sci-biology/vaal: [QA] Move the patch to a distfile

Closes: https://bugs.gentoo.org/620620

3 files changed, 6 insertions, 915 deletions

diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
index 8276750cfdc6..592353792452 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,2 +1,3 @@
-DIST VAAL_manual.doc 48128 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 WHIRLPOOL 3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175
-DIST vaal-46233.tar.gz 1148052 SHA256 a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 WHIRLPOOL e848bcd6b2dd0c0c52142a3d55acef6a98b816e37355d22386bf3a2fac21e1318a821a394ebd5851cd530aa9afb0d178debc3f74638ee0d0820209a0f432f59f
+DIST VAAL_manual.doc 48128 BLAKE2B cc31bcdfd4d6faa8c247a9d23a6254ac8a8f8f5de20f8d188c7ed57b9f8231920b4fc7e246394b1bb48ebf457a777d82e704b51b91feb6191e5da331e5765aa9 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171
+DIST vaal-46233.tar.gz 1148052 BLAKE2B c3fa8ebd722e41bfa1e821d988316900a07d502b6a6b2be394b7227f269ae60a47645b45b6616a782189dcef8a1ea341265e40f257d2ee3f005e8d023273e0b6 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321
+DIST vaal-46233_remove-namespace-std.patch.bz2 5879 BLAKE2B eb10f5cec8c65c12461346b151dc2c6d60a6f980cdfda78bd97bf0cc33451f808481763e5766b76a78d3d8ef6d5f2f8798bf7b8a7b605e0d32867fdaa9073e3a SHA512 4141094b68b4f9c643abf15d2c5e1486525a69b9d8762cd8034abd3e6f85726ed50d7f25edfcf88fc429ab90db288a583f14b2b5d8e6605cdbfab515f295979c
diff --git a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
deleted file mode 100644
index c3c3ec032481..000000000000
--- a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
+++ /dev/null
@@ -1,911 +0,0 @@
-Remove 'using namespace std' causing massive havoc with newly
-introduced std::align in GCC-5. Fix bug
-https://bugs.gentoo.org/show_bug.cgi?id=568438
-
---- vaal-46233/src/efasta/EfastaTools.cc
-+++ vaal-46233/src/efasta/EfastaTools.cc
-@@ -18,6 +18,8 @@
- #include "math/Functions.h"
- #include "math/Array.h"
- 
-+using std::set;
-+
- #define Err(message)                                      \
- {    cout << message << endl << "\nInvalid.\n" << endl;   \
-      TracebackThisProcess( );    }
---- vaal-46233/src/Equiv.cc
-+++ vaal-46233/src/Equiv.cc
-@@ -9,6 +9,8 @@
- #include "Equiv.h"
- #include "Vec.h"
- 
-+using std::swap;
-+
- bool equivalence_relation::equiv(int a, int b) const
- {    if ( a == b ) return true;
-      int c = a;
---- vaal-46233/src/FastaFilestream.cc
-+++ vaal-46233/src/FastaFilestream.cc
-@@ -13,6 +13,8 @@
- 
- #include <strstream>
- 
-+using std::string;
-+
- template <typename vecT, typename seqT, typename convT, typename verifT>
- FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename,
-                                                           FastaNameParser* name_parser )
---- vaal-46233/src/FastaFilestreamPreview.cc
-+++ vaal-46233/src/FastaFilestreamPreview.cc
-@@ -11,6 +11,8 @@
- 
- #include <algorithm>
- 
-+using std::streamoff;
-+
- FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream)
-   : max_sequence_size_(0), start_offset_(0)
- {
---- vaal-46233/src/FastaFilestreamPreview.h
-+++ vaal-46233/src/FastaFilestreamPreview.h
-@@ -12,6 +12,8 @@
- 
- #include "Vec.h"
- 
-+using std::streampos;
-+
- // FastaFilestreamPreview understands just enough about the fasta
- // format to be able to count the number of sequences in the specified
- // filestream and to know where each sequence starts in that filestream.
---- vaal-46233/src/Fastavector.cc
-+++ vaal-46233/src/Fastavector.cc
-@@ -14,6 +14,8 @@
- #include <istream>
- #include <string>
- 
-+using std::max;
-+
- // Split this into chunks, separated by gaps ('n'), and return each chunk as a
- // gapless fastavector.
- // TODO: generalize this into a templatized STL algorithm.
---- vaal-46233/src/Fastavector.h
-+++ vaal-46233/src/Fastavector.h
-@@ -24,6 +24,9 @@
- #include <iostream>
- #include <unistd.h>
- 
-+using std::string;
-+using std::istringstream;
-+
- typedef std::tuple<String, int, int> FastaRegion;
- 
- class fastaindex {
---- vaal-46233/src/FetchReads.cc
-+++ vaal-46233/src/FetchReads.cc
-@@ -36,6 +36,8 @@
- #include "Qualvector.h"
- #include "random/Random.h"
- 
-+using std::istringstream;
-+
- // Heuristic constants:
- 
- namespace
---- vaal-46233/src/feudal/BaseVec.cc
-+++ vaal-46233/src/feudal/BaseVec.cc
-@@ -21,6 +21,7 @@
- using std::ostream;
- using std::cout;
- using std::endl;
-+using std::max_element;
- 
- // Cap: in a given basevector, replace any sequence of N > n identical
- // bases by n of the same base.
---- vaal-46233/src/graph/Digraph.cc
-+++ vaal-46233/src/graph/Digraph.cc
-@@ -16,6 +16,8 @@
- #include "graph/Digraph.h"
- #include "math/Functions.h"
- 
-+using std::make_pair;
-+
- Bool digraph::HasEdge( int v, int w ) const {
-   return find( from_[v].begin(),  from_[v].end(), w ) != from_[v].end();
- }
---- vaal-46233/src/graph/DigraphTemplate.h
-+++ vaal-46233/src/graph/DigraphTemplate.h
-@@ -34,6 +34,8 @@
- #include "graph/Digraph.h"
- #include <cstddef>
- 
-+using std::make_pair;
-+
- template<class E> vec<int> digraphE<E>::EdgesConnectedTo( const vec<int>& v ) const
- {    vec<int> G = VerticesConnectedTo(v), e;
-      for ( int x = 0; x < G.isize( ); x++ )
---- vaal-46233/src/IndexedAlignmentPlusVector.cc
-+++ vaal-46233/src/IndexedAlignmentPlusVector.cc
-@@ -9,6 +9,8 @@
- #include "IndexedAlignmentPlusVector.h"
- #include "VecAlignmentPlus.h"
- 
-+using std::streamoff;
-+
- // These strings are at the head of the vector and index files for verification purposes.
- 
- const String VecAlignmentPlusHeaderIO::mStrVectorHeader( "alignment_plus vector V.2\n" );
---- vaal-46233/src/IndexedAlignmentPlusVector.h
-+++ vaal-46233/src/IndexedAlignmentPlusVector.h
-@@ -15,6 +15,7 @@
- 
- #include "Alignment.h"
- 
-+using std::streampos;
- 
- // This class encapsulates the header information for both vectors and indices.
- 
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc
-@@ -10,6 +10,7 @@
- #include "kmers/KmerParcels.h"
- #include "system/WorklistN.h"
- 
-+using std::fixed;
- 
- inline String Tag(String S = "KPs") { return Date() + " (" + S + "): "; } 
- 
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h
-@@ -6,6 +6,9 @@
- //   Institute is not responsible for its use, misuse, or functionality.     //
- ///////////////////////////////////////////////////////////////////////////////
- 
-+using std::hex;
-+using std::dec;
-+
- // ---------------------------------
- // NaifTimer
- // ---------------------------------
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h
-@@ -10,7 +10,7 @@
- #ifndef KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H
- #define KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H
- 
--
-+using std::map;
- 
- // --------------------------------------
- // MapOfCounters
---- vaal-46233/src/layout/ContigActualloc.h
-+++ vaal-46233/src/layout/ContigActualloc.h
-@@ -17,6 +17,8 @@
- #include "system/Crash.h"
- #include "Misc.h"
- 
-+using std::set;
-+using std::map;
- 
- //
- // Class contig_actualloc
---- vaal-46233/src/lookup/ImperfectLookup.h
-+++ vaal-46233/src/lookup/ImperfectLookup.h
-@@ -52,6 +52,8 @@
- #include "lookup/AlignCollector.h"
- #include "solid/Solid.h"
- 
-+using std::unique_ptr;
-+
- class TaskTimer;
- 
- 
-@@ -534,7 +536,7 @@
-       aligns.resize( nqueries );
-     }
- 
--    auto_ptr<TaskTimer> t1, t2;
-+    unique_ptr<TaskTimer> t1, t2;
- 
-     if ( m_instr_level & IO_TIMER != 0 ) t1.reset( new TaskTimer() );
-     if ( m_instr_level & CPU_TIMER != 0 ) t2.reset( new TaskTimer() );
---- vaal-46233/src/lookup/LookAlign.cc
-+++ vaal-46233/src/lookup/LookAlign.cc
-@@ -29,6 +29,8 @@
- #include "random/Random.h"
- #include "system/ParsedArgs.h"
- 
-+using std::istrstream;
-+
- String QUERY("QUERY");
- 
- void look_align::ResetFromAlign(const align & al, const basevector & b1,
---- vaal-46233/src/lookup/LookAlignFinder.h
-+++ vaal-46233/src/lookup/LookAlignFinder.h
-@@ -12,6 +12,8 @@
- #include "lookup/LookAlign.h"
- #include "Vec.h"
- 
-+using std::set;
-+
- /**
-    Class: LookAlignFinder
- 
---- vaal-46233/src/lookup/LookAlignSort.h
-+++ vaal-46233/src/lookup/LookAlignSort.h
-@@ -15,6 +15,8 @@
- 
- #include <functional>
- 
-+using std::set;
-+
- /// Read in look_aligns from file, sort, and load into vecs
- /// \param fname name of look_align text file
- /// \param aligns vector into which to put the alignments
---- vaal-46233/src/lookup/LookupTable.h
-+++ vaal-46233/src/lookup/LookupTable.h
-@@ -18,6 +18,8 @@
- 
- #include <set>
- 
-+using std::set;
-+
- typedef pair<unsigned int, unsigned int> LocSeq;
- 
- ///
---- vaal-46233/src/lookup/QueryLookupTableCore.cc
-+++ vaal-46233/src/lookup/QueryLookupTableCore.cc
-@@ -456,6 +456,9 @@
- #include "system/ParsedArgs.h"
- #include "system/file/FileReader.h"
- 
-+using std::istrstream;
-+using std::less_equal;
-+
- #define ABORT(MSG)                                 \
- {    out << MSG << "  Abort." << endl << endl;     \
-      exit(1);    }
---- vaal-46233/src/lookup/ShortQueryLookup.cc
-+++ vaal-46233/src/lookup/ShortQueryLookup.cc
-@@ -32,6 +32,8 @@
- #include "lookup/AlignCollector.h"
- #include "lookup/ImperfectLookup.h"
- 
-+using std::ios_base;
-+
- // Run an alignment processing chain: seqs -> look -> receiver -> aligns
- // That is, look turns seqs into hits, which receiver accepts
- // and turns into alignments which are passed to aligns.  The
---- vaal-46233/src/Map.h
-+++ vaal-46233/src/Map.h
-@@ -21,7 +21,7 @@
- #include <map>
- #include <ext/hash_map>
- using namespace __gnu_cxx;
--
-+using std::map;
- 
- ///Return true if k is a key in map m
- template<class Key, class Value, typename Cmp> 
---- vaal-46233/src/math/Array.h
-+++ vaal-46233/src/math/Array.h
-@@ -12,6 +12,9 @@
- #include "CoreTools.h"
- #include "Vec.h"
- 
-+using std::map;
-+using std::fill;
-+
- // ==============================================================================
- // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> >
- // The elements are uninitialized.
---- vaal-46233/src/math/Functions.cc
-+++ vaal-46233/src/math/Functions.cc
-@@ -10,8 +10,8 @@
- #include "STLExtensions.h"
- #include "math/Functions.h"
- 
--
--
-+using std::isfinite;
-+using std::make_pair;
- 
- /*  CombineNormalDistribution              Filipe Ribeiro 2009-06-22
-  *
---- vaal-46233/src/math/Functions.h
-+++ vaal-46233/src/math/Functions.h
-@@ -14,6 +14,10 @@
- #include <cmath>
- #include <numeric>
- 
-+using std::min;
-+using std::cerr;
-+using std::swap;
-+
- // ===========================================================================
- //
- // Min functions
---- vaal-46233/src/math/HoInterval.cc
-+++ vaal-46233/src/math/HoInterval.cc
-@@ -10,6 +10,8 @@
- #include "math/HoInterval.h"
- #include "STLExtensions.h"
- 
-+using std::make_pair;
-+
- bool ho_interval::Merge(const ho_interval & o) {
-   if (!Meets(*this,o)) return false;
-   *this = Span(*this, o);
---- vaal-46233/src/math/HoInterval.h
-+++ vaal-46233/src/math/HoInterval.h
-@@ -14,6 +14,8 @@
- #include "feudal/MasterVec.h"
- #include "feudal/SerfVec.h"
- 
-+using std::max;
-+
- /// Class: ho_interval
- /// A half-open interval [a, b).
- class ho_interval {
---- vaal-46233/src/PackAlign.h
-+++ vaal-46233/src/PackAlign.h
-@@ -133,6 +133,8 @@
- #include "pairwise_aligners/Mutmer.h"
- #include "feudal/BinaryStream.h"
- 
-+using std::make_pair;
-+
- const int Bits2  = 3, Bits3  = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, 
-   Bits16 = 65535;
- 
---- vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc
-+++ vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc
-@@ -19,6 +19,9 @@
- #include "pairwise_aligners/AlignFromMutmers.h"
- #include "pairwise_aligners/SmithWatBandedA.h"
- 
-+using std::map;
-+using std::set;
-+
- // If there's a perfect match of length at least perf but we produced no proper 
- // alignment, use banded Smith-Waterman to create one.
- 
---- vaal-46233/src/pairwise_aligners/MatchList.cc
-+++ vaal-46233/src/pairwise_aligners/MatchList.cc
-@@ -9,6 +9,8 @@
- 
- #include "pairwise_aligners/MatchList.h"
- 
-+using std::max;
-+
- bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const 
- {
-   const vec<Match>& sortedMatches = m_sortedMatches[id1];
---- vaal-46233/src/pairwise_aligners/SuffixTree.h
-+++ vaal-46233/src/pairwise_aligners/SuffixTree.h
-@@ -23,6 +23,8 @@
- #include <list>
- #include <string>
- 
-+using std::list;
-+
- /**
-  * Implementation of a suffix tree for basevectors.
-  * This is a data structure for exact (sub)string matching.
---- vaal-46233/src/paths/AlignHyperKmerPath.cc
-+++ vaal-46233/src/paths/AlignHyperKmerPath.cc
-@@ -23,6 +23,9 @@
- #include "paths/KmerBaseBroker.h"
- #include "paths/KmerPath.h"
- 
-+using std::ostringstream;
-+using std::set;
-+
- // Function: AlignHyperKmerPath
- //
- // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed
---- vaal-46233/src/paths/AlignSeqsToHyper.cc
-+++ vaal-46233/src/paths/AlignSeqsToHyper.cc
-@@ -26,6 +26,7 @@
- #include "paths/ReadsToPathsCoreX.h"
- #include "paths/SeqOnHyper.h"
- 
-+using std::multimap;
- 
- // Local class: simple_align
- //
---- vaal-46233/src/paths/HyperKmerPath.cc
-+++ vaal-46233/src/paths/HyperKmerPath.cc
-@@ -19,6 +19,8 @@
- #include "paths/HyperKmerPath.h"
- #include "paths/KmerBaseBroker.h"
- 
-+using std::ostrstream;
-+using std::ends;
- 
- void HyperKmerPath::ReduceLoops( )
- {    for ( int v = 0; v < N( ); v++ )
---- vaal-46233/src/paths/KmerBaseBroker.h
-+++ vaal-46233/src/paths/KmerBaseBroker.h
-@@ -20,6 +20,8 @@
- #include <algorithm>  // for set_union
- #include <map>
- 
-+using std::map;
-+
- /**
-    Class: KmerBaseBrokerTemplate
- 
---- vaal-46233/src/paths/KmerPath.h
-+++ vaal-46233/src/paths/KmerPath.h
-@@ -22,6 +22,8 @@
- #include "HashSimple.h"
- #include "graph/Digraph.h"
- 
-+using std::make_pair;
-+
- class KmerPathLoc;  // forward declaration
- 
- /**
---- vaal-46233/src/paths/KmerPathInterval.h
-+++ vaal-46233/src/paths/KmerPathInterval.h
-@@ -8,6 +8,8 @@
- #include "CommonSemanticTypes.h"
- #include "feudal/BinaryStreamTraits.h"
- 
-+using std::max;
-+
- // Portability note: endianness
- // The implementations here would need to be changed for big endian architectures.
- 
-@@ -285,6 +287,12 @@
-    Models <tagged read path interval>.
- */
- // TODO: potentially dangerous truncation of index by PathId, ReadId
-+template<class TAG>
-+void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 );
-+
-+template<class TAG>
-+void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 );
-+
- class tagged_rpint {
- 
-      public: /* PUBLIC METHODS */
-@@ -362,11 +370,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
-@@ -489,11 +497,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
-@@ -620,11 +628,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k );
---- vaal-46233/src/paths/ReadsToPathsCoreX.cc
-+++ vaal-46233/src/paths/ReadsToPathsCoreX.cc
-@@ -20,6 +20,8 @@
- #include "paths/MakeAlignsPathsParallelX.h"
- #include "paths/ReadsToPathsCoreX.h"
- 
-+using std::map;
-+
- static inline 
- String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } 
- 
---- vaal-46233/src/paths/SuperBaseVector.h
-+++ vaal-46233/src/paths/SuperBaseVector.h
-@@ -10,6 +10,8 @@
- #include <numeric>
- #include <functional>
- 
-+using std::mem_fun_ref;
-+
- /// A simple class which holds a series of basevectors with
- /// (possibly negative) gaps between them.  This is what a 
- /// KmerPath logically maps to in sequence space.  The function
---- vaal-46233/src/polymorphism/VAAL2.cc
-+++ vaal-46233/src/polymorphism/VAAL2.cc
-@@ -42,7 +42,7 @@
- #include "feudal/BinaryStream.h"
- #include "feudal/VirtualMasterVec.h"
- 
--using namespace std;
-+
- 
- // Trim reads so that they contain only kmers in the unipaths.
- 
---- vaal-46233/src/polymorphism/VAAL3.cc
-+++ vaal-46233/src/polymorphism/VAAL3.cc
-@@ -29,6 +29,8 @@
- #include "polymorphism/VAALTools.h"
- #include "solexa/SolexaTools.h"
- 
-+using std::ostringstream;
-+
- int main( int argc, char *argv[] )
- {
-      RunTime( );
---- vaal-46233/src/PrintAlignment.h
-+++ vaal-46233/src/PrintAlignment.h
-@@ -14,6 +14,8 @@
- #include "CoreTools.h"
- #include "Qualvector.h"
- 
-+using std::ostringstream;
-+
- void PrintBlanks( ostream& out, int n );
- 
- template<class BASEVEC>
---- vaal-46233/src/Qualvector.cc
-+++ vaal-46233/src/Qualvector.cc
-@@ -10,6 +10,8 @@
- #include "FastIfstream.h"
- #include "Qualvector.h"
- 
-+using std::istrstream;
-+
- /// \file
- /// \ingroup grp_quals
- /// \copydoc Qualvector.h
---- vaal-46233/src/SeqInterval.cc
-+++ vaal-46233/src/SeqInterval.cc
-@@ -9,6 +9,8 @@
- #include "SeqInterval.h"
- #include "Vec.h"
- 
-+using std::max;
-+using std::min;
- 
- /*
-  * seq_interval
---- vaal-46233/src/SeqInterval.h
-+++ vaal-46233/src/SeqInterval.h
-@@ -14,7 +14,9 @@
- #include <algorithm>
- #include <iostream>
- 
--using namespace std;
-+using std::binary_function;
-+using std::ostream;
-+using std::istream;
- 
- /*
-  * class seq_interval
---- vaal-46233/src/Set.h
-+++ vaal-46233/src/Set.h
-@@ -16,7 +16,7 @@
- #include <set>
- #include "CoreTools.h"
- 
--using namespace std;
-+using std::set;
- 
- template<class T> bool Member( const set<T>& the_set, const T& value )
- {    return the_set.find(value) != the_set.end( );    }  // Breaks cxx 
---- vaal-46233/src/ShortVector.h
-+++ vaal-46233/src/ShortVector.h
-@@ -14,6 +14,8 @@
- #include "system/Types.h"
- #include "feudal/BinaryStream.h"
- 
-+using std::uninitialized_fill_n;
-+
- // ================================================================================
- //
- // A shortvector holds a list of up to 255 things of any type T.  
---- vaal-46233/src/solexa/FourBase2.h
-+++ vaal-46233/src/solexa/FourBase2.h
-@@ -15,6 +15,10 @@
- #include "feudal/MasterVec.h"
- #include "feudal/SerfVec.h"
- 
-+using std::max_element;
-+using std::min_element;
-+using std::accumulate;
-+
- class four_base2 {
- 
- public:
---- vaal-46233/src/solexa/FourBase.cc
-+++ vaal-46233/src/solexa/FourBase.cc
-@@ -9,6 +9,9 @@
- 
- #include "solexa/FourBase.h"
- 
-+using std::string;
-+using std::istringstream;
-+
- int four_base::Call( ) const
- {
-     int result = 0;
---- vaal-46233/src/solexa/FourBase.h
-+++ vaal-46233/src/solexa/FourBase.h
-@@ -16,6 +16,8 @@
- #include "feudal/MasterVec.h"
- #include "feudal/SerfVec.h"
- 
-+using std::max;
-+
- /*
-    Class: four_base
- 
---- vaal-46233/src/solexa/SolexaMetrics.h
-+++ vaal-46233/src/solexa/SolexaMetrics.h
-@@ -42,6 +42,8 @@
- #include "CommonSemanticTypes.h"
- #include <map>
- 
-+using std::map;
-+
- /// Definition of general macros.
- 
- class solexa_metric_db {
---- vaal-46233/src/solexa/SolexaTools.cc
-+++ vaal-46233/src/solexa/SolexaTools.cc
-@@ -20,6 +20,8 @@
- #include "FastaFileset.h"
- #include "util/BaitMap.h"
- 
-+using std::ostringstream;
-+
- void SolexaPredictorParameters::SetFromFile(const String & fname) {
-   Ifstream(is, fname);
-   String params = Slurp(is);
---- vaal-46233/src/STLExtensions.h
-+++ vaal-46233/src/STLExtensions.h
-@@ -9,7 +9,7 @@
- #ifndef STLEXTENSIONS_H
- #define STLEXTENSIONS_H
- 
--using namespace std;
-+
- 
- #include <functional>
- #include <vector>
-@@ -21,6 +21,13 @@
- #include "feudal/BinaryStream.h"
- #include "system/StaticAssert.h"
- 
-+using std::binary_function;
-+using std::unary_function;
-+using std::pair;
-+using std::bitset;
-+using std::vector;
-+using std::ostream;
-+
- /// minimum<T> is a function object.  
- ///
- /// If f is an object of class minimum<T> and x and y are objects of
---- vaal-46233/src/system/ParsedArgs.cc
-+++ vaal-46233/src/system/ParsedArgs.cc
-@@ -26,6 +26,9 @@
- #include "system/HostName.h"
- #include "system/UseGDB.h"
- 
-+using std::istrstream;
-+using std::mem_fun_ref;
-+
- #ifndef FatalErr
-      #define FatalErr(message) { cout << message << endl << endl; exit(-1); }
- #endif
---- vaal-46233/src/system/ParsedArgs.h
-+++ vaal-46233/src/system/ParsedArgs.h
-@@ -97,6 +97,8 @@
- #include "TokenizeString.h"
- #include "ParseSet.h"
- 
-+using std::stringstream;
-+
- class parsed_arg_help {
- 
-  public:
---- vaal-46233/src/system/ProcBuf.cc
-+++ vaal-46233/src/system/ProcBuf.cc
-@@ -15,6 +15,8 @@
- #include <sys/wait.h>
- #include <unistd.h>
- 
-+using std::ios_base;
-+
- namespace
- {
- size_t const BUFFER_SIZE = 8192;
---- vaal-46233/src/system/RunTime.cc
-+++ vaal-46233/src/system/RunTime.cc
-@@ -41,6 +41,10 @@
-      #include <unwind.h>
- #endif
- 
-+using std::strstream;
-+using std::hex;
-+using std::setw;
-+
- /// ===========================================================================
- ///
- /// ReturnAddress(i), where 0 <= i <= 100: get the return address.  The
---- vaal-46233/src/system/RunTime.h
-+++ vaal-46233/src/system/RunTime.h
-@@ -14,6 +14,8 @@
- #include "system/Exit.h"
- #include "system/Types.h"
- 
-+using std::ostream;
-+
- typedef void ArachneSignalHandler(int, siginfo_t*, void*);
- 
- void arachne_signal_handler( int signal_number, siginfo_t* info, void* context,
---- vaal-46233/src/system/System.cc
-+++ vaal-46233/src/system/System.cc
-@@ -35,6 +35,11 @@
- 
- #include <dirent.h>
- 
-+using std::istringstream;
-+using std::istream_iterator;
-+using std::ostrstream;
-+using std::ends;
-+
- int SystemInternal( String command, const char *shell )
- {
-   flush(cout);
---- vaal-46233/src/system/System.h
-+++ vaal-46233/src/system/System.h
-@@ -21,6 +21,17 @@
- #include "system/Exit.h"
- #include "system/file/TempFile.h"
- 
-+using std::vector;
-+using std::ostream;
-+using std::ofstream;
-+using std::cout;
-+using std::flush;
-+using std::endl;
-+using std::istream;
-+using std::ifstream;
-+using std::ios;
-+using std::setprecision;
-+
- #ifndef InputErr
-      #define InputErr(message)                                               \
-      {    cout << "\nFatal error at " << Date( ) << ": " << message << endl; \
---- vaal-46233/src/system/TraceVal.h
-+++ vaal-46233/src/system/TraceVal.h
-@@ -24,6 +24,9 @@
- #include "system/Types.h"
- #include "system/Assert.h"
- 
-+using std::cout;
-+using std::endl;
-+
- // Macros: Tracing macros
- //   TRACEVAL_ON - undefine if you're not doing tracing
- //   TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles
---- vaal-46233/src/system/Types.h
-+++ vaal-46233/src/system/Types.h
-@@ -14,7 +14,7 @@
- #include <cstdlib>
- #include <netinet/in.h>
- 
--using namespace std;
-+
- 
- // This assumes that all suns run Solaris...
- #if __sun == 1
---- vaal-46233/src/util/BaitMap.cc
-+++ vaal-46233/src/util/BaitMap.cc
-@@ -236,7 +236,7 @@
- bool BaitMap::write(String file_name)
- {
-     std::ofstream out(file_name.c_str());
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     for (unsigned int i = 0; i < this->size(); i++)
-     {
-@@ -250,7 +250,7 @@
-     }
- 
-     out.close();
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     return true;
- }
-@@ -260,7 +260,7 @@
- bool BaitMap::write_names(String file_name)
- {
-     std::ofstream out(file_name.c_str());
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     for (unsigned int i = 0; i < this->size(); i++)
-     {
-@@ -268,7 +268,7 @@
-     }
- 
-     out.close();
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     return true;
- }
---- vaal-46233/src/util/BaitMap.h
-+++ vaal-46233/src/util/BaitMap.h
-@@ -20,6 +20,8 @@
- 
- #include <map>
- 
-+using std::map;
-+
- class BaitMap
- {
- public:
---- vaal-46233/src/util/Qualb.cc
-+++ vaal-46233/src/util/Qualb.cc
-@@ -10,6 +10,8 @@
- #include "FastIfstream.h"
- #include "Qualvector.h"
- 
-+using std::istrstream;
-+
- int main( int argc, char *argv[] )
- {
-      RunTime( );
---- vaal-46233/src/Vec.h
-+++ vaal-46233/src/Vec.h
-@@ -48,6 +48,14 @@
- #include "Compare.h"
- #include "system/file/FileReader.h"
- 
-+using std::initializer_list;
-+using std::numeric_limits;
-+using std::ostream_iterator;
-+using std::less;
-+using std::equal_to;
-+using std::setfill;
-+using std::setw;
-+
- /////////////////////////////////////////////////////////////////////////////
- //
- //  vec Class Declaration and Template Definitions
---- vaal-46233/src/VecUtilities.h
-+++ vaal-46233/src/VecUtilities.h
-@@ -37,6 +37,7 @@
- #include "Vec.h"
- #include <cstddef>
- 
-+using std::greater;
- 
- /////////////////////////////////////////////////////////////////////////////
- //
diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild b/sci-biology/vaal/vaal-46233-r2.ebuild
index 7185fc1c24df..85076f330579 100644
--- a/sci-biology/vaal/vaal-46233-r2.ebuild
+++ b/sci-biology/vaal/vaal-46233-r2.ebuild
@@ -9,7 +9,8 @@ DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms"
 HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
 SRC_URI="
 	ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
-	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
+	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc
+	https://dev.gentoo.org/~mgorny/dist/${P}_remove-namespace-std.patch.bz2"
 
 LICENSE="Whitehead-MIT"
 SLOT="0"
@@ -25,7 +26,7 @@ DEPEND="
 
 DOCS=( "${DISTDIR}/VAAL_manual.doc" )
 PATCHES=(
-	"${FILESDIR}/${P}_remove-namespace-std.patch"
+	"${WORKDIR}/${P}_remove-namespace-std.patch"
 )
 
 src_prepare() {