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

1 files changed, 71 insertions, 0 deletions

diff --git a/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch b/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch
new file mode 100644
index 000000000000..ec620ebb35aa
--- /dev/null
+++ b/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch
@@ -0,0 +1,71 @@
+ libMems/CompactGappedAlignment.h | 36 ++++++++++++++++++------------------
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/libMems/CompactGappedAlignment.h b/libMems/CompactGappedAlignment.h
+index bf78477..942d4aa 100644
+--- a/libMems/CompactGappedAlignment.h
++++ b/libMems/CompactGappedAlignment.h
+@@ -13,7 +13,7 @@
+ #include "config.h"

+ #endif

+ 

+-#include "libGenome/gnDebug.h"
++#include "libGenome/gnDebug.h"

+ #include "libGenome/gnFilter.h"

+ #include "libGenome/gnSequence.h"

+ #include "libMems/SparseAbstractMatch.h"

+@@ -103,15 +103,15 @@ public:
+ 	/** Eliminates any columns that contain only gap characters */

+ 	void CondenseGapColumns();

+ 

+-	void swap( CompactGappedAlignment& other ){ swap(&other); }
+-
+-protected:
+-	// for use by derived classes in order to swap contents
+-	void swap( CompactGappedAlignment* other ){
+-		std::swap( align_matrix, other->align_matrix );
+-		std::swap( bcount, other->bcount );
+-		BaseType::swap( other );
+-	}
++	void swap( CompactGappedAlignment& other ){ swap(&other); }

++

++protected:

++	// for use by derived classes in order to swap contents

++	void swap( CompactGappedAlignment* other ){

++		std::swap( align_matrix, other->align_matrix );

++		std::swap( bcount, other->bcount );

++		BaseType::swap( other );

++	}

+ 

+ 	std::vector< bitset_t > align_matrix;		/**< aligned positions have true values, gaps are false */

+ 	std::vector< std::vector< size_t > > bcount;

+@@ -572,7 +572,7 @@ void CompactGappedAlignment<BaseType>::CropEnd(gnSeqI crop_amount){
+ 			this->SetStart(i, 0);

+ 		}

+ 	}

+-	SetAlignmentLength( this->AlignmentLength() - crop_amount );

++	this->SetAlignmentLength( this->AlignmentLength() - crop_amount );

+ 	this->create_bitcount();

+ 	if( !this->validate() )

+ 		std::cerr << "CropEnd error\n";

+@@ -806,13 +806,13 @@ void CompactGappedAlignment<BaseType>::CondenseGapColumns()
+ 

+ }

+ 

+-namespace std {
+-template<> inline
+-void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b )
+-{
+-	a.swap(b);
+-}
+-}
++namespace std {

++template<> inline

++void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b )

++{

++	a.swap(b);

++}

++}

+ 

+ 

+ #endif // __CompactGappedAlignment_h__