diff options
Diffstat (limited to 'sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch')
| -rw-r--r-- | sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch | 911 |
1 files changed, 0 insertions, 911 deletions
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; - - ///////////////////////////////////////////////////////////////////////////// - // |