Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package octave-forge-nan for openSUSE:Factory checked in at 2022-07-12 11:12:45 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/octave-forge-nan (Old) and /work/SRC/openSUSE:Factory/.octave-forge-nan.new.1523 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "octave-forge-nan" Tue Jul 12 11:12:45 2022 rev:15 rq:988500 version:3.7.0 Changes: -------- --- /work/SRC/openSUSE:Factory/octave-forge-nan/octave-forge-nan.changes 2021-11-18 10:34:00.091916779 +0100 +++ /work/SRC/openSUSE:Factory/.octave-forge-nan.new.1523/octave-forge-nan.changes 2022-07-12 11:12:59.147741348 +0200 @@ -1,0 +2,6 @@ +Fri Jul 8 17:38:37 UTC 2022 - Atri Bhattacharya <badshah...@gmail.com> + +- Update to version 3.7.0: + * minor improvements (kappa, cdfplot, signrank). + +------------------------------------------------------------------- Old: ---- nan-3.6.1.tar.gz New: ---- nan-3.7.0.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ octave-forge-nan.spec ++++++ --- /var/tmp/diff_new_pack.cwaYR0/_old 2022-07-12 11:12:59.603741945 +0200 +++ /var/tmp/diff_new_pack.cwaYR0/_new 2022-07-12 11:12:59.607741950 +0200 @@ -1,7 +1,7 @@ # -# spec file +# spec file for package octave-forge-nan # -# Copyright (c) 2021 SUSE LLC +# Copyright (c) 2022 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -18,7 +18,7 @@ %define octpkg nan Name: octave-forge-%{octpkg} -Version: 3.6.1 +Version: 3.7.0 Release: 0 Summary: A statistics and machine learning toolbox License: GPL-3.0-or-later ++++++ nan-3.6.1.tar.gz -> nan-3.7.0.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/DESCRIPTION new/nan-3.7.0/DESCRIPTION --- old/nan-3.6.1/DESCRIPTION 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/DESCRIPTION 2022-05-21 12:49:30.000000000 +0200 @@ -1,6 +1,6 @@ Name: NaN -Version: 3.6.1 -Date: 2021-11-03 +Version: 3.7.0 +Date: 2022-05-09 Author: Alois Schl??gl <alois.schlo...@gmail.com> Maintainer: Alois Schl??gl Title: The NaN-toolbox diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/NEWS new/nan-3.7.0/NEWS --- old/nan-3.6.1/NEWS 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/NEWS 2022-05-21 12:49:30.000000000 +0200 @@ -1,4 +1,10 @@ +2022-05-09: Release of NaN-toolbox 3.7.0 + +* minor improvements (kappa, cdfplot, signrank) +* fix installation when matlab is in non-default location + + 2021-11-03: Release of NaN-toolbox 3.6.1 * signrank: update computation of p-value diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/doc/README.TXT new/nan-3.7.0/doc/README.TXT --- old/nan-3.6.1/doc/README.TXT 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/doc/README.TXT 2022-05-21 12:49:30.000000000 +0200 @@ -276,10 +276,17 @@ This is useful to improve speed, and is required if you used weighted samples. Check if precompiled binaries are provided. If your platform is not supported, compile the C-Mex-functions using "make". + + If matlab is not available in the default location, it can be compiled + with these commands: + cd src + ./configure + make MATLABDIR=/usr/local/MATLAB/R2021b/ mex4m + Run NANINSTTEST again to check the stability of the compiled SUMSKIPNAN. - Copyright (C) 2000-2021 by Alois Schl??gl <alois.schlo...@gmail.com> + Copyright (C) 2000-2022 by Alois Schl??gl <alois.schlo...@gmail.com> http://pub.ist.ac.at/~schloegl/matlab/NaN/ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/inst/cdfplot.m new/nan-3.7.0/inst/cdfplot.m --- old/nan-3.6.1/inst/cdfplot.m 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/inst/cdfplot.m 2022-05-21 12:49:30.000000000 +0200 @@ -20,8 +20,7 @@ % % References: -% $Id$ -% Copyright (C) 2009,2010 by Alois Schloegl <alois.schlo...@gmail.com> +% Copyright (C) 2009,2010,2021,2022 by Alois Schloegl <alois.schlo...@gmail.com> % This function is part of the NaN-toolbox % http://pub.ist.ac.at/~schloegl/matlab/NaN/ @@ -40,7 +39,7 @@ % Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA 02110-1301, USA. -his = histo(X(:)); +his = histo3(X(:)); cdf = cumsum(his.H,1) ./ sum(his.H,1); ix1 = ceil ([1:2*size(his.X,1)]'/2); ix2 = floor([2:2*size(his.X,1)]'/2); diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/inst/kappa.m new/nan-3.7.0/inst/kappa.m --- old/nan-3.6.1/inst/kappa.m 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/inst/kappa.m 2022-05-21 12:49:30.000000000 +0200 @@ -192,7 +192,7 @@ R(isnan(R)) = 0; tmp = 1 - R.*R; tmp(tmp<0) = 0; % prevent tmp<0 i.e. imag(t)~=0 - t = R.*sqrt(max(NN-2,0)./tmp) + t = R.*sqrt(max(NN-2,0)./tmp); sig = tcdf(t,NN-2); sig = 2 * min(sig,1 - sig); X.MCC_p_value = sig; diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/inst/signrank.m new/nan-3.7.0/inst/signrank.m --- old/nan-3.6.1/inst/signrank.m 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/inst/signrank.m 2022-05-21 12:49:30.000000000 +0200 @@ -120,7 +120,12 @@ Tplus = sumskipnan((x>0) .* Rix, DIM); Tminus = sumskipnan((x<0) .* Rix, DIM); - stats.signedrank = min(Tplus, Tminus); + % t = -(min(Tplus,Tminus) + 0.5 + Nr.*(Nr+1)/4) ./ sqrt(Nr.*(Nr+1).*(2*Nr+1)/6); + t = W ./ sqrt(Nr.*(Nr+1).*(2*Nr+1)/6); + n = Nr; + cdf0 = normcdf(-z) .* ( 1 + (3*n.*n + 3.*n - 1) ./ ( 10.*n.*(n+1).*(2*n+1) ) .*t.*(t.*t - 3) ); + + stats.signedrank = min(Tplus, Tminus); # # simple formula is: # z = (Tplus - Nr.*(Nr+1)/4)./sqrt(Nr.*(Nr+1).*(2*Nr+1)/24); diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/src/Makefile.in new/nan-3.7.0/src/Makefile.in --- old/nan-3.6.1/src/Makefile.in 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/src/Makefile.in 2022-05-21 12:49:30.000000000 +0200 @@ -1,5 +1,5 @@ #################################################### -# Copyright 2010,2011,2012,2015,2019 Alois Schloegl +# Copyright 2010-2022 Alois Schloegl # This is part of the NaN-toolbox - a statistics and machine learning toolbox for data with and without missing values. # http://pub.ist.ac.at/~schloegl/matlab/NaN/ #################################################### @@ -27,11 +27,21 @@ # Better alternative: define an OCTAVE_VERSION bash variable (or in .bashrc or .profile) # OCTAVE_VERSION=-3.6.3 -# Matlab configuration -#MATLABDIR = /usr/local/MATLAB/R2010b -# comment the following line if you use MATLAB on 32-bit operating system +########################################################## +## Matlab configuration +## set Matlab and Octave variables +MATLABDIR ?= $(shell dirname @MATLAB@) + +ifeq (.,$(MATLABDIR)) + #$(warning MATLABDIR is not defined) +else + MEX = $(MATLABDIR)/mex + MEX_EXT := $(shell $(MATLABDIR)/bin/mexext) +endif #MEX_OPTION += -largeArrayDims MEX_OPTION += -R2017b +########################################################## + # Mingw crosscompiler: available at http://www.nongnu.org/mingw-cross-env/ CROSS = $(HOME)/src/mxe/usr/bin/i686-w64-mingw32.static- @@ -77,7 +87,7 @@ #MEX_OPTION += CC\#$(CXX) CXX\#$(CXX) CFLAGS\#"$(CFLAGS) " CXXFLAGS\#"$(CFLAGS) " endif -###REMOVE### MATMEX = $(MATLABDIR)/bin/mex $(MEX_OPTION) +MATMEX = $(MATLABDIR)/bin/mex $(MEX_OPTION) PROGS = histo_mex.mex covm_mex.mex kth_element.mex sumskipnan_mex.mex str2array.mex train.mex svmtrain_mex.mex svmpredict_mex.mex xptopen.mex @@ -128,16 +138,16 @@ CFLAGS += -fexceptions -fPIC -fno-omit-frame-pointer -pthread COPTIMFLAGS := -O -DNDEBUG CDEBUGFLAGS := -g -INCLUDE := -I"$(MWROOT)/extern/include" -I"$(MWROOT)/simulink/include" +INCLUDE := -I"$(MATLABDIR)/extern/include" -I"$(MATLABDIR)/simulink/include" LD := gcc LDFLAGS += -pthread LDTYPE := -shared -LINKEXPORTVER := -Wl,--version-script,"$(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++ +LINKEXPORTVER := -Wl,--version-script,"$(MATLABDIR)/extern/lib/glnxa64/c_exportsmexfileversion.map" +LINKLIBS := -Wl,--as-needed -Wl,-rpath-link,$(MATLABDIR)/bin/glnxa64 -L"$(MATLABDIR)/bin/glnxa64" -Wl,-rpath-link,$(MATLABDIR)/extern/bin/glnxa64 -L"$(MATLABDIR)/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 +c_mexapi_version.o : $(MATLABDIR)/extern/version/c_mexapi_version.c Makefile $(CC) -c $< -o $@ $(MATLABMEX) $(DEFINES) $(CFLAGS) $(COPTIMFLAGS) $(INCLUDE) %.$(MEX_EXT) : %.o c_mexapi_version.o $(LD) $(LDFLAGS) $(LDTYPE) $(LINKEXPORTVER) $< $(LINKLIBS) -o $@ @@ -173,14 +183,15 @@ train.$(MEX_EXT) predict.$(MEX_EXT): train.c tron.o linear_model_matlab.c $(CXX) $(CFLAGS) -I $(MATLABDIR)/extern/include -c linear_model_matlab.c $(MATMEX) -lblas train.c tron.o -llinear linear_model_matlab.o - #$(MATMEX) -lblas predict.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_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 +# $(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) $(BLAS_LIBS) train.c tron.o linear.o linear_model_matlab.c linear.o: linear.cpp diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/src/configure new/nan-3.7.0/src/configure --- old/nan-3.6.1/src/configure 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/src/configure 2022-05-21 12:49:30.000000000 +0200 @@ -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 3.7.0. # # Report bugs to <alois.schlo...@gmail.com>. # @@ -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='3.7.0' +PACKAGE_STRING='nan-toolbox 3.7.0' PACKAGE_BUGREPORT='alois.schlo...@gmail.com' PACKAGE_URL='' @@ -630,6 +630,9 @@ EGREP GREP CPP +OCTAVE +MKOCTFILE +MATLAB ac_ct_CC CFLAGS CC @@ -1245,7 +1248,7 @@ # 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 3.7.0 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1307,7 +1310,7 @@ if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of nan-toolbox 3.2.0:";; + short | recursive ) echo "Configuration of nan-toolbox 3.7.0:";; esac cat <<\_ACEOF @@ -1389,7 +1392,7 @@ test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -nan-toolbox configure 3.2.0 +nan-toolbox configure 3.7.0 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -1980,7 +1983,7 @@ 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 3.7.0, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -3788,6 +3791,127 @@ fi +# Extract the first word of "matlab", so it can be a program name with args. +set dummy matlab; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_MATLAB+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$MATLAB"; then + ac_cv_prog_MATLAB="$MATLAB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_MATLAB="$(readlink -f $(which matlab))" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + + test -z "$ac_cv_prog_MATLAB" && ac_cv_prog_MATLAB=":" +fi +fi +MATLAB=$ac_cv_prog_MATLAB +if test -n "$MATLAB"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MATLAB" >&5 +$as_echo "$MATLAB" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +# AC_CHECK_PROG([MATLAB], [matlab], [$(matlab -n|awk '/^-> r MATLAB = / {printf("%s/bin/matlab",$5)}')], [:]) +# Extract the first word of "mkoctfile", so it can be a program name with args. +set dummy mkoctfile; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_path_MKOCTFILE+:} false; then : + $as_echo_n "(cached) " >&6 +else + case $MKOCTFILE in + [\\/]* | ?:[\\/]*) + ac_cv_path_MKOCTFILE="$MKOCTFILE" # Let the user override the test with a path. + ;; + *) + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_path_MKOCTFILE="$as_dir/$ac_word$ac_exec_ext" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + + test -z "$ac_cv_path_MKOCTFILE" && ac_cv_path_MKOCTFILE=":" + ;; +esac +fi +MKOCTFILE=$ac_cv_path_MKOCTFILE +if test -n "$MKOCTFILE"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKOCTFILE" >&5 +$as_echo "$MKOCTFILE" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +# Extract the first word of "octave", so it can be a program name with args. +set dummy octave; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_path_OCTAVE+:} false; then : + $as_echo_n "(cached) " >&6 +else + case $OCTAVE in + [\\/]* | ?:[\\/]*) + ac_cv_path_OCTAVE="$OCTAVE" # Let the user override the test with a path. + ;; + *) + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_path_OCTAVE="$as_dir/$ac_word$ac_exec_ext" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + + test -z "$ac_cv_path_OCTAVE" && ac_cv_path_OCTAVE=":" + ;; +esac +fi +OCTAVE=$ac_cv_path_OCTAVE +if test -n "$OCTAVE"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OCTAVE" >&5 +$as_echo "$OCTAVE" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + # Checks for header files. ac_ext=c @@ -5249,7 +5373,7 @@ # 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 3.7.0, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -5311,7 +5435,7 @@ cat >>$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 3.7.0 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/nan-3.6.1/src/configure.ac new/nan-3.7.0/src/configure.ac --- old/nan-3.6.1/src/configure.ac 2021-11-03 21:09:44.000000000 +0100 +++ new/nan-3.7.0/src/configure.ac 2022-05-21 12:49:30.000000000 +0200 @@ -2,7 +2,7 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ([2.69]) -AC_INIT([nan-toolbox], [3.5.3], [alois.schlo...@gmail.com]) +AC_INIT([nan-toolbox], [3.7.0], [alois.schlo...@gmail.com]) AC_CONFIG_SRCDIR([train.c]) AC_CONFIG_HEADERS([config.h]) @@ -21,6 +21,10 @@ AC_CHECK_LIB([linear], [train]) AC_CHECK_LIB([svm], [svm_train]) +AC_CHECK_PROG([MATLAB], [matlab], [$(readlink -f $(which matlab))], [:]) +# AC_CHECK_PROG([MATLAB], [matlab], [$(matlab -n|awk '/^-> r MATLAB = / {printf("%s/bin/matlab",$5)}')], [:]) +AC_PATH_PROG([MKOCTFILE], [mkoctfile], [:]) +AC_PATH_PROG([OCTAVE], [octave], [:]) # Checks for header files. AC_CHECK_HEADERS([float.h limits.h locale.h stdint.h stdlib.h string.h sys/param.h])