Changeset 2103
- Timestamp:
- Nov 6, 2009, 1:40:26 PM (13 years ago)
- Location:
- trunk
- Files:
-
- 10 edited
- 4 copied
Legend:
- Unmodified
- Added
- Removed
-
trunk/NEWS
r2089 r2103 17 17 A complete list of closed tickets can be found here [[br]] 18 18 http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.6 19 20 Version 0.5.5 (released 5 November 2009) 21 22 - SVM::predict is calculated as geometric distance (issue #542) 23 - detection of GSL is improved (issue #558) 24 25 A complete list of closed tickets can be found here [[br]] 26 http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.5.5 19 27 20 28 Version 0.5.4 (released 12 June 2009) -
trunk/build_support/svn_support.am
r2056 r2103 65 65 exit 1;; \ 66 66 esac 67 @date=`date -u "+% d%B %Y"` &&\67 @date=`date -u "+%e %B %Y"` &&\ 68 68 case `sed 15q $(srcdir)/NEWS` in \ 69 69 *"$$date"*);; \ -
trunk/configure.ac
r2088 r2103 113 113 dx_enable_ps=$dx_enable_dvi 114 114 ACLTX_PROG_DVIPS([dx_enable_ps=no]) 115 AS_IF([test "x$dx_enable_ps" != xno], [ 116 YAT_PROG_DVIPS_PSPICTURE([], [dx_enable_ps=no 117 AC_MSG_NOTICE([ps generation turned off])]) 118 ]) 115 119 ] 116 120 ) … … 124 128 AC_CONFIG_FILES([test/documentation_test.sh], 125 129 [chmod +x test/documentation_test.sh]) 126 127 # Save user-defined environment settings for later restoration128 APR_SAVE_THE_ENVIRONMENT(CPPFLAGS)129 APR_SAVE_THE_ENVIRONMENT(CXXFLAGS)130 APR_SAVE_THE_ENVIRONMENT(LDFLAGS)131 APR_SAVE_THE_ENVIRONMENT(LIBS)132 133 # Checks for libraries.134 AC_MSG_NOTICE([checking for libraries])135 AC_CHECK_LIBM136 137 # find library implementing BLAS C API, or use gslcblas138 YAT_LIB_CBLAS([YAT_CBLAS_LIB=$CBLAS_LIB], [YAT_CBLAS_LIB=-lgslcblas])139 140 # GNU Scientific Library, GSL http://www.gnu.org/software/gsl/, checks141 # Including AX_PATH_GSL macro from gsl.m4 distributed by GSL142 gsl_version="1.8"143 AC_SUBST(gsl_version)144 gsl_ok=yes145 YAT_CHECK_GSL([$gsl_version],[gsl_ok=yes],[gsl_ok=no])146 147 # Boost http://www.boost.org148 boost_version=1.33149 AC_SUBST(boost_version)150 AX_BOOST_BASE(["$boost_version"])151 boost_version_check=$succeeded;152 YAT_CPP_ADD_FLAG([CPPFLAGS], [$BOOST_CPPFLAGS])153 154 #support for large files155 AC_SYS_LARGEFILE156 if test "$enable_largefile" = "no"; then157 AC_DEFINE([YAT_LFS_DISABLED], 1,158 [defined to 1 if large file support is disabled])159 fi160 161 # we use prefix INTERNAL_ for variables that are solely needed for162 # building yat, i.e., they are not needed for a user of yat and are163 # not propagated to yat-config or yat.m4.164 YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wall -pedantic])165 YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DHAVE_INLINE=1])166 AC_ARG_ENABLE([debug],167 [AS_HELP_STRING([--enable-debug],[turn on debug options and code])])168 if test "${enable_debug}" = "yes" ; then169 YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DYAT_DEBUG=1])170 YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-g -O])171 else172 # avoid defining GSL_RANGE_CHECK_OFF if GSL_RANGE_CHECK is already defined173 AX_C_IFDEF([GSL_RANGE_CHECK],[],174 [YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DGSL_RANGE_CHECK_OFF])] )175 YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DNDEBUG])176 YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-O3])177 fi178 179 AC_ARG_ENABLE([svn-support],180 [AS_HELP_STRING([--enable-svn-support],181 [enable svn support - used by yat maintainer])])182 183 if test "x$enable_svn-support" = "xyes"; then184 svn_error_msg="svn support cannot be enabled:"185 AS_IF([test "x$MD5" = "xno"],186 [AC_MSG_ERROR([$svn_error_msg tool to create md5 file not found])])187 188 AC_CHECK_FILE([$srcdir/.svn], ,189 AC_MSG_ERROR([$svn_error_msg `$srcdir' is not an svn wc.]))190 fi191 AM_CONDITIONAL([ENABLE_SVN_SUPPORT], [test "x$enable_svn_support" = "xyes"])192 193 130 194 131 # check for quiet_NaN support in OS … … 261 198 [AC_MSG_RESULT([no])] ) 262 199 200 # Save user-defined environment settings for later restoration 201 APR_SAVE_THE_ENVIRONMENT(CPPFLAGS) 202 APR_SAVE_THE_ENVIRONMENT(CXXFLAGS) 203 APR_SAVE_THE_ENVIRONMENT(LDFLAGS) 204 APR_SAVE_THE_ENVIRONMENT(LIBS) 205 206 # Checks for libraries. 207 AC_MSG_NOTICE([checking for libraries]) 208 AC_CHECK_LIBM 209 210 # find library implementing BLAS C API, or use gslcblas 211 YAT_LIB_CBLAS([YAT_CBLAS_LIB=$CBLAS_LIB], [YAT_CBLAS_LIB=-lgslcblas]) 212 213 # GNU Scientific Library, GSL http://www.gnu.org/software/gsl/, checks 214 # Including AX_PATH_GSL macro from gsl.m4 distributed by GSL 215 gsl_version="1.8" 216 AC_SUBST(gsl_version) 217 gsl_ok=yes 218 YAT_CHECK_GSL([$gsl_version],[gsl_ok=yes],[gsl_ok=no]) 219 220 # Boost http://www.boost.org 221 boost_version=1.33 222 AC_SUBST(boost_version) 223 AX_BOOST_BASE(["$boost_version"]) 224 boost_version_check=$succeeded; 225 YAT_CPP_ADD_FLAG([CPPFLAGS], [$BOOST_CPPFLAGS]) 226 227 #support for large files 228 AC_SYS_LARGEFILE 229 if test "$enable_largefile" = "no"; then 230 AC_DEFINE([YAT_LFS_DISABLED], 1, 231 [defined to 1 if large file support is disabled]) 232 fi 233 234 # we use prefix INTERNAL_ for variables that are solely needed for 235 # building yat, i.e., they are not needed for a user of yat and are 236 # not propagated to yat-config or yat.m4. 237 YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wall -pedantic]) 238 YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DHAVE_INLINE=1]) 239 AC_ARG_ENABLE([debug], 240 [AS_HELP_STRING([--enable-debug],[turn on debug options and code])]) 241 if test "${enable_debug}" = "yes" ; then 242 YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DYAT_DEBUG=1]) 243 YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-g -O]) 244 else 245 # avoid defining GSL_RANGE_CHECK_OFF if GSL_RANGE_CHECK is already defined 246 AX_C_IFDEF([GSL_RANGE_CHECK],[], 247 [YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DGSL_RANGE_CHECK_OFF])] ) 248 YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DNDEBUG]) 249 YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-O3]) 250 fi 251 252 # some versions of boost uses long long - turn off compiler warnings 253 # with -Wno-long-long 254 yat_save_CXXFLAGS=$CXXFLAGS 255 # use -pedantic and friends in CXXFLAGS temporarily 256 CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS" 257 # turn warnings into errors 258 YAT_CXX_ADD_FLAG([CXXFLAGS], [-Werror]) 259 AC_COMPILE_IFELSE([AC_LANG_PROGRAM( 260 [ 261 @%:@include <boost/iterator/transform_iterator.hpp> 262 @%:@include <cmath> 263 @%:@include <functional> 264 @%:@include <vector> 265 ],[ 266 using namespace boost; 267 typedef std::pointer_to_unary_function<double, double> F; 268 std::vector<double> vec; 269 transform_iterator<F, std::vector<double>::iterator> 270 i(vec.begin(), std::ptr_fun(fabs)); 271 ])], 272 [], 273 [YAT_CXX_ADD_FLAG([AM_CXXFLAGS], [-Wno-long-long])]) 274 # restore CXXFLAGS 275 CXXFLAGS=$yat_save_CXXFLAGS 276 277 AC_ARG_ENABLE([svn-support], 278 [AS_HELP_STRING([--enable-svn-support], 279 [enable svn support - used by yat maintainer])]) 280 281 if test "x$enable_svn-support" = "xyes"; then 282 svn_error_msg="svn support cannot be enabled:" 283 AS_IF([test "x$MD5" = "xno"], 284 [AC_MSG_ERROR([$svn_error_msg tool to create md5 file not found])]) 285 286 AC_CHECK_FILE([$srcdir/.svn], , 287 AC_MSG_ERROR([$svn_error_msg `$srcdir' is not an svn wc.])) 288 fi 289 AM_CONDITIONAL([ENABLE_SVN_SUPPORT], [test "x$enable_svn_support" = "xyes"]) 290 291 263 292 # yat specific settings 264 293 YAT_LIBNAME="yat" -
trunk/doc/Makefile.am
r2082 r2103 6 6 # Copyright (C) 2005 Peter Johansson 7 7 # Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson 8 # Copyright (C) 2009 Peter Johansson 8 9 # 9 10 # This file is part of the yat library, http://dev.thep.lu.se/yat … … 25 26 DOXYGEN_FILES = $(srcdir)/build_tool.doxygen \ 26 27 $(builddir)/first_page.doxygen \ 28 $(srcdir)/footer.html \ 27 29 $(srcdir)/namespaces.doxygen \ 28 30 $(srcdir)/concepts.doxygen \ -
trunk/doc/doxygen.config.in
r1905 r2103 479 479 # standard footer. 480 480 481 HTML_FOOTER = 481 HTML_FOOTER = @srcdir@/footer.html 482 482 483 483 # The HTML_STYLESHEET tag can be used to specify a user defined cascading -
trunk/m4/gsl.m4
r1954 r2103 9 9 AC_ARG_WITH(gsl-exec-prefix,[ --with-gsl-exec-prefix=PFX Exec prefix where GSL is installed (optional)], 10 10 gsl_exec_prefix="$withval", gsl_exec_prefix="") 11 AC_ARG_ENABLE(gsltest, [ --disable-gsltest Do not try to compile and run a test GSL program],12 , enable_gsltest=yes)13 11 14 12 if test "x${GSL_CONFIG+set}" != xset ; then … … 27 25 if test "$GSL_CONFIG" = "no" ; then 28 26 no_gsl=yes 27 AC_MSG_RESULT([no]) 28 AC_MSG_WARN([ 29 The gsl-config script installed by GSL could not be found 30 If GSL was installed in PREFIX, make sure PREFIX/bin is in 31 your path, or set the GSL_CONFIG environment variable to the 32 full path to gsl-config. 33 ]) 29 34 else 30 35 GSL_CFLAGS=`$GSL_CONFIG --cflags` 31 36 GSL_LIBS=`$GSL_CONFIG --libs` 37 ac_save_LIBS="$LIBS" 38 CXXFLAGS="$CXXFLAGS $GSL_CFLAGS" 39 LIBS="$GSL_LIBS $LIBS" 40 AC_LINK_IFELSE([AC_LANG_PROGRAM(, [return 0])],,[no_gsl=yes]) 41 LIBS="$ac_save_LIBS" 42 fi 32 43 33 gsl_major_version=`$GSL_CONFIG --version | \ 34 sed 's/^\([[0-9]]*\).*/\1/'` 35 if test "x${gsl_major_version}" = "x" ; then 36 gsl_major_version=0 37 fi 44 if test "x$no_gsl" = xyes ; then 45 AC_MSG_RESULT([no]) 46 AC_MSG_WARN([ 47 The test program failed to compile or link. See the config.log 48 for the exact error that occured. This usually means GSL was 49 incorrectly installed or that you have moved GSL since it was 50 installed. In the latter case, you may want to edit the 51 gsl-config script: $GSL_CONFIG. 52 ]) 53 else 54 ac_gsl_version=`$GSL_CONFIG --version` 55 AX_COMPARE_VERSION([$ac_gsl_version], [ge], [$min_gsl_version],,[no_gsl=yes]) 56 AC_MSG_RESULT([$ac_gsl_version]) 57 if test "x$no_gsl" = xyes ; then 58 AC_MSG_WARN([ 59 gsl-config --version returned $ac_gsl_version, but the minimum 60 version of GSL required is $min_gsl_version. If gsl-config is 61 correct, then it is best to upgrade to the required version. If 62 gsl-config was wrong, set the environment variable GSL_CONFIG to 63 point to the correct copy of gsl-config, and remove the file 64 config.cache before re-running configure. 65 ]) 66 fi 67 fi 38 68 39 gsl_minor_version=`$GSL_CONFIG --version | \40 sed 's/^\([[0-9]]*\)\.\{0,1\}\([[0-9]]*\).*/\2/'`41 if test "x${gsl_minor_version}" = "x" ; then42 gsl_minor_version=043 fi44 45 gsl_micro_version=`$GSL_CONFIG --version | \46 sed 's/^\([[0-9]]*\)\.\{0,1\}\([[0-9]]*\)\.\{0,1\}\([[0-9]]*\).*/\3/'`47 if test "x${gsl_micro_version}" = "x" ; then48 gsl_micro_version=049 fi50 51 if test "x$enable_gsltest" = "xyes" ; then52 ac_save_CFLAGS="$CFLAGS"53 ac_save_LIBS="$LIBS"54 CFLAGS="$CFLAGS $GSL_CFLAGS"55 LIBS="$GSL_LIBS $LIBS"56 57 rm -f conf.gsltest58 AC_TRY_RUN([59 #include <stdio.h>60 #include <stdlib.h>61 #include <string.h>62 63 char* my_strdup (const char *str);64 65 char*66 my_strdup (const char *str)67 {68 char *new_str;69 70 if (str)71 {72 new_str = (char *)malloc ((strlen (str) + 1) * sizeof(char));73 strcpy (new_str, str);74 }75 else76 new_str = NULL;77 78 return new_str;79 }80 81 int main (void)82 {83 int major = 0, minor = 0, micro = 0;84 int n;85 char *tmp_version;86 87 system ("touch conf.gsltest");88 89 /* HP/UX 9 (%@#!) writes to sscanf strings */90 tmp_version = my_strdup("$min_gsl_version");91 92 n = sscanf(tmp_version, "%d.%d.%d", &major, &minor, µ) ;93 94 if (n != 2 && n != 3) {95 printf("%s, bad version string\n", "$min_gsl_version");96 exit(1);97 }98 99 if (($gsl_major_version > major) ||100 (($gsl_major_version == major) && ($gsl_minor_version > minor)) ||101 (($gsl_major_version == major) && ($gsl_minor_version == minor) && ($gsl_micro_version >= micro)))102 {103 exit(0);104 }105 else106 {107 printf("\n*** 'gsl-config --version' returned %d.%d.%d, but the minimum version\n", $gsl_major_version, $gsl_minor_version, $gsl_micro_version);108 printf("*** of GSL required is %d.%d.%d. If gsl-config is correct, then it is\n", major, minor, micro);109 printf("*** best to upgrade to the required version.\n");110 printf("*** If gsl-config was wrong, set the environment variable GSL_CONFIG\n");111 printf("*** to point to the correct copy of gsl-config, and remove the file\n");112 printf("*** config.cache before re-running configure\n");113 exit(1);114 }115 }116 117 ],, no_gsl=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])118 CFLAGS="$ac_save_CFLAGS"119 LIBS="$ac_save_LIBS"120 fi121 fi122 69 if test "x$no_gsl" = x ; then 123 AC_MSG_RESULT(yes)124 70 ifelse([$2], , :, [$2]) 125 71 else 126 AC_MSG_RESULT(no)127 if test "$GSL_CONFIG" = "no" ; then128 echo "*** The gsl-config script installed by GSL could not be found"129 echo "*** If GSL was installed in PREFIX, make sure PREFIX/bin is in"130 echo "*** your path, or set the GSL_CONFIG environment variable to the"131 echo "*** full path to gsl-config."132 else133 if test -f conf.gsltest ; then134 :135 else136 echo "*** Could not run GSL test program, checking why..."137 CFLAGS="$CFLAGS $GSL_CFLAGS"138 LIBS="$GSL_LIBS $LIBS"139 AC_TRY_LINK([140 #include <stdio.h>141 ], [ return 0; ],142 [ echo "*** The test program compiled, but did not run. This usually means"143 echo "*** that the run-time linker is not finding GSL or finding the wrong"144 echo "*** version of GSL. If it is not finding GSL, you'll need to set your"145 echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"146 echo "*** to the installed location Also, make sure you have run ldconfig if that"147 echo "*** is required on your system"148 echo "***"149 echo "*** If you have an old version installed, it is best to remove it, although"150 echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"],151 [ echo "*** The test program failed to compile or link. See the file config.log for the"152 echo "*** exact error that occured. This usually means GSL was incorrectly installed"153 echo "*** or that you have moved GSL since it was installed. In the latter case, you"154 echo "*** may want to edit the gsl-config script: $GSL_CONFIG" ])155 CFLAGS="$ac_save_CFLAGS"156 LIBS="$ac_save_LIBS"157 fi158 fi159 # GSL_CFLAGS=""160 # GSL_LIBS=""161 72 ifelse([$3], , :, [$3]) 162 73 fi 163 74 AC_SUBST(GSL_CFLAGS) 164 75 AC_SUBST(GSL_LIBS) 165 rm -f conf.gsltest166 76 ]) 167 77 -
trunk/m4/gsl_license.txt
r1785 r2103 1 1 We have copied gsl.m4 (CVS revision 1.11) from the GNU Scientific 2 Library, GSL http://www.gnu.org/software/gsl/. No modification is made 3 to the file. 2 Library, GSL http://www.gnu.org/software/gsl/. The file has been 3 modified to suit our needs; the exact modifications can be traced 4 using the source code revision system. 4 5 5 6 GSL is distributed under the GNU General License v3, -
trunk/m4/version.m4
r1998 r2103 58 58 # yat-0.5.3 2:2:0 59 59 # yat-0.5.4 2:3:0 60 # yat-0.5.5 2:4:0 60 61 # 61 62 # *Accidently, the libtool number was not updated for yat 0.5 -
trunk/yat/classifier/SVM.cc
r1863 r2103 90 90 margin_ += 2*alpha_(i)*target(i)*kernel_mod(i,j)*alpha_(j)*target(j); 91 91 } 92 margin_ = std::sqrt(margin_); 92 93 } 93 94 -
trunk/yat/normalizer/qQuantileNormalizer.cc
r1813 r2103 96 96 std::stringstream ss; 97 97 ss << "yat::normalizer::qQuantileNormalizer: relative weight too " 98 << "large in\n"; 98 << "large. See qQuantileNormalizer constructor documentation " 99 << "for details on weights.\n"; 99 100 throw std::runtime_error(ss.str()); 100 101 }
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