[Pkg-octave-commit] [SCM] dynare branch, master, updated. bb6bcc2ad7229f408a124db6d4962e4a769cd5d8
Sébastien Villemot
sebastien.villemot at ens.fr
Wed Jan 13 17:47:58 UTC 2010
The following commit has been merged in the master branch:
commit 0a928b422b0b1f8ec1f77fee5ec3359dfb9b3efa
Author: Sébastien Villemot <sebastien.villemot at ens.fr>
Date: Mon Jan 11 15:50:59 2010 +0100
Removed patches incorporated upstream
diff --git a/debian/changelog b/debian/changelog
index 8bd5d93..1a41943 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,13 @@
dynare (4.1.0-1) UNRELEASED; urgency=low
* New upstream version
+ * debian/patches/testsuite-octave3.2-crash-workaround,
+ debian/patches/mcmcdiagnostics,
+ debian/patches/manual-fix-for-debian,
+ debian/patches/rows-name-clash:
+ Removed patches, incorporated upstream.
- -- Sébastien Villemot <sebastien.villemot at ens.fr> Mon, 11 Jan 2010 15:27:08 +0100
+ -- Sébastien Villemot <sebastien.villemot at ens.fr> Mon, 11 Jan 2010 15:47:50 +0100
dynare (4.0.4-6) unstable; urgency=low
diff --git a/debian/patches/manual-fix-for-debian b/debian/patches/manual-fix-for-debian
deleted file mode 100644
index f39d293..0000000
--- a/debian/patches/manual-fix-for-debian
+++ /dev/null
@@ -1,36 +0,0 @@
-Fix reference manual with respect to Debian packaging.
---- a/doc/manual.xml
-+++ b/doc/manual.xml
-@@ -167,9 +167,9 @@
- </sect2>
-
- <sect2><title>On Debian GNU/Linux and Ubuntu</title>
--<para>Please refer to <ulink url="http://www.dynare.org/DynareWiki/InstallOnDebianOrUbuntu">InstallOnDebianOrUbuntu</ulink> on Dynare Wiki for detailed instructions.</para>
-+<para>Install the <literal>dynare</literal> package. Documentation is in the <literal>dynare-doc</literal> package. MATLAB users should install the <literal>dynare-matlab</literal> package.</para>
-
--<para>Dynare will be installed under <filename>/usr/lib/dynare</filename>. Documentation will be under <filename>/usr/share/doc/dynare</filename>.</para>
-+<para>Dynare will be installed under <filename>/usr/share/dynare</filename> and <filename>/usr/lib/dynare</filename>. Documentation will be under <filename>/usr/share/doc/dynare-doc</filename>.</para>
- </sect2>
-
- <sect2 id="install_other_systems"><title>For other systems</title>
-@@ -196,7 +196,7 @@
-
- <para>Under Debian GNU/Linux or Ubuntu, type:</para>
- <programlisting>
-- addpath /usr/lib/dynare/matlab
-+ addpath /usr/share/dynare/matlab
- </programlisting>
-
- <para><trademark class="registered">Matlab</trademark> will not remember this setting next time you run it, and you will have
-@@ -221,10 +221,7 @@
- addpath c:\dynare\4.x.y\matlab
- </programlisting>
-
--<para>Under Debian GNU/Linux or Ubuntu, type:</para>
--<programlisting>
-- addpath /usr/lib/dynare/matlab
--</programlisting>
-+<para>Under Debian GNU/Linux or Ubuntu, there is no need to use <command>addpath</command>; the packaging does it for you.</para>
-
- <para>You will also want to tell to Octave to accept the short syntax (without parentheses and quotes) for the <command>dynare</command> command, by typing:</para>
- <programlisting>
diff --git a/debian/patches/mcmcdiagnostics b/debian/patches/mcmcdiagnostics
deleted file mode 100644
index fbfae77..0000000
--- a/debian/patches/mcmcdiagnostics
+++ /dev/null
@@ -1,25 +0,0 @@
-Fix bug in McMCDiagnostics.m
---- a/matlab/McMCDiagnostics.m
-+++ b/matlab/McMCDiagnostics.m
-@@ -48,13 +48,16 @@
-
- load([MhDirectoryName '/' M_.fname '_mh_history.mat'])
-
--mcfiles = [];
--for blck = 1:nblck
-- mcfiles = cat(3,mcfiles,dir([MhDirectoryName '/' M_.fname '_mh*_blck' int2str(blck) '.mat']));
-+NumberOfMcFilesPerBlock = size(dir([MhDirectoryName ,filesep, M_.fname '_mh*_blck1.mat']),1);
-+for blck = 2:nblck
-+ tmp = size(dir([MhDirectoryName ,filesep, M_.fname '_mh*_blck' int2str(blck) '.mat']),1);
-+ if tmp~=NumberOfMcFilesPerBlock
-+ disp(['McMCDiagnostics:: The number of mh files in chain ' int2str(blck) ' is ' int2str(tmp) ' while'])
-+ disp([' the number of mh files in chain 1 is ' int2str(mcfiles) '!'])
-+ error('The number of mh files has to be constant across chains!')
-+ end
- end
--NumberOfMcFilesPerBlock = size(mcfiles,1);
-
--
- PastDraws = sum(record.MhDraws,1);
- LastFileNumber = PastDraws(2);
- LastLineNumber = record.MhDraws(end,3);
diff --git a/debian/patches/rows-name-clash b/debian/patches/rows-name-clash
deleted file mode 100644
index 7102f17..0000000
--- a/debian/patches/rows-name-clash
+++ /dev/null
@@ -1,186 +0,0 @@
-Fixes the name clash of Dynare rows.m function with Octave's by renaming it to dynrows.m
---- a/matlab/compute_moments_varendo.m
-+++ b/matlab/compute_moments_varendo.m
-@@ -31,7 +31,7 @@
- %
- % You should have received a copy of the GNU General Public License
- % along with Dynare. If not, see <http://www.gnu.org/licenses/>.
-- NumberOfEndogenousVariables = rows(var_list_);
-+ NumberOfEndogenousVariables = dynrows(var_list_);
- NumberOfExogenousVariables = M_.exo_nbr;
- list_of_exogenous_variables = M_.exo_names;
- NumberOfLags = options_.ar;
---- a/matlab/correlation_posterior_analysis.m
-+++ b/matlab/correlation_posterior_analysis.m
-@@ -72,7 +72,7 @@
- i1 = 1; tmp = zeros(SampleSize,1);
- for file = 1:NumberOfFiles
- load([ dname '/metropolis/' fname '_PosteriorCorrelations' int2str(file) '.mat']);
-- i2 = i1 + rows(Correlation_array) - 1;
-+ i2 = i1 + dynrows(Correlation_array) - 1;
- tmp(i1:i2) = Correlation_array(:,indx1,indx2,nar);
- i1 = i2+1;
- end
---- a/matlab/covariance_posterior_analysis.m
-+++ b/matlab/covariance_posterior_analysis.m
-@@ -58,7 +58,7 @@
- i1 = 1; tmp = zeros(NumberOfSimulations,1);
- for file = 1:NumberOfFiles
- load([ dname '/metropolis/' fname '_Posterior2ndOrderMoments' int2str(file) '.mat']);
-- i2 = i1 + rows(Covariance_matrix) - 1;
-+ i2 = i1 + dynrows(Covariance_matrix) - 1;
- tmp(i1:i2) = Covariance_matrix(:,symmetric_matrix_index(indx1,indx2,nvar));
- i1 = i2+1;
- end
---- a/matlab/dsge_posterior_theoretical_correlation.m
-+++ b/matlab/dsge_posterior_theoretical_correlation.m
-@@ -63,14 +63,14 @@
- NumberOfCorrFiles = ceil(SampleSize/MaXNumberOfCorrLines);
- end
-
--NumberOfCorrLines = rows(Correlation_array);
-+NumberOfCorrLines = dynrows(Correlation_array);
- CorrFileNumber = 1;
-
- % Compute 2nd order moments and save them in *_PosteriorCorrelations* files
- linea = 0;
- for file = 1:NumberOfDrawsFiles
- load([M_.dname '/metropolis/' DrawsFiles(file).name ]);
-- NumberOfDraws = rows(pdraws);
-+ NumberOfDraws = dynrows(pdraws);
- isdrsaved = cols(pdraws)-1;
- for linee = 1:NumberOfDraws
- linea = linea+1;
---- a/matlab/dsge_posterior_theoretical_covariance.m
-+++ b/matlab/dsge_posterior_theoretical_covariance.m
-@@ -62,14 +62,14 @@
- NumberOfCovarFiles = ceil(SampleSize/MaXNumberOfCovarLines);
- end
-
--NumberOfCovarLines = rows(Covariance_matrix);
-+NumberOfCovarLines = dynrows(Covariance_matrix);
- CovarFileNumber = 1;
-
- % Compute 2nd order moments and save them in *_Posterior2ndOrderMoments* files
- linea = 0;
- for file = 1:NumberOfDrawsFiles
- load([M_.dname '/metropolis/' DrawsFiles(file).name ],'pdraws');
-- NumberOfDraws = rows(pdraws);
-+ NumberOfDraws = dynrows(pdraws);
- isdrsaved = cols(pdraws)-1;
- for linee = 1:NumberOfDraws
- linea = linea+1;
---- a/matlab/dsge_posterior_theoretical_variance_decomposition.m
-+++ b/matlab/dsge_posterior_theoretical_variance_decomposition.m
-@@ -52,7 +52,7 @@
- nexo = M_.exo_nbr;
-
-
--NumberOfDrawsFiles = rows(DrawsFiles);
-+NumberOfDrawsFiles = dynrows(DrawsFiles);
- NumberOfSavedElementsPerSimulation = nvar*(nexo+1);
- MaXNumberOfDecompLines = ceil(options_.MaxNumberOfBytes/NumberOfSavedElementsPerSimulation/8);
-
-@@ -65,7 +65,7 @@
- NumberOfDecompFiles = ceil(SampleSize/MaXNumberOfDecompLines);
- end
-
--NumberOfDecompLines = rows(Decomposition_array);
-+NumberOfDecompLines = dynrows(Decomposition_array);
- DecompFileNumber = 1;
-
-
-@@ -75,7 +75,7 @@
- for file = 1:NumberOfDrawsFiles
- load([M_.dname '/metropolis/' DrawsFiles(file).name ]);
- isdrsaved = cols(pdraws)-1;
-- NumberOfDraws = rows(pdraws);
-+ NumberOfDraws = dynrows(pdraws);
- for linee = 1:NumberOfDraws
- linea = linea+1;
- if isdrsaved
---- /dev/null
-+++ b/matlab/dynrows.m
-@@ -0,0 +1,20 @@
-+function nr=dynrows(x)
-+
-+% Copyright (C) 2005 Dynare Team
-+%
-+% This file is part of Dynare.
-+%
-+% Dynare is free software: you can redistribute it and/or modify
-+% it under the terms of the GNU General Public License as published by
-+% the Free Software Foundation, either version 3 of the License, or
-+% (at your option) any later version.
-+%
-+% Dynare is distributed in the hope that it will be useful,
-+% but WITHOUT ANY WARRANTY; without even the implied warranty of
-+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-+% GNU General Public License for more details.
-+%
-+% You should have received a copy of the GNU General Public License
-+% along with Dynare. If not, see <http://www.gnu.org/licenses/>.
-+
-+ nr = size(x,1);
-\ No newline at end of file
---- a/matlab/generalized_cholesky.m
-+++ b/matlab/generalized_cholesky.m
-@@ -21,7 +21,7 @@
- % You should have received a copy of the GNU General Public License
- % along with Dynare. If not, see <http://www.gnu.org/licenses/>.
-
--n = rows(A);
-+n = dynrows(A);
- R = eye(n);
- E = zeros(n,n);
- norm_A = max(transpose(sum(abs(A))));
---- a/matlab/rows.m
-+++ /dev/null
-@@ -1,20 +0,0 @@
--function nr=rows(x)
--
--% Copyright (C) 2005 Dynare Team
--%
--% This file is part of Dynare.
--%
--% Dynare is free software: you can redistribute it and/or modify
--% it under the terms of the GNU General Public License as published by
--% the Free Software Foundation, either version 3 of the License, or
--% (at your option) any later version.
--%
--% Dynare is distributed in the hope that it will be useful,
--% but WITHOUT ANY WARRANTY; without even the implied warranty of
--% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
--% GNU General Public License for more details.
--%
--% You should have received a copy of the GNU General Public License
--% along with Dynare. If not, see <http://www.gnu.org/licenses/>.
--
-- nr = size(x,1);
-\ No newline at end of file
---- a/matlab/set_stationary_variables_list.m
-+++ b/matlab/set_stationary_variables_list.m
-@@ -39,7 +39,7 @@
- varlist = options_.varobs;
- options_.varlist = varlist;
- end
--nvar = rows(varlist);
-+nvar = dynrows(varlist);
- if ~isempty(options_.unit_root_vars)
- vartan = [];
- for i=1:nvar
---- a/matlab/variance_decomposition_posterior_analysis.m
-+++ b/matlab/variance_decomposition_posterior_analysis.m
-@@ -31,10 +31,10 @@
- tmp = dir([ dname '/metropolis/' fname '_PosteriorVarianceDecomposition*.mat']);
- NumberOfFiles = length(tmp);
- i1 = 1; tmp = zeros(NumberOfSimulations,1);
-- indice = (indx-1)*rows(exonames)+jndx;
-+ indice = (indx-1)*dynrows(exonames)+jndx;
- for file = 1:NumberOfFiles
- load([dname '/metropolis/' fname '_PosteriorVarianceDecomposition' int2str(file) '.mat']);
-- i2 = i1 + rows(Decomposition_array) - 1;
-+ i2 = i1 + dynrows(Decomposition_array) - 1;
- tmp(i1:i2) = Decomposition_array(:,indice);
- i1 = i2+1;
- end
diff --git a/debian/patches/series b/debian/patches/series
index cb5b509..85424f9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,8 +1,4 @@
-testsuite-octave3.2-crash-workaround
-mcmcdiagnostics
testsuite-fs2000
-rows-name-clash
build-matlab
-manual-fix-for-debian
extra-addpath # This patch needs to be on top of stack
fhs-compliance # This patch needs to be on top of stack
diff --git a/debian/patches/testsuite-octave3.2-crash-workaround b/debian/patches/testsuite-octave3.2-crash-workaround
deleted file mode 100644
index 2cc978c..0000000
--- a/debian/patches/testsuite-octave3.2-crash-workaround
+++ /dev/null
@@ -1,17 +0,0 @@
-Workaround for Octave 3.2 bug reported as #550823 in the BTS.
---- a/matlab/dynare.m
-+++ b/matlab/dynare.m
-@@ -89,6 +89,13 @@
- for i=2:nargin
- command = [command ' ' varargin{i-1}];
- end
-+
-+if exist('OCTAVE_VERSION')
-+ % Workaround for Octave 3.2 bug
-+ % See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=550823
-+ sleep(2);
-+end
-+
- [status, result] = system(command);
- disp(result)
- if status
--
dynare
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