reinit the tree, so we can have metadata

3 files changed, 63 insertions, 0 deletions

diff --git a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
new file mode 100644
index 000000000000..50f83c9021dc
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
@@ -0,0 +1,22 @@
+ax_boost_regex.m4 |    4 ++--
+1 file changed, 2 insertions(+), 2 deletions(-)
+
+--- mira-4.0.2/m4/ax_boost_regex.m4
++++ mira-4.0.2/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@
+                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 if test "x$link_regex" != "xyes"; then
+                 for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 fi
diff --git a/sci-biology/mira/files/mira-4.0.2-cmath.patch b/sci-biology/mira/files/mira-4.0.2-cmath.patch
new file mode 100644
index 000000000000..a4a020177af7
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cmath.patch
@@ -0,0 +1,14 @@
+--- mira-4.0.2/src/mira/ads.C
++++ mira-4.0.2/src/mira/ads.C
+@@ -31,10 +31,11 @@
+  * Routines for computing scores and some other classification number are
+  *  provided, too.
+  *
+  */
+ 
++#include <cmath>
+ 
+ #include "ads.H"
+ 
+ #include "errorhandling/errorhandling.H"
+ #include "util/dptools.H"
diff --git a/sci-biology/mira/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch
new file mode 100644
index 000000000000..78e7168cb49d
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cout.patch
@@ -0,0 +1,27 @@
+ src/progs/quirks.C | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/progs/quirks.C b/src/progs/quirks.C
+index 47e5ee8..060b6f3 100644
+--- a/src/progs/quirks.C
++++ b/src/progs/quirks.C
+@@ -25,6 +25,8 @@
+ 
+ #include <boost/filesystem.hpp>
+ 
++#include <iostream>
++
+ // make the "tcmalloc: large alloc" messages from TCMallom disappear
+ // by setting the reporting environment variable to a very large value
+ // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
+--- a/src/mira/parameters.C
++++ b/src/mira/parameters.C
+@@ -2222,7 +2222,7 @@
+     MIRANOTIFY(Notify::FATAL, "File not found: " << pfile);
+   }
+ 
+-  parse(fin, Pv, nullptr);
++  parse(fin, Pv, false);
+ 
+   fin.close();
+