Changeset 3018
- Timestamp:
- Apr 4, 2013, 6:46:38 AM (10 years ago)
- Location:
- trunk
- Files:
-
- 1 deleted
- 14 edited
- 1 copied
Legend:
- Unmodified
- Added
- Removed
-
trunk
- Property svn:mergeinfo changed
/branches/0.10-stable merged: 2991,2996-2997,3000,3003,3008-3016
- Property svn:mergeinfo changed
-
trunk/Makefile.am
r2984 r3018 8 8 # Copyright (C) 2006 Jari Häkkinen 9 9 # Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson 10 # Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson10 # Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson 11 11 # 12 12 # This file is part of the yat library, http://dev.thep.lu.se/yat … … 113 113 yat-pc-check: 114 114 $(SHELL) $(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) \ 115 && rm -f build_support/yat.pc && make\115 && rm -f build_support/yat.pc && $(MAKE) $(AM_MAKEFLAGS) \ 116 116 && $(GREP) '^prefix=/usr/local' build_support/yat.pc \ 117 117 && $(GREP) '^exec_prefix=$${prefix}' build_support/yat.pc \ 118 118 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 119 119 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 120 && rm -f build_support/yat.pc && makeprefix=foo \120 && rm -f build_support/yat.pc && $(MAKE) $(AM_MAKEFLAGS) prefix=foo \ 121 121 && $(GREP) '^prefix=foo' build_support/yat.pc \ 122 122 && $(GREP) '^exec_prefix=$${prefix}' build_support/yat.pc \ 123 123 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 124 124 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 125 && rm -f build_support/yat.pc && make prefix=foo exec_prefix=bar \ 126 && $(GREP) '^prefix=foo' build_support/yat.pc \ 127 && $(GREP) '^exec_prefix=bar' build_support/yat.pc \ 128 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 129 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 130 && rm -f build_support/yat.pc \ 131 && make prefix=foo exec_prefix=bar libdir=baz includedir=quz \ 125 && rm -f build_support/yat.pc \ 126 && $(MAKE) $(AM_MAKEFLAGS) prefix=foo exec_prefix=bar \ 127 && $(GREP) '^prefix=foo' build_support/yat.pc \ 128 && $(GREP) '^exec_prefix=bar' build_support/yat.pc \ 129 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 130 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 131 && rm -f build_support/yat.pc \ 132 && $(MAKE) $(AM_MAKEFLAGS) prefix=foo exec_prefix=bar libdir=baz includedir=quz \ 132 133 && $(GREP) '^prefix=foo' build_support/yat.pc \ 133 134 && $(GREP) '^exec_prefix=bar' build_support/yat.pc \ … … 135 136 && $(GREP) '^includedir=quz' build_support/yat.pc \ 136 137 && $(SHELL) $(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) exec_prefix=/t \ 137 && rm -f build_support/yat.pc && make\138 && rm -f build_support/yat.pc && $(MAKE) $(AM_MAKEFLAGS) \ 138 139 && $(GREP) '^prefix=/usr/local' build_support/yat.pc \ 139 140 && $(GREP) '^exec_prefix=/t' build_support/yat.pc \ 140 141 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 141 142 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 142 && rm -f build_support/yat.pc && makeprefix=foo \143 && rm -f build_support/yat.pc && $(MAKE) $(AM_MAKEFLAGS) prefix=foo \ 143 144 && $(GREP) '^prefix=foo' build_support/yat.pc \ 144 145 && $(GREP) '^exec_prefix=/t' build_support/yat.pc \ 145 146 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 146 147 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 147 && rm -f build_support/yat.pc && make prefix=foo exec_prefix=bar \ 148 && $(GREP) '^prefix=foo' build_support/yat.pc \ 149 && $(GREP) '^exec_prefix=bar' build_support/yat.pc \ 150 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 151 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 152 && rm -f build_support/yat.pc \ 153 && make prefix=foo exec_prefix=bar libdir=baz includedir=quz \ 148 && rm -f build_support/yat.pc \ 149 && $(MAKE) $(AM_MAKEFLAGS) prefix=foo exec_prefix=bar \ 150 && $(GREP) '^prefix=foo' build_support/yat.pc \ 151 && $(GREP) '^exec_prefix=bar' build_support/yat.pc \ 152 && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \ 153 && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \ 154 && rm -f build_support/yat.pc \ 155 && $(MAKE) $(AM_MAKEFLAGS) prefix=foo exec_prefix=bar libdir=baz includedir=quz \ 154 156 && $(GREP) '^prefix=foo' build_support/yat.pc \ 155 157 && $(GREP) '^exec_prefix=bar' build_support/yat.pc \ … … 159 161 SVN = svn 160 162 SVNCOPYRIGHT = svncopyright 163 SCP = scp 161 164 162 165 copyright: 163 166 $(SVNCOPYRIGHT) -v -r $(srcdir) 167 168 ## FIXME perhaps incorporate this target into release 169 release-tag-upload: 170 $(MAKE) $(AM_MAKEFLAGS) release 171 $(MAKE) $(AM_MAKEFLAGS) svn-tag 172 $(MAKE) $(AM_MAKEFLAGS) annaounce.txt 173 $(MAKE) $(AM_MAKEFLAGS) upload 174 175 announce.txt: build_support/gen_announce.sh $(distdir).tar.gz.MD5 176 $(SHELL) build_support/gen_announce.sh > $@ 177 178 sf_user = peter31042 179 180 upload: $(distdir).tar.gz $(distdir).tar.gz.MD5 181 $(SCP) $(distdir).tar.gz $(distdir).tar.gz.MD5 \ 182 $(sf_user),libyat@frs.sourceforge.net:/home/frs/project/l/li/libyat/. 164 183 165 184 svn-tag: check-version check-svn-diff -
trunk/NEWS
r3006 r3018 14 14 yat 0.10.x series from http://dev.thep.lu.se/yat/svn/branches/0.10-stable 15 15 16 version 0.10.2 (released 4 April 2013) 17 - On OSX yat is built using flat_namespace (see bug #745) 18 - BamRead::mtid(void) is now implemented (see bug #743) 19 - Fixed bug in KolmogorovSmirnov::remove (see bug #753) 20 21 A complete list of closed tickets can be found here [[br]] 22 http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.10.2 23 16 24 version 0.10.1 (released 17 January 2013) 17 25 - libyat is no longer linked against -lbam (bug #733) … … 52 60 - utility::SmartPtr was marked internal (see r2778) 53 61 - ssearch now takes parameter setting mismatch (r2792) 54 - RNG class is no tmultithread safe (ticket #568)62 - RNG class is now multithread safe (ticket #568) 55 63 - The build system now uses a non-recursive Makefile (ticket #703) 56 64 -
trunk/build_support/Makefile.am
r2960 r3018 18 18 # along with yat. If not, see <http://www.gnu.org/licenses/>. 19 19 20 noinst_SCRIPTS = build_support/ tag_and_release.sh20 noinst_SCRIPTS = build_support/gen_announce.sh 21 21 bin_SCRIPTS = build_support/for_installation/yat-config 22 22 -
trunk/configure.ac
r2986 r3018 210 210 APR_SAVE_THE_ENVIRONMENT(LIBS) 211 211 212 AS_CASE([$host_os], [darwin*], [ 213 YAT_LD_ADD_FLAG([LDFLAGS], [-Wl,-flat_namespace]) 214 ]) 215 212 216 # Checks for libraries. 213 217 AC_MSG_NOTICE([checking for libraries]) … … 407 411 AC_CONFIG_FILES([build_support/gen_yat_pc.sh], 408 412 [chmod +x build_support/gen_yat_pc.sh]) 409 AC_CONFIG_FILES([build_support/ tag_and_release.sh],410 [chmod +x-w build_support/ tag_and_release.sh])413 AC_CONFIG_FILES([build_support/gen_announce.sh], 414 [chmod +x-w build_support/gen_announce.sh]) 411 415 AC_CONFIG_FILES([Makefile 412 416 doc/doxygen.config -
trunk/doc/Makefile.am
r2932 r3018 80 80 $(AM_V_at) test -r "$(DESTDIR)/$(htmldir)/index.html" \ 81 81 || { echo "no documentation installed" 1>&2; exit 1; } 82 $(AM_V_at)grep "yat.*$(VERSION)" "$(DESTDIR)/$(htmldir)/index.html" \83 || { echo $(DESTDIR)/$(htmldir)/index.html not updated 1>&2; exit 1; }84 82 85 83 MOSTLYCLEANFILES += doc/doxygen.error -
trunk/m4/version.m4
r2960 r3018 71 71 # yat-0.10 7:0:0 72 72 # yat-0.10.1 7:1:0 73 # yat-0.10.2 7:2:0 73 74 # 74 75 # *Accidently, the libtool number was not updated for yat 0.5 -
trunk/test/Makefile.am
r2995 r3018 198 198 199 199 $(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps) 200 $(AM_V_GEN) cd $(srcdir)/test/yat-hello\201 && $(MKDIR_P) m4\200 $(AM_V_GEN)$(MKDIR_P) $(srcdir)/test/yat-hello/m4 \ 201 && cd $(srcdir)/test/yat-hello \ 202 202 && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \ 203 203 && autoreconf -if $(yat_dev_null) \ -
trunk/test/common_defs.sh.in
r2981 r3018 163 163 AM_CPPFLAGS = \$(YAT_CPPFLAGS) 164 164 AM_CXXFLAGS = \$(YAT_CXXFLAGS) 165 AM_LDFLAGS = \$(YAT_LDFLAGS) 165 166 LDADD = \$(YAT_LDADD) 166 167 bin_PROGRAMS = hello -
trunk/test/kolmogorov_smirnov.cc
r2998 r3018 209 209 suite.out() << "test remove\n"; 210 210 KolmogorovSmirnov ks; 211 ks.add(0, true); 211 212 ks.add(1, true); 212 213 ks.add(2, false); … … 214 215 ks.add(3, false); 215 216 double score = ks.score(); 216 ks.add(4, false); 217 double x = 0; 218 ks.add(x, false); 217 219 218 220 try { 219 ks.remove( 4, false);221 ks.remove(x, false); 220 222 } 221 223 catch (std::runtime_error& e) { -
trunk/test/yat_m4_test.sh
r2805 r3018 2 2 # $Id$ 3 3 # 4 # Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson4 # Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson 5 5 # 6 6 # This file is part of the yat library, http://dev.thep.lu.se/yat … … 35 35 [AC_MSG_ERROR([could not find required version of yat])]) 36 36 YAT_CHECK_HEADER(,[AC_MSG_ERROR([could not find yat headers])]) 37 YAT_LDFLAGS=\`\$yat_config --ldflags\` 38 AC_SUBST([YAT_LDFLAGS]) 37 39 YAT_LDADD=\`\$yat_config --link-libtool\` 38 40 AC_SUBST(YAT_LDADD) -
trunk/yat/omic/BamReadIterator.h
r2993 r3018 5 5 6 6 /* 7 Copyright (C) 2012 Peter Johansson7 Copyright (C) 2012, 2013 Peter Johansson 8 8 9 9 This file is part of the yat library, http://dev.thep.lu.se/yat -
trunk/yat/statistics/KolmogorovSmirnov.cc
r2837 r3018 3 3 /* 4 4 Copyright (C) 2008 Jari Häkkinen, Peter Johansson 5 Copyright (C) 2009, 2011, 2012 Peter Johansson5 Copyright (C) 2009, 2011, 2012, 2013 Peter Johansson 6 6 7 7 This file is part of the yat library, http://dev.thep.lu.se/yat … … 34 34 #include <functional> 35 35 #include <limits> 36 #include <sstream> 36 37 #include <vector> 37 38 … … 112 113 return; 113 114 Element e(value, class_label, weight); 114 typedef std::multiset<Element>:: const_iterator iterator;115 typedef std::multiset<Element>::iterator iterator; 115 116 std::pair<iterator, iterator> iter = data_.equal_range(e); 116 117 while (iter.first!=iter.second) { … … 120 121 else 121 122 sum_w2_-=weight; 123 data_.erase(iter.first); 122 124 cached_=false; 123 125 return; … … 125 127 ++iter.first; 126 128 } 127 throw utility::runtime_error("bajs"); 129 std::ostringstream ss; 130 ss << "KolmogorovSmirnov::remove: " << value << " " << class_label 131 << " " << weight; 132 throw utility::runtime_error(ss.str()); 128 133 } 129 134 -
trunk/yat/statistics/KolmogorovSmirnov.h
r2912 r3018 6 6 /* 7 7 Copyright (C) 2008 Jari Häkkinen, Peter Johansson 8 Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson8 Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson 9 9 10 10 This file is part of the yat library, http://dev.thep.lu.se/yat … … 141 141 value, \a class_label, and \a weight. 142 142 143 \since New in yat 0. 0143 \since New in yat 0.9 144 144 */ 145 145 void remove(double value, bool class_label, double weight=1.0);
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