[Bug 207567] [NEW] Please sync gromacs 3.3.3-2 (universe) from Debian unstable (main)

[Jordan Mantha]

Public bug reported:

Binary package hint: gromacs

Please sync gromacs 3.3.3-2 from Debian unstable. This is a part of the
gfortran, bug #201962, (blanket FFe)  and mpich (Bug #202817)
transitions.

I have verified that the package builds/installs/works in Hardy. It has
no reverse dependencies other than metapackages.

Relevant changelong entries:

gromacs (3.3.3-2) unstable; urgency=low

  * debian/control: Eliminate unneeded Build-Depends on libxml-dev.
    Spotted by Pierre Habouzit.  (Closes: #470000)
  * debian/rules: Force --with-gsl in configuration.

 -- Nicholas Breen <nbreen at ofb.net>  Sat, 08 Mar 2008 12:34:36 -0800

gromacs (3.3.3-1) unstable; urgency=low

  [ Nicholas Breen ]
  * New upstream release.
  * debian/rules, debian/control: Reconfigure gromacs-doc as gromacs-data.
    This moves all architecture independent files into a single package,
    including many topology files formerly shipped in gromacs instead.
    - Rename debian/*gromacs-doc* to debian/*gromacs-data* .
    - debian/gromacs-doc.preinst: no longer necessary, removed.
  * Remove PDF manual for the time being, as modifiable sources are not
    currently available.
    - debian/gromacs.README.Debian, debian/man/gromacs.7: Provide pointers
      to its location online instead.
    - debian/control: Drop build dependency on sharutils, which was used
      only to provide the manual.
    - debian/gromacs-data.doc-base: Remove reference to PDF.
  * debian/control: Add Build-Depends on libgsl0-dev to support addition
    of /usr/bin/g_kinetics.
  * debian/gromacs.README.Debian: Update suggested MPI implementations.
  * debian/man: write preliminary man pages for undocumented new commands,
    g_kinetics.1 g_spatial.1 g_sdf.1
  * debian/patches/10_manpages: Update with ROFF fixes to 18 files; fix a 
    few minor typos; resync patch against upstream CVS.
  * debian/man/mdrun_mpi.{mpich,lam,openmpi}.1: Propagate those fixes.
  * debian/lintian-overrides.gromacs: Drop binary-without-manpage override.
  * debian/linda-overrides.gromacs, debian/rules: Remove linda override.

  [ Daniel Leidert ]
  * debian/man/average.1: Minor ROFF improvements, hyphen/minus and typo
    fixes.
  * debian/man/g_nmtraj.1: Ditto.
  * debian/man/luck.1: Ditto.

 -- Nicholas Breen <nbreen at ofb.net>  Mon, 03 Mar 2008 21:23:01 -0800

gromacs (3.3.3~pre1-1) unstable; urgency=low

  [ Nicholas Breen ]
  * New upstream release.
    - Remove obsolete patches now incorporated upstream:
      50_xtcio_double_range_checking, 51_180_degree_angle,
      52_pme_spline, 53_pbc_compiler.
  * debian/rules: 
    - Clean up patch syntax to prevent double compilations.
    - Add .NOTPARALLEL target to prevent the various MPI builds from
      compiling on the same source tree simultaneously, while still
      allowing -j options to be passed to sublevel targets.
    - Improve DEB_BUILD_OPTIONS=parallel=X handling, now in line with
      the example proposed for policy.
    - Disable FORTRAN inner loops for gromacs-openmpi on alpha.  This
      is a temporary workaround to avoid lingering linking problems
      regarding libmpi.so and the update-alternatives system.
    - Add support for DEB_BUILD_OPTIONS=noopt.
    - Additional rewrite work (see below): use new format for build
      commands, but split for individual MPI implementations.
    - Run autotools between patch and configuration steps.
    - New format for MPI library suffix configuration.
  * debian/control:
    - Add versioned Build-Depends on libmpich1.0-dev for its 
      g77 -> gfortran transition.
    - Add Build-Depends on autoconf and automake, and Build-Conflicts
      on autoconf2.13, to support updated mpisuffix patch.
    - Downgrade gromacs-doc Depends: on gromacs to a Recommends:, as -doc
      now ships its own copyright file.
  * debian/patches/04_autoconf_mpisuffix.dpatch: Apply dleidert's improved
    patch to allow arbitrary overrides of LIBSUFFIX; reduce patch to only
    the directly changed code in configure.ac, and add an invocation of
    autotools during the build process rather than patching configure
    itself directly.
  * debian/gromacs-{doc,dev}.preinst: Remove symlinks for package doc
    directories on upgrade, in order to replace them with actual directories.

  [ Daniel Leidert ]
  * debian/control (Suggests): Fixed a debcheck issue - gromacs-openmpi should
    only be suggested on supported architectures.
  * debian/copyright: Added copyright information to satisfy lintian.
  * debian/gromacs-doc.doc-base (Section): Fixed accordingly to menu policy.
    (Format): Fixed path to HTML files.
  * debian/rules: Major rewrite. Changes/improvements include:
    - drop dpatch target definitions in favour of dpatch.make
    - put all configure flags to the top of the file
    - moved all configure related commands into configure-stamp
    - moved all build related commands into build-stamp
    - moved all install related commands into separate install targets
    - configure and build in sub-directories to avoid $(MAKE) clean calls
    - clean target removes build/ instead to run clean/distclean
    - replaced ln with dh_link and gzip with dh_installman
    - adjusted target requirements for binary* and install*
    - install a /usr/share/doc/$package directory for gromacs-doc and -dev
      too; put the HTML into the -doc documentation directory; add links to
      the HTML directory for the gromacs and the -dev package pointing to the
      -doc directory
    - fixed .PHONY target for above
  * debian/watch: Added pre-release version handling.

 -- Nicholas Breen <nbreen at ofb.net>  Wed, 13 Feb 2008 15:01:50 -0800

gromacs (3.3.2-3) unstable; urgency=low

  * Package transferred to Debichem team maintenance.
  * debian/control:
    - Switched Maintainer to Debichem Team, moved myself to
      Uploaders.  Added Vcs-Browser, Vcs-Svn fields.
    - Increase Standards-Version to 3.7.3.  No changes required.
    - Build-Depend on libopenmpi-dev >= 1.2.4-5 (Closes: #456860).
  * debian/rules: include kfreebsd-* variants explicitly in OPENMPI_ARCH.
  * debian/patches/11_readme.dpatch: change edited README to an explicit
    patch, rather than modifying it directly in the .diff.gz.
  * Multiple bugfixes from upstream CVS:
    - 51_180_degree_angle.dpatch: apply upstream patches to avoid crashes
      crashes when operating on precisely linear 2-bond pairs.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=172,
           http://bugzilla.gromacs.org/show_bug.cgi?id=177)
    - 52_pme_spline.dpatch: calculate mesh contribution when charges
      are 0 in A state, but non-zero in B state.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=175)
    - 53_pbc_compiler: Solve regression in gmxlib/pbc.c introduced by a
      previous compiler workaround.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=179)
  * debian/gromacs-doc.doc-base: remove extraneous spaces.

 -- Nicholas Breen <nbreen at ofb.net>  Wed, 26 Dec 2007 12:26:09 -0800

** Affects: gromacs (Ubuntu)
     Importance: Wishlist
         Status: Confirmed

-- 
Please sync gromacs 3.3.3-2 (universe) from Debian unstable (main)
https://bugs.launchpad.net/bugs/207567
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