
543059: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=543059
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: gromacs
Version: 4.0.5-3
Severity: serious
User: [email protected]
Usertags: qa-ftbfs-20090822 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part:
> make[4]: Entering directory
> `/build/user-gromacs_4.0.5-3-amd64-USJwHp/gromacs-4.0.5/build/basic/include'
> make[4]: Nothing to be done for `install-exec-am'.
> test -z "/usr/include/gromacs" || /bin/mkdir -p
> "/build/user-gromacs_4.0.5-3-amd64-USJwHp/gromacs-4.0.5/debian/gromacs/usr/include/gromacs"
> /usr/bin/install -c -m 644 ../../../include/3dview.h
> ../../../include/assert.h ../../../include/atomprop.h
> ../../../include/bondf.h ../../../include/calcgrid.h ../../../include/calch.h
> ../../../include/calcmu.h ../../../include/checkpoint.h
> ../../../include/confio.h ../../../include/constr.h
> ../../../include/copyrite.h ../../../include/coulomb.h
> ../../../include/dihre.h ../../../include/disre.h ../../../include/domdec.h
> ../../../include/domdec_network.h ../../../include/do_fit.h
> ../../../include/ebin.h ../../../include/edsam.h ../../../include/enxio.h
> ../../../include/gmx_fatal.h ../../../include/ffscanf.h
> ../../../include/fftgrid.h ../../../include/filenm.h ../../../include/force.h
> ../../../include/futil.h ../../../include/gbutil.h ../../../include/gmx_ana.h
> ../../../include/gmx_arpack.h ../../../include/gmx_blas.h
> ../../../include/gmxcomplex.h ../../../include/gmx_cyclecounter.h
> ../../../include/gmxfio.h ../../../include/gmx_fft.h
> ../../../include/gmx_lapack.h ../../../include/gmx_random.h
> ../../../include/gmx_parallel_3dfft.h ../../../include/gmx_system_xdr.h
> ../../../include/gmx_thread.h ../../../include/gmx_parallel_3dfft.h
> '/build/user-gromacs_4.0.5-3-amd64-USJwHp/gromacs-4.0.5/debian/gromacs/usr/include/gromacs'
> /usr/bin/install: will not overwrite just-created
> `/build/user-gromacs_4.0.5-3-amd64-USJwHp/gromacs-4.0.5/debian/gromacs/usr/include/gromacs/gmx_parallel_3dfft.h'
> with `../../../include/gmx_parallel_3dfft.h'
> make[4]: *** [install-pkgincludeHEADERS] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2009/08/22/gromacs_4.0.5-3_lsid64.buildlog
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on about 50 AMD64 nodes
of the Grid'5000 platform, using a clean chroot. Internet was not
accessible from the build systems.
--
| Lucas Nussbaum
| [email protected] http://www.lucas-nussbaum.net/ |
| jabber: [email protected] GPG: 1024D/023B3F4F |
--- End Message ---
--- Begin Message ---
Source: gromacs
Source-Version: 4.0.5-4
We believe that the bug you reported is fixed in the latest version of
gromacs, which is due to be installed in the Debian FTP archive:
gromacs-data_4.0.5-4_all.deb
to pool/main/g/gromacs/gromacs-data_4.0.5-4_all.deb
gromacs-dev_4.0.5-4_i386.deb
to pool/main/g/gromacs/gromacs-dev_4.0.5-4_i386.deb
gromacs-lam_4.0.5-4_i386.deb
to pool/main/g/gromacs/gromacs-lam_4.0.5-4_i386.deb
gromacs-mpich_4.0.5-4_i386.deb
to pool/main/g/gromacs/gromacs-mpich_4.0.5-4_i386.deb
gromacs-openmpi_4.0.5-4_i386.deb
to pool/main/g/gromacs/gromacs-openmpi_4.0.5-4_i386.deb
gromacs_4.0.5-4.diff.gz
to pool/main/g/gromacs/gromacs_4.0.5-4.diff.gz
gromacs_4.0.5-4.dsc
to pool/main/g/gromacs/gromacs_4.0.5-4.dsc
gromacs_4.0.5-4_i386.deb
to pool/main/g/gromacs/gromacs_4.0.5-4_i386.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nicholas Breen <[email protected]> (supplier of updated gromacs package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: RIPEMD160
Format: 1.8
Date: Tue, 25 Aug 2009 12:30:15 -0700
Source: gromacs
Binary: gromacs gromacs-data gromacs-dev gromacs-mpich gromacs-lam
gromacs-openmpi
Architecture: source all i386
Version: 4.0.5-4
Distribution: unstable
Urgency: low
Maintainer: Debichem Team <[email protected]>
Changed-By: Nicholas Breen <[email protected]>
Description:
gromacs - Molecular dynamics simulator, with building and analysis tools
gromacs-data - GROMACS molecular dynamics sim, data and documentation
gromacs-dev - GROMACS molecular dynamics sim, development kit
gromacs-lam - Molecular dynamics sim, binaries for LAM-MPI parallelization
gromacs-mpich - Molecular dynamics sim, binaries for MPICH parallelization
gromacs-openmpi - Molecular dynamics sim, binaries for OpenMPI parallelization
Closes: 543059
Changes:
gromacs (4.0.5-4) unstable; urgency=low
.
* patches/21_makefile_dups.dpatch: Eliminate duplicated files in the
installation list of include/Makefile.am. Automake 1.11 now passes
multiple files to `install' at once, causing failures when one name
is given twice. (Closes: #543059)
* control: Increment S-V to 3.8.3. No changes required.
* rules: Remove obsolete --disable-nice option from *_CONFIG_PARAMS.
* man/gromacs.7: Update macros for lintian cleanliness.
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gromacs-lam_4.0.5-4_i386.deb
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gromacs-openmpi_4.0.5-4_i386.deb
Files:
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9a68882031c6e1275beeb5d20b7e36f8 37744 science extra gromacs_4.0.5-4.diff.gz
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gromacs-data_4.0.5-4_all.deb
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1067ccba2c0ccb111054e08330f11e04 10902264 devel extra
gromacs-dev_4.0.5-4_i386.deb
57e77622e4bc8279a12f6fb10a0574e7 2334342 science extra
gromacs-mpich_4.0.5-4_i386.deb
553f19e92d8946c8860a6d1f383d84e9 2044428 science extra
gromacs-lam_4.0.5-4_i386.deb
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gromacs-openmpi_4.0.5-4_i386.deb
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