diff options
author | Justin Lecher <jlec@gentoo.org> | 2015-12-27 17:34:31 +0100 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2015-12-27 17:34:31 +0100 |
commit | a32dafa1efb3a3f3bb748ae86f39ffd4fc6928f3 (patch) | |
tree | f8924f84ecd8c8f474426b31986c098a798d91e2 | |
parent | media-radio/xlog: move patch for underlinking to src_prepare phase (diff) | |
parent | sci-biology/vaal: Remove old patches (diff) | |
download | gentoo-a32dafa1efb3a3f3bb748ae86f39ffd4fc6928f3.tar.gz gentoo-a32dafa1efb3a3f3bb748ae86f39ffd4fc6928f3.tar.bz2 gentoo-a32dafa1efb3a3f3bb748ae86f39ffd4fc6928f3.zip |
Merge branch 'SoapZaNet-bug-568438'
* SoapZaNet-bug-568438:
sci-biology/vaal: Remove old patches
sci-biology/vaal: Gentoo-Bug: 568438, fix global namespace std:: clash.
-rw-r--r-- | sci-biology/vaal/files/vaal-1.2-as-needed.patch | 22 | ||||
-rw-r--r-- | sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch | 39 | ||||
-rw-r--r-- | sci-biology/vaal/files/vaal-1.2-respect-flags.patch | 60 | ||||
-rw-r--r-- | sci-biology/vaal/files/vaal-1.6-gcc47.patch | 153 | ||||
-rw-r--r-- | sci-biology/vaal/files/vaal-1.6-respect-flags.patch | 12 | ||||
-rw-r--r-- | sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch | 911 | ||||
-rw-r--r-- | sci-biology/vaal/vaal-46233-r1.ebuild | 42 |
7 files changed, 953 insertions, 286 deletions
diff --git a/sci-biology/vaal/files/vaal-1.2-as-needed.patch b/sci-biology/vaal/files/vaal-1.2-as-needed.patch deleted file mode 100644 index 31649010dbe3..000000000000 --- a/sci-biology/vaal/files/vaal-1.2-as-needed.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- VAAL.orig/MakeDepend.cc 2008-12-18 17:05:48.000000000 +0100 -+++ VAAL/MakeDepend.cc 2010-02-14 13:42:23.734370178 +0100 -@@ -1195,9 +1195,6 @@ - } - } - mf << " -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; -- for ( set<string>::iterator dep_iter = lib_deps.begin(); -- dep_iter != lib_deps.end(); ++dep_iter ) -- mf << " " << "$(" << *dep_iter << "_LFLAGS)"; - for ( set<string>::iterator dep_iter = sharedlib_deps.begin(); - dep_iter != sharedlib_deps.end(); ++dep_iter ) { - // Extract the symbolic name of this library from its filename. -@@ -1208,6 +1205,9 @@ - mf << " -l" << sharedlib_name; - } - mf << " -l" << libname; -+ for ( set<string>::iterator dep_iter = lib_deps.begin(); -+ dep_iter != lib_deps.end(); ++dep_iter ) -+ mf << " " << "$(" << *dep_iter << "_LFLAGS)"; - mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n"; - } - } diff --git a/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch deleted file mode 100644 index c021fadb44b1..000000000000 --- a/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff -durr VAAL.orig/SortKmersImpl.h VAAL/SortKmersImpl.h ---- VAAL.orig/SortKmersImpl.h 2009-11-12 13:02:40.116993289 +0000 -+++ VAAL/SortKmersImpl.h 2009-11-12 13:04:59.416388534 +0000 -@@ -98,7 +98,7 @@ - { if ( reads[l].size( ) < KSPAN ) continue; - unsigned int N = reads[l].size( ) - KSPAN + 1; - if ( S + 2*N >= R.size( ) ) { -- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); -+ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); - if ( nn < R.size( ) ) FatalErr( "SortKmers<1>: Unsigned-int overflow (R=" << R.size( ) << ")" ); - R.resize(nn); - } -@@ -180,7 +180,7 @@ - } - if ( q == N ) break; - if ( S + 2*N >= R.size( ) ) { -- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); -+ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); - if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" ); - R.resize(nn); - } -@@ -207,7 +207,7 @@ - top += Min( N - top, (unsigned int) 10000 ); - - if ( S + 20000 >= R.size( ) || S + 2*N >= R.size( ) ) { -- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); -+ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); - if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" ); - R.resize(nn); - } -@@ -318,7 +318,7 @@ - - top += Min( N - top, 10000 ); - if ( S + 2*(top - q) >= R.size( ) ) { -- unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (S + 2*(top - q)) ); -+ unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (unsigned) (S + 2*(top - q)) ); - if ( nn < R.size( ) ) FatalErr( "SortKmers<100>: Unsigned-int overflow (R=" << R.size( ) << ")" ); - R.resize(nn); - } diff --git a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch deleted file mode 100644 index d3420556b608..000000000000 --- a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch +++ /dev/null @@ -1,60 +0,0 @@ ---- VAAL.orig/Makefile.in 2009-04-02 21:43:42.000000000 +0200 -+++ VAAL/Makefile.in 2010-02-14 14:20:26.222370302 +0100 -@@ -161,12 +161,16 @@ - COMPILER = @CC@ - CPLUSPLUS = @CXX@ - -+CFLAGS = @CFLAGS@ -+CXXFLAGS = @CXXFLAGS@ -+LDFLAGS = @LDFLAGS@ -+ - # QUIET=yes causes the compiler to be less verbose about warnings. - QUIET = no - - # DEBUG=yes forces out-of-date executables to be built with symbolic - # debugging information. Any other value is ignored. --DEBUG = yes -+DEBUG = no - - # OPTIM=<compiler optimization> forces user-defined optimizations to be used, - # rather than the compiler-specific default. -@@ -174,7 +178,7 @@ - # If OPTIM=none, then no optimization is used. - # If unset, defaults are used. - # -fno-exceptions --OPTIM = -+OPTIM = none - - # PROFILE=yes builds sampled-profiling (i.e. gprof) executables. Any other - # value is ignored. -@@ -317,6 +321,7 @@ - # Setup final compilation options: - - CPP_OPTIONS = \ -+ $(CXXFLAGS) \ - $(SYS_WARN) \ - $(SYS_OPT) \ - $(SYS_DEBUG) \ -@@ -328,6 +333,7 @@ - @INCLUDES@ - - LINK_OPTIONS = \ -+ $(LDFLAGS) \ - $(SYS_DEBUG) \ - $(SYS_LINK) \ - $(OMP_LINK) \ -@@ -406,12 +406,12 @@ - $(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc - - checkLock: $(SRC)/util/checkLock.cc -- $(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock -+ $(CPLUSPLUS) $(CXXFLAGS) $(SRC)/util/checkLock.cc $(LDFLAGS) -o $(BIN)/checkLock - - random/Random.o: random/Random.cc - @ mkdir -p $(OBJ)/${@D} - cp $(SRC)/random/Random.cc $(SRC)/random/Random.c -- $(CC) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o -+ $(CC) $(CFLAGS) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o - rm $(SRC)/random/Random.c - - MemTracker.o: MemTracker.cc diff --git a/sci-biology/vaal/files/vaal-1.6-gcc47.patch b/sci-biology/vaal/files/vaal-1.6-gcc47.patch deleted file mode 100644 index 0d80f08d3c21..000000000000 --- a/sci-biology/vaal/files/vaal-1.6-gcc47.patch +++ /dev/null @@ -1,153 +0,0 @@ -Fix building with gcc-4.7 - -https://bugs.gentoo.org/show_bug.cgi?id=423497 - -Patch written by Kacper Kowalik <xarthisius@gentoo.org> ---- a/src/feudal/MasterVec.h -+++ b/src/feudal/MasterVec.h -@@ -62,20 +62,20 @@ - /// This function is deprecated: Use reserve() instead. - /// The pool size argument is ignored, anyway. - MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity ) -- { reserve(capacity); return *this; } -+ { this->reserve(capacity); return *this; } - - /// This function is deprecated: Use clear().shrink_to_fit(). - MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; } - - /// This function is deprecated: Use push_back(). - MasterVec& push_back_external( T const& val ) -- { push_back(val); return *this; } -+ { this->push_back(val); return *this; } - - /// This function is deprecated: Use push_back(). - MasterVec& push_back_reserve( T const& val, - size_type growthIncr = 0, - float growthFact = 1.3f ) -- { push_back(val,growthFact,growthIncr); return *this; } -+ { this->push_back(val,growthFact,growthIncr); return *this; } - - /// This function is deprecated: Use append(). - MasterVec& Append( MasterVec const& that ) -@@ -83,7 +83,7 @@ - - /// This function is deprecated: Use append(). - MasterVec& Append( MasterVec const& that, size_type from, size_type to ) -- { append(that.begin(from),that.begin(to)); return *this; } -+ { this->append(that.begin(from),that.begin(to)); return *this; } - - MasterVec const& WriteAll( String const& fileName ) const - { return WriteRange(fileName,0UL,BaseT::size()); return *this; } -@@ -108,7 +108,7 @@ - { if ( !append ) BaseT::clear(); - FeudalFileReader rdr(fileName.c_str()); - size_type siz = rdr.getNElements(); -- reserve(BaseT::size()+siz); -+ this->reserve(BaseT::size()+siz); - preAlloc(rdr,0,siz); - for ( size_type iii = 0; iii < siz; ++iii ) - appendFromReader(rdr,iii); ---- a/src/feudal/FeudalControlBlock.cc -+++ b/src/feudal/FeudalControlBlock.cc -@@ -24,6 +24,7 @@ - #include <string.h> - #include <errno.h> - #include <iostream> -+#include <unistd.h> - - using std::cout; - using std::endl; ---- a/src/feudal/SerfVec.h -+++ b/src/feudal/SerfVec.h -@@ -83,9 +83,9 @@ - { AssertLe(pos,that.size()); - AssertLe(len,that.size()-pos); - if ( this != &that ) -- { assign(that.begin(pos),that.begin(pos+len)); } -+ { this->assign(that.begin(pos),that.begin(pos+len)); } - else -- { erase(BaseT::begin(),BaseT::begin(pos)); -+ { this->erase(BaseT::begin(),BaseT::begin(pos)); - BaseT::resize(len); } - return *this; } - ---- a/src/system/ProcBuf.cc -+++ b/src/system/ProcBuf.cc -@@ -195,12 +195,12 @@ - Assert(M_internal_put_buffer == NULL); - M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE]; - M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE; -- setp(M_internal_put_buffer, -+ this->setp(M_internal_put_buffer, - M_internal_put_buffer_end); - } else if (!flush()) - return traits_type::eof(); - if (!traits_type::eq_int_type(c, traits_type::eof())) -- return sputc(c); -+ return this->sputc(c); - else - return traits_type::not_eof(c); - } -@@ -240,7 +240,7 @@ - // (which is start of buffer) - std::copy_backward(this->eback(), this->egptr(), this->egptr()+1); - *(this->gptr()) = traits_type::to_char_type(c); -- setg(this->eback(), this->gptr(), this->egptr()+1); -+ this->setg(this->eback(), this->gptr(), this->egptr()+1); - return traits_type::not_eof(c); - } else - return traits_type::eof(); -@@ -269,7 +269,7 @@ - // doing wchars and we write an odd # of bytes? - return false; - } else { -- setp(this->pbase(), this->epptr()); -+ this->setp(this->pbase(), this->epptr()); - return true; - } - } -@@ -283,7 +283,7 @@ - Assert(M_internal_get_buffer == NULL); - M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE]; - M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE; -- setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end); -+ this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end); - } - // The "get" pointer should be at the end of the buffer - that's - // why we need to fill it. -@@ -318,7 +318,7 @@ - // - // reset the get pointers - // -- setg(M_internal_get_buffer, -+ this->setg(M_internal_get_buffer, - M_internal_get_buffer, - M_internal_get_buffer+numusable/sizeof(char_type)); - return true; ---- a/src/system/SysConf.cc -+++ b/src/system/SysConf.cc -@@ -19,6 +19,7 @@ - #include "system/SysConf.h" - #include "system/Exit.h" - #include <iostream> -+#include <unistd.h> - - namespace - { ---- a/src/Vec.h -+++ b/src/Vec.h -@@ -261,11 +261,11 @@ - - template <class U> - void append( const vec<U>& y ) -- { insert( this->end( ), y.begin( ), y.end( ) ); } -+ { this->insert( this->end( ), y.begin( ), y.end( ) ); } - - void append( const vec<T>& y, size_type i, size_type j ) { -- if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) ); -- else insert( this->end( ), y.begin( ) + i, y.begin( ) + j ); -+ if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) ); -+ else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j ); - } - - // appends values in y, but only those whose indices are in entries diff --git a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch deleted file mode 100644 index 152fb423e924..000000000000 --- a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac ---- vaal-33805.orig/configure.ac 2010-09-20 04:37:49.858059826 +0000 -+++ vaal-33805/configure.ac 2010-09-20 04:39:41.178059477 +0000 -@@ -14,7 +14,7 @@ - AC_OPENMP - AC_OPENMP_CEHCK - --CXXFLAGS=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ." -+CXXFLAGS+=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ." - - OS_RELEASE="`uname -r`" - AC_SUBST(CXXFLAGS) diff --git a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch new file mode 100644 index 000000000000..c3c3ec032481 --- /dev/null +++ b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch @@ -0,0 +1,911 @@ +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-r1.ebuild b/sci-biology/vaal/vaal-46233-r1.ebuild new file mode 100644 index 000000000000..20b3bf0de466 --- /dev/null +++ b/sci-biology/vaal/vaal-46233-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit autotools + +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/${P}.tar.gz + ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc" + +LICENSE="Whitehead-MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="openmp" + +DEPEND=">=dev-libs/boost-1.41.0-r3" +RDEPEND="${DEPEND}" + +DOCS=( "${DISTDIR}/VAAL_manual.doc" ) +PATCHES=( "${FILESDIR}/${P}_remove-namespace-std.patch" ) + +src_prepare() { + sed \ + -e '/COPYING/d' \ + -i src/Makefile.am || die + + sed \ + -e 's:-ggdb::g' \ + -e '/AC_OPENMP_CEHCK/d' \ + -i configure.ac || die + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable openmp) +} |