proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 148 insertions, 0 deletions

diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
new file mode 100644
index 000000000000..9bbd267cf4c8
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
@@ -0,0 +1,56 @@
+http://bugs.gentoo.org/show_bug.cgi?id=305547
+
+--- config/m4/ax_lib_expat.m4
++++ config/m4/ax_lib_expat.m4
+@@ -96,6 +99,7 @@
+ 
+     EXPAT_CFLAGS=""
+     EXPAT_LDFLAGS=""
++    EXPAT_LIBS=""
+     EXPAT_VERSION=""
+ 
+     dnl
+@@ -105,7 +109,8 @@
+ 
+     if test -n "$expat_prefix"; then
+         expat_include_dir="$expat_prefix/include"
+-        expat_lib_flags="-L$expat_prefix/lib -lexpat"
++        expat_lib_flags="-L$expat_prefix/lib"
++        expat_libs="-lexpat"
+         run_expat_test="yes"
+     elif test "$expat_requested" = "yes"; then
+         if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then
+@@ -126,6 +131,8 @@
+         saved_LDFLAGS="$LDFLAGS"
+         LDFLAGS="$LDFLAGS $expat_lib_flags"
+ 
++        saved_LIBS="$LIBS"
++        LIBS="$LIBS $expat_libs"
+         dnl
+         dnl Check Expat headers
+         dnl
+@@ -171,7 +178,8 @@
+                     ]]
+                 )],
+                 [
+                 EXPAT_LDFLAGS="$expat_lib_flags"
++                EXPAT_LIBS="$expat_libs"
+                 expat_lib_found="yes"
+                 AC_MSG_RESULT([found])
+                 ],
+@@ -185,6 +193,7 @@
+ 
+         CPPFLAGS="$saved_CPPFLAGS"
+         LDFLAGS="$saved_LDFLAGS"
++        LIBS="$saved_LIBS"
+     fi
+ 
+     AC_MSG_CHECKING([for Expat XML Parser])
+@@ -194,6 +203,7 @@
+ 
+             AC_SUBST([EXPAT_CFLAGS])
+             AC_SUBST([EXPAT_LDFLAGS])
++            AC_SUBST([EXPAT_LIBS])
+ 
+             HAVE_EXPAT="yes"
+         else
diff --git a/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch
new file mode 100644
index 000000000000..27fb36467c8f
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch
@@ -0,0 +1,52 @@
+ config/m4/ax_boost_regex.m4          | 4 ++--
+ src/examples_programming/Makefile.am | 2 +-
+ src/examples_programming/Makefile.in | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 3c4a999..a3bb19b 100644
+--- a/config/m4/ax_boost_regex.m4
++++ b/config/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
+                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.{so,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/src/examples_programming/Makefile.am b/src/examples_programming/Makefile.am
+index d77daaf..09c9965 100644
+--- a/src/examples_programming/Makefile.am
++++ b/src/examples_programming/Makefile.am
+@@ -11,7 +11,7 @@ AM_LDFLAGS= -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L..
+ 
+ mira_101.C: 
+ mira_101_SOURCES= mira_101.C
+-mira_101_LDADD= -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK)
++mira_101_LDADD= -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system
+ 
+ read_101.C: 
+ read_101_SOURCES= read_101.C
+diff --git a/src/examples_programming/Makefile.in b/src/examples_programming/Makefile.in
+index 27e6515..7dae4c4 100644
+--- a/src/examples_programming/Makefile.in
++++ b/src/examples_programming/Makefile.in
+@@ -222,7 +222,7 @@ AM_CXXFLAGS = $(BOOST_CPPFLAGS)
+ INCLUDES = -I$(top_srcdir)/src $(all_includes)
+ AM_LDFLAGS = -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L../EdIt/ -L../caf/ -L../knn_abi373 -L../knn_alf $(BOOST_LDFLAGS)
+ mira_101_SOURCES = mira_101.C
+-mira_101_LDADD = -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK)
++mira_101_LDADD = -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system
+ read_101_SOURCES = read_101.C
+ read_101_LDADD = -lmirasupport -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lm -lz
+ readpool_101_SOURCES = readpool_101.C
diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
new file mode 100644
index 000000000000..427192294c81
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
@@ -0,0 +1,24 @@
+ config/m4/ax_boost_regex.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 1ac06af..5b7be93 100644
+--- a/config/m4/ax_boost_regex.m4
++++ b/config/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
+                 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-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch
new file mode 100644
index 000000000000..14feb0284c9f
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cout.patch
@@ -0,0 +1,16 @@
+ 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