sci-biology/ncbi-tools++ removal. This version doesn't build with gnutls-3. See bug #421777.

10 files changed, 0 insertions, 1173 deletions

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
deleted file mode 100644
index 7331c537bbf6..000000000000
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ /dev/null
@@ -1,158 +0,0 @@
-# ChangeLog for sci-biology/ncbi-tools++
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.29 2014/05/14 12:06:42 jlec Exp $
-
-  14 May 2014; Justin Lecher <jlec@gentoo.org>
-  ncbi-tools++-0.2010.06.15-r1.ebuild:
-  Block sci-biology/update-blastdb
-
-  11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
-  Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
-
-  28 Feb 2013; Justin Lecher <jlec@gentoo.org>
-  -ncbi-tools++-2010.06.15-r1.ebuild, metadata.xml:
-  Drop old
-
-  05 Nov 2012; Justin Lecher <jlec@gentoo.org>
-  ncbi-tools++-0.2010.06.15-r1.ebuild:
-  Correct patch naming again
-
-  03 Nov 2012; Justin Lecher <jlec@gentoo.org>
-  ncbi-tools++-0.2010.06.15-r1.ebuild:
-  Correct for new version number
-
-*ncbi-tools++-0.2010.06.15-r1 (02 Nov 2012)
-
-  02 Nov 2012; Justin Lecher <jlec@gentoo.org>
-  +ncbi-tools++-0.2010.06.15-r1.ebuild, -ncbi-tools++-2010.06.15.ebuild:
-  Drop old, duplicate with lower version number for new versioning schema
-
-  03 Jun 2012; Justin Lecher <jlec@gentoo.org>
-  ncbi-tools++-2010.06.15-r1.ebuild,
-  +files/ncbi-tools++-2010.06.15-gcc47.patch:
-  Fix for gcc-4.7; add rpath on prefix
-
-  24 Nov 2011; Justin Lecher <jlec@gentoo.org>
-  ncbi-tools++-2010.06.15-r1.ebuild,
-  +files/ncbi-tools++-2010.06.15-glibc-214.patch:
-  Fix compilation against glbc-2.1.4 (changed declaration of type for
-  __malloc_initialize_hook from void to volatile
-
-  23 Sep 2011; Lars Wendler <polynomial-c@gentoo.org>
-  ncbi-tools++-2010.06.15-r1.ebuild,
-  +files/ncbi-tools++-2010.06.15-libpng15.patch:
-  non-maintainer commit: Added a patch to fix compilation with libpng15 (bug
-  #383721).
-
-  05 May 2011; Justin Lecher <jlec@gentoo.org>
-  ncbi-tools++-2010.06.15-r1.ebuild,
-  -files/ncbi-tools++-2010.06.15-asneeded.patch,
-  -files/ncbi-tools++-2010.06.15-asneeded-ng.patch:
-  Mirrored large patches
-
-*ncbi-tools++-2010.06.15-r1 (04 May 2011)
-
-  04 May 2011; Justin Lecher <jlec@gentoo.org>
-  -ncbi-tools++-2009.05.15-r6.ebuild, ncbi-tools++-2010.06.15.ebuild,
-  +ncbi-tools++-2010.06.15-r1.ebuild,
-  +files/ncbi-tools++-2010.06.15-asneeded.patch,
-  +files/ncbi-tools++-2010.06.15-asneeded-ng.patch:
-  Fix for asneeded, #297193; removed old, #312921
-
-  02 May 2011; Justin Lecher <jlec@gentoo.org> ncbi-tools++-2010.06.15.ebuild,
-  +files/ncbi-tools++-2010.06.15-gcc46.patch:
-  Fix for gcc46
-
-*ncbi-tools++-2010.06.15 (26 Sep 2010)
-
-  26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org>
-  +ncbi-tools++-2010.06.15.ebuild:
-  Version bump
-
-*ncbi-tools++-2009.05.15-r6 (26 Jun 2010)
-
-  26 Jun 2010; Justin Lecher <jlec@gentoo.org>
-  -ncbi-tools++-2009.05.15-r5.ebuild, +ncbi-tools++-2009.05.15-r6.ebuild,
-  +files/ncbi-tools++-2009.05.15-asneeded.patch:
-  Fixed as-needed problem
-
-  26 Jun 2010; Justin Lecher <jlec@gentoo.org>
-  ncbi-tools++-2009.05.15-r5.ebuild:
-  Added no-as-needed
-
-*ncbi-tools++-2009.05.15-r5 (24 Jun 2010)
-
-  24 Jun 2010; Justin Lecher <jlec@gentoo.org>
-  -ncbi-tools++-2009.05.15-r4.ebuild, +ncbi-tools++-2009.05.15-r5.ebuild:
-  Never set LD_LIBRARY_PATH, use LDPATH
-
-*ncbi-tools++-2009.05.15-r4 (31 May 2010)
-
-  31 May 2010; Andrey Kislyuk <weaver@gentoo.org>
-  -ncbi-tools++-2009.05.15-r3.ebuild, +ncbi-tools++-2009.05.15-r4.ebuild:
-  Address bug 300722, bug 312921
-
-*ncbi-tools++-2009.05.15-r3 (11 Mar 2010)
-
-  11 Mar 2010; Andrey Kislyuk <weaver@gentoo.org>
-  -ncbi-tools++-2009.05.15-r2.ebuild, +ncbi-tools++-2009.05.15-r3.ebuild:
-  Enable --with-mt
-
-  07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
-  ncbi-tools++-2009.05.15-r2.ebuild:
-  Moved to EAPI=3 for PREFIX support, keyworded for *-linux, tested by me
-
-*ncbi-tools++-2009.05.15-r2 (26 Feb 2010)
-
-  26 Feb 2010; Andrey Kislyuk <weaver@gentoo.org>
-  -ncbi-tools++-2009.05.15-r1.ebuild, +ncbi-tools++-2009.05.15-r2.ebuild:
-  Set custom lib dir, bug 306595
-
-  12 Jan 2010; Andrey Kislyuk <weaver@gentoo.org>
-  ncbi-tools++-2009.05.15-r1.ebuild:
-  Postpone stabilization due to QA problems
-
-  29 Dec 2009; Christian Faulhammer <fauli@gentoo.org>
-  ncbi-tools++-2009.05.15-r1.ebuild:
-  stable x86, bug 298778
-
-  02 Oct 2009; Andrey Kislyuk <weaver@gentoo.org>
-  ncbi-tools++-2009.05.15-r1.ebuild:
-  Update description
-
-  19 Aug 2009; Andrey Kislyuk <weaver@gentoo.org>
-  ncbi-tools++-2009.05.15-r1.ebuild:
-  Fix collision with dynamic libs
-
-*ncbi-tools++-2009.05.15-r1 (18 Aug 2009)
-
-  18 Aug 2009; Andrey Kislyuk <weaver@gentoo.org>
-  -ncbi-tools++-2009.05.15.ebuild, +ncbi-tools++-2009.05.15-r1.ebuild:
-  Remove static linking and fix fPIC issues, re-keyword amd64
-
-  10 Aug 2009; Samuli Suominen <ssuominen@gentoo.org>
-  ncbi-tools++-2009.05.15.ebuild,
-  +files/ncbi-tools++-2009.05.15-gcc44.patch:
-  Fix building with GCC 4.4+ wrt #280237. Keyword -amd64 because the build
-  system doesn't support x86_64 (relocation R_X86_64_32S -fPIC issues).
-
-  27 Jul 2009; Andrey Kislyuk <weaver@gentoo.org>
-  ncbi-tools++-2009.05.15.ebuild:
-  Avoid collision with openrc
-
-  27 Jul 2009; Andrey Kislyuk <weaver@gentoo.org>
-  ncbi-tools++-2009.05.15.ebuild:
-  Fix typo
-
-*ncbi-tools++-2009.05.15 (27 Jul 2009)
-
-  27 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
-  +ncbi-tools++-2009.05.15.ebuild:
-  Import from Science overlay
-
-  25 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
-  Version bump
-
-  28 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
-  New package, ebuild written by me
-
diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
deleted file mode 100644
index 131a28443b97..000000000000
--- a/sci-biology/ncbi-tools++/Manifest
+++ /dev/null
@@ -1,33 +0,0 @@
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diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-asneeded.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-asneeded.patch
deleted file mode 100644
index fde794b1a20e..000000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-asneeded.patch
+++ /dev/null
@@ -1,123 +0,0 @@
---- src/build-system/Makefile.mk.in
-+++ src/build-system/Makefile.mk.in
-@@ -547,7 +547,7 @@
- #################################
- # Useful sets of object libraries
- # Interdependent sequence libraries + seqcode.  Does not include seqset.
--COMPRESS_LDEP = $(CMPRS_LIB)
-+COMPRESS_LDEP = $(CMPRS_LIB) xutil xncbi
- COMPRESS_LIBS = xcompress $(COMPRESS_LDEP)
- 
- GENBANK_LDEP = \
---- src/util/compress/Makefile.compress.lib
-+++ src/util/compress/Makefile.compress.lib
-@@ -4,7 +4,7 @@
- 
- LIB = xcompress
- 
--DLL_LIB = 
--#$(COMPRESS_LDEP)
-+DLL_LIB = $(COMPRESS_LDEP)
-+LIBS = $(CMPRS_LIBS)
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
---- src/serial/Makefile.serial.lib
-+++ src/serial/Makefile.serial.lib
-@@ -17,3 +17,5 @@
- 	objostrjson serializable serialobject pathhook
- 
- LIB    = xser
-+
-+DLL_LIB = xutil xncbi
---- src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-+++ src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -12,4 +12,4 @@
- LIB_OR_DLL = both
- 
- # Dependencies for shared library
--DLL_LIB = 
-+DLL_LIB = xcompress
---- src/objtools/readers/Makefile.xobjread.lib
-+++ src/objtools/readers/Makefile.xobjread.lib
-@@ -8,4 +8,4 @@
-       wiggle_reader wiggle_data gff3_reader \
-       ucscid idmap idmapper idmapper_builtin idmapper_user idmapper_site \
-       idmapper_database
--DLL_LIB = creaders
-+DLL_LIB = creaders seq seqset
---- src/objects/seq/Makefile.seq.lib
-+++ src/objects/seq/Makefile.seq.lib
-@@ -10,3 +10,5 @@
- SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \
-       seq_id_tree seq_id_handle seq_id_mapper \
-       seq_loc_mapper_base seq_align_mapper_base
-+
-+DLL_LIB = biblio general pub seqcode sequtil xncbi
---- src/objects/pub/Makefile.pub.lib
-+++ src/objects/pub/Makefile.pub.lib
-@@ -1,2 +1,4 @@
- LIB = pub
- SRC = pub__ pub___
-+
-+DLL_LIB = medline
---- src/objects/general/Makefile.general.lib
-+++ src/objects/general/Makefile.general.lib
-@@ -1,2 +1,4 @@
- LIB = general
- SRC = general__ general___ uoconv
-+
-+DLL_LIB = xsoap xser
---- src/objects/omssa/Makefile.omssa.lib
-+++ src/objects/omssa/Makefile.omssa.lib
-@@ -2,3 +2,5 @@
- 
- LIB = omssa
- SRC = omssa__ omssa___
-+
-+DLL_LIB = seq
---- src/algo/blast/api/Makefile.xblast.lib
-+++ src/algo/blast/api/Makefile.xblast.lib
-@@ -73,7 +73,8 @@
- 
- LIB = xblast
- 
--DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgodustmask xalgowinmask xobjutil xnetblast xnetblastcli blastdb composition_adjustment \
-+   blast tables xalgoblastdbindex_search xalgoblastdbindex $(OBJMGR_LIBS)
- 
- CFLAGS   = $(FAST_CFLAGS)
- # Strict gcc flags
---- src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-+++ src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -12,3 +12,4 @@
- LDFLAGS  = $(FAST_LDFLAGS)
- 
- ASN_DEP = seqset
-+DLL_LIB = xobjread
---- src/objects/biblio/Makefile.biblio.lib
-+++ src/objects/biblio/Makefile.biblio.lib
-@@ -1,2 +1,4 @@
- LIB = biblio
- SRC = biblio__ biblio___ label_util
-+
-+DLL_LIB = general
---- src/objects/medline/Makefile.medline.lib
-+++ src/objects/medline/Makefile.medline.lib
-@@ -1,2 +1,4 @@
- LIB = medline
- SRC = medline__ medline___
-+
-+DLL_LIB = biblio
---- src/objects/Makefile.in
-+++ src/objects/Makefile.in
-@@ -5,8 +5,8 @@
- 
- USR_PROJ = sources
- 
--SUB_PROJ = tinyseq omssa general biblio medline pub pubmed \
--           featdef seqcode seqset seq genomecoll biotree \
-+SUB_PROJ = tinyseq general biblio medline pub pubmed \
-+           featdef seqcode seqset seq omssa genomecoll biotree \
-            id1 id2 gbseq insdseq entrez2 submit medlars mla proj mmdb \
-            cdd cn3d scoremat ncbimime access objprt docsum taxon1 mim \
-            entrezgene blast blastdb blastxml pcsubstance pcassay remap \
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-gcc44.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-gcc44.patch
deleted file mode 100644
index 9ab210d338e0..000000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-gcc44.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ur ncbi_cxx--May_15_2009.orig/src/dbapi/driver/dblib/context.cpp ncbi_cxx--May_15_2009/src/dbapi/driver/dblib/context.cpp
---- ncbi_cxx--May_15_2009.orig/src/dbapi/driver/dblib/context.cpp	2008-11-13 23:13:10.000000000 +0200
-+++ ncbi_cxx--May_15_2009/src/dbapi/driver/dblib/context.cpp	2009-08-10 16:54:33.000000000 +0300
-@@ -781,7 +781,7 @@
- #  elif NCBI_FTDS == 8
- #    define NCBI_FTDS_DRV_NAME    "ftds8"
- #    define NCBI_FTDS_ENTRY_POINT DBAPI_E_ftds8
--#  elif
-+#  else
- #    error "This version of FreeTDS is not supported"
- #  endif
- #endif
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc46.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc46.patch
deleted file mode 100644
index abc12ccb5fb9..000000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc46.patch
+++ /dev/null
@@ -1,71 +0,0 @@
- include/dbapi/driver/dbapi_object_convert.hpp    |    8 ++++----
- include/dbapi/driver/impl/dbapi_driver_utils.hpp |    2 +-
- src/objtools/blast/seqdb_reader/seqdbimpl.hpp    |    2 +-
- 3 files changed, 6 insertions(+), 6 deletions(-)
-
-diff --git a/include/dbapi/driver/dbapi_object_convert.hpp b/include/dbapi/driver/dbapi_object_convert.hpp
-index b66a3b0..667a133 100644
---- a/include/dbapi/driver/dbapi_object_convert.hpp
-+++ b/include/dbapi/driver/dbapi_object_convert.hpp
-@@ -67,7 +67,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -92,7 +92,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -133,7 +133,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -174,7 +174,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-diff --git a/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-index ee22035..c2e21e7 100644
---- a/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-+++ b/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-@@ -231,7 +231,7 @@ protected:
- 
- private:
-     const string& m_SPName;
--    mutable impl::CConnection& m_Conn;
-+    impl::CConnection& m_Conn;
- };
- 
- 
-diff --git a/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-index 7070fdb..814658b 100644
---- a/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-+++ b/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-@@ -1234,7 +1234,7 @@ private:
-     CSeqDBAtlasHolder m_AtlasHolder;
-     
-     /// Reference to memory management layer.
--    mutable CSeqDBAtlas & m_Atlas;
-+    CSeqDBAtlas & m_Atlas;
-     
-     /// The list of database names provided to the constructor.
-     string m_DBNames;
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch
deleted file mode 100644
index 36718d161ac0..000000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch
+++ /dev/null
@@ -1,643 +0,0 @@
- include/algo/gnomon/gnomon_model.hpp          |    8 +-
- include/corelib/ncbiexpt.hpp                  |    4 +-
- include/corelib/ncbimisc.hpp                  |    2 +
- include/corelib/ncbiobj.hpp                   |    2 +-
- include/corelib/ncbistl.hpp                   |    2 +-
- include/corelib/ncbistr.hpp                   |    2 +-
- include/serial/impl/stltypes.hpp              |   14 +-
- include/serial/iterator.hpp                   |    6 +-
- include/util/bitset/bmfunc.h                  |  263 +++++++++++++------------
- include/util/bitset/bmserial.h                |    6 +-
- include/util/linkedset.hpp                    |    8 +-
- include/util/rangemap.hpp                     |    2 +-
- src/algo/blast/gumbel_params/njn_approx.hpp   |    1 +
- src/algo/blast/gumbel_params/sls_alp_data.hpp |    1 +
- src/serial/stdtypes.cpp                       |    8 +-
- 15 files changed, 167 insertions(+), 162 deletions(-)
-
-diff --git a/include/algo/gnomon/gnomon_model.hpp b/include/algo/gnomon/gnomon_model.hpp
-index 66e7765..ca4d765 100644
---- a/include/algo/gnomon/gnomon_model.hpp
-+++ b/include/algo/gnomon/gnomon_model.hpp
-@@ -627,11 +627,11 @@ public:
-     CModelCluster(TSignedSeqRange limits) : m_limits(limits) {}
-     void Insert(const Model& a) {
-         m_limits.CombineWith(a.Limits());
--        push_back(a);
-+        this->push_back(a);
-     }
-     void Splice(CModelCluster& c) { // elements removed from c and inserted into *this
-         m_limits.CombineWith(c.Limits());
--        splice(list<Model>::end(),c);
-+        this->splice(list<Model>::end(),c);
-     }
-     TSignedSeqRange Limits() const { return m_limits; }
-     bool operator<(const CModelCluster& c) const { return Precede(m_limits, c.m_limits); }
-@@ -663,9 +663,9 @@ class NCBI_XALGOGNOMON_EXPORT CModelClusterSet : public set<Cluster> {
-         pair<Titerator,Titerator> lim = set<Cluster>::equal_range(clust);
-         for(Titerator it = lim.first; it != lim.second;) {
-             clust.Splice(const_cast<Cluster&>(*it));
--            erase(it++);
-+            this->erase(it++);
-         }
--        const_cast<Cluster&>(*insert(lim.second,Cluster(clust.Limits()))).Splice(clust);
-+        const_cast<Cluster&>(*this->insert(lim.second,Cluster(clust.Limits()))).Splice(clust);
-     }
- };
- 
-diff --git a/include/corelib/ncbiexpt.hpp b/include/corelib/ncbiexpt.hpp
-index 1d3cce3..1055d66 100644
---- a/include/corelib/ncbiexpt.hpp
-+++ b/include/corelib/ncbiexpt.hpp
-@@ -843,7 +843,7 @@ const TTo* UppermostCast(const TFrom& from)
-     exception_class(const exception_class& other) \
-        : base_class(other) \
-     { \
--        x_Assign(other); \
-+        this->x_Assign(other); \
-     } \
- public: \
-     virtual ~exception_class(void) throw() {} \
-@@ -1166,7 +1166,7 @@ public:
-         : TBase( other)
-     {
-         m_Errno = other.m_Errno;
--        x_Assign(other);
-+        this->x_Assign(other);
-     }
- 
-     /// Destructor.
-diff --git a/include/corelib/ncbimisc.hpp b/include/corelib/ncbimisc.hpp
-index 87236c7..b540038 100644
---- a/include/corelib/ncbimisc.hpp
-+++ b/include/corelib/ncbimisc.hpp
-@@ -47,6 +47,8 @@
- #  include <ctype.h>
- #endif
- 
-+// for free()
-+#include <stdlib.h>
- 
- #if defined(_DEBUG)  &&  !defined(NCBI_NO_STRICT_CTYPE_ARGS)
- #  define NCBI_STRICT_CTYPE_ARGS
-diff --git a/include/corelib/ncbiobj.hpp b/include/corelib/ncbiobj.hpp
-index de4c454..084a041 100644
---- a/include/corelib/ncbiobj.hpp
-+++ b/include/corelib/ncbiobj.hpp
-@@ -2128,7 +2128,7 @@ public:
-         CIRef<Interface, TThisType> ref(
-                    dynamic_cast<Interface*>(proxy->GetLockedObject()), *this);
-         if (ref.NotNull()) {
--            Unlock(ref.GetPointer());
-+            this->Unlock(ref.GetPointer());
-         }
-         return ref;
-     }
-diff --git a/include/corelib/ncbistl.hpp b/include/corelib/ncbistl.hpp
-index afd71d2..38768c4 100644
---- a/include/corelib/ncbistl.hpp
-+++ b/include/corelib/ncbistl.hpp
-@@ -36,7 +36,7 @@
- 
- 
- #include <common/ncbi_export.h>
--
-+#include <string>
- 
- // Get rid of some warnings in MSVC++ 6.00
- #if (_MSC_VER >= 1200)
-diff --git a/include/corelib/ncbistr.hpp b/include/corelib/ncbistr.hpp
-index e515dc6..5800223 100644
---- a/include/corelib/ncbistr.hpp
-+++ b/include/corelib/ncbistr.hpp
-@@ -2439,7 +2439,7 @@ public:
-         : TBase(other)
-     {
-         m_Pos = other.m_Pos;
--        x_Assign(other);
-+        this->x_Assign(other);
-     }
- 
-     /// Destructor.
-diff --git a/include/serial/impl/stltypes.hpp b/include/serial/impl/stltypes.hpp
-index abfa8b8..28254ae 100644
---- a/include/serial/impl/stltypes.hpp
-+++ b/include/serial/impl/stltypes.hpp
-@@ -437,7 +437,7 @@ public:
-         }
-     static bool InitIterator(TTypeInfoIterator& iter)
-         {
--            TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin();
-+            TStlIterator stl_iter = CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).begin();
-             if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) {
-                 void* data = &iter.m_IteratorData;
-                 new (data) TStlIterator(stl_iter);
-@@ -445,7 +445,7 @@ public:
-             else {
-                 iter.m_IteratorData = new TStlIterator(stl_iter);
-             }
--            return stl_iter != Get(iter.GetContainerPtr()).end();
-+            return stl_iter != CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).end();
-         }
-     static void ReleaseIterator(TTypeInfoIterator& iter)
-         {
-@@ -466,7 +466,7 @@ public:
- 
-     static bool NextElement(TTypeInfoIterator& iter)
-         {
--            return ++It(iter) != Get(iter.GetContainerPtr()).end();
-+            return ++It(iter) != CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).end();
-         }
-     static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter)
-         {
-@@ -503,7 +503,7 @@ public:
-     
-     static bool EraseElement(TTypeInfoIterator& iter)
-         {
--            TStlIterator& it = It(iter);
-+            TStlIterator& it = CStlClassInfoFunctionsI::It(iter);
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
-             it = c->erase(it);
-             return it != c->end();
-@@ -511,7 +511,7 @@ public:
-     static void EraseAllElements(TTypeInfoIterator& iter)
-         {
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
--            c->erase(It(iter), c->end());
-+            c->erase(CStlClassInfoFunctionsI::It(iter), c->end());
-         }
- 
-     static void SetIteratorFunctions(CStlOneArgTemplate* info)
-@@ -542,7 +542,7 @@ public:
-         }
-     static bool EraseElement(TTypeInfoIterator& iter)
-         {
--            TStlIterator& it = It(iter);
-+            TStlIterator& it = CStlClassInfoFunctionsI_set::It(iter);
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
-             TStlIterator erase = it++;
-             c->erase(erase);
-@@ -551,7 +551,7 @@ public:
-     static void EraseAllElements(TTypeInfoIterator& iter)
-         {
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
--            c->erase(It(iter), c->end());
-+            c->erase(CStlClassInfoFunctionsI_set::It(iter), c->end());
-         }
- 
-     static void SetIteratorFunctions(CStlOneArgTemplate* info)
-diff --git a/include/serial/iterator.hpp b/include/serial/iterator.hpp
-index eabb01b..402d7ac 100644
---- a/include/serial/iterator.hpp
-+++ b/include/serial/iterator.hpp
-@@ -491,13 +491,13 @@ protected:
-     CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo)
-         : m_NeedType(needType)
-         {
--            Init(beginInfo);
-+            this->Init(beginInfo);
-         }
-     CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo,
-                       const string& filter)
-         : m_NeedType(needType)
-         {
--            Init(beginInfo, filter);
-+            this->Init(beginInfo, filter);
-         }
- 
-     virtual bool CanSelect(const CConstObjectInfo& object)
-@@ -599,7 +599,7 @@ public:
- 
-     CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo)
-         {
--            Init(beginInfo);
-+            this->Init(beginInfo);
-             return *this;
-         }
- 
-diff --git a/include/util/bitset/bmfunc.h b/include/util/bitset/bmfunc.h
-index bf09e2d..5489213 100644
---- a/include/util/bitset/bmfunc.h
-+++ b/include/util/bitset/bmfunc.h
-@@ -1794,6 +1794,72 @@ void gap_and_to_bitset(unsigned* dest, const T*  buf)
-     }
- }
- 
-+/*!
-+	Function calculates number of 1 bits in the given array of words in
-+    the range between left anf right bits (borders included)
-+    Make sure the addresses are aligned.
-+
-+    @ingroup bitfunc
-+*/
-+inline 
-+bm::id_t bit_block_calc_count_range(const bm::word_t* block,
-+                                    bm::word_t left,
-+                                    bm::word_t right)
-+{
-+    BM_ASSERT(left <= right);
-+    unsigned nword, nbit;    
-+    nbit = left & bm::set_word_mask;
-+    const bm::word_t* word = 
-+        block + (nword = unsigned(left >> bm::set_word_shift));
-+    if (left == right)  // special case (only 1 bit to check)
-+    {
-+        return (*word >> nbit) & 1;
-+    }
-+	bm::id_t count = 0;
-+
-+    unsigned acc;
-+    unsigned bitcount = right - left + 1;
-+
-+    if (nbit) // starting position is not aligned
-+    {
-+        unsigned right_margin = nbit + (right - left);
-+
-+        if (right_margin < 32)
-+        {
-+            unsigned mask =
-+                block_set_table<true>::_right[nbit] &
-+                block_set_table<true>::_left[right_margin];
-+            acc = *word & mask;
-+            
-+            BM_INCWORD_BITCOUNT(count, acc);
-+            return count;
-+        }
-+        else
-+        {
-+            acc = *word & block_set_table<true>::_right[nbit];
-+            BM_INCWORD_BITCOUNT(count, acc);
-+            bitcount -= 32 - nbit;
-+        }
-+        ++word;
-+    }
-+
-+    // now when we are word aligned, we can count bits the usual way
-+    for ( ;bitcount >= 32; bitcount -= 32)
-+    {
-+        acc = *word++;
-+        BM_INCWORD_BITCOUNT(count, acc);
-+    }
-+
-+    if (bitcount)  // we have a tail to count
-+    {
-+        acc = (*word) & block_set_table<true>::_left[bitcount-1];
-+        BM_INCWORD_BITCOUNT(count, acc);
-+    }
-+
-+    return count;
-+}
-+
-+
- 
- /*!
-    \brief Compute bitcount of bit block AND masked by GAP block.
-@@ -1825,6 +1891,72 @@ bm::id_t gap_bitset_and_count(const unsigned* block, const T*  buf)
-     return count;
- }
- 
-+/*!
-+	Function calculates if there is any number of 1 bits 
-+    in the given array of words in the range between left anf right bits 
-+    (borders included). Make sure the addresses are aligned.
-+
-+    @ingroup bitfunc
-+*/
-+inline 
-+bm::id_t bit_block_any_range(const bm::word_t* block,
-+                             bm::word_t left,
-+                             bm::word_t right)
-+{
-+    BM_ASSERT(left <= right);
-+    
-+    unsigned nbit  = left; // unsigned(left & bm::set_block_mask);
-+    unsigned nword = unsigned(nbit >> bm::set_word_shift);
-+    nbit &= bm::set_word_mask;
-+
-+    const bm::word_t* word = block + nword;
-+
-+    if (left == right)  // special case (only 1 bit to check)
-+    {
-+        return (*word >> nbit) & 1;
-+    }
-+    unsigned acc;
-+    unsigned bitcount = right - left + 1;
-+
-+    if (nbit) // starting position is not aligned
-+    {
-+        unsigned right_margin = nbit + (right - left);
-+        if (right_margin < 32)
-+        {
-+            unsigned mask =
-+                block_set_table<true>::_right[nbit] &
-+                block_set_table<true>::_left[right_margin];
-+            acc = *word & mask;
-+            return acc;
-+        }
-+        else
-+        {
-+            acc = *word & block_set_table<true>::_right[nbit];
-+            if (acc) 
-+                return acc;
-+            bitcount -= 32 - nbit;
-+        }
-+        ++word;
-+    }
-+
-+    // now when we are word aligned, we can check bits the usual way
-+    for ( ;bitcount >= 32; bitcount -= 32)
-+    {
-+        acc = *word++;
-+        if (acc) 
-+            return acc;
-+    }
-+
-+    if (bitcount)  // we have a tail to count
-+    {
-+        acc = (*word) & block_set_table<true>::_left[bitcount-1];
-+        if (acc) 
-+            return acc;
-+    }
-+
-+    return 0;
-+}
-+
- 
- /*!
-    \brief Bitcount test of bit block AND masked by GAP block.
-@@ -2939,137 +3071,6 @@ bm::id_t bit_block_calc_count_change(const bm::word_t* block,
- }
- 
- 
--/*!
--	Function calculates number of 1 bits in the given array of words in
--    the range between left anf right bits (borders included)
--    Make sure the addresses are aligned.
--
--    @ingroup bitfunc
--*/
--inline 
--bm::id_t bit_block_calc_count_range(const bm::word_t* block,
--                                    bm::word_t left,
--                                    bm::word_t right)
--{
--    BM_ASSERT(left <= right);
--    unsigned nword, nbit;    
--    nbit = left & bm::set_word_mask;
--    const bm::word_t* word = 
--        block + (nword = unsigned(left >> bm::set_word_shift));
--    if (left == right)  // special case (only 1 bit to check)
--    {
--        return (*word >> nbit) & 1;
--    }
--	bm::id_t count = 0;
--
--    unsigned acc;
--    unsigned bitcount = right - left + 1;
--
--    if (nbit) // starting position is not aligned
--    {
--        unsigned right_margin = nbit + (right - left);
--
--        if (right_margin < 32)
--        {
--            unsigned mask =
--                block_set_table<true>::_right[nbit] &
--                block_set_table<true>::_left[right_margin];
--            acc = *word & mask;
--            
--            BM_INCWORD_BITCOUNT(count, acc);
--            return count;
--        }
--        else
--        {
--            acc = *word & block_set_table<true>::_right[nbit];
--            BM_INCWORD_BITCOUNT(count, acc);
--            bitcount -= 32 - nbit;
--        }
--        ++word;
--    }
--
--    // now when we are word aligned, we can count bits the usual way
--    for ( ;bitcount >= 32; bitcount -= 32)
--    {
--        acc = *word++;
--        BM_INCWORD_BITCOUNT(count, acc);
--    }
--
--    if (bitcount)  // we have a tail to count
--    {
--        acc = (*word) & block_set_table<true>::_left[bitcount-1];
--        BM_INCWORD_BITCOUNT(count, acc);
--    }
--
--    return count;
--}
--
--
--/*!
--	Function calculates if there is any number of 1 bits 
--    in the given array of words in the range between left anf right bits 
--    (borders included). Make sure the addresses are aligned.
--
--    @ingroup bitfunc
--*/
--inline 
--bm::id_t bit_block_any_range(const bm::word_t* block,
--                             bm::word_t left,
--                             bm::word_t right)
--{
--    BM_ASSERT(left <= right);
--    
--    unsigned nbit  = left; // unsigned(left & bm::set_block_mask);
--    unsigned nword = unsigned(nbit >> bm::set_word_shift);
--    nbit &= bm::set_word_mask;
--
--    const bm::word_t* word = block + nword;
--
--    if (left == right)  // special case (only 1 bit to check)
--    {
--        return (*word >> nbit) & 1;
--    }
--    unsigned acc;
--    unsigned bitcount = right - left + 1;
--
--    if (nbit) // starting position is not aligned
--    {
--        unsigned right_margin = nbit + (right - left);
--        if (right_margin < 32)
--        {
--            unsigned mask =
--                block_set_table<true>::_right[nbit] &
--                block_set_table<true>::_left[right_margin];
--            acc = *word & mask;
--            return acc;
--        }
--        else
--        {
--            acc = *word & block_set_table<true>::_right[nbit];
--            if (acc) 
--                return acc;
--            bitcount -= 32 - nbit;
--        }
--        ++word;
--    }
--
--    // now when we are word aligned, we can check bits the usual way
--    for ( ;bitcount >= 32; bitcount -= 32)
--    {
--        acc = *word++;
--        if (acc) 
--            return acc;
--    }
--
--    if (bitcount)  // we have a tail to count
--    {
--        acc = (*word) & block_set_table<true>::_left[bitcount-1];
--        if (acc) 
--            return acc;
--    }
--
--    return 0;
--}
- 
- 
- 
-diff --git a/include/util/bitset/bmserial.h b/include/util/bitset/bmserial.h
-index 519cd2b..00f6c01 100644
---- a/include/util/bitset/bmserial.h
-+++ b/include/util/bitset/bmserial.h
-@@ -1381,7 +1381,7 @@ deserializer<BV, DEC>::deserialize_gap(unsigned char btype, decoder_type& dec,
-     case set_block_arrgap: 
-     case set_block_arrgap_egamma:
-         {
--        	unsigned arr_len = read_id_list(dec, btype, this->id_array_);
-+        	unsigned arr_len = this->read_id_list(dec, btype, this->id_array_);
-             gap_len = gap_set_array(gap_temp_block_, this->id_array_, arr_len);
-             break;
-         }
-@@ -1390,7 +1390,7 @@ deserializer<BV, DEC>::deserialize_gap(unsigned char btype, decoder_type& dec,
-             (sizeof(gap_word_t) == 2 ? dec.get_16() : dec.get_32());
-     case set_block_arrgap_egamma_inv:
-     case set_block_arrgap_inv:
--        gap_len = read_gap_block(dec, btype, gap_temp_block_, gap_head);
-+        gap_len = this->read_gap_block(dec, btype, gap_temp_block_, gap_head);
-         break;
-     default:
-         BM_ASSERT(0);
-@@ -2763,7 +2763,7 @@ serial_stream_iterator<DEC>::get_gap_block(bm::gap_word_t* dst_block)
-               this->block_type_ == set_block_bit_1bit);
-     BM_ASSERT(dst_block);
- 
--    read_gap_block(this->decoder_,
-+    this->read_gap_block(this->decoder_,
-                    this->block_type_,
-                    dst_block,
-                    this->gap_head_);
-diff --git a/include/util/linkedset.hpp b/include/util/linkedset.hpp
-index 0d2cba1..1d09a28 100644
---- a/include/util/linkedset.hpp
-+++ b/include/util/linkedset.hpp
-@@ -422,10 +422,10 @@ public:
-         {
-             iterator iter = m_Container.insert(value);
-             if ( iter == begin() )
--                insertToStart(get(iter));
-+                this->insertToStart(get(iter));
-             else {
-                 iterator prev = iter;
--                insertAfter(get(--prev), get(iter));
-+                this->insertAfter(get(--prev), get(iter));
-             }
-             return iter;
-         }
-@@ -433,10 +433,10 @@ public:
-     void erase(iterator iter)
-         {
-             if ( iter == begin() )
--                removeFromStart(get(iter));
-+                this->removeFromStart(get(iter));
-             else {
-                 iterator prev = iter;
--                removeAfter(get(--prev), get(iter));
-+                this->removeAfter(get(--prev), get(iter));
-             }
-             m_Container.erase(iter);
-         }
-diff --git a/include/util/rangemap.hpp b/include/util/rangemap.hpp
-index 22cf3dd..b30b39d 100644
---- a/include/util/rangemap.hpp
-+++ b/include/util/rangemap.hpp
-@@ -640,7 +640,7 @@ public:
-             // insert element
-             iterator ret;
-             ret.m_Range = range_type::GetWhole();
--            ret.m_SelectIter = insertLevel(selectKey);
-+            ret.m_SelectIter = this->insertLevel(selectKey);
-             ret.m_SelectIterEnd = this->m_SelectMap.end();
-             ret.m_LevelIter = ret.m_SelectIter->second.insert(value);
-             return ret;
-diff --git a/src/algo/blast/gumbel_params/njn_approx.hpp b/src/algo/blast/gumbel_params/njn_approx.hpp
-index a79da93..5909cdf 100644
---- a/src/algo/blast/gumbel_params/njn_approx.hpp
-+++ b/src/algo/blast/gumbel_params/njn_approx.hpp
-@@ -38,6 +38,7 @@ Contents:
- 
- #include <corelib/ncbistl.hpp>
- #include <float.h>
-+#include <math.h>
- 
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(blast)
-diff --git a/src/algo/blast/gumbel_params/sls_alp_data.hpp b/src/algo/blast/gumbel_params/sls_alp_data.hpp
-index 5cee936..9ff4a4c 100644
---- a/src/algo/blast/gumbel_params/sls_alp_data.hpp
-+++ b/src/algo/blast/gumbel_params/sls_alp_data.hpp
-@@ -44,6 +44,7 @@ Contents: Contains input data
- #include <float.h>
- #include <ctime>
- #include <stdlib.h>
-+#include <math.h>
- #include <limits>
- 
- #ifndef NCBI_OS_MSWIN
-diff --git a/src/serial/stdtypes.cpp b/src/serial/stdtypes.cpp
-index 6eb0ac3..cdf5356 100644
---- a/src/serial/stdtypes.cpp
-+++ b/src/serial/stdtypes.cpp
-@@ -720,7 +720,7 @@ public:
-             if ( IsSigned() ) {
-                 // signed -> unsigned
-                 // check for negative value
--                if ( IsNegative(value) )
-+                if ( CPrimitiveTypeInfoIntFunctions::IsNegative(value) )
-                     ThrowIntegerOverflow();
-             }
-             if ( sizeof(value) > sizeof(result) ) {
-@@ -751,7 +751,7 @@ public:
-                 // unsigned -> signed
-                 if ( sizeof(value) == sizeof(result) ) {
-                     // same size - check for sign change only
--                    if ( IsNegative(result) )
-+                    if ( CPrimitiveTypeInfoIntFunctions::IsNegative(result) )
-                         ThrowIntegerOverflow();
-                 }
-             }
-@@ -786,7 +786,7 @@ public:
-             if ( IsSigned() ) {
-                 // signed -> unsigned
-                 // check for negative value
--                if ( IsNegative(value) )
-+                if ( CPrimitiveTypeInfoIntFunctions::IsNegative(value) )
-                     ThrowIntegerOverflow();
-             }
-             if ( sizeof(value) > sizeof(result) ) {
-@@ -817,7 +817,7 @@ public:
-                 // unsigned -> signed
-                 if ( sizeof(value) == sizeof(result) ) {
-                     // same size - check for sign change only
--                    if ( IsNegative(result) )
-+                    if ( CPrimitiveTypeInfoIntFunctions::IsNegative(result) )
-                         ThrowIntegerOverflow();
-                 }
-             }
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-glibc-214.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-glibc-214.patch
deleted file mode 100644
index 2275cdefb550..000000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-glibc-214.patch
+++ /dev/null
@@ -1,22 +0,0 @@
- src/app/netcache/nc_memory.cpp |    8 +++++++-
- 1 files changed, 7 insertions(+), 1 deletions(-)
-
-diff --git a/src/app/netcache/nc_memory.cpp b/src/app/netcache/nc_memory.cpp
-index bb602ee..468b44d 100644
---- a/src/app/netcache/nc_memory.cpp
-+++ b/src/app/netcache/nc_memory.cpp
-@@ -3329,7 +3329,13 @@ void s_NCInitMallocHook(void)
-     __free_hook    = s_NCFreeHook;
- }
- 
--void (*__malloc_initialize_hook) (void) = s_NCInitMallocHook;
-+/* GNU libc 2.14 defines this macro to declare hook variables as volatile.
-+   Define it as empty for older libc versions.  */
-+#ifndef __MALLOC_HOOK_VOLATILE
-+# define __MALLOC_HOOK_VOLATILE
-+#endif
-+
-+void (*__MALLOC_HOOK_VOLATILE __malloc_initialize_hook) (void) = s_NCInitMallocHook;
- 
- #elif !defined(NCBI_OS_MSWIN)
- // Changing of C library allocation functions on Windows is very tricky (if
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-libpng15.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-libpng15.patch
deleted file mode 100644
index d0f9c80894bf..000000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-libpng15.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Index: ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp
-===================================================================
---- ncbi_cxx--Jun_15_2010.orig/src/util/image/image_io_png.cpp
-+++ ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp
-@@ -34,6 +34,7 @@
- #include <util/image/image.hpp>
- #include <util/image/image_exception.hpp>
- #include <util/error_codes.hpp>
-+#include <zlib.h>
- 
- #define NCBI_USE_ERRCODE_X   Util_Image
- 
-@@ -177,11 +178,11 @@ static void s_PngReadValidate(png_struct
-                               size_t& x, size_t& y, size_t& w, size_t& h)
- {
-     // store and validate our image's parameters
--    width        = info_ptr->width;
--    height       = info_ptr->height;
--    depth        = info_ptr->channels;
--    png_byte color_type = info_ptr->color_type;
--    png_byte bit_depth  = info_ptr->bit_depth;
-+    width        = png_get_image_width(png_ptr,info_ptr);
-+    height       = png_get_image_height(png_ptr,info_ptr);
-+    depth        = png_get_channels(png_ptr,info_ptr);
-+    png_byte color_type = png_get_color_type(png_ptr,info_ptr);
-+    png_byte bit_depth  = png_get_bit_depth(png_ptr,info_ptr);
- 
-     // we support only RGB and RGBA images
-     if ( color_type != PNG_COLOR_TYPE_RGB  &&
diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
deleted file mode 100644
index f17a827e3101..000000000000
--- a/sci-biology/ncbi-tools++/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild
deleted file mode 100644
index 9fe756ac8a6e..000000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.4 2014/05/14 12:06:42 jlec Exp $
-
-EAPI="3"
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-MY_TAG="Jun_15_2010"
-MY_Y="${MY_TAG/*_/}"
-MY_P="ncbi_cxx--${MY_TAG}"
-
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/${MY_Y}/${MY_TAG}/${MY_P}.tar.gz
-	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-LICENSE="public-domain"
-SLOT="0"
-IUSE="sqlite mysql"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND="
-	!sci-biology/update-blastdb
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-	sed -i -e 's/-print-file-name=libstdc++.a//' \
-		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-		src/build-system/configure || die
-	epatch \
-		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-}
-
-src_configure() {
-	tc-export CXX CC
-# conf check for sqlite and mysql
-	"${S}"/configure --without-debug \
-		--with-bin-release \
-		--with-bincopy \
-		--without-static \
-		--with-dll \
-		--with-mt \
-		--prefix="${ED}"/usr \
-		--libdir="${ED}"/usr/$(get_libdir)/${PN} \
-		|| die
-}
-
-src_compile() {
-	emake all_r -C GCC*-Release*/build || die
-}
-
-src_install() {
-	emake install || die
-	# File collisions with sci-biology/ncbi-tools
-	rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-}