path: root/sci-biology/generecon/files/1.2.1-gcc4.patch

diff --git a/affected_unaffected_genotype_cluster_test.cc b/affected_unaffected_genotype_cluster_test.cc
index 646af06..4e5fbde 100644
--- a/affected_unaffected_genotype_cluster_test.cc
+++ b/affected_unaffected_genotype_cluster_test.cc
@@ -32,6 +32,7 @@
 # include "random_tree_builder.hh"
 #endif
 
+#include <cstring>
 
 void test_tree(const CoalescentTree &tree,
 	       const Haplotype &h0, const Haplotype &h1,
diff --git a/affected_unaffected_genotype_set_test.cc b/affected_unaffected_genotype_set_test.cc
index 07fa122..5f333f5 100644
--- a/affected_unaffected_genotype_set_test.cc
+++ b/affected_unaffected_genotype_set_test.cc
@@ -19,6 +19,8 @@
 # include "region.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/affected_unaffected_haplotype_cluster_test.cc b/affected_unaffected_haplotype_cluster_test.cc
index 145e05f..b5dddaa 100644
--- a/affected_unaffected_haplotype_cluster_test.cc
+++ b/affected_unaffected_haplotype_cluster_test.cc
@@ -32,6 +32,7 @@
 # include "random_tree_builder.hh"
 #endif
 
+#include <cstring>
 
 void test_tree(const CoalescentTree &tree,
 	       const Haplotype &h0, const Haplotype &h1,
diff --git a/affected_unaffected_haplotype_set_test.cc b/affected_unaffected_haplotype_set_test.cc
index fda6173..8489c54 100644
--- a/affected_unaffected_haplotype_set_test.cc
+++ b/affected_unaffected_haplotype_set_test.cc
@@ -19,6 +19,8 @@
 # include "region.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/au_random_tree_builder_test.cc b/au_random_tree_builder_test.cc
index a2d4daa..d6689e0 100644
--- a/au_random_tree_builder_test.cc
+++ b/au_random_tree_builder_test.cc
@@ -30,6 +30,7 @@
 # include "test_random.hh"
 #endif
 
+#include <cstring>
 
 void test_tree(const CoalescentTree *tree,
 	       const Haplotype &h0, const Haplotype &h1,
diff --git a/change_selector_test.cc b/change_selector_test.cc
index 5f655d1..9004bef 100644
--- a/change_selector_test.cc
+++ b/change_selector_test.cc
@@ -23,6 +23,8 @@
 # include "change.hh"
 #endif
 
+#include <cstring>
+
 // dummy class for testing
 struct DummyChange : public Change {
     DummyChange() : Change("Dummy change") {}
diff --git a/coalescent_tree.cc b/coalescent_tree.cc
index eb937e5..9e54a2b 100644
--- a/coalescent_tree.cc
+++ b/coalescent_tree.cc
@@ -7,6 +7,7 @@
 
 #include "coalescent_tree.hh"
 
+#include <algorithm>
 
 /** \file
  * \brief Implementation of the coalescent tree.
diff --git a/coalescent_tree_test.cc b/coalescent_tree_test.cc
index 20059e9..2971ead 100644
--- a/coalescent_tree_test.cc
+++ b/coalescent_tree_test.cc
@@ -30,6 +30,8 @@
 # define CMATH_INCLUDED
 #endif
 
+#include <cstring>
+
 namespace {
 
     CoalescentTree *test_tree(HaplotypePool &pool)
diff --git a/distance_matrix_test.cc b/distance_matrix_test.cc
index e2e8435..9d367ee 100644
--- a/distance_matrix_test.cc
+++ b/distance_matrix_test.cc
@@ -15,6 +15,8 @@
 # include "haplotype_pool.hh"
 #endif
 
+#include <cstring>
+
 namespace {
     int distance(const Haplotype &h1, const Haplotype &h2)
     {
diff --git a/distance_tree_builder_test.cc b/distance_tree_builder_test.cc
index e252c3e..3f589f4 100644
--- a/distance_tree_builder_test.cc
+++ b/distance_tree_builder_test.cc
@@ -15,6 +15,8 @@
 # include "test_random.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/filter_iterator_test.cc b/filter_iterator_test.cc
index bf5097b..e74a29f 100644
--- a/filter_iterator_test.cc
+++ b/filter_iterator_test.cc
@@ -21,6 +21,8 @@
 # define FUNCTIONAL_INCLUDED
 #endif
 
+#include <cstring>
+
 namespace {
   struct even : public std::unary_function<int,bool> {
     bool operator () (int i) const { return i % 2 == 0; }
diff --git a/genotype_pool_test.cc b/genotype_pool_test.cc
index e62a03f..9a2badb 100644
--- a/genotype_pool_test.cc
+++ b/genotype_pool_test.cc
@@ -22,6 +22,8 @@
 # include "genotype.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/genotype_test.cc b/genotype_test.cc
index 3d704e4..64b3343 100644
--- a/genotype_test.cc
+++ b/genotype_test.cc
@@ -22,6 +22,8 @@
 # include "haplotype.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/guile_sampler.cc b/guile_sampler.cc
index b0d19f1..ffbec86 100644
--- a/guile_sampler.cc
+++ b/guile_sampler.cc
@@ -26,6 +26,7 @@
 # define CASSERT_INCLUDED
 #endif
 
+#include <memory>
 
 /** \file
  * \brief Implementation of the guile sampler wrapper.
diff --git a/haplotype.cc b/haplotype.cc
index a38541f..7810642 100644
--- a/haplotype.cc
+++ b/haplotype.cc
@@ -12,6 +12,8 @@
 # define SSTREAM_INCLUDED
 #endif
 
+#include <algorithm>
+
 /** \file
  * \brief Implementation of haplotype functionality.
  */
diff --git a/haplotype_pool.cc b/haplotype_pool.cc
index ceef1b9..42c6125 100644
--- a/haplotype_pool.cc
+++ b/haplotype_pool.cc
@@ -7,6 +7,8 @@
 
 #include "haplotype_pool.hh"
 
+#include <algorithm>
+
 /** \file
  * \brief Implementation of haplotype pool functionality.
  */
diff --git a/haplotype_pool_test.cc b/haplotype_pool_test.cc
index a774809..4527d23 100644
--- a/haplotype_pool_test.cc
+++ b/haplotype_pool_test.cc
@@ -19,6 +19,8 @@
 # include "region.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/haplotype_test.cc b/haplotype_test.cc
index 134a601..b7f5b63 100644
--- a/haplotype_test.cc
+++ b/haplotype_test.cc
@@ -19,6 +19,8 @@
 # include "region.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/marker_test.cc b/marker_test.cc
index ff34d7c..317385d 100644
--- a/marker_test.cc
+++ b/marker_test.cc
@@ -13,6 +13,7 @@
 #include "testing.hh"
 
 #include <cmath>
+#include <cstring>
 
 int main(int argc, const char *argv[])
 {
diff --git a/markov_region_test.cc b/markov_region_test.cc
index 58e0278..db0f9ba 100644
--- a/markov_region_test.cc
+++ b/markov_region_test.cc
@@ -11,7 +11,7 @@
 
 #include "region.hh"
 #include "testing.hh"
-
+#include <cstring>
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/qtl_haplotype_pool_test.cc b/qtl_haplotype_pool_test.cc
index 72f763d..8c058af 100644
--- a/qtl_haplotype_pool_test.cc
+++ b/qtl_haplotype_pool_test.cc
@@ -19,6 +19,8 @@
 # include "region.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/random_set_test.cc b/random_set_test.cc
index 7eae435..b7a3451 100644
--- a/random_set_test.cc
+++ b/random_set_test.cc
@@ -15,6 +15,8 @@
 # include "test_random.hh"
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/random_tree_builder_test.cc b/random_tree_builder_test.cc
index e8c5957..7c95519 100644
--- a/random_tree_builder_test.cc
+++ b/random_tree_builder_test.cc
@@ -28,6 +28,7 @@
 # include "test_random.hh"
 #endif
 
+#include <cstring>
 
 void test_tree(const CoalescentTree *tree,
 	       const Haplotype &h0, const Haplotype &h1,
diff --git a/region.cc b/region.cc
index df22885..94bce6f 100644
--- a/region.cc
+++ b/region.cc
@@ -22,6 +22,8 @@
 # define CMATH_INCLUDED
 #endif
 
+#include <algorithm>
+
 
 /** \file
  * \brief Implementation of region functionality.
diff --git a/region_test.cc b/region_test.cc
index 25f6cf0..e21084f 100644
--- a/region_test.cc
+++ b/region_test.cc
@@ -11,6 +11,7 @@
 
 #include "region.hh"
 #include "testing.hh"
+#include <cstring>
 
 int main(int argc, const char *argv[])
 {
diff --git a/selection_if_test.cc b/selection_if_test.cc
index a9a6377..0fb8052 100644
--- a/selection_if_test.cc
+++ b/selection_if_test.cc
@@ -24,6 +24,8 @@
 # define VECTOR_INCLUDED
 #endif
 
+#include <cstring>
+
 namespace {
   struct even : public std::unary_function<int,bool> {
     bool operator () (int i) const { return i % 2 == 0; }
diff --git a/selection_test.cc b/selection_test.cc
index 3bf673a..579931c 100644
--- a/selection_test.cc
+++ b/selection_test.cc
@@ -28,6 +28,8 @@
 # define LIST_INCLUDED
 #endif
 
+#include <cstring>
+
 int main(int argc, const char *argv[])
 {
     HANDLE_TEST_OPTIONS;
diff --git a/testing.hh b/testing.hh
index fbdcd87..c86dbc6 100644
--- a/testing.hh
+++ b/testing.hh
@@ -23,6 +23,8 @@
 # define CSTDLIB_INCLUDED
 #endif
 
+#include <cstring>
+
 /// \brief Verboseness flag for running tests.
 ///
 /// If set, the test will report the failed tests, otherwise it will
diff --git a/tree_builder.hh b/tree_builder.hh
index 4b0ec01..c0bdc5a 100644
--- a/tree_builder.hh
+++ b/tree_builder.hh
@@ -34,6 +34,7 @@
 # include "meta_programming.hh"
 #endif
 
+#include <limits>
 
 /**
  * \brief Abstract class for tree builders.