Commit 7ccdc735 authored by Nicholas Breen's avatar Nicholas Breen

* 21_makefile_dups.dpatch: Actually "svn add" it this time.

* rules: Remove obsolete --disable-nice option from *_CONFIG_PARAMS.
* man/gromacs.7: Update macros for lintian cleanliness.
* changelog: Update date stamp for release.
parent 24c05cdf
gromacs (4.0.5-4) unstable; urgency=low
* patches/21_makefile_dups.dpatch: Eliminate duplicated files in the
installation list of include/Makefile.am. Autoconf 1.11 now passes
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.
-- Nicholas Breen <nbreen@ofb.net> Sat, 22 Aug 2009 13:12:18 -0700
-- Nicholas Breen <nbreen@ofb.net> Tue, 25 Aug 2009 12:30:15 -0700
gromacs (4.0.5-3) unstable; urgency=low
......
.\" Automatically generated by Pod::Man v1.37, Pod::Parser v1.14
.\" Automatically generated by Pod::Man 2.1801 (Pod::Simple 3.05)
.\" (and then reused elsewhere, since this isn't a perl package)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sh \" Subsection heading
.br
.if t .Sp
.ne 5
.PP
\fB\\$1\fR
.PP
..
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
......@@ -26,11 +18,11 @@
..
.\" Set up some character translations and predefined strings. \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote. | will give a
.\" real vertical bar. \*(C+ will give a nicer C++. Capital omega is used to
.\" do unbreakable dashes and therefore won't be available. \*(C` and \*(C'
.\" expand to `' in nroff, nothing in troff, for use with C<>.
.tr \(*W-|\(bv\*(Tr
.\" double quote, and \*(R" will give a right double quote. \*(C+ will
.\" give a nicer C++. Capital omega is used to do unbreakable dashes and
.\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
. ds -- \(*W-
......@@ -49,22 +41,25 @@
. ds R" ''
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el .ds Aq '
.\"
.\" If the F register is turned on, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD. Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.if \nF \{\
.ie \nF \{\
. de IX
. tm Index:\\$1\t\\n%\t"\\$2"
..
. nr % 0
. rr F
.\}
.\"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.hy 0
.if n .na
.el \{\
. de IX
..
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear. Run. Save yourself. No user-serviceable parts.
......@@ -131,6 +126,10 @@
.\"
.IX Title "GROMACS 7"
.TH GROMACS 7 "2008-10-12" "gromacs" "GROMACS suite, Version 4.0"
\" For nroff, turn off justification. Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
gromacs \- molecular dynamics simulation suite
.SH "DESCRIPTION"
......@@ -146,7 +145,7 @@ to a wide variety of chemical and biological research questions.
.PP
The following commands make up the GROMACS suite. Please refer to their
individual man pages for further details.
.Sh "Generating topologies and coordinates"
.SH "Generating topologies and coordinates"
.IX Subsection "Generating topologies and coordinates"
.Vb 7
\& pdb2gmx converts pdb files to topology and coordinate files
......@@ -157,7 +156,7 @@ individual man pages for further details.
\& genconf multiplies a conformation in 'random' orientations
\& protonate protonates structures
.Ve
.Sh "Running a simulation"
.SH "Running a simulation"
.IX Subsection "Running a simulation"
.Vb 4
\& grompp makes a run input file
......@@ -165,21 +164,21 @@ individual man pages for further details.
\& mdrun performs a simulation
\& mdrun_mpi performs a sim across multiple CPUs or systems (in separate package)
.Ve
.Sh "Viewing trajectories"
.SH "Viewing trajectories"
.IX Subsection "Viewing trajectories"
.Vb 3
\& ngmx displays a trajectory
\& trjconv converts trajectories to e.g. pdb which can be viewed with e.g. rasmol
\& g_nmtraj generate a virtual trajectory from an eigenvector
.Ve
.Sh "Processing energies"
.SH "Processing energies"
.IX Subsection "Processing energies"
.Vb 3
\& g_energy writes energies to xvg files and displays averages
\& g_enemat extracts an energy matrix from an energy file
\& mdrun with \-rerun (re)calculates energies for trajectory frames
.Ve
.Sh "Converting files"
.SH "Converting files"
.IX Subsection "Converting files"
.Vb 5
\& editconf converts and manipulates structure files
......@@ -189,7 +188,7 @@ individual man pages for further details.
\& xpm2ps converts XPM matrices to encapsulated postscript (or XPM)
\& sigeps convert c6/12 or c6/cn combinations to and from sigma/epsilon
.Ve
.Sh "Tools"
.SH "Tools"
.IX Subsection "Tools"
.Vb 18
\& make_ndx makes index files
......@@ -211,7 +210,7 @@ individual man pages for further details.
\& g_spatial calculates the spatial distribution function (more control than g_sdf)
\& g_sdf calculates the spatial distribution function (faster than g_spatial)
.Ve
.Sh "Distances between structures"
.SH "Distances between structures"
.IX Subsection "Distances between structures"
.Vb 4
\& g_rms calculates rmsd's with a reference structure and rmsd matrices
......@@ -219,7 +218,7 @@ individual man pages for further details.
\& g_cluster clusters structures
\& g_rmsf calculates atomic fluctuations
.Ve
.Sh "Distances in structures over time"
.SH "Distances in structures over time"
.IX Subsection "Distances in structures over time"
.Vb 6
\& g_mindist calculates the minimum distance between two groups
......@@ -229,7 +228,7 @@ individual man pages for further details.
\& g_polystat plot average static properties of polymers
\& g_rmsdist calculates atom pair distances averaged with power \-2, \-3 or \-6
.Ve
.Sh "Mass distribution properties over time"
.SH "Mass distribution properties over time"
.IX Subsection "Mass distribution properties over time"
.Vb 5
\& g_traj plots x, v, f, box, temperature and rotational energy
......@@ -238,7 +237,7 @@ individual man pages for further details.
\& g_rotacf calculates the rotational correlation function for molecules
\& g_vanhove compute Van Hove correlation function
.Ve
.Sh "Analyzing bonded interactions"
.SH "Analyzing bonded interactions"
.IX Subsection "Analyzing bonded interactions"
.Vb 4
\& g_bond calculates bond length distributions
......@@ -246,7 +245,7 @@ individual man pages for further details.
\& g_angle calculates distributions and correlations for angles and dihedrals
\& g_dih analyzes dihedral transitions
.Ve
.Sh "Structural properties"
.SH "Structural properties"
.IX Subsection "Structural properties"
.Vb 13
\& g_hbond computes and analyzes hydrogen bonds
......@@ -263,7 +262,7 @@ individual man pages for further details.
\& g_clustsize calculate size distributions of atomic clusters
\& anadock cluster structures from Autodock runs
.Ve
.Sh "Kinetic properties"
.SH "Kinetic properties"
.IX Subsection "Kinetic properties"
.Vb 4
\& g_traj plots x, v, f, box, temperature and rotational energy
......@@ -271,7 +270,7 @@ individual man pages for further details.
\& g_tcaf calculates viscosities of liquids
\& g_kinetics calculate kinetic rate constants (experimental)
.Ve
.Sh "Electrostatic properties"
.SH "Electrostatic properties"
.IX Subsection "Electrostatic properties"
.Vb 5
\& genion generates mono atomic ions on energetically favorable positions
......@@ -280,7 +279,7 @@ individual man pages for further details.
\& g_dielectric calculates frequency dependent dielectric constants
\& g_current calculate current autocorrelation function of system
.Ve
.Sh "Protein specific analysis"
.SH "Protein specific analysis"
.IX Subsection "Protein specific analysis"
.Vb 7
\& do_dssp assigns secondary structure and calculates solvent accessible surface area
......@@ -291,7 +290,7 @@ individual man pages for further details.
\& xrama shows animated Ramachandran plots
\& wheel plots helical wheels
.Ve
.Sh "Interfaces"
.SH "Interfaces"
.IX Subsection "Interfaces"
.Vb 6
\& g_potential calculates the electrostatic potential across the box
......@@ -301,14 +300,14 @@ individual man pages for further details.
\& g_h2order computes the orientation of water molecules
\& g_bundle analyzes bundles of axes, e.g. transmembrane helices
.Ve
.Sh "Covariance analysis"
.SH "Covariance analysis"
.IX Subsection "Covariance analysis"
.Vb 3
\& g_covar calculates and diagonalizes the covariance matrix
\& g_anaeig analyzes the eigenvectors
\& make_edi generate essential-dynamics input file from g_covar output
.Ve
.Sh "Normal modes"
.SH "Normal modes"
.IX Subsection "Normal modes"
.Vb 8
\& grompp makes a run input file
......
#! /bin/sh /usr/share/dpatch/dpatch-run
## 21_makefile_dups.dpatch by Nicholas Breen <nbreen@ofb.net>
##
## All lines beginning with `## DP:' are a description of the patch.
## DP: Delete duplicate install entries from Makefile.am. Autotools
## DP: >= 1.11 passes multiple files to install at once, causing errors
## DP: when the same filename appears twice in one run.
## DP: After applying this patch, the autotools must be re-run.
## DP: Last updated 24-Aug-2009 for upstream release 4.0.5
@DPATCH@
diff -Nru gromacs-4.0.5_orig/include/Makefile.am gromacs-4.0.5/include/Makefile.am
--- gromacs-4.0.5_orig/include/Makefile.am 2009-05-08 08:45:07.000000000 -0700
+++ gromacs-4.0.5/include/Makefile.am 2009-08-24 15:10:02.609412273 -0700
@@ -45,7 +45,6 @@
gmx_parallel_3dfft.h \
gmx_system_xdr.h \
gmx_thread.h \
-gmx_parallel_3dfft.h \
gmx_wallcycle.h \
gpp_atomtype.h \
gpp_nextnb.h \
@@ -109,7 +108,6 @@
sysstuff.h \
tags.h \
tgroup.h \
-tgroup.h \
topsort.h \
tpxio.h \
transfer.h \
......@@ -43,7 +43,6 @@ endif
LAM_CONFIG_PARAMS = \
--enable-mpi \
--disable-nice \
--without-x \
--without-gsl \
MPICC=/usr/bin/mpicc.lam \
......@@ -52,7 +51,6 @@ LAM_CONFIG_PARAMS = \
MPICH_CONFIG_PARAMS = \
--enable-mpi \
--disable-nice \
--without-x \
--without-gsl \
MPICC=/usr/bin/mpicc.mpich \
......@@ -60,7 +58,6 @@ MPICH_CONFIG_PARAMS = \
OPENMPI_CONFIG_PARAMS = \
--enable-mpi \
--disable-nice \
--disable-fortran \
--without-x \
--without-gsl \
......
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