path: root/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch

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;
 
 /////////////////////////////////////////////////////////////////////////////
 //