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, 53 insertions, 0 deletions

diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
new file mode 100644
index 000000000000..5baee4d8ebc0
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch
@@ -0,0 +1,16 @@
+ core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
+index 4a6c2e6..8cc9a42 100644
+--- a/core/include/seqan/index/index_qgram_openaddressing.h
++++ b/core/include/seqan/index/index_qgram_openaddressing.h
+@@ -35,6 +35,8 @@
+ #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ 
++#include <smmintrin.h>
++
+ namespace SEQAN_NAMESPACE_MAIN
+ {
+ 
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
new file mode 100644
index 000000000000..0f438ff07bce
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
@@ -0,0 +1,22 @@
+ util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
+index bcba2c0..d53cd01 100644
+--- a/util/cmake/SeqAnBuildSystem.cmake
++++ b/util/cmake/SeqAnBuildSystem.cmake
+@@ -144,10 +144,10 @@ macro (seqan_register_apps)
+     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
+ 
+     # enable static linkage for seqan apps
+-    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
+-      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+-    endif ()
++#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
++#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++#    endif ()
+ 
+     # Get all direct entries of the current source directory into ENTRIES.
+     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
new file mode 100644
index 000000000000..de14e9d58b8e
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
@@ -0,0 +1,15 @@
+ include/seqan/stream/zipstream/zutil.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/seqan/stream/zipstream/zutil.h b/include/seqan/stream/zipstream/zutil.h
+index 2806344..f8b41e6 100644
+--- a/include/seqan/stream/zipstream/zutil.h
++++ b/include/seqan/stream/zipstream/zutil.h
+@@ -152,6 +152,7 @@ extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */
+ 
+          /* functions */
+ 
++#define OF(x) x
+ #ifdef HAVE_STRERROR
+    extern char *strerror OF((int));
+ #  define zstrerror(errnum) strerror(errnum)