[Pkg-octave-commit] [octave-statistics] 04/04: Drop patches applied upstream.
Sébastien Villemot
sebastien at debian.org
Wed Oct 12 12:09:01 UTC 2016
This is an automated email from the git hooks/post-receive script.
sebastien pushed a commit to branch master
in repository octave-statistics.
commit 401250f9ea4c17013e6758e20de6989fb841b31d
Author: Sébastien Villemot <sebastien at debian.org>
Date: Wed Oct 12 13:58:35 2016 +0200
Drop patches applied upstream.
+ d/p/combnk-implicit-conversion-warn.patch
+ d/p/expected-linkage-warning.patch
+ d/p/small-k-in-gev-functions.patch
+ d/p/use-corr-instead-of-cor.patch
+ d/p/use-corr-instead-of-corrcoef.patch
Gbp-Dch: Full
---
.../patches/combnk-implicit-conversion-warn.patch | 20 --------
debian/patches/expected-linkage-warning.patch | 21 ---------
debian/patches/series | 5 --
debian/patches/small-k-in-gev-functions.patch | 55 ----------------------
debian/patches/use-corr-instead-of-cor.patch | 29 ------------
debian/patches/use-corr-instead-of-corrcoef.patch | 18 -------
6 files changed, 148 deletions(-)
diff --git a/debian/patches/combnk-implicit-conversion-warn.patch b/debian/patches/combnk-implicit-conversion-warn.patch
deleted file mode 100644
index 307b38a..0000000
--- a/debian/patches/combnk-implicit-conversion-warn.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Description: Avoid warning when calling combnk on strings
-Author: Rafael Laboissiere <rafael at debian.org>
-Forwarded: https://savannah.gnu.org/bugs/?45670
-Last-Update: 2015-09-13
-
---- octave-statistics-1.2.4.orig/inst/combnk.m
-+++ octave-statistics-1.2.4/inst/combnk.m
-@@ -60,7 +60,11 @@ function retval = __combnk__ (data, k)
- C = __combnk__ (data ((j+1):end), k-1);
- C = cat (2, repmat (data (j), rows (C), 1), C);
- if (!isempty (C))
-- retval = [retval; C];
-+ if (isempty (retval))
-+ retval = C;
-+ else
-+ retval = [retval; C];
-+ endif
- endif
- endfor
- endif
diff --git a/debian/patches/expected-linkage-warning.patch b/debian/patches/expected-linkage-warning.patch
deleted file mode 100644
index dd4d2b8..0000000
--- a/debian/patches/expected-linkage-warning.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Description: Fix expected warnings in unit tests for the linkage function
-Author: Rafael Laboissiere <rafael at debian.org>
-Forwarded: https://savannah.gnu.org/bugs/?45671
-Last-Update: 2016-09-13
-
---- octave-statistics-1.2.4.orig/inst/linkage.m
-+++ octave-statistics-1.2.4/inst/linkage.m
-@@ -217,11 +217,11 @@ endfunction
- %!assert (cond (linkage (pdist (x), "average")), 27.045012,t);
- %!assert (cond (linkage (pdist (x), "weighted")), 27.412889,t);
- %! lastwarn(); # Clear last warning before the test
--%!warning <monotonically> linkage (pdist (x), "centroid");
-+%!warning <clustering> linkage (pdist (x), "centroid");
- %!test warning off clustering
- %! assert (cond (linkage (pdist (x), "centroid")), 27.457477,t);
- %! warning on clustering
--%!warning <monotonically> linkage (pdist (x), "median");
-+%!warning <clustering> linkage (pdist (x), "median");
- %!test warning off clustering
- %! assert (cond (linkage (pdist (x), "median")), 27.683325,t);
- %! warning on clustering
diff --git a/debian/patches/series b/debian/patches/series
index 00a4553..f28ddb0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1,2 @@
data-files-for-tests.diff
expose-tbl-delim-tests.patch
-use-corr-instead-of-cor.patch
-small-k-in-gev-functions.patch
-use-corr-instead-of-corrcoef.patch
-expected-linkage-warning.patch
-combnk-implicit-conversion-warn.patch
diff --git a/debian/patches/small-k-in-gev-functions.patch b/debian/patches/small-k-in-gev-functions.patch
deleted file mode 100644
index 7c4575e..0000000
--- a/debian/patches/small-k-in-gev-functions.patch
+++ /dev/null
@@ -1,55 +0,0 @@
-Description: Appropriate results of gev(c|p)df function for small values of k
- When computing the cdf and pdf of the GEV distributions, in functions
- gevcdf and gevpdf, respectively, the parameter k appears in the
- denominator of a division operation. To avoid division by zero, the
- condition k==0 is tested and an alternative formula is used for it.
- .
- However, this test should be extended to values very close to zero.
- Doing some non-extensive tests, I concluded that the function returns
- wrong results for values of abs(k) lesser than 1e-11. Nir Krakauer
- has set the limit as a funciton of eps.
- .
- This problem was evidenced in unit tests of the gevcdf and gevpdf
- functions. In one case, we have:
- .
- k = -0.03 : 0.01 : 0.03;
- .
- In my system (Octave 4.0 on Debian i386), the fourth element of k is
- different from zero (it is equal 3.4694e-18) and the result of gevcdf
- is clearly wrong, and the unit test fails.
-Author: Rafael Laboissiere <rafael at debian.org>
-Origin: upstream, http://sourceforge.net/p/octave/statistics/ci/{eff9575,298bde9}
-Bug: https://savannah.gnu.org/bugs/index.php?44986
-Last-Update: 2015-05-02
-
---- octave-statistics-1.2.4.orig/inst/gevcdf.m
-+++ octave-statistics-1.2.4/inst/gevcdf.m
-@@ -94,7 +94,7 @@ function p = gevcdf (x, k, sigma, mu)
- p(z <= 0 & x < mu) = 0;
- p(z <= 0 & x > mu) = 1;
-
-- inds = (k == 0); %use a different formula
-+ inds = (abs (k) < (eps^0.7)); %use a different formula if k is very close to zero
- if any(inds)
- z = (mu(inds) - x(inds)) ./ sigma(inds);
- p(inds) = exp(-exp(z));
---- octave-statistics-1.2.4.orig/inst/gevpdf.m
-+++ octave-statistics-1.2.4/inst/gevpdf.m
-@@ -78,7 +78,7 @@ function y = gevpdf (x, k, sigma, mu)
- endif
-
- if (isempty (x) || isempty (k) || isempty (sigma) || isempty (mu) || ~ismatrix (x) || ~ismatrix (k) || ~ismatrix (sigma) || ~ismatrix (mu))
-- error ("gevpdf: inputs must be a numeric matrices");
-+ error ("gevpdf: inputs must be numeric matrices");
- endif
-
- [retval, x, k, sigma, mu] = common_size (x, k, sigma, mu);
-@@ -93,7 +93,7 @@ function y = gevpdf (x, k, sigma, mu)
-
- y(z <= 0) = 0;
-
-- inds = (k == 0); %use a different formula
-+ inds = (abs (k) < (eps^0.7)); %use a different formula if k is very close to zero
- if any(inds)
- z = (mu(inds) - x(inds)) ./ sigma(inds);
- y(inds) = exp(z-exp(z)) ./ sigma(inds);
diff --git a/debian/patches/use-corr-instead-of-cor.patch b/debian/patches/use-corr-instead-of-cor.patch
deleted file mode 100644
index 056f7a2..0000000
--- a/debian/patches/use-corr-instead-of-cor.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Description: Use corr() instead of the deprecated cor() function
- The cor() function has been removed from Octave 4.0. .
-Author: Rafael Laboissiere <rafael at debian.org>
-Origin: upstream, http://sourceforge.net/p/octave/statistics/ci/2372ef1
-Bug: https://savannah.gnu.org/bugs/index.php?44985
-Last-Update: 2015-05-01
-
---- octave-statistics-1.2.4.orig/inst/pdist.m
-+++ octave-statistics-1.2.4/inst/pdist.m
-@@ -169,15 +169,15 @@ function y = pdist (x, metric, varargin)
- if (rows(X) == 1)
- error ("pdist: correlation distance between scalars not defined")
- endif
-- corr = cor (X);
-- y = 1 - corr (sub2ind (size (corr), Xi, Yi))';
-+ cor = corr (X);
-+ y = 1 - cor (sub2ind (size (cor), Xi, Yi))';
-
- case "spearman"
- if (rows(X) == 1)
- error ("pdist: spearman distance between scalars not defined")
- endif
-- corr = spearman (X);
-- y = 1 - corr (sub2ind (size (corr), Xi, Yi))';
-+ cor = spearman (X);
-+ y = 1 - cor (sub2ind (size (cor), Xi, Yi))';
-
- case "hamming"
- d = logical (X(:,Xi) - X(:,Yi));
diff --git a/debian/patches/use-corr-instead-of-corrcoef.patch b/debian/patches/use-corr-instead-of-corrcoef.patch
deleted file mode 100644
index f452bcc..0000000
--- a/debian/patches/use-corr-instead-of-corrcoef.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Description: Use corr() instead of the deprecated corrcoef() function
- The corrcoef() function has been removed from Octave 4.0.
-Author: Rafael Laboissiere <rafael at debian.org>
-Origin: upstream, http://sourceforge.net/p/octave/statistics/ci/f26c570
-Bug: https://savannah.gnu.org/bugs/index.php?44987
-Last-Update: 2015-05-02
-
---- octave-statistics-1.2.4.orig/inst/stepwisefit.m
-+++ octave-statistics-1.2.4/inst/stepwisefit.m
-@@ -75,7 +75,7 @@ while 1
- added = false;
- if numel(X_use) < k
- X_inds = zeros(k, 1, "logical"); X_inds(X_use) = 1;
-- [~, i_max_corr] = max(abs(corrcoef(X(:, ~X_inds), r))); #try adding the variable with the highest correlation to the residual from current regression
-+ [~, i_max_corr] = max(abs(corr(X(:, ~X_inds), r))); #try adding the variable with the highest correlation to the residual from current regression
- i_max_corr = (1:k)(~X_inds)(i_max_corr); #index within the original predictor set
- [b_new, bint_new, r_new, rint_new, stats_new] = regress(y, [ones(n, 1) X(:, [X_use i_max_corr])], penter);
- z_new = abs(b_new(end)) / (bint_new(end, 2) - b_new(end));
--
Alioth's /home/groups/pkg-octave/bin/git-commit-notice on /srv/git.debian.org/git/pkg-octave/octave-statistics.git
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