make c++11 compatible

28 files changed, 72 insertions, 86 deletions

diff --git a/decoder/decoder.cc b/decoder/decoder.cc
index 69fbaf85..d4f8f06d 100644
--- a/decoder/decoder.cc
+++ b/decoder/decoder.cc
@@ -57,7 +57,6 @@ static const double kMINUS_EPSILON = -1e-6;  // don't be too strict
 
 using namespace std;
 using namespace std::tr1;
-using boost::shared_ptr;
 namespace po = boost::program_options;
 
 static bool verbose_feature_functions=true;
@@ -101,7 +100,7 @@ inline string str(char const* name,po::variables_map const& conf) {
 
 // print just the --long_opt names suitable for bash compgen
 inline void print_options(std::ostream &out,po::options_description const& opts) {
-  typedef std::vector< shared_ptr<po::option_description> > Ds;
+  typedef std::vector< boost::shared_ptr<po::option_description> > Ds;
   Ds const& ds=opts.options();
   out << '"';
   for (unsigned i=0;i<ds.size();++i) {
@@ -120,13 +119,13 @@ inline bool store_conf(po::variables_map const& conf,std::string const& name,V *
   return false;
 }
 
-inline shared_ptr<FeatureFunction> make_ff(string const& ffp,bool verbose_feature_functions,char const* pre="") {
+inline boost::shared_ptr<FeatureFunction> make_ff(string const& ffp,bool verbose_feature_functions,char const* pre="") {
   string ff, param;
   SplitCommandAndParam(ffp, &ff, &param);
   cerr << pre << "feature: " << ff;
   if (param.size() > 0) cerr << " (with config parameters '" << param << "')\n";
   else cerr << " (no config parameters)\n";
-  shared_ptr<FeatureFunction> pf = ff_registry.Create(ff, param);
+  boost::shared_ptr<FeatureFunction> pf = ff_registry.Create(ff, param);
   if (!pf) exit(1);
   int nbyte=pf->NumBytesContext();
   if (verbose_feature_functions)
@@ -135,13 +134,13 @@ inline shared_ptr<FeatureFunction> make_ff(string const& ffp,bool verbose_featur
 }
 
 #ifdef FSA_RESCORING
-inline shared_ptr<FsaFeatureFunction> make_fsa_ff(string const& ffp,bool verbose_feature_functions,char const* pre="") {
+inline boost::shared_ptr<FsaFeatureFunction> make_fsa_ff(string const& ffp,bool verbose_feature_functions,char const* pre="") {
   string ff, param;
   SplitCommandAndParam(ffp, &ff, &param);
   cerr << "FSA Feature: " << ff;
   if (param.size() > 0) cerr << " (with config parameters '" << param << "')\n";
   else cerr << " (no config parameters)\n";
-  shared_ptr<FsaFeatureFunction> pf = fsa_ff_registry.Create(ff, param);
+  boost::shared_ptr<FsaFeatureFunction> pf = fsa_ff_registry.Create(ff, param);
   if (!pf) exit(1);
   if (verbose_feature_functions)
     cerr<<"State is "<<pf->state_bytes()<<" bytes for "<<pre<<"feature "<<ffp<<endl;
@@ -156,10 +155,10 @@ inline shared_ptr<FsaFeatureFunction> make_fsa_ff(string const& ffp,bool verbose
 // passes are carried over into subsequent passes (where they may have different weights).
 struct RescoringPass {
   RescoringPass() : fid_summary(), density_prune(), beam_prune() {}
-  shared_ptr<ModelSet> models;
-  shared_ptr<IntersectionConfiguration> inter_conf;
+  boost::shared_ptr<ModelSet> models;
+  boost::shared_ptr<IntersectionConfiguration> inter_conf;
   vector<const FeatureFunction*> ffs;
-  shared_ptr<vector<weight_t> > weight_vector;
+  boost::shared_ptr<vector<weight_t> > weight_vector;
   int fid_summary;            // 0 == no summary feature
   double density_prune;       // 0 == don't density prune
   double beam_prune;          // 0 == don't beam prune
@@ -293,15 +292,15 @@ struct DecoderImpl {
   po::variables_map& conf;
   OracleBleu oracle;
   string formalism;
-  shared_ptr<Translator> translator;
-  shared_ptr<vector<weight_t> > init_weights; // weights used with initial parse
-  vector<shared_ptr<FeatureFunction> > pffs;
+  boost::shared_ptr<Translator> translator;
+  boost::shared_ptr<vector<weight_t> > init_weights; // weights used with initial parse
+  vector<boost::shared_ptr<FeatureFunction> > pffs;
 #ifdef FSA_RESCORING
   CFGOptions cfg_options;
-  vector<shared_ptr<FsaFeatureFunction> > fsa_ffs;
+  vector<boost::shared_ptr<FsaFeatureFunction> > fsa_ffs;
   vector<string> fsa_names;
 #endif
-  shared_ptr<RandomNumberGenerator<boost::mt19937> > rng;
+  boost::shared_ptr<RandomNumberGenerator<boost::mt19937> > rng;
   int sample_max_trans;
   bool aligner_mode;
   bool graphviz; 
@@ -310,7 +309,7 @@ struct DecoderImpl {
   bool kbest;
   bool unique_kbest;
   bool get_oracle_forest;
-  shared_ptr<WriteFile> extract_file;
+  boost::shared_ptr<WriteFile> extract_file;
   int combine_size;
   int sent_id;
   SparseVector<prob_t> acc_vec;  // accumulate gradient
@@ -622,7 +621,7 @@ DecoderImpl::DecoderImpl(po::variables_map& conf, int argc, char** argv, istream
   }
 
   // set up weight vectors since later phases may reuse weights from earlier phases
-  shared_ptr<vector<weight_t> > prev_weights = init_weights;
+  boost::shared_ptr<vector<weight_t> > prev_weights = init_weights;
   for (int pass = 0; pass < rescoring_passes.size(); ++pass) {
     RescoringPass& rp = rescoring_passes[pass];
     if (!rp.weight_vector) {
diff --git a/decoder/earley_composer.cc b/decoder/earley_composer.cc
index b7af801a..385baf8b 100644
--- a/decoder/earley_composer.cc
+++ b/decoder/earley_composer.cc
@@ -16,8 +16,6 @@
 #include "tdict.h"
 #include "hg.h"
 
-using boost::shared_ptr;
-namespace po = boost::program_options;
 using namespace std;
 using namespace std::tr1;
 
@@ -111,7 +109,7 @@ struct Edge {
   const Edge* const active_parent;    // back pointer, NULL for PREDICT items
   const Edge* const passive_parent;   // back pointer, NULL for SCAN and PREDICT items
   const TargetPhraseSet* const tps;   // translations
-  shared_ptr<SparseVector<double> > features; // features from CFG rule
+  boost::shared_ptr<SparseVector<double> > features; // features from CFG rule
 
   bool IsPassive() const {
     // when a rule is completed, this value will be set
diff --git a/decoder/phrasetable_fst.cc b/decoder/phrasetable_fst.cc
index f421e941..b3bec86b 100644
--- a/decoder/phrasetable_fst.cc
+++ b/decoder/phrasetable_fst.cc
@@ -9,7 +9,6 @@
 #include "filelib.h"
 #include "tdict.h"
 
-using boost::shared_ptr;
 using namespace std;
 
 TargetPhraseSet::~TargetPhraseSet() {}
@@ -46,7 +45,7 @@ class TextFSTNode : public FSTNode {
   void ClearPassThroughTranslations();
  private:
   vector<WordID> passthroughs;
-  shared_ptr<TargetPhraseSet> data;
+  boost::shared_ptr<TargetPhraseSet> data;
   map<WordID, TextFSTNode> ptr;
 };
 
diff --git a/dpmert/ces.cc b/dpmert/ces.cc
index a85454da..c6cb1cdf 100644
--- a/dpmert/ces.cc
+++ b/dpmert/ces.cc
@@ -11,7 +11,6 @@
 #include "error_surface.h"
 #include "ns.h"
 
-using boost::shared_ptr;
 using namespace std;
 
 const bool minimize_segments = true;    // if adjacent segments have equal scores, merge them
@@ -22,7 +21,7 @@ void ComputeErrorSurface(const SegmentEvaluator& ss,
                          const EvaluationMetric* metric,
                          const Hypergraph& hg) {
   vector<WordID> prev_trans;
-  const vector<shared_ptr<MERTPoint> >& ienv = ve.GetSortedSegs();
+  const vector<boost::shared_ptr<MERTPoint> >& ienv = ve.GetSortedSegs();
   env->resize(ienv.size());
   SufficientStats prev_score; // defaults to 0
   int j = 0;
diff --git a/dpmert/lo_test.cc b/dpmert/lo_test.cc
index d9b909b8..5d90aabb 100644
--- a/dpmert/lo_test.cc
+++ b/dpmert/lo_test.cc
@@ -19,7 +19,6 @@
 #include "line_optimizer.h"
 
 using namespace std;
-using boost::shared_ptr;
 
 class OptTest : public testing::Test {
  protected:
@@ -44,12 +43,12 @@ TEST_F(OptTest, TestCheckNaN) {
 }
 
 TEST_F(OptTest,TestConvexHull) {
-  shared_ptr<MERTPoint> a1(new MERTPoint(-1, 0));
-  shared_ptr<MERTPoint> b1(new MERTPoint(1, 0));
-  shared_ptr<MERTPoint> a2(new MERTPoint(-1, 1));
-  shared_ptr<MERTPoint> b2(new MERTPoint(1, -1));
-  vector<shared_ptr<MERTPoint> > sa; sa.push_back(a1); sa.push_back(b1);
-  vector<shared_ptr<MERTPoint> > sb; sb.push_back(a2); sb.push_back(b2);
+  boost::shared_ptr<MERTPoint> a1(new MERTPoint(-1, 0));
+  boost::shared_ptr<MERTPoint> b1(new MERTPoint(1, 0));
+  boost::shared_ptr<MERTPoint> a2(new MERTPoint(-1, 1));
+  boost::shared_ptr<MERTPoint> b2(new MERTPoint(1, -1));
+  vector<boost::shared_ptr<MERTPoint> > sa; sa.push_back(a1); sa.push_back(b1);
+  vector<boost::shared_ptr<MERTPoint> > sb; sb.push_back(a2); sb.push_back(b2);
   ConvexHull a(sa);
   cerr << a << endl;
   ConvexHull b(sb);
diff --git a/dpmert/mert_geometry.cc b/dpmert/mert_geometry.cc
index 81b25af9..d6973658 100644
--- a/dpmert/mert_geometry.cc
+++ b/dpmert/mert_geometry.cc
@@ -4,13 +4,12 @@
 #include <limits>
 
 using namespace std;
-using boost::shared_ptr;
 
 ConvexHull::ConvexHull(int i) {
   if (i == 0) {
     // do nothing - <>
   } else if (i == 1) {
-    points.push_back(shared_ptr<MERTPoint>(new MERTPoint(0, 0, 0, shared_ptr<MERTPoint>(), shared_ptr<MERTPoint>())));
+    points.push_back(boost::shared_ptr<MERTPoint>(new MERTPoint(0, 0, 0, boost::shared_ptr<MERTPoint>(), boost::shared_ptr<MERTPoint>())));
     assert(this->IsMultiplicativeIdentity());
   } else {
     cerr << "Only can create ConvexHull semiring 0 and 1 with this constructor!\n";
@@ -27,7 +26,7 @@ const ConvexHull ConvexHullWeightFunction::operator()(const Hypergraph::Edge& e)
 
 ostream& operator<<(ostream& os, const ConvexHull& env) {
   os << '<';
-  const vector<shared_ptr<MERTPoint> >& points = env.GetSortedSegs();
+  const vector<boost::shared_ptr<MERTPoint> >& points = env.GetSortedSegs();
   for (int i = 0; i < points.size(); ++i)
     os << (i==0 ? "" : "|") << "x=" << points[i]->x << ",b=" << points[i]->b << ",m=" << points[i]->m << ",p1=" << points[i]->p1 << ",p2=" << points[i]->p2;
   return os << '>';
@@ -37,7 +36,7 @@ ostream& operator<<(ostream& os, const ConvexHull& env) {
 #ifdef ORIGINAL_MERT_IMPLEMENTATION
 
 struct SlopeCompare {
-  bool operator() (const shared_ptr<MERTPoint>& a, const shared_ptr<MERTPoint>& b) const {
+  bool operator() (const boost::shared_ptr<MERTPoint>& a, const boost::shared_ptr<MERTPoint>& b) const {
     return a->m < b->m;
   }
 };
@@ -93,7 +92,7 @@ const ConvexHull& ConvexHull::operator*=(const ConvexHull& other) {
   if (this->IsEdgeEnvelope()) {
 //    if (other.size() > 1)
 //      cerr << *this << " (TIMES) " << other << endl;
-    shared_ptr<MERTPoint> edge_parent = points[0];
+    boost::shared_ptr<MERTPoint> edge_parent = points[0];
     const double& edge_b = edge_parent->b;
     const double& edge_m = edge_parent->m;
     points.clear();
@@ -102,13 +101,13 @@ const ConvexHull& ConvexHull::operator*=(const ConvexHull& other) {
       const double m = p.m + edge_m;
       const double b = p.b + edge_b;
       const double& x = p.x;       // x's don't change with *
-      points.push_back(shared_ptr<MERTPoint>(new MERTPoint(x, m, b, edge_parent, other.points[i])));
+      points.push_back(boost::shared_ptr<MERTPoint>(new MERTPoint(x, m, b, edge_parent, other.points[i])));
       assert(points.back()->p1->edge);
     }
 //    if (other.size() > 1)
 //      cerr << " = " << *this << endl;
   } else {
-    vector<shared_ptr<MERTPoint> > new_points;
+    vector<boost::shared_ptr<MERTPoint> > new_points;
     int this_i = 0;
     int other_i = 0;
     const int this_size  = points.size();
@@ -124,7 +123,7 @@ const ConvexHull& ConvexHull::operator*=(const ConvexHull& other) {
       const double m = this_point.m + other_point.m;
       const double b = this_point.b + other_point.b;
  
-      new_points.push_back(shared_ptr<MERTPoint>(new MERTPoint(cur_x, m, b, points[this_i], other.points[other_i])));
+      new_points.push_back(boost::shared_ptr<MERTPoint>(new MERTPoint(cur_x, m, b, points[this_i], other.points[other_i])));
       int comp = 0;
       if (this_next_val < other_next_val) comp = -1; else
         if (this_next_val > other_next_val) comp = 1;
diff --git a/extools/extract.cc b/extools/extract.cc
index f6c121b4..49542fed 100644
--- a/extools/extract.cc
+++ b/extools/extract.cc
@@ -131,16 +131,16 @@ lookup_and_append(const map<K, V> &dict, const K &key, V &output)
 // phrases if there is more than one annotation.
 // TODO: support source annotation
 void Extract::AnnotatePhrasesWithCategoryTypes(const WordID default_cat,
-                                      const map< tuple<short,short,short,short>, vector<WordID> > &types,
+                                      const map< boost::tuple<short,short,short,short>, vector<WordID> > &types,
                                       vector<ParallelSpan>* phrases) {
   const int num_unannotated_phrases = phrases->size();
   // have to use num_unannotated_phrases since we may grow the vector
   for (int i = 0; i < num_unannotated_phrases; ++i) {
     ParallelSpan& phrase = (*phrases)[i];
     vector<WordID> cats;
-    lookup_and_append(types, make_tuple(phrase.i1, phrase.i2, phrase.j1, phrase.j2), cats);
-    lookup_and_append(types, make_tuple((short)-1, (short)-1, phrase.j1, phrase.j2), cats);
-    lookup_and_append(types, make_tuple(phrase.i1, phrase.i2, (short)-1, (short)-1), cats);
+    lookup_and_append(types, boost::make_tuple(phrase.i1, phrase.i2, phrase.j1, phrase.j2), cats);
+    lookup_and_append(types, boost::make_tuple((short)-1, (short)-1, phrase.j1, phrase.j2), cats);
+    lookup_and_append(types, boost::make_tuple(phrase.i1, phrase.i2, (short)-1, (short)-1), cats);
     if (cats.empty() && default_cat != 0) {
       cats = vector<WordID>(1, default_cat);
     }
diff --git a/extools/featurize_grammar.cc b/extools/featurize_grammar.cc
index ebae9fdc..78175202 100644
--- a/extools/featurize_grammar.cc
+++ b/extools/featurize_grammar.cc
@@ -136,8 +136,8 @@ class FERegistry {
  public:
   FERegistry() {}
   boost::shared_ptr<FeatureExtractor> Create(const std::string& ffname) const {
-    map<string, shared_ptr<FEFactoryBase> >::const_iterator it = reg_.find(ffname);
-    shared_ptr<FeatureExtractor> res;
+    map<string, boost::shared_ptr<FEFactoryBase> >::const_iterator it = reg_.find(ffname);
+    boost::shared_ptr<FeatureExtractor> res;
     if (it == reg_.end()) {
       cerr << "I don't know how to create feature " << ffname << endl;
     } else {
@@ -147,7 +147,7 @@ class FERegistry {
   }
   void DisplayList(ostream* out) const {
     bool first = true;
-    for (map<string, shared_ptr<FEFactoryBase> >::const_iterator it = reg_.begin();
+    for (map<string, boost::shared_ptr<FEFactoryBase> >::const_iterator it = reg_.begin();
         it != reg_.end(); ++it) {
       if (first) {first=false;} else {*out << ' ';}
       *out << it->first;
diff --git a/extools/sentence_pair.cc b/extools/sentence_pair.cc
index d5ebe48f..7d60715a 100644
--- a/extools/sentence_pair.cc
+++ b/extools/sentence_pair.cc
@@ -71,8 +71,7 @@ int AnnotatedParallelSentence::ReadAlignmentPoint(const char* buf,
     exit(1);
   }
   (*b) = 0;
-  //TODO: is this what is intended?  parses as A && B || C && D.
-  while(ch < end && (c == 0 && (!permit_col || (permit_col && buf[ch] != ':')) || c != 0 && buf[ch] != '-')) {
+  while((ch < end) && (c == 0 && (!permit_col || (permit_col && buf[ch] != ':')) || c != 0 && buf[ch] != '-')) {
     if ((buf[ch] < '0') || (buf[ch] > '9')) {
       cerr << "Alignment point badly formed 4: " << string(buf, start, end-start) << endl << buf << endl << buf[ch] << endl;
       exit(1);
@@ -151,7 +150,7 @@ void AnnotatedParallelSentence::ParseSpanLabel(const char* buf, int start, int e
     exit(1);
   }
   // cerr << a << " " << b << " " << string(buf,c,end-c) << endl;
-  span_types[make_tuple(a,b,c,d)].push_back(-TD::Convert(string(buf, ch, end-ch)));
+  span_types[boost::make_tuple(a,b,c,d)].push_back(-TD::Convert(string(buf, ch, end-ch)));
 }
 
 // INPUT FORMAT
diff --git a/gi/pf/align-tl.cc b/gi/pf/align-tl.cc
index cbe8c6c8..f6608f1d 100644
--- a/gi/pf/align-tl.cc
+++ b/gi/pf/align-tl.cc
@@ -58,7 +58,7 @@ void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   }
 }
 
-shared_ptr<MT19937> prng;
+boost::shared_ptr<MT19937> prng;
 
 struct LexicalAlignment {
   unsigned char src_index;
diff --git a/gi/pf/brat.cc b/gi/pf/brat.cc
index c2c52760..832f22cf 100644
--- a/gi/pf/brat.cc
+++ b/gi/pf/brat.cc
@@ -489,7 +489,7 @@ int main(int argc, char** argv) {
     cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
     return 1;
   }
-  shared_ptr<MT19937> prng;
+  boost::shared_ptr<MT19937> prng;
   if (conf.count("random_seed"))
     prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
   else
diff --git a/gi/pf/cfg_wfst_composer.cc b/gi/pf/cfg_wfst_composer.cc
index a31b5be8..20520c81 100644
--- a/gi/pf/cfg_wfst_composer.cc
+++ b/gi/pf/cfg_wfst_composer.cc
@@ -16,7 +16,6 @@
 #include "tdict.h"
 #include "hg.h"
 
-using boost::shared_ptr;
 namespace po = boost::program_options;
 using namespace std;
 using namespace std::tr1;
@@ -114,7 +113,7 @@ struct Edge {
   const Edge* const active_parent;    // back pointer, NULL for PREDICT items
   const Edge* const passive_parent;   // back pointer, NULL for SCAN and PREDICT items
   TRulePtr tps;   // translations
-  shared_ptr<SparseVector<double> > features; // features from CFG rule
+  boost::shared_ptr<SparseVector<double> > features; // features from CFG rule
 
   bool IsPassive() const {
     // when a rule is completed, this value will be set
diff --git a/gi/pf/condnaive.cc b/gi/pf/condnaive.cc
index 3ea88016..419731ac 100644
--- a/gi/pf/condnaive.cc
+++ b/gi/pf/condnaive.cc
@@ -55,7 +55,7 @@ void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   }
 }
 
-shared_ptr<MT19937> prng;
+boost::shared_ptr<MT19937> prng;
 
 struct ModelAndData {
   explicit ModelAndData(ConditionalParallelSegementationModel<PhraseConditionalBase>& m, const vector<vector<int> >& ce, const vector<vector<int> >& cf, const set<int>& ve, const set<int>& vf) :
diff --git a/gi/pf/dpnaive.cc b/gi/pf/dpnaive.cc
index 469dff5c..75ccad72 100644
--- a/gi/pf/dpnaive.cc
+++ b/gi/pf/dpnaive.cc
@@ -55,7 +55,7 @@ void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   }
 }
 
-shared_ptr<MT19937> prng;
+boost::shared_ptr<MT19937> prng;
 
 template <typename Base>
 struct ModelAndData {
diff --git a/gi/pf/itg.cc b/gi/pf/itg.cc
index a38fe672..29ec3860 100644
--- a/gi/pf/itg.cc
+++ b/gi/pf/itg.cc
@@ -231,7 +231,7 @@ int main(int argc, char** argv) {
     cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
     return 1;
   }
-  shared_ptr<MT19937> prng;
+  boost::shared_ptr<MT19937> prng;
   if (conf.count("random_seed"))
     prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
   else
diff --git a/gi/pf/learn_cfg.cc b/gi/pf/learn_cfg.cc
index ed1772bf..44eaa162 100644
--- a/gi/pf/learn_cfg.cc
+++ b/gi/pf/learn_cfg.cc
@@ -24,7 +24,7 @@ using namespace std;
 using namespace tr1;
 namespace po = boost::program_options;
 
-shared_ptr<MT19937> prng;
+boost::shared_ptr<MT19937> prng;
 vector<int> nt_vocab;
 vector<int> nt_id_to_index;
 static unsigned kMAX_RULE_SIZE = 0;
diff --git a/gi/pf/pfbrat.cc b/gi/pf/pfbrat.cc
index c2c52760..832f22cf 100644
--- a/gi/pf/pfbrat.cc
+++ b/gi/pf/pfbrat.cc
@@ -489,7 +489,7 @@ int main(int argc, char** argv) {
     cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
     return 1;
   }
-  shared_ptr<MT19937> prng;
+  boost::shared_ptr<MT19937> prng;
   if (conf.count("random_seed"))
     prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
   else
diff --git a/gi/pf/pfdist.cc b/gi/pf/pfdist.cc
index 3d578db2..a3e46064 100644
--- a/gi/pf/pfdist.cc
+++ b/gi/pf/pfdist.cc
@@ -23,7 +23,7 @@ using namespace std;
 using namespace tr1;
 namespace po = boost::program_options;
 
-shared_ptr<MT19937> prng;
+boost::shared_ptr<MT19937> prng;
 
 void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   po::options_description opts("Configuration options");
diff --git a/gi/pf/pfnaive.cc b/gi/pf/pfnaive.cc
index e1a53f5c..958ec4e2 100644
--- a/gi/pf/pfnaive.cc
+++ b/gi/pf/pfnaive.cc
@@ -25,7 +25,7 @@ using namespace std;
 using namespace tr1;
 namespace po = boost::program_options;
 
-shared_ptr<MT19937> prng;
+boost::shared_ptr<MT19937> prng;
 
 void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   po::options_description opts("Configuration options");
diff --git a/gi/pf/pyp_lm.cc b/gi/pf/pyp_lm.cc
index 91029688..e2b67e17 100644
--- a/gi/pf/pyp_lm.cc
+++ b/gi/pf/pyp_lm.cc
@@ -25,7 +25,7 @@ using namespace std;
 using namespace tr1;
 namespace po = boost::program_options;
 
-shared_ptr<MT19937> prng;
+boost::shared_ptr<MT19937> prng;
 
 void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   po::options_description opts("Configuration options");
diff --git a/mira/kbest_mira.cc b/mira/kbest_mira.cc
index 904eba74..dc0200d6 100644
--- a/mira/kbest_mira.cc
+++ b/mira/kbest_mira.cc
@@ -3,10 +3,10 @@
 #include <vector>
 #include <cassert>
 #include <cmath>
+#include <tr1/memory>
 
 #include "config.h"
 
-#include <boost/shared_ptr.hpp>
 #include <boost/program_options.hpp>
 #include <boost/program_options/variables_map.hpp>
 
@@ -27,11 +27,10 @@
 #include "sampler.h"
 
 using namespace std;
-using boost::shared_ptr;
 namespace po = boost::program_options;
 
 bool invert_score;
-boost::shared_ptr<MT19937> rng;
+std::tr1::shared_ptr<MT19937> rng;
 
 void RandomPermutation(int len, vector<int>* p_ids) {
   vector<int>& ids = *p_ids;
@@ -89,15 +88,15 @@ struct HypothesisInfo {
 };
 
 struct GoodBadOracle {
-  shared_ptr<HypothesisInfo> good;
-  shared_ptr<HypothesisInfo> bad;
+  std::tr1::shared_ptr<HypothesisInfo> good;
+  std::tr1::shared_ptr<HypothesisInfo> bad;
 };
 
 struct TrainingObserver : public DecoderObserver {
   TrainingObserver(const int k, const DocScorer& d, bool sf, vector<GoodBadOracle>* o) : ds(d), oracles(*o), kbest_size(k), sample_forest(sf) {}
   const DocScorer& ds;
   vector<GoodBadOracle>& oracles;
-  shared_ptr<HypothesisInfo> cur_best;
+  std::tr1::shared_ptr<HypothesisInfo> cur_best;
   const int kbest_size;
   const bool sample_forest;
 
@@ -109,16 +108,16 @@ struct TrainingObserver : public DecoderObserver {
     UpdateOracles(smeta.GetSentenceID(), *hg);
   }
 
-  shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score) {
-    shared_ptr<HypothesisInfo> h(new HypothesisInfo);
+  std::tr1::shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score) {
+    std::tr1::shared_ptr<HypothesisInfo> h(new HypothesisInfo);
     h->features = feats;
     h->mt_metric = score;
     return h;
   }
 
   void UpdateOracles(int sent_id, const Hypergraph& forest) {
-    shared_ptr<HypothesisInfo>& cur_good = oracles[sent_id].good;
-    shared_ptr<HypothesisInfo>& cur_bad = oracles[sent_id].bad;
+    std::tr1::shared_ptr<HypothesisInfo>& cur_good = oracles[sent_id].good;
+    std::tr1::shared_ptr<HypothesisInfo>& cur_bad = oracles[sent_id].bad;
     cur_bad.reset();  // TODO get rid of??
 
     if (sample_forest) {
diff --git a/mteval/ns.cc b/mteval/ns.cc
index 788f809a..8d354677 100644
--- a/mteval/ns.cc
+++ b/mteval/ns.cc
@@ -14,7 +14,6 @@
 #include "stringlib.h"
 
 using namespace std;
-using boost::shared_ptr;
 
 map<string, EvaluationMetric*> EvaluationMetric::instances_;
 
@@ -35,8 +34,8 @@ struct DefaultSegmentEvaluator : public SegmentEvaluator {
   const EvaluationMetric* em_;
 };
 
-shared_ptr<SegmentEvaluator> EvaluationMetric::CreateSegmentEvaluator(const vector<vector<WordID> >& refs) const {
-  return shared_ptr<SegmentEvaluator>(new DefaultSegmentEvaluator(refs, this));
+boost::shared_ptr<SegmentEvaluator> EvaluationMetric::CreateSegmentEvaluator(const vector<vector<WordID> >& refs) const {
+  return boost::shared_ptr<SegmentEvaluator>(new DefaultSegmentEvaluator(refs, this));
 }
 
 #define MAX_SS_VECTOR_SIZE 50
@@ -184,8 +183,8 @@ template <unsigned int N = 4u, BleuType BrevityType = IBM>
 struct BleuMetric : public EvaluationMetric {
   BleuMetric() : EvaluationMetric(BrevityType == IBM ? "IBM_BLEU" : (BrevityType == Koehn ? "KOEHN_BLEU" : "NIST_BLEU")) {}
   unsigned SufficientStatisticsVectorSize() const { return N*2 + 2; }
-  shared_ptr<SegmentEvaluator> CreateSegmentEvaluator(const vector<vector<WordID> >& refs) const {
-    return shared_ptr<SegmentEvaluator>(new BleuSegmentEvaluator<N,BrevityType>(refs, this));
+  boost::shared_ptr<SegmentEvaluator> CreateSegmentEvaluator(const vector<vector<WordID> >& refs) const {
+    return boost::shared_ptr<SegmentEvaluator>(new BleuSegmentEvaluator<N,BrevityType>(refs, this));
   }
   float ComputeBreakdown(const SufficientStats& stats, float* bp, vector<float>* out) const {
     if (out) { out->clear(); }
diff --git a/phrasinator/gibbs_train_plm.cc b/phrasinator/gibbs_train_plm.cc
index 3b99e1b6..86fd7865 100644
--- a/phrasinator/gibbs_train_plm.cc
+++ b/phrasinator/gibbs_train_plm.cc
@@ -269,7 +269,7 @@ struct UniphraseLM {
 int main(int argc, char** argv) {
   po::variables_map conf;
   InitCommandLine(argc, argv, &conf);
-  shared_ptr<MT19937> prng;
+  boost::shared_ptr<MT19937> prng;
   if (conf.count("random_seed"))
     prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
   else
diff --git a/phrasinator/gibbs_train_plm.notables.cc b/phrasinator/gibbs_train_plm.notables.cc
index 4b431b90..9dca9e8d 100644
--- a/phrasinator/gibbs_train_plm.notables.cc
+++ b/phrasinator/gibbs_train_plm.notables.cc
@@ -293,7 +293,7 @@ struct UniphraseLM {
 int main(int argc, char** argv) {
   po::variables_map conf;
   InitCommandLine(argc, argv, &conf);
-  shared_ptr<MT19937> prng;
+  boost::shared_ptr<MT19937> prng;
   if (conf.count("random_seed"))
     prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
   else
diff --git a/training/mpi_batch_optimize.cc b/training/mpi_batch_optimize.cc
index 046e921c..9f12dba9 100644
--- a/training/mpi_batch_optimize.cc
+++ b/training/mpi_batch_optimize.cc
@@ -29,7 +29,6 @@ namespace mpi = boost::mpi;
 #include "sparse_vector.h"
 
 using namespace std;
-using boost::shared_ptr;
 namespace po = boost::program_options;
 
 bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
@@ -270,7 +269,7 @@ int main(int argc, char** argv) {
     }
     Weights::InitFromFile(conf["means"].as<string>(), &means);
   }
-  shared_ptr<BatchOptimizer> o;
+  boost::shared_ptr<BatchOptimizer> o;
   if (rank == 0) {
     const string omethod = conf["optimization_method"].as<string>();
     if (omethod == "rprop")
diff --git a/training/mr_optimize_reduce.cc b/training/mr_optimize_reduce.cc
index 15e28fa1..461e6b5f 100644
--- a/training/mr_optimize_reduce.cc
+++ b/training/mr_optimize_reduce.cc
@@ -15,7 +15,6 @@
 #include "sparse_vector.h"
 
 using namespace std;
-using boost::shared_ptr;
 namespace po = boost::program_options;
 
 void SanityCheck(const vector<double>& w) {
@@ -102,7 +101,7 @@ int main(int argc, char** argv) {
     }
     Weights::InitFromFile(conf["means"].as<string>(), &means);
   }
-  shared_ptr<BatchOptimizer> o;
+  boost::shared_ptr<BatchOptimizer> o;
   const string omethod = conf["optimization_method"].as<string>();
   if (omethod == "rprop")
     o.reset(new RPropOptimizer(num_feats));  // TODO add configuration
diff --git a/training/optimize_test.cc b/training/optimize_test.cc
index fe7ca70f..bff2ca03 100644
--- a/training/optimize_test.cc
+++ b/training/optimize_test.cc
@@ -102,7 +102,7 @@ void TestOnline() {
   size_t N = 20;
   double C = 1.0;
   double eta0 = 0.2;
-  shared_ptr<LearningRateSchedule> r(new ExponentialDecayLearningRate(N, eta0, 0.85));
+  std::tr1::shared_ptr<LearningRateSchedule> r(new ExponentialDecayLearningRate(N, eta0, 0.85));
   //shared_ptr<LearningRateSchedule> r(new StandardLearningRate(N, eta0));
   CumulativeL1OnlineOptimizer opt(r, N, C, std::vector<int>());
   assert(r->eta(10) < r->eta(1));
diff --git a/utils/atools.cc b/utils/atools.cc
index c0a91731..ba56dd6c 100644
--- a/utils/atools.cc
+++ b/utils/atools.cc
@@ -12,7 +12,6 @@
 
 namespace po = boost::program_options;
 using namespace std;
-using boost::shared_ptr;
 
 struct Command {
   virtual ~Command() {}
@@ -348,10 +347,10 @@ int main(int argc, char **argv) {
       }
     }
     if (line1.empty() && !*in1) break;
-    shared_ptr<Array2D<bool> > out(new Array2D<bool>);
-    shared_ptr<Array2D<bool> > a1 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line1);
+    boost::shared_ptr<Array2D<bool> > out(new Array2D<bool>);
+    boost::shared_ptr<Array2D<bool> > a1 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line1);
     if (in2) {
-      shared_ptr<Array2D<bool> > a2 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line2);
+      boost::shared_ptr<Array2D<bool> > a2 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line2);
       cmd.Apply(*a1, *a2, out.get());
     } else {
       Array2D<bool> dummy;