diff options
author | Manuel Rüger <mrueg@gentoo.org> | 2014-06-30 08:04:50 +0000 |
---|---|---|
committer | Manuel Rüger <mrueg@gentoo.org> | 2014-06-30 08:04:50 +0000 |
commit | ae2a5e77e478a36248fb076af18538f62b4b74ad (patch) | |
tree | c023e5c15a56c07c78fe3381d63c1052f4c17cb2 /sci-biology/ncbi-tools++ | |
parent | drop py2.6 pypy2_0 (diff) | |
download | gentoo-2-ae2a5e77e478a36248fb076af18538f62b4b74ad.tar.gz gentoo-2-ae2a5e77e478a36248fb076af18538f62b4b74ad.tar.bz2 gentoo-2-ae2a5e77e478a36248fb076af18538f62b4b74ad.zip |
sci-biology/ncbi-tools++ removal. This version doesn't build with gnutls-3. See bug #421777.
Diffstat (limited to 'sci-biology/ncbi-tools++')
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 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 - -AUX ncbi-tools++-2009.05.15-asneeded.patch 3620 SHA256 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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.' -} |