Changeset 3018


Ignore:
Timestamp:
Apr 4, 2013, 6:46:38 AM (8 years ago)
Author:
Peter
Message:

merge patch release 0.10.2 into trunk

Location:
trunk
Files:
1 deleted
14 edited
1 copied

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/Makefile.am

    r2984 r3018  
    88# Copyright (C) 2006 Jari Häkkinen
    99# Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    10 # Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     10# Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
    1111#
    1212# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    113113yat-pc-check:
    114114  $(SHELL) $(srcdir)/configure $(DISTCHECK_CONFIGURE_FLAGS) \
    115   && rm -f build_support/yat.pc && make \
     115  && rm -f build_support/yat.pc && $(MAKE) $(AM_MAKEFLAGS) \
    116116  && $(GREP) '^prefix=/usr/local' build_support/yat.pc \
    117117  && $(GREP) '^exec_prefix=$${prefix}' build_support/yat.pc \
    118118  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
    119119  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
    120   && rm -f build_support/yat.pc && make prefix=foo \
     120  && rm -f build_support/yat.pc && $(MAKE) $(AM_MAKEFLAGS) prefix=foo \
    121121  && $(GREP) '^prefix=foo' build_support/yat.pc \
    122122  && $(GREP) '^exec_prefix=$${prefix}' build_support/yat.pc \
    123123  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
    124124  && $(GREP) '^includedir=$${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 \
    132133  && $(GREP) '^prefix=foo' build_support/yat.pc \
    133134  && $(GREP) '^exec_prefix=bar' build_support/yat.pc \
     
    135136  && $(GREP) '^includedir=quz' build_support/yat.pc \
    136137  && $(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) \
    138139  && $(GREP) '^prefix=/usr/local' build_support/yat.pc \
    139140  && $(GREP) '^exec_prefix=/t' build_support/yat.pc \
    140141  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
    141142  && $(GREP) '^includedir=$${prefix}/include' build_support/yat.pc \
    142   && rm -f build_support/yat.pc && make prefix=foo \
     143  && rm -f build_support/yat.pc && $(MAKE) $(AM_MAKEFLAGS) prefix=foo \
    143144  && $(GREP) '^prefix=foo' build_support/yat.pc \
    144145  && $(GREP) '^exec_prefix=/t' build_support/yat.pc \
    145146  && $(GREP) '^libdir=$${exec_prefix}/lib' build_support/yat.pc \
    146147  && $(GREP) '^includedir=$${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 \
    154156  && $(GREP) '^prefix=foo' build_support/yat.pc \
    155157  && $(GREP) '^exec_prefix=bar' build_support/yat.pc \
     
    159161SVN = svn
    160162SVNCOPYRIGHT = svncopyright
     163SCP = scp
    161164
    162165copyright:
    163166  $(SVNCOPYRIGHT) -v -r $(srcdir)
     167
     168## FIXME perhaps incorporate this target into release
     169release-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
     175announce.txt: build_support/gen_announce.sh $(distdir).tar.gz.MD5
     176  $(SHELL) build_support/gen_announce.sh > $@
     177
     178sf_user = peter31042
     179
     180upload: $(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/.
    164183
    165184svn-tag: check-version check-svn-diff
  • trunk/NEWS

    r3006 r3018  
    1414yat 0.10.x series from http://dev.thep.lu.se/yat/svn/branches/0.10-stable
    1515
     16version 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
    1624version 0.10.1 (released 17 January 2013)
    1725  - libyat is no longer linked against -lbam (bug #733)
     
    5260  - utility::SmartPtr was marked internal (see r2778)
    5361  - ssearch now takes parameter setting mismatch (r2792)
    54   - RNG class is not multithread safe (ticket #568)
     62  - RNG class is now multithread safe (ticket #568)
    5563  - The build system now uses a non-recursive Makefile (ticket #703)
    5664
  • trunk/build_support/Makefile.am

    r2960 r3018  
    1818# along with yat. If not, see <http://www.gnu.org/licenses/>.
    1919
    20 noinst_SCRIPTS = build_support/tag_and_release.sh
     20noinst_SCRIPTS = build_support/gen_announce.sh
    2121bin_SCRIPTS = build_support/for_installation/yat-config
    2222
  • trunk/configure.ac

    r2986 r3018  
    210210APR_SAVE_THE_ENVIRONMENT(LIBS)
    211211
     212AS_CASE([$host_os], [darwin*], [
     213  YAT_LD_ADD_FLAG([LDFLAGS], [-Wl,-flat_namespace])
     214])
     215
    212216# Checks for libraries.
    213217AC_MSG_NOTICE([checking for libraries])
     
    407411AC_CONFIG_FILES([build_support/gen_yat_pc.sh],
    408412                [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])
     413AC_CONFIG_FILES([build_support/gen_announce.sh],
     414                [chmod +x-w build_support/gen_announce.sh])
    411415AC_CONFIG_FILES([Makefile
    412416     doc/doxygen.config
  • trunk/doc/Makefile.am

    r2932 r3018  
    8080  $(AM_V_at) test -r "$(DESTDIR)/$(htmldir)/index.html" \
    8181  || { 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; }
    8482
    8583MOSTLYCLEANFILES += doc/doxygen.error
  • trunk/m4/version.m4

    r2960 r3018  
    7171# yat-0.10   7:0:0
    7272# yat-0.10.1 7:1:0
     73# yat-0.10.2 7:2:0
    7374#
    7475# *Accidently, the libtool number was not updated for yat 0.5
  • trunk/test/Makefile.am

    r2995 r3018  
    198198
    199199$(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 \
    202202  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
    203203  && autoreconf -if $(yat_dev_null) \
  • trunk/test/common_defs.sh.in

    r2981 r3018  
    163163AM_CPPFLAGS = \$(YAT_CPPFLAGS)
    164164AM_CXXFLAGS = \$(YAT_CXXFLAGS)
     165AM_LDFLAGS = \$(YAT_LDFLAGS)
    165166LDADD = \$(YAT_LDADD)
    166167bin_PROGRAMS = hello
  • trunk/test/kolmogorov_smirnov.cc

    r2998 r3018  
    209209  suite.out() << "test remove\n";
    210210  KolmogorovSmirnov ks;
     211  ks.add(0, true);
    211212  ks.add(1, true);
    212213  ks.add(2, false);
     
    214215  ks.add(3, false);
    215216  double score = ks.score();
    216   ks.add(4, false);
     217  double x = 0;
     218  ks.add(x, false);
    217219
    218220  try {
    219     ks.remove(4, false);
     221    ks.remove(x, false);
    220222  }
    221223  catch (std::runtime_error& e) {
  • trunk/test/yat_m4_test.sh

    r2805 r3018  
    22# $Id$
    33#
    4 # Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     4# Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    3535                  [AC_MSG_ERROR([could not find required version of yat])])
    3636YAT_CHECK_HEADER(,[AC_MSG_ERROR([could not find yat headers])])
     37YAT_LDFLAGS=\`\$yat_config --ldflags\`
     38AC_SUBST([YAT_LDFLAGS])
    3739YAT_LDADD=\`\$yat_config --link-libtool\`
    3840AC_SUBST(YAT_LDADD)
  • trunk/yat/omic/BamReadIterator.h

    r2993 r3018  
    55
    66/*
    7   Copyright (C) 2012 Peter Johansson
     7  Copyright (C) 2012, 2013 Peter Johansson
    88
    99  This file is part of the yat library, http://dev.thep.lu.se/yat
  • trunk/yat/statistics/KolmogorovSmirnov.cc

    r2837 r3018  
    33/*
    44  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    5   Copyright (C) 2009, 2011, 2012 Peter Johansson
     5  Copyright (C) 2009, 2011, 2012, 2013 Peter Johansson
    66
    77  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    3434#include <functional>
    3535#include <limits>
     36#include <sstream>
    3637#include <vector>
    3738
     
    112113      return;
    113114    Element e(value, class_label, weight);
    114     typedef std::multiset<Element>::const_iterator iterator;
     115    typedef std::multiset<Element>::iterator iterator;
    115116    std::pair<iterator, iterator> iter = data_.equal_range(e);
    116117    while (iter.first!=iter.second) {
     
    120121        else
    121122          sum_w2_-=weight;
     123        data_.erase(iter.first);
    122124        cached_=false;
    123125        return;
     
    125127      ++iter.first;
    126128    }
    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());
    128133  }
    129134
  • trunk/yat/statistics/KolmogorovSmirnov.h

    r2912 r3018  
    66/*
    77  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    8   Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
     8  Copyright (C) 2009, 2010, 2011, 2012, 2013 Peter Johansson
    99
    1010  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    141141       value, \a class_label, and \a weight.
    142142
    143        \since New in yat 0.0
     143       \since New in yat 0.9
    144144     */
    145145    void remove(double value, bool class_label, double weight=1.0);
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