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

3 files changed, 80 insertions, 0 deletions

diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt
new file mode 100644
index 000000000000..e7c53afdaf36
--- /dev/null
+++ b/sci-biology/fasttree/files/CMakeLists.txt
@@ -0,0 +1,30 @@
+cmake_minimum_required (VERSION 2.6)
+project(fasttree C)
+
+option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON)
+option(USE_DOUBLE "Use double precission" OFF)
+option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON)
+
+if(USE_OPENMP)
+	SET( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" )
+	SET( CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" )
+endif(USE_OPENMP)
+
+if(USE_DOUBLE)
+	SET( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DUSE_DOUBLE" )
+endif(USE_DOUBLE)
+
+if(NOT HAS_SSE3)
+	SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" )
+endif(NOT HAS_SSE3)
+
+
+add_executable(FastTree FastTree-${VERSION}.c)
+add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c)
+
+target_link_libraries(FastTree m)
+target_link_libraries(FastTreeUPGMA m)
+
+install (TARGETS FastTree FastTreeUPGMA DESTINATION bin)
+
+install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree)
diff --git a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch
new file mode 100644
index 000000000000..31dafdad46de
--- /dev/null
+++ b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch
@@ -0,0 +1,25 @@
+ FastTreeUPGMA-2.1.7.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c
+index af76cb1..4065f42 100644
+--- a/FastTreeUPGMA-2.1.7.c
++++ b/FastTreeUPGMA-2.1.7.c
+@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
+       break;
+   }
+   if(iArg < argc-1) {
+-    fprintf(stderr, usage);
++    fprintf(stderr, "%s", usage);
+     exit(1);
+   }
+ 
+@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
+       assert(first >= 0);
+       /* Print the name, or the subtree of duplicate names */
+       if (nameNext[first] == -1) {
+-	fprintf(fp, names[uniqueFirst[node]]);
++	fprintf(fp, "%s", names[uniqueFirst[node]]);
+       } else {
+ 	fprintf(fp,"(%s:0.0",names[first]);
+ 	int iName = nameNext[first];
diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch
new file mode 100644
index 000000000000..15f5c174ec40
--- /dev/null
+++ b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch
@@ -0,0 +1,25 @@
+ FastTreeUPGMA-2.1.8.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c
+index af76cb1..4065f42 100644
+--- a/FastTreeUPGMA-2.1.8.c
++++ b/FastTreeUPGMA-2.1.8.c
+@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
+       break;
+   }
+   if(iArg < argc-1) {
+-    fprintf(stderr, usage);
++    fprintf(stderr, "%s", usage);
+     exit(1);
+   }
+ 
+@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
+       assert(first >= 0);
+       /* Print the name, or the subtree of duplicate names */
+       if (nameNext[first] == -1) {
+-	fprintf(fp, names[uniqueFirst[node]]);
++	fprintf(fp, "%s", names[uniqueFirst[node]]);
+       } else {
+ 	fprintf(fp,"(%s:0.0",names[first]);
+ 	int iName = nameNext[first];