Hello community,
here is the log from the commit of package octave-forge-nan for
openSUSE:Factory checked in at 2019-12-09 21:37:36
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/octave-forge-nan (Old)
and /work/SRC/openSUSE:Factory/.octave-forge-nan.new.4691 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "octave-forge-nan"
Mon Dec 9 21:37:36 2019 rev:9 rq:755318 version:3.4.5
Changes:
--------
--- /work/SRC/openSUSE:Factory/octave-forge-nan/octave-forge-nan.changes
2019-11-28 10:15:37.151638078 +0100
+++
/work/SRC/openSUSE:Factory/.octave-forge-nan.new.4691/octave-forge-nan.changes
2019-12-09 21:38:16.806025926 +0100
@@ -1,0 +2,18 @@
+Mon Dec 9 15:40:02 UTC 2019 - Stefan Brüns <[email protected]>
+
+- Update to version 3.4.5:
+ * fishers_exact_test: added <NEW>
+ * bug fixes for:
+ + #57263: [octave forge] (nan) fails to build on a system
+ without libblas (Octave built with OpenBLAS)
+ + #57232: [octave forge] (nan) Spelling error in message of
+ function str2array
+ + #50248: [octave forge] (nan) Spelling error in the help
+ string of the train function
+ + #57228 "[octave forge] (nan) fails to build with undefined
+ references in Octave 5 when LDFLAGS is set"
+ * gscatter: fix use of argument "doleg"
+ * address "warning: no return statement in function returning non-void"
+- Drop fix_missing_return.patch, fixed upstream
+
+-------------------------------------------------------------------
Old:
----
fix_missing_return.patch
nan-3.4.3.tar.gz
New:
----
nan-3.4.5.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ octave-forge-nan.spec ++++++
--- /var/tmp/diff_new_pack.Ok5pJ2/_old 2019-12-09 21:38:18.186025382 +0100
+++ /var/tmp/diff_new_pack.Ok5pJ2/_new 2019-12-09 21:38:18.190025381 +0100
@@ -18,14 +18,13 @@
%define octpkg nan
Name: octave-forge-%{octpkg}
-Version: 3.4.3
+Version: 3.4.5
Release: 0
Summary: A statistics and machine learning toolbox
License: GPL-3.0-or-later
Group: Productivity/Scientific/Math
-URL: https://octave.sourceforge.io
+URL: https://octave.sourceforge.io/%{octpkg}/index.html
Source0:
https://downloads.sourceforge.net/octave/%{octpkg}-%{version}.tar.gz
-Patch0: fix_missing_return.patch
BuildRequires: libsvm-devel
BuildRequires: octave-devel >= 3.8.0
Requires: octave-cli >= 3.8.0
@@ -36,10 +35,6 @@
%prep
%setup -q -c %{name}-%{version}
-pushd %{octpkg}-%{version}
-%patch0 -p1
-popd
-sed -i 's/-lblas/-l%{octave_blas}/g' %{octpkg}-%{version}/src/Makefile.in
%octave_pkg_src
%build
++++++ nan-3.4.3.tar.gz -> nan-3.4.5.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/DESCRIPTION new/nan-3.4.5/DESCRIPTION
--- old/nan-3.4.3/DESCRIPTION 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/DESCRIPTION 2019-11-21 13:54:16.000000000 +0100
@@ -1,6 +1,6 @@
Name: NaN
-Version: 3.4.3
-Date: 2019-10-27
+Version: 3.4.5
+Date: 2019-11-21
Author: Alois Schloegl <[email protected]>
Maintainer: Alois Schloegl
Title: The NaN-toolbox
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/INDEX new/nan-3.4.5/INDEX
--- old/nan-3.4.3/INDEX 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/INDEX 2019-11-21 13:54:16.000000000 +0100
@@ -13,5 +13,6 @@
bland_altman cumsumskipnan range signrank histo
histo2 histo3 histo4 kolmogorov_smirnov kstest2 roc
kappa load_cifar100 load_cifar10 load_mnist
+ fishers_exact_test
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/NEWS new/nan-3.4.5/NEWS
--- old/nan-3.4.3/NEWS 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/NEWS 2019-11-21 13:54:16.000000000 +0100
@@ -1,3 +1,16 @@
+
+2019-11-16: Release of NaN-Tb v3.4.5
+
+- fishers_exact_test: added <NEW>
+
+- bug fixes for:
+ #57263: [octave forge] (nan) fails to build on a system without libblas
(Octave built with OpenBLAS)
+ #57232: [octave forge] (nan) Spelling error in message of function str2array
+ #50248: [octave forge] (nan) Spelling error in the help string of the train
function
+ #57228 "[octave forge] (nan) fails to build with undefined references in
Octave 5 when LDFLAGS is set"
+- gscatter: fix use of argument "doleg"
+- address "warning: no return statement in function returning non-void"
+
2019-10-27: Release of NaN-Tb v3.4.3
- Makefile.*
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/inst/fishers_exact_test.m
new/nan-3.4.5/inst/fishers_exact_test.m
--- old/nan-3.4.3/inst/fishers_exact_test.m 1970-01-01 01:00:00.000000000
+0100
+++ new/nan-3.4.5/inst/fishers_exact_test.m 2019-11-21 13:54:16.000000000
+0100
@@ -0,0 +1,68 @@
+function p = fishers_exact_test(a,b,c,d)
+% FISHERS_EXACT_TEST implements Fisher's exact test for the analysis of
+% contincency tables e.g. "Lady tasting tea" experiment [1-6].
+%
+% Usage:
+% p = fishers_exact_test(H)
+% p = fishers_exact_test(a,b,c,d)
+%
+% with H being a 2x2 matrix representing a contincency table H = [[a,b];[c,d]]
+% and p is the resulting p-value. The implementation provides exact results
+% for small sample sizes, and might be subject to the limited accuracy of
+% floating point numbers for large sample sizes (a warning might be shown).
+%
+% Reference:
+% [1] https://en.wikipedia.org/wiki/Fisher%27s_exact_test
+% [2] https://en.wikipedia.org/wiki/Lady_tasting_tea
+% [3] Fisher, R. A. (1922). "On the interpretation of χ2 from contingency
+% tables, and the calculation of P".
+% Journal of the Royal Statistical Society. 85 (1): 87–94.
+% doi:10.2307/2340521. JSTOR 2340521.
+% [4] Fisher, R.A. (1954). Statistical Methods for Research Workers.
+% Oliver and Boyd. ISBN 0-05-002170-2.
+% [5] Agresti, Alan (1992). "A Survey of Exact Inference for Contingency
Tables".
+% Statistical Science. 7 (1): 131–153.
+% CiteSeerX 10.1.1.296.874. doi:10.1214/ss/1177011454. JSTOR 2246001.
+% [6] Fisher, Sir Ronald A. (1956) [The Design of Experiments (1935)].
+% "Mathematics of a Lady Tasting Tea". In James Roy Newman (ed.).
+% The World of Mathematics, volume 3. Courier Dover Publications.
+% ISBN 978-0-486-41151-4.
+
+% Copyright (C) 2019 Alois Schloegl <[email protected]>
+% This is part of the BIOSIG-toolbox http://biosig.sf.net/
+%
+% This library is free software; you can redistribute it and/or
+% modify it under the terms of the GNU Library General Public
+% License as published by the Free Software Foundation; either
+% version 3 of the License, or (at your option) any later version.
+%
+% This library 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
+% Library General Public License for more details.
+%
+% You should have received a copy of the GNU Library General Public
+% License along with this library; if not, write to the
+% Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+% Boston, MA 02111-1307, USA.
+
+if (nargin==1) && isequal(size(a),[2,2]),
+ H = a;
+ a=H(1,1);
+ b=H(1,2);
+ c=H(2,1);
+ d=H(2,2);
+elseif (nargin==4) && isscalar(a) && isscalar(b) && isscalar(c) && isscalar(d)
+ H=[[a,b];[c,d]];
+else
+ error('invalid input argument')
+end
+n = sum(H(:));
+
+u = nchoosek(a+b,a);
+v = nchoosek(c+d,c);
+w = nchoosek(n,a+c);
+
+p = u*v / w;
+
+
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/inst/gscatter.m
new/nan-3.4.5/inst/gscatter.m
--- old/nan-3.4.3/inst/gscatter.m 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/inst/gscatter.m 2019-11-21 13:54:16.000000000 +0100
@@ -78,7 +78,7 @@
end;
hold off;
-if ~strcmpi(doleg,'off')
+if strcmpi(doleg,'off')
if isnumeric(b)
b={num2str(b(:))};
end;
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/src/Makefile.in
new/nan-3.4.5/src/Makefile.in
--- old/nan-3.4.3/src/Makefile.in 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/src/Makefile.in 2019-11-21 13:54:16.000000000 +0100
@@ -130,10 +130,11 @@
CDEBUGFLAGS := -g
INCLUDE := -I"$(MWROOT)/extern/include" -I"$(MWROOT)/simulink/include"
LD := gcc
-LDFLAGS := -pthread -Wl,--no-undefined
+LDFLAGS += -pthread
LDTYPE := -shared
LINKEXPORTVER :=
-Wl,--version-script,"$(MWROOT)/extern/lib/glnxa64/c_exportsmexfileversion.map"
LINKLIBS := -Wl,--as-needed -Wl,-rpath-link,$(MWROOT)/bin/glnxa64
-L"$(MWROOT)/bin/glnxa64" -Wl,-rpath-link,$(MWROOT)/extern/bin/glnxa64
-L"$(MWROOT)/extern/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++
+BLAS_LIBS := $(shell $(MKOCTFILE) -p BLAS_LIBS)
c_mexapi_version.o : $(MWROOT)/extern/version/c_mexapi_version.c Makefile
@@ -174,14 +175,14 @@
$(MATMEX) -lblas train.c tron.o -llinear linear_model_matlab.o
#$(MATMEX) -lblas predict.c tron.o linear.o linear_model_matlab.o
train.mex predict.mex: train.c tron.o linear_model_matlab.c
- $(OCTMEX) -lblas train.c tron.o -llinear linear_model_matlab.c
+ $(OCTMEX) $(BLAS_LIBS) train.c tron.o -llinear linear_model_matlab.c
else
train.$(MEX_EXT) predict.$(MEX_EXT): train.c tron.o linear.o
linear_model_matlab.c
$(CXX) $(CFLAGS) -I $(MATLABDIR)/extern/include -c linear_model_matlab.c
$(MATMEX) -lblas train.c tron.o linear.o linear_model_matlab.o
#$(MATMEX) -lblas predict.c tron.o linear.o linear_model_matlab.o
train.mex predict.mex: train.c tron.o linear.o linear_model_matlab.c
- $(OCTMEX) -lblas train.c tron.o linear.o linear_model_matlab.c
+ $(OCTMEX) $(BLAS_LIBS) train.c tron.o linear.o linear_model_matlab.c
linear.o: linear.cpp
$(CXX) $(CFLAGS) -c linear.cpp
endif
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/src/configure new/nan-3.4.5/src/configure
--- old/nan-3.4.3/src/configure 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/src/configure 2019-12-08 19:21:34.000000000 +0100
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for nan-toolbox 3.2.0.
+# Generated by GNU Autoconf 2.69 for nan-toolbox 3.4.5.
#
# Report bugs to <[email protected]>.
#
@@ -580,8 +580,8 @@
# Identity of this package.
PACKAGE_NAME='nan-toolbox'
PACKAGE_TARNAME='nan-toolbox'
-PACKAGE_VERSION='3.2.0'
-PACKAGE_STRING='nan-toolbox 3.2.0'
+PACKAGE_VERSION='3.4.5'
+PACKAGE_STRING='nan-toolbox 3.4.5'
PACKAGE_BUGREPORT='[email protected]'
PACKAGE_URL=''
@@ -1245,7 +1245,7 @@
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures nan-toolbox 3.2.0 to adapt to many kinds of systems.
+\`configure' configures nan-toolbox 3.4.5 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1307,7 +1307,7 @@
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of nan-toolbox 3.2.0:";;
+ short | recursive ) echo "Configuration of nan-toolbox 3.4.5:";;
esac
cat <<\_ACEOF
@@ -1389,7 +1389,7 @@
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-nan-toolbox configure 3.2.0
+nan-toolbox configure 3.4.5
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1980,7 +1980,7 @@
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by nan-toolbox $as_me 3.2.0, which was
+It was created by nan-toolbox $as_me 3.4.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -5249,7 +5249,7 @@
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by nan-toolbox $as_me 3.2.0, which was
+This file was extended by nan-toolbox $as_me 3.4.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -5311,7 +5311,7 @@
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //;
s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-nan-toolbox config.status 3.2.0
+nan-toolbox config.status 3.4.5
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/src/configure.ac
new/nan-3.4.5/src/configure.ac
--- old/nan-3.4.3/src/configure.ac 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/src/configure.ac 2019-12-08 19:21:01.000000000 +0100
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.69])
-AC_INIT([nan-toolbox], [3.2.0], [[email protected]])
+AC_INIT([nan-toolbox], [3.4.5], [[email protected]])
AC_CONFIG_SRCDIR([train.c])
AC_CONFIG_HEADERS([config.h])
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/src/str2array.cpp
new/nan-3.4.5/src/str2array.cpp
--- old/nan-3.4.3/src/str2array.cpp 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/src/str2array.cpp 2019-11-21 13:54:16.000000000 +0100
@@ -160,7 +160,7 @@
mexPrintf("\t[...] = STR2ARRAY(s,cdelim,rdelim)\n");
mexPrintf("\t[...] = STR2ARRAY(s,cdelim,rdelim,ddelim)\n");
mexPrintf("\t[num,status,strarray] = STR2ARRAY(...)\n");
- mexPrintf(" Input:\n\ts\tstring\n\tsa\tcell array of
strings\n\tcdelim\tlist of column delimiters (default:
\"<Tab>,\"\n\trdelim\tlist of row delimiter (defautlt: \"<LF><CR>;\")");
+ mexPrintf(" Input:\n\ts\tstring\n\tsa\tcell array of
strings\n\tcdelim\tlist of column delimiters (default:
\"<Tab>,\"\n\trdelim\tlist of row delimiter (default: \"<LF><CR>;\")");
mexPrintf("\n\tddelim\tdecimal delimiter (default: \".\"). This
is useful if decimal delimiter is a comma (e.g. after Excel export in
Europe)\n");
mexPrintf(" Output:\n\tnum\tnumeric array\n\tstatus\tflag
failing conversion\n\tstrarray\tcell array of strings contains strings of
failed conversions\n");
mexPrintf("\nExamples:\n\tSTR2ARRAY('4.12')\n\tSTR2ARRAY('1.2 -
3.4e2i') complex numbers\n\tSTR2ARRAY('101.01 , 0-i4; 1.2 - i * 3.4,
abc')\n\tSTR2ARRAY({'101.01', '0-i4'; '1.2 - i * 3.4',
'abc'})\n\tSTR2ARRAY('1,2;a,b,c;3,4')\n");
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/src/svmpredict_mex.cpp
new/nan-3.4.5/src/svmpredict_mex.cpp
--- old/nan-3.4.3/src/svmpredict_mex.cpp 2019-10-27 23:26:24.000000000
+0100
+++ new/nan-3.4.5/src/svmpredict_mex.cpp 2019-11-21 13:54:16.000000000
+0100
@@ -52,7 +52,7 @@
#define CMD_LEN 2048
-int print_null(const char *s,...) {}
+int print_null(const char *s,...) {return 0;}
int (*info)(const char *fmt,...) = &mexPrintf;
void read_sparse_instance(const mxArray *prhs, int index, struct svm_node *x)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nan-3.4.3/src/train.c new/nan-3.4.5/src/train.c
--- old/nan-3.4.3/src/train.c 2019-10-27 23:26:24.000000000 +0100
+++ new/nan-3.4.5/src/train.c 2019-11-21 13:54:16.000000000 +0100
@@ -98,7 +98,7 @@
"-C : find parameter C (only for -s 0 and 2)\n"
"-q : quiet mode (no outputs)\n"
"col:\n"
- " if 'col' is setted, training_instance_matrix is parsed in
column format, otherwise is in row format\n"
+ " if 'col' is set, training_instance_matrix is parsed in column
format, otherwise is in row format\n"
);
}
