[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/

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From: "Andrew Ammerlaan" <andrewammerlaan@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
Date: Tue,  2 May 2023 12:15:40 +0000 (UTC)	[thread overview]
Message-ID: <1683029714.7e108279bb4d8cacad16e51875e704c885edc2e7.andrewammerlaan@gentoo> (raw)

commit:     7e108279bb4d8cacad16e51875e704c885edc2e7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:10:02 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:15:14 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e108279

sci-biology/ncbi-tools++: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/ncbi-tools++/files/curl-types.patch    |  24 --
 .../files/disable-testsuite-compilation.txt        |   8 -
 sci-biology/ncbi-tools++/files/make_install.patch  |  14 -
 .../files/malloc_initialize_upstream_fix.patch     | 100 -----
 .../files/ncbi-tools++-12.0.0-bdb6.patch           | 114 ------
 .../files/ncbi-tools++-12.0.0-conf-opts.patch      |  64 ----
 .../files/ncbi-tools++-12.0.0-configure.patch      | 216 -----------
 .../ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch |  44 ---
 .../ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch |  19 -
 .../ncbi-tools++-12.0.0-fix-creaders-linking.patch |  11 -
 .../files/ncbi-tools++-12.0.0-fix-install.patch    |  11 -
 .../ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch |  10 -
 ...cbi-tools++-12.0.0-linkage-tuneups-addons.patch |  13 -
 .../ncbi-tools++-12.0.0-linkage-tuneups.patch      | 421 ---------------------
 .../files/ncbi-tools++-12.0.0-more-patches.patch   | 136 -------
 ...cbi-tools++-12.0.0-never_build_test_boost.patch |  11 -
 ...ncbi-tools++-12.0.0-support-autoconf-2.60.patch | 296 ---------------
 .../files/ncbi-tools++-18.0.0-configure.patch      |  20 -
 ...bi-tools++-18.0.0-fix-annotwriter-linking.patch |  15 -
 ...ols++-18.0.0-fix-app-blast_sample-linking.patch |  26 --
 ...i-tools++-18.0.0-fix-app-compartp-linking.patch |  29 --
 ...ools++-18.0.0-fix-app-convert_seq-linking.patch |  11 -
 ...bi-tools++-18.0.0-fix-app-hfilter-linking.patch |  14 -
 ...bi-tools++-18.0.0-fix-app-igblast-linking.patch |  28 --
 ...i-tools++-18.0.0-fix-app-rmblastn-linking.patch |  11 -
 ...-tools++-18.0.0-fix-app-table2asn-linking.patch |  13 -
 .../ncbi-tools++-18.0.0-fix-app-tls-linking.patch  |  11 -
 ...-tools++-18.0.0-fix-app-vecscreen-linking.patch |  13 -
 ...cbi-tools++-18.0.0-fix-apps-blast-linking.patch | 130 -------
 .../files/ncbi-tools++-18.0.0-fix-install.patch    |  11 -
 .../ncbi-tools++-18.0.0-fix-ncfetch-linking.patch  |  11 -
 ...++-18.0.0-fix-netcache_cgi_sample-linking.patch |  11 -
 ...-tools++-18.0.0-fix-netstorage_gc-linking.patch |  11 -
 ...tools++-18.0.0-fix-sample-app-cgi-linking.patch |  11 -
 ...ncbi-tools++-18.0.0-fix-speedtest-linking.patch |  11 -
 .../ncbi-tools++-18.0.0-fix-splign-linking.patch   |  11 -
 .../ncbi-tools++-18.0.0-fix-srcchk-linking.patch   |  15 -
 .../ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch |  10 -
 ...cbi-tools++-18.0.0-fix-undefined-xobjread.patch |  11 -
 ...cbi-tools++-18.0.0-never_build_test_boost.patch |  11 -
 .../ncbi-tools++-18.0.0-remove-old-symlinks.patch  |  10 -
 .../report_project_settings_configure.ac.patch     |  64 ----
 .../files/report_project_settings_configure.patch  |  66 ----
 .../files/respect_CXXFLAGS_configure.ac.patch      |  54 ---
 .../files/respect_CXXFLAGS_configure.patch         |  53 ---
 sci-biology/ncbi-tools++/metadata.xml              |  19 -
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        | 364 ------------------
 .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild        | 383 -------------------
 .../ncbi-tools++/ncbi-tools++-22.0.0.ebuild        | 388 -------------------
 49 files changed, 3358 deletions(-)

diff --git a/sci-biology/ncbi-tools++/files/curl-types.patch b/sci-biology/ncbi-tools++/files/curl-types.patch
deleted file mode 100644
index 3e6079057..000000000
--- a/sci-biology/ncbi-tools++/files/curl-types.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Index: libs/kns/url-fetcher-curl.c
-===================================================================
---- src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11878)
-+++ src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11880)
-@@ -38,7 +38,6 @@
- #include <string.h>
- 
- #include <curl/curl.h>
--#include <curl/types.h>
- #include <curl/easy.h>
- 
- /*--------------------------------------------------------------------------
-Index: tools/refseq-load/refseq-load.c
-===================================================================
---- src/sra/sdk/tools/refseq-load/refseq-load.c     (revision 11878)
-+++ src/sra/sdk/tools/refseq-load/refseq-load.c     (revision 11880)
-@@ -41,7 +41,6 @@
- #include <sysalloc.h>
- 
- #include <curl/curl.h>
--#include <curl/types.h>
- #include <curl/easy.h>
- 
- #include <stdlib.h>

diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
deleted file mode 100644
index fa27aa13b..000000000
--- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-.*
--.*/test
--.*/unit_test
--.*/unit_tests
--dbapi/driver/ftds.*/freetds/.*/unittests
--sample
--.*/demo
--.*/samples

diff --git a/sci-biology/ncbi-tools++/files/make_install.patch b/sci-biology/ncbi-tools++/files/make_install.patch
deleted file mode 100644
index e98f1110d..000000000
--- a/sci-biology/ncbi-tools++/files/make_install.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/build-system/Makefile.in.top.old	2013-01-07 23:07:29.970141951 +0100
-+++ src/build-system/Makefile.in.top	2013-01-07 23:08:37.940990190 +0100
-@@ -39,7 +39,10 @@
- 	-$(RMDIR) $(pincludedir)
- 	$(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
- 	$(INSTALL) $(lbindir)/* $(bindir)
--	$(INSTALL) -m 644 $(llibdir)/* $(libdir)
-+	$(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
-+	if test -d $(llibdir)/ncbi; then \
-+	    cp -pPR $(llibdir)/ncbi $(libdir)/; \
-+	fi
- 	-rm -f $(libdir)/lib*-static.a
- 	cd $(libdir)  && \
- 	    for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done

diff --git a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch b/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch
deleted file mode 100644
index 4900e529a..000000000
--- a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch
+++ /dev/null
@@ -1,100 +0,0 @@
---- trunk/c++/src/app/netcache/nc_memory.cpp    2011/12/16 17:42:54     52330
-+++ trunk/c++/src/app/netcache/nc_memory.cpp    2012/02/27 14:38:30     53136
-@@ -360,7 +360,7 @@
-     m_ObjLock.Lock();
-     ++m_SysFrees;
-     m_SystemMem -= alloced_size;
--    m_LostMem   -= alloced_size -= asked_size;
-+    m_LostMem   -= alloced_size - asked_size;
-     m_ObjLock.Unlock();
- }
- 
-@@ -2539,7 +2539,7 @@
- bool
- CNCMemManager::InitializeApp(void)
- {
--    try {
-+    /*try {
-         CSQLITE_Global::SetCustomMallocFuncs(&s_NCMallocMethods);
-     }
-     catch (CSQLITE_Exception& ex) {
-@@ -2547,13 +2547,15 @@
-         return false;
-     }
- 
--    return CNCMMCentral::RunLateInit();
-+    return CNCMMCentral::RunLateInit();*/
-+    g_InitNCThreadIndexes();
-+    return true;
- }
- 
- void
- CNCMemManager::FinalizeApp(void)
- {
--    CNCMMCentral::PrepareToStop();
-+    //CNCMMCentral::PrepareToStop();
- }
- 
- void
-@@ -2571,28 +2573,29 @@
- void
- CNCMemManager::PrintStats(CPrintTextProxy& proxy)
- {
--    CNCMMStats stats_sum;
-+    /*CNCMMStats stats_sum;
-     CNCMMStats::CollectAllStats(&stats_sum);
--    stats_sum.Print(proxy);
-+    stats_sum.Print(proxy);*/
- }
- 
- size_t
- CNCMemManager::GetMemoryLimit(void)
- {
--    return CNCMMCentral::GetMemLimit();
-+    return 0;//CNCMMCentral::GetMemLimit();
- }
- 
- size_t
- CNCMemManager::GetMemoryUsed(void)
- {
--    CNCMMStats stat;
-+    /*CNCMMStats stat;
-     CNCMMStats::CollectAllStats(&stat);
--    return stat.GetSystemMem();
-+    return stat.GetSystemMem();*/
-+    return 0;
- }
- 
- END_NCBI_SCOPE
- 
--
-+/*
- void*
- operator new (size_t size)
- #ifndef NCBI_COMPILER_MSVC
-@@ -2626,13 +2629,13 @@
- {
-     NCBI_NS_NCBI::CNCMMCentral::DeallocMemory(ptr);
- }
--
-+*/
- #ifdef __GLIBC__
- // glibc has special method of overriding C library allocation functions.
- 
- #include <malloc.h>
- 
--
-+/*
- void* s_NCMallocHook(size_t size, const void* caller)
- {
-     return NCBI_NS_NCBI::CNCMMCentral::AllocMemory(size);
-@@ -2656,7 +2659,7 @@
- }
- 
- void (*__malloc_initialize_hook) (void) = s_NCInitMallocHook;
--
-+*/
- #elif !defined(NCBI_OS_MSWIN)
- // Changing of C library allocation functions on Windows is very tricky (if
- // possible at all) and NetCache will never run in production on Windows. So
-

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch
deleted file mode 100644
index 9589481d4..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch
+++ /dev/null
@@ -1,114 +0,0 @@
-Index: include/db/bdb/bdb_file.hpp
-===================================================================
---- include/db/bdb/bdb_file.hpp	(revision 470126)
-+++ include/db/bdb/bdb_file.hpp	(working copy)
-@@ -660,6 +660,9 @@
-     void x_ConstructKeyBuf();
-     void x_ConstructDataBuf();
- 
-+    static int x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2,
-+                             size_t* locp);
-+
- private:
-     auto_ptr<CBDB_BufferManager>   m_KeyBuf;
-     auto_ptr<CBDB_BufferManager>   m_DataBuf;
-Index: src/db/bdb/bdb_blob.cpp
-===================================================================
---- src/db/bdb/bdb_blob.cpp	(revision 470126)
-+++ src/db/bdb/bdb_blob.cpp	(working copy)
-@@ -583,12 +583,31 @@
-     return m_DBT_Data->size;
- }
- 
-+#if DB_VERSION_MAJOR >= 6
-+extern "C" {
-+    typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*,
-+                                          size_t*);
-+    int BDB_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*)
-+        { return BDB_Uint4Compare(db, dbt1, dbt2); }
-+    int BDB_ByteSwap_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2,
-+                                    size_t*)
-+        { return BDB_ByteSwap_Uint4Compare(db, dbt1, dbt2); }
-+}
-+#endif
-+
- void CBDB_LobFile::SetCmp(DB*)
- {
-+#if DB_VERSION_MAJOR >= 6
-+    BDB_CompareFunction_V6 func = BDB_Uint4Compare_V6;
-+    if (IsByteSwapped()) {
-+        func = BDB_ByteSwap_Uint4Compare_V6;
-+    }
-+#else
-     BDB_CompareFunction func = BDB_Uint4Compare;
-     if (IsByteSwapped()) {
-         func = BDB_ByteSwap_Uint4Compare;
-     }
-+#endif
- 
-     _ASSERT(func);
-     int ret = m_DB->set_bt_compare(m_DB, func);
-Index: src/db/bdb/bdb_file.cpp
-===================================================================
---- src/db/bdb/bdb_file.cpp	(revision 470126)
-+++ src/db/bdb/bdb_file.cpp	(working copy)
-@@ -1535,12 +1535,27 @@
- }
- 
- 
-+#if DB_VERSION_MAJOR >= 6
-+int CBDB_File::x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*)
-+{
-+    const CBDB_BufferManager* key_buf
-+        = static_cast<const CBDB_BufferManager*>(db->app_private);
-+    _ASSERT(key_buf);
-+    return (key_buf->GetCompareFunction())(db, dbt1, dbt2);
-+}
-+#endif
-+
-+
- void CBDB_File::SetCmp(DB* db)
- {
-     _ASSERT(m_DB_Type == eBtree);
-+#if DB_VERSION_MAJOR >= 6
-+    int ret = db->set_bt_compare(db, x_CompareShim);
-+#else
-     BDB_CompareFunction func = m_KeyBuf->GetCompareFunction();
-     _ASSERT(func);
-     int ret = db->set_bt_compare(db, func);
-+#endif
-     BDB_CHECK(ret, 0);
- 
-     if (m_PrefixCompress) {
-@@ -2056,12 +2071,31 @@
-     BindKey("id", &IdKey);
- }
- 
-+#if DB_VERSION_MAJOR >= 6
-+extern "C" {
-+    typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*,
-+                                          size_t*);
-+    int BDB_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*)
-+        { return BDB_Int4Compare(db, dbt1, dbt2); }
-+    int BDB_ByteSwap_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2,
-+                                    size_t*)
-+        { return BDB_ByteSwap_Int4Compare(db, dbt1, dbt2); }
-+}
-+#endif
-+
- void CBDB_IdFile::SetCmp(DB* /* db */)
- {
-+#if DB_VERSION_MAJOR >= 6
-+    BDB_CompareFunction_V6 func = BDB_Int4Compare_V6;
-+    if (IsByteSwapped()) {
-+        func = BDB_ByteSwap_Int4Compare_V6;
-+    }
-+#else
-     BDB_CompareFunction func = BDB_Int4Compare;
-     if (IsByteSwapped()) {
-         func = BDB_ByteSwap_Int4Compare;
-     }
-+#endif
- 
-     _ASSERT(func);
-     int ret = m_DB->set_bt_compare(m_DB, func);

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch
deleted file mode 100644
index 3ed3e7d5f..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch
+++ /dev/null
@@ -1,64 +0,0 @@
- src/build-system/configure.ac | 17 ++++++++++++++---
- 1 file changed, 14 insertions(+), 3 deletions(-)
-
-diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac
-index 03e34b4..336453d 100644
---- a/src/build-system/configure.ac
-+++ b/src/build-system/configure.ac
-@@ -224,7 +224,7 @@ AC_ARG_WITH(ncbi-c,
- AC_ARG_WITH(sss,
-    [ --without-sss           do not use NCBI SSS libraries])
- AC_ARG_WITH(sssutils,
--   [ --without-utils         do not use NCBI SSS UTIL library])
-+   [ --without-sssutils      do not use NCBI SSS UTIL library])
- AC_ARG_WITH(sssdb,
-    [ --without-sssdb         do not use NCBI SSS DB library])
- AC_ARG_WITH(included-sss,
-@@ -490,13 +490,13 @@ check ncbi-public strip pch caution ccache distcc \
- ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
- geo included-geo \
- z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
- bdb python perl jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt libexslt xerces xalan zorba \
- oechem sge muparser hdf5 \
- gif jpeg tiff png xpm magic curl mimetic 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench"
-+serial objects dbapi app ctools gui algo internal gbench x"
- 
- changequote(, )dnl
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-@@ -522,6 +522,7 @@ for x_arg in "$@" ; do
-    case "$x_arg" in
-       --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
-       | --cache-file= | --build= | --host= | --target= | --with-runpath= \
-+      | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
-       | --with-relative-runpath= | --x-includes= | --x-libraries= )
-       AC_MSG_ERROR([$x_arg:  requires value;  use --help to show usage])
-       ;;
-@@ -532,6 +533,7 @@ for x_arg in "$@" ; do
-       | --with-universal=* | --with-tcheck=* \
-       | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
-       | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
-+      | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
-       | [[A-Z]*=*] \
-       | --with-z=* | --with-bz2=* | --with-lzo=* \
-       | --with-pcre=* \
-@@ -647,6 +649,15 @@ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-       *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-    esac
- fi
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
-+fi
- 
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
deleted file mode 100644
index d44993da2..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
+++ /dev/null
@@ -1,216 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ori	2014-06-25 23:47:05.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure	2014-06-25 23:52:35.000000000 +0200
-@@ -927,7 +927,7 @@
-  --without-distcc        do not automatically use distcc if available
-  --without-ncbi-c        do not use NCBI C Toolkit
-  --without-sss           do not use NCBI SSS libraries
-- --without-utils         do not use NCBI SSS UTIL library
-+ --without-sssutils      do not use NCBI SSS UTIL library
-  --without-sssdb         do not use NCBI SSS DB library
-  --with-included-sss     use the in-tree copy of SSS
-  --with-z=DIR            use zlib installation in DIR
-@@ -2965,13 +2965,13 @@
- ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
- geo included-geo \
- z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
- bdb python perl jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt libexslt xerces xalan zorba \
- oechem sge muparser hdf5 \
- gif jpeg tiff png xpm magic curl mimetic 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench"
-+serial objects dbapi app ctools gui algo internal gbench x"
- 
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
- 
-@@ -2995,6 +2995,7 @@
-    case "$x_arg" in
-       --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
-       | --cache-file= | --build= | --host= | --target= | --with-runpath= \
-+      | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
-       | --with-relative-runpath= | --x-includes= | --x-libraries= )
-       { { echo "$as_me:$LINENO: error: $x_arg:  requires value;  use --help to show usage" >&5
- echo "$as_me: error: $x_arg:  requires value;  use --help to show usage" >&2;}
-@@ -3007,6 +3008,7 @@
-       | --with-universal=* | --with-tcheck=* \
-       | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
-       | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
-+      | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
-       | [A-Z]*=* \
-       | --with-z=* | --with-bz2=* | --with-lzo=* \
-       | --with-pcre=* \
-@@ -3201,6 +3203,17 @@
-       *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-    esac
- fi
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5
-+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;}
-+   { (exit 1); exit 1; }; }
-+fi
- 
- #### Always define this
- 
-@@ -17878,68 +17891,6 @@
- fi
- 
- 
--echo "$as_me:$LINENO: checking for std::is_sorted<> in <algorithm>" >&5
--echo $ECHO_N "checking for std::is_sorted<> in <algorithm>... $ECHO_C" >&6
--if test "${ncbi_cv_func_is_sorted+set}" = set; then
--  echo $ECHO_N "(cached) $ECHO_C" >&6
--else
--  cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h.  */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h.  */
--#include <algorithm>
--int
--main ()
--{
--int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;
--  ;
--  return 0;
--}
--_ACEOF
--rm -f conftest.$ac_objext
--if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
--  (eval $ac_compile) 2>conftest.er1
--  ac_status=$?
--  grep -v '^ *+' conftest.er1 >conftest.err
--  rm -f conftest.er1
--  cat conftest.err >&5
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); } &&
--	 { ac_try='test -z "$ac_cxx_werror_flag"
--			 || test ! -s conftest.err'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; } &&
--	 { ac_try='test -s conftest.$ac_objext'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; }; then
--  ncbi_cv_func_is_sorted=yes
--else
--  echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--ncbi_cv_func_is_sorted=no
--fi
--rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
--fi
--echo "$as_me:$LINENO: result: $ncbi_cv_func_is_sorted" >&5
--echo "${ECHO_T}$ncbi_cv_func_is_sorted" >&6
--if test "$ncbi_cv_func_is_sorted" = yes; then
--
--cat >>confdefs.h <<\_ACEOF
--#define HAVE_IS_SORTED 1
--_ACEOF
--
--fi
--
--
- 
- echo "$as_me:$LINENO: checking for SysV semaphores" >&5
- echo $ECHO_N "checking for SysV semaphores... $ECHO_C" >&6
-@@ -18550,7 +18501,7 @@
-   echo $ECHO_N "(cached) $ECHO_C" >&6
- else
-   ncbi_cv_c_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_c_restrict" = "no" || break
-        cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
-@@ -18620,7 +18571,7 @@
-   echo $ECHO_N "(cached) $ECHO_C" >&6
- else
-   ncbi_cv_cxx_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_cxx_restrict" = "no" || break
-        cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
-@@ -19046,67 +18997,6 @@
- _ACEOF
- 
- fi
--
--echo "$as_me:$LINENO: checking whether $CXX supports C++0x nullptr" >&5
--echo $ECHO_N "checking whether $CXX supports C++0x nullptr... $ECHO_C" >&6
--if test "${ncbi_cv_cxx_nullptr+set}" = set; then
--  echo $ECHO_N "(cached) $ECHO_C" >&6
--else
--  cat >conftest.$ac_ext <<_ACEOF
--/* confdefs.h.  */
--_ACEOF
--cat confdefs.h >>conftest.$ac_ext
--cat >>conftest.$ac_ext <<_ACEOF
--/* end confdefs.h.  */
--
--int
--main ()
--{
--void * p = nullptr;
--  ;
--  return 0;
--}
--_ACEOF
--rm -f conftest.$ac_objext
--if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
--  (eval $ac_compile) 2>conftest.er1
--  ac_status=$?
--  grep -v '^ *+' conftest.er1 >conftest.err
--  rm -f conftest.er1
--  cat conftest.err >&5
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); } &&
--	 { ac_try='test -z "$ac_cxx_werror_flag"
--			 || test ! -s conftest.err'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; } &&
--	 { ac_try='test -s conftest.$ac_objext'
--  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
--  (eval $ac_try) 2>&5
--  ac_status=$?
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); }; }; then
--  ncbi_cv_cxx_nullptr=yes
--else
--  echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--ncbi_cv_cxx_nullptr=no
--fi
--rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
--fi
--echo "$as_me:$LINENO: result: $ncbi_cv_cxx_nullptr" >&5
--echo "${ECHO_T}$ncbi_cv_cxx_nullptr" >&6
--if test "$ncbi_cv_cxx_nullptr" = yes; then
--
--cat >>confdefs.h <<\_ACEOF
--#define HAVE_NULLPTR 1
--_ACEOF
--
--fi
- 
- ### Check for the availability of other packages
- ### --------------------------------------------

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
deleted file mode 100644
index fad02c38e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
+++ /dev/null
@@ -1,44 +0,0 @@
---- ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app.ori	2014-06-26 16:46:27.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app	2014-06-26 16:47:26.000000000 +0200
-@@ -9,7 +9,7 @@
- APP = speedtest
- SRC = speedtest
- LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \
--      xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
-+      xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
- 
---- ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app.ori	2014-06-26 16:47:53.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app	2014-06-26 16:48:07.000000000 +0200
-@@ -7,7 +7,7 @@
- 
- LIB =  xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \
-        taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \
--       $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC))
-+       $(BLAST_LIBS) $(OBJMGR_LIBS)
- 
- LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-
---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app.ori	2014-06-26 17:45:11.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app	2014-06-26 17:48:26.000000000 +0200
-@@ -3,7 +3,7 @@
- APP = igblastp
- SRC = igblastp_app
- LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
--LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
-+LIB = blast_app_util igblast $(LIB_)
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
- CFLAGS   = $(FAST_CFLAGS:ppc=i386)
---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app.ori	2014-06-26 17:47:53.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app	2014-06-26 17:49:31.000000000 +0200
-@@ -3,7 +3,7 @@
- APP = igblastn
- SRC = igblastn_app
- LIB_ = $(BLAST_INPUT_LIBS)  xalgoalignutil xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) 
--LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
-+LIB = blast_app_util igblast $(LIB_)
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
- CFLAGS   = $(FAST_CFLAGS:ppc=i386)

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch
deleted file mode 100644
index fede70e51..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- src/app/agpconvert/Makefile.agpconvert.app.ori	2013-09-13 23:56:22.660032261 +0200
-+++ src/app/agpconvert/Makefile.agpconvert.app	2013-09-13 23:57:31.340032441 +0200
-@@ -6,13 +6,12 @@
- APP = agpconvert
- SRC = agpconvert
- 
--LIB  = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \
--    ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
--LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+LIB  = $(OBJREAD_LIBS) taxon1 xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
-+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
--REQUIRES = objects algo
-+REQUIRES = objects
- 
- WATCHERS = xiangcha

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch
deleted file mode 100644
index 46c2e83fb..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/objtools/alnmgr/demo/Makefile.alnmrg.app.ori	2013-09-13 23:51:34.340031508 +0200
-+++ src/objtools/alnmgr/demo/Makefile.alnmrg.app	2013-09-13 23:51:36.660031514 +0200
-@@ -5,7 +5,7 @@
- SRC = alnmrg
- 
- LIB = xalnmgr $(OBJREAD_LIBS) ncbi_xloader_blastdb seqdb xobjutil submit blastdb \
--      tables $(OBJMGR_LIBS)
-+      tables creaders $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
deleted file mode 100644
index 97e845fdb..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori	2014-06-26 22:49:49.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top	2014-06-26 22:50:57.000000000 +0200
-@@ -48,7 +48,7 @@
- 	    for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
- 	cd $(includedir0) && find * -name CVS -prune -o -print |\
-             cpio -pd $(pincludedir)
--	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)
-+	$(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
- ## set up appropriate build and status directories somewhere under $(libdir)?
- 
- install-gbench:

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch
deleted file mode 100644
index 8bba91f1d..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- scripts/common/new_project.sh      (revision 408264)
-+++ scripts/common/new_project.sh      (working copy)
-@@ -6,7 +6,7 @@
- svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"`
- def_builddir="$NCBI/c++/Debug/build"
- 
--repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit'
-+repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1'
- tmp_app_checkout_dir='tmp_app_sample'
- stem='sample/app'

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch
deleted file mode 100644
index 553e41d29..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori     (revision 439078)
-+++ ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app     (working copy)
-@@ -7,8 +7,8 @@
- SRC = agpconvert
- 
- LIB  = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \
--    ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
--LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+       tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
-+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch
deleted file mode 100644
index 86e96b865..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch
+++ /dev/null
@@ -1,421 +0,0 @@
-Index: src/algo/blast/format/Makefile.xblastformat.lib
-===================================================================
---- src/algo/blast/format/Makefile.xblastformat.lib	(revision 439078)
-+++ src/algo/blast/format/Makefile.xblastformat.lib	(working copy)
-@@ -7,6 +7,6 @@
- 
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
- 
--DLL_LIB = align_format blastxml xhtml xcgi
-+DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi
- 
- WATCHERS = jianye zaretska madden camacho fongah2
-Index: src/app/compart/Makefile.compart.app
-===================================================================
---- src/app/compart/Makefile.compart.app	(revision 439078)
-+++ src/app/compart/Makefile.compart.app	(working copy)
-@@ -5,11 +5,11 @@
- APP = compart
- SRC = compart
- 
--LIB =  xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \
--       $(BLAST_LIBS:%=%$(STATIC)) \
--       $(OBJMGR_LIBS:%=%$(STATIC))
-+LIB =  xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \
-+       taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \
-+       $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC))
- 
--LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
-Index: src/app/compart/Makefile.compartp.app
-===================================================================
---- src/app/compart/Makefile.compartp.app	(revision 439078)
-+++ src/app/compart/Makefile.compartp.app	(working copy)
-@@ -5,7 +5,8 @@
- APP = compartp
- SRC = compartp
- 
--LIB = prosplign  xalgoalignutil $(BLAST_LIBS)  xqueryparse $(OBJMGR_LIBS)
-+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \
-+      xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: src/app/grid/util/Makefile.ncfetch.app
-===================================================================
---- src/app/grid/util/Makefile.ncfetch.app	(revision 439078)
-+++ src/app/grid/util/Makefile.ncfetch.app	(working copy)
-@@ -5,7 +5,7 @@
- APP = ncfetch.cgi
- SRC = ncfetch
- 
--LIB = xcgi xconnserv xconnect xutil xncbi
-+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- WATCHERS = kazimird
-Index: src/app/hfilter/Makefile.hfilter.app
-===================================================================
---- src/app/hfilter/Makefile.hfilter.app	(revision 439078)
-+++ src/app/hfilter/Makefile.hfilter.app	(working copy)
-@@ -5,9 +5,10 @@
- APP = hfilter
- SRC = hitfilter_app
- 
--LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS)
-+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \
-+      xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
--LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
-Index: src/app/speedtest/Makefile.speedtest.app
-===================================================================
---- src/app/speedtest/Makefile.speedtest.app	(revision 439078)
-+++ src/app/speedtest/Makefile.speedtest.app	(working copy)
-@@ -8,7 +8,7 @@
- 
- APP = speedtest
- SRC = speedtest
--LIB = prosplign xalgoalignutil xcleanup submit $(BLAST_LIBS) \
-+LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \
-       xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
- 
- LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
-Index: src/app/splign/Makefile.splign.app
-===================================================================
---- src/app/splign/Makefile.splign.app	(revision 439078)
-+++ src/app/splign/Makefile.splign.app	(working copy)
-@@ -12,7 +12,7 @@
- LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \
-       $(BLAST_DB_DATA_LOADER_LIBS) \
-       ncbi_xloader_lds2 lds2 sqlitewrapp \
--      xqueryparse xalgoseq $(PCRE_LIB) \
-+      xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \
-       $(BLAST_LIBS:%=%$(STATIC)) submit \
-       $(OBJMGR_LIBS:%=%$(STATIC))
- 
-Index: src/connect/services/test/Makefile.test_nsstorage.app
-===================================================================
---- src/connect/services/test/Makefile.test_nsstorage.app	(revision 439078)
-+++ src/connect/services/test/Makefile.test_nsstorage.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = test_nsstorage
- SRC = test_nsstorage
--LIB = xconnserv xconnect xutil xncbi
-+LIB = xconnserv xthrserv xconnect xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: src/misc/hgvs/test/Makefile.hgvs2variation.app
-===================================================================
---- src/misc/hgvs/test/Makefile.hgvs2variation.app	(revision 439078)
-+++ src/misc/hgvs/test/Makefile.hgvs2variation.app	(working copy)
-@@ -6,7 +6,7 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB_ = hgvs variation \
-+LIB_ = hgvs objcoords variation \
-        entrez2cli entrez2 xregexp $(PCRE_LIB) xobjutil $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- 
-Index: src/misc/hgvs/test/Makefile.test_hgvs_parser.app
-===================================================================
---- src/misc/hgvs/test/Makefile.test_hgvs_parser.app	(revision 439078)
-+++ src/misc/hgvs/test/Makefile.test_hgvs_parser.app	(working copy)
-@@ -5,7 +5,7 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB_ = hgvs variation test_boost xregexp $(PCRE_LIB) xobjutil \
-+LIB_ = hgvs objcoords variation test_boost xregexp $(PCRE_LIB) xobjutil \
-        entrez2cli entrez2 $(OBJMGR_LIBS)
- 
- LIB = $(LIB_:%=%$(STATIC))
-Index: src/objects/biblio/Makefile.biblio.lib
-===================================================================
---- src/objects/biblio/Makefile.biblio.lib	(revision 439078)
-+++ src/objects/biblio/Makefile.biblio.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-+
-+DLL_LIB = general
-Index: src/objects/blast/Makefile.blast.lib
-===================================================================
---- src/objects/blast/Makefile.blast.lib	(revision 439078)
-+++ src/objects/blast/Makefile.blast.lib	(working copy)
-@@ -1,4 +1,6 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
- 
-+DLL_LIB = scoremat seqset
-+
- WATCHERS = camacho
-Index: src/objects/blast/Makefile.xnetblastcli.lib
-===================================================================
---- src/objects/blast/Makefile.xnetblastcli.lib	(revision 439078)
-+++ src/objects/blast/Makefile.xnetblastcli.lib	(working copy)
-@@ -2,3 +2,5 @@
- 
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-+
-+DLL_LIB = xnetblast xconnect
-Index: src/objects/blastdb/Makefile.blastdb.lib
-===================================================================
---- src/objects/blastdb/Makefile.blastdb.lib	(revision 439078)
-+++ src/objects/blastdb/Makefile.blastdb.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = blastdb
- SRC = blastdb__ blastdb___
-+
-+DLL_LIB = seq
-Index: src/objects/general/Makefile.general.lib
-===================================================================
---- src/objects/general/Makefile.general.lib	(revision 439078)
-+++ src/objects/general/Makefile.general.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = general
- SRC = general__ general___ uoconv
-+
-+DLL_LIB = xser
-Index: src/objects/medline/Makefile.medline.lib
-===================================================================
---- src/objects/medline/Makefile.medline.lib	(revision 439078)
-+++ src/objects/medline/Makefile.medline.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = medline
- SRC = medline__ medline___
-+
-+DLL_LIB = biblio general
-Index: src/objects/pub/Makefile.pub.lib
-===================================================================
---- src/objects/pub/Makefile.pub.lib	(revision 439078)
-+++ src/objects/pub/Makefile.pub.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = pub
- SRC = pub__ pub___
-+
-+DLL_LIB = medline biblio
-Index: src/objects/scoremat/Makefile.scoremat.lib
-===================================================================
---- src/objects/scoremat/Makefile.scoremat.lib	(revision 439078)
-+++ src/objects/scoremat/Makefile.scoremat.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-+
-+DLL_LIB = seqset
-Index: src/objects/seq/Makefile.seq.lib
-===================================================================
---- src/objects/seq/Makefile.seq.lib	(revision 439078)
-+++ src/objects/seq/Makefile.seq.lib	(working copy)
-@@ -13,3 +13,5 @@
-       seq_loc_from_string seq_loc_reverse_complementer
- 
- WATCHERS = vasilche grichenk
-+
-+DLL_LIB = seqcode pub biblio general xser sequtil
-Index: src/objects/seqset/Makefile.seqset.lib
-===================================================================
---- src/objects/seqset/Makefile.seqset.lib	(revision 439078)
-+++ src/objects/seqset/Makefile.seqset.lib	(working copy)
-@@ -1,2 +1,4 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-+
-+DLL_LIB = xser
-Index: src/objects/taxon1/Makefile.taxon1.lib
-===================================================================
---- src/objects/taxon1/Makefile.taxon1.lib	(revision 439078)
-+++ src/objects/taxon1/Makefile.taxon1.lib	(working copy)
-@@ -3,4 +3,6 @@
- LIB = taxon1
- SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont
- 
-+DLL_LIB = xconnect
-+
- WATCHERS = domrach
-Index: src/objmgr/util/Makefile.util.lib
-===================================================================
---- src/objmgr/util/Makefile.util.lib	(revision 439078)
-+++ src/objmgr/util/Makefile.util.lib	(working copy)
-@@ -8,5 +8,7 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
- LIB = xobjutil
- 
-+DLL_LIB = xobjmgr
-+
- WATCHERS = ucko vasilche
- 
-Index: src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-===================================================================
---- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib	(revision 439078)
-+++ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib	(working copy)
-@@ -29,4 +29,6 @@
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
-+DLL_LIB = xobjmgr blastdb
-+
- WATCHERS = maning camacho
-Index: src/objtools/blast/services/Makefile.blast_services.lib
-===================================================================
---- src/objtools/blast/services/Makefile.blast_services.lib	(revision 439078)
-+++ src/objtools/blast/services/Makefile.blast_services.lib	(working copy)
-@@ -13,3 +13,4 @@
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
-+DLL_LIB = xnetblastcli xconnect
-Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-===================================================================
---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib	(revision 439078)
-+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib	(working copy)
-@@ -7,4 +7,6 @@
- 
- ASN_DEP = blastdb seqset
- 
-+DLL_LIB = seqdb
-+
- WATCHERS = camacho
-Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-===================================================================
---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib	(revision 439078)
-+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib	(working copy)
-@@ -7,4 +7,6 @@
- 
- ASN_DEP = blastdb xnetblast
- 
-+DLL_LIB = blast_services
-+
- WATCHERS = camacho
-Index: src/objtools/lds2/Makefile.lds2.lib
-===================================================================
---- src/objtools/lds2/Makefile.lds2.lib	(revision 439078)
-+++ src/objtools/lds2/Makefile.lds2.lib	(working copy)
-@@ -8,9 +8,9 @@
- SRC = lds2 lds2_db lds2_handlers
- 
- # Dependencies for shared library
--#DLL_LIB = sqlitewrapp
-+DLL_LIB = sqlitewrapp $(COMPRESS_LIBS)
- 
--LIBS = $(CMPRS_LIBS) $(ORIG_LIBS)
-+LIBS = $(SQLITE3_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS)
- 
- CPPFLAGS = $(SQLITE3_INCLUDE) $(CMPRS_INCLUDE) $(ORIG_CPPFLAGS)
- 
-Index: src/objtools/readers/Makefile.xobjread.lib
-===================================================================
---- src/objtools/readers/Makefile.xobjread.lib	(revision 439078)
-+++ src/objtools/readers/Makefile.xobjread.lib	(working copy)
-@@ -19,5 +19,6 @@
-       best_feat_finder source_mod_parser fasta_exception
- 
- 
--DLL_LIB = creaders
-+DLL_LIB = seqset $(SEQ_LIBS) pub general creaders xutil
- 
-+
-Index: src/sample/app/cgi/Makefile.cgi_session_sample.app
-===================================================================
---- src/sample/app/cgi/Makefile.cgi_session_sample.app	(revision 439078)
-+++ src/sample/app/cgi/Makefile.cgi_session_sample.app	(working copy)
-@@ -11,7 +11,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
-+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: src/sample/app/netcache/Makefile.netcache_cgi_sample.app
-===================================================================
---- src/sample/app/netcache/Makefile.netcache_cgi_sample.app	(revision 439078)
-+++ src/sample/app/netcache/Makefile.netcache_cgi_sample.app	(working copy)
-@@ -4,7 +4,7 @@
- SRC = netcache_cgi_sample
- 
- ### BEGIN COPIED SETTINGS
--LIB = xconnserv xconnect xcgi xhtml xutil xncbi
-+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- ### END COPIED SETTINGS
-Index: src/serial/Makefile.serial.lib
-===================================================================
---- src/serial/Makefile.serial.lib	(revision 439078)
-+++ src/serial/Makefile.serial.lib	(working copy)
-@@ -19,3 +19,5 @@
- LIB    = xser
- 
- WATCHERS = gouriano
-+
-+DLL_LIB = xutil xncbi
-Index: src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app
-===================================================================
---- src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app	(revision 439078)
-+++ src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app	(working copy)
-@@ -7,7 +7,8 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB = ncbi_xloader_bam bamread $(BAM_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS)
-+LIB = ncbi_xloader_bam bamread $(BAM_LIBS) \
-+      xobjreadex $(OBJREAD_LIBS) xobjutil test_boost $(OBJMGR_LIBS)
- 
- LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 
-Index: src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app
-===================================================================
---- src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app	(revision 439078)
-+++ src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app	(working copy)
-@@ -5,7 +5,8 @@
- 
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
- 
--LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS)
-+LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil \
-+      test_boost $(OBJMGR_LIBS)
- 
- LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 
-Index: src/sra/readers/bam/test/Makefile.bam_test.app
-===================================================================
---- src/sra/readers/bam/test/Makefile.bam_test.app	(revision 439078)
-+++ src/sra/readers/bam/test/Makefile.bam_test.app	(working copy)
-@@ -9,7 +9,8 @@
- APP = bam_test
- SRC = bam_test
- 
--LIB =   bamread xobjreadex xobjutil xobjsimple $(OBJMGR_LIBS) $(BAM_LIBS)
-+LIB =   bamread $(BAM_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil xobjsimple \
-+        $(OBJMGR_LIBS)
- LIBS =  $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
- 
- REQUIRES = objects
-Index: src/sra/sdk/libs/vfs/Makefile.vfs.lib
-===================================================================
---- src/sra/sdk/libs/vfs/Makefile.vfs.lib	(revision 16076)
-+++ src/sra/sdk/libs/vfs/Makefile.vfs.lib	(working copy)
-@@ -8,6 +8,9 @@
- CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \
-            $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS)
- 
--DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
-+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) \
-+          krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
- 
-+LIBS = $(SRA_SDK_SYSLIBS)
-+
- LIB_OR_DLL = both

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch
deleted file mode 100644
index 449bbc5a9..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch
+++ /dev/null
@@ -1,136 +0,0 @@
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h.ori     2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h     2013/09/30 14:10:44     59962
-@@ -62,10 +62,6 @@
- #define HAVE_SYS_TYPES_H 1
- #define HAVE_VSNPRINTF   1
- 
--#if _MSC_VER >= 1600
--#  define HAVE_IS_SORTED   1
--#endif
--
- #if _MSC_VER < 1500
- #  define vsnprintf        _vsnprintf
- #endif
-@@ -136,10 +132,6 @@
- 
- #endif
- 
--#if _MSC_VER >= 1600
--#  define HAVE_NULLPTR  1
--#endif
--
- /* Windows XP and above */
- #define NCBI_WIN32_WINNT 0x0501
- #if !defined(_WIN32_WINNT)
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori    2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h    2013/09/30 14:10:44     59962
-@@ -258,9 +258,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #define HAVE_IOS_REGISTER_CALLBACK 1
- 
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--/* #undef HAVE_IS_SORTED */
--
- /* Define to 1 if you have the `lchown' function. */
- /* #undef HAVE_LCHOWN */
- 
-@@ -595,9 +592,6 @@
- /* Define to 1 if wxWidgets is available. */
- /* #undef HAVE_WXWIDGETS */
- 
--/* Define to 1 if nullptr keyword is available. */
--/* #undef HAVE_NULLPTR */
--
- /* Define as const if the declaration of iconv() needs const. */
- #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
- #  define ICONV_CONST
---- ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h.ori    2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h    2013/09/30 14:10:44     59962
-@@ -115,6 +115,11 @@
-       || defined(__GXX_EXPERIMENTAL_CPP0X__)
- #    define NCBI_HAVE_CXX11 1
- #  endif
-+#  if defined(NCBI_HAVE_CXX11) \
-+      ||  (defined(NCBI_COMPILER_MSVC)  &&  _MSC_VER >= 1600)
-+#    define HAVE_IS_SORTED 1
-+#    define HAVE_NULLPTR 1
-+#  endif
- #endif
- 
- #include <common/ncbi_skew_guard.h>
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori      2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in      2013/09/30 14:10:44     59962
-@@ -179,9 +179,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #undef HAVE_IOS_REGISTER_CALLBACK
- 
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--#undef HAVE_IS_SORTED
--
- /* Define to 1 if you have the `lchown' function. */
- #undef HAVE_LCHOWN
- 
-@@ -391,9 +388,6 @@
- /* Define to 1 if `min'/`max' templates are not implemented. */
- #undef HAVE_NO_MINMAX_TEMPLATE
- 
--/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
--#undef HAVE_NULLPTR
--
- /* Define to 1 if ODBC libraries are available. */
- #undef HAVE_ODBC
- 
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori     2013/09/30 13:46:04     59961
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac     2013/09/30 14:10:44     59962
-@@ -3351,17 +3351,6 @@
- fi
- 
- 
--AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
--   [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
--       [[#include <algorithm>]],
--       [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
--       [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
--if test "$ncbi_cv_func_is_sorted" = yes; then
--   AC_DEFINE(HAVE_IS_SORTED, 1,
--             [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
--fi
--
--
- 
- AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
-    AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
-@@ -3498,7 +3487,7 @@
- AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
-    ncbi_cv_c_restrict,
-    [ncbi_cv_c_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_c_restrict" = "no" || break
-        AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
-           [ncbi_cv_c_restrict=$restrict], [])
-@@ -3518,7 +3507,7 @@
- AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
-    ncbi_cv_cxx_restrict,
-    [ncbi_cv_cxx_restrict=no
--    for restrict in restrict __restrict__ __restrict; do
-+    for restrict in __restrict__ __restrict restrict; do
-        test "$ncbi_cv_cxx_restrict" = "no" || break
-        AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
-           [ncbi_cv_cxx_restrict=$restrict], [])
-@@ -3623,14 +3612,6 @@
-               unaligned addresses.])
- fi
- 
--AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
--   [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
--       [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
--if test "$ncbi_cv_cxx_nullptr" = yes; then
--   AC_DEFINE(HAVE_NULLPTR, 1,
--      [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
--fi
--
- ### Check for the availability of other packages
- ### --------------------------------------------
- 
-

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
deleted file mode 100644
index 68baea046..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori	2016-12-01 20:28:33.239758102 +0100
-+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in	2016-12-01 20:28:46.330110659 +0100
-@@ -7,7 +7,7 @@
- #################################
- 
- USR_PROJ = precompile
--LIB_PROJ = corelib test_mt test_boost
-+LIB_PROJ = corelib test_mt
- SUB_PROJ = test
- PROJ_TAG = core
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
deleted file mode 100644
index 9047c3384..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
+++ /dev/null
@@ -1,296 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori       2014/05/05 12:38:59     62744
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4       2014/05/05 13:59:33     62745
-@@ -1,126 +1,44 @@
--# Hacked up in various ways, since Autoconf's version doesn't quite
--# suit our (unusual) conventions.  (Originally from status.m4)
--m4_define([_AC_SRCPATHS],
--[#ac_builddir=. # Useless!
--ac_builddir=$builddir
--dnl Base source directories on path to *input* file.
--if test -n "$ac_file_in"; then
--   ac_dir_in=`AS_DIRNAME(["$ac_file_in"])`
-+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS)
-+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly.
-+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS])
-+m4_define([_AC_SRCDIRS],
-+[# Base source directories on path to *input* file.
-+if test -n "$ac_f"; then
-+   ac_dir_in=`AS_DIRNAME(["$ac_f"])`
- else
-    ac_dir_in=$1
- fi
- 
--if test $ac_dir_in != .; then
--  ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'`
--  # A "../" for each directory in $ac_dir_suffix.
--  ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'`
--else
--  ac_dir_suffix= ac_top_builddir=
--fi
-+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
- 
--case $srcdir in
--  .)  # No --srcdir option.  We are building in place.
--    ac_srcdir=.
--    if test -z "$ac_top_builddir"; then
--       ac_top_srcdir=.
--    else
--       ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
--    fi ;;
--  [[\\/]]* | ?:[[\\/]]* )  # Absolute path.
--    ac_srcdir=$srcdir/$ac_dir_suffix;
--    ac_top_srcdir=$srcdir ;;
--  *) # Relative path.
--    ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix
--    ac_top_srcdir=$ac_top_builddir$srcdir ;;
--esac
--# Do not use `cd foo && pwd` to compute absolute paths, because
--# the directories may not exist.
--AS_SET_CATFILE([ac_abs_builddir],   [$builddir],        [$1])
--AS_SET_CATFILE([ac_abs_top_builddir],
--                                    [$ac_abs_builddir], [${ac_top_builddir}.])
--AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in],       [$real_srcdir])
--AS_SET_CATFILE([ac_abs_srcdir],     [$ac_abs_top_srcdir], [$ac_dir_suffix])
--])# _AC_SRCPATHS
--
--
--# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a
--# last resort due to issues with sourcing .bashrc.
--m4_define([_AS_LINENO_PREPARE],
--[_AS_LINENO_WORKS || {
--  # Find who we are.  Look in the path if we contain no path at all
--  # relative or not.
--  case $[0] in
--    *[[\\/]]* ) as_myself=$[0] ;;
--    *) _AS_PATH_WALK([],
--                   [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break])
--       ;;
--  esac
--  # We did not find ourselves, most probably we were run as `sh COMMAND'
--  # in which case we are not to be found in the path.
--  if test "x$as_myself" = x; then
--    as_myself=$[0]
--  fi
--  if test ! -f "$as_myself"; then
--    AS_ERROR([cannot find myself; rerun with an absolute path])
--  fi
--  case $CONFIG_SHELL in
--  '')
--    AS_UNSET(ZSH_VERSION)
--    for as_base in sh ksh sh5 bash; do
--      _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH],
--         [case $as_dir in
--         /*)
--           if ("$as_dir/$as_base" -c \
--                 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null
--           then
--             AS_UNSET(BASH_ENV)
--             AS_UNSET(ENV)
--             CONFIG_SHELL=$as_dir/$as_base
--             export CONFIG_SHELL
--             exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"}
--           fi;;
--         esac
--       done]);;
--  esac
--
--  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
--  # uniformly replaced by the line number.  The first 'sed' inserts a
--  # line-number line before each line; the second 'sed' does the real
--  # work.  The second script uses 'N' to pair each line-number line
--  # with the numbered line, and appends trailing '-' during
--  # substitution so that $LINENO is not a special case at line end.
--  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
--  # second 'sed' script.  Blame Lee E. McMahon for sed's syntax.  :-)
--  sed '=' <$as_myself |
--    sed '
--      N
--      s,$,-,
--      : loop
--      s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3,
--      t loop
--      s,-$,,
--      s,^[['$as_cr_digits']]*\n,,
--    ' >$as_me.lineno &&
--  chmod +x $as_me.lineno ||
--    AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell])
--
--  # Don't try to exec as it changes $[0], causing all sort of problems
--  # (the dirname of $[0] is not the place where we might find the
--  # original and so on.  Autoconf is especially sensible to this).
--  . ./$as_me.lineno
--  # Exit status is that of the last command.
--  exit
--}
--])# _AS_LINENO_PREPARE
-+ac_builddir=$builddir
-+])
-+
-+
-+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
-+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
-+# bash a last resort due to issues with sourcing .bashrc while entirely
-+# avoiding zsh, which passes itself off as ksh on some systems but runs
-+# parent shells' exit handlers from subshells, resulting in premature
-+# cleanup of temporary files (notably confdefs.h).
-+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL])
-+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN])
-+
-+m4_define([_AS_DETECT_BETTER_SHELL],
-+  [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]),
-+     [sh bash ksh sh5], [sh ksh sh5 bash])])
-+m4_define([_AS_RUN],
-+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl
-+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])])
- 
- 
- # One more hack: suppress PACKAGE_*, as we don't use them and some
- # third-party libraries expose their corresponding settings, leading
- # to preprocessor warnings.
--m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED]))
-+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED])
- m4_define([AC_DEFINE_UNQUOTED],
-    [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [],
--       [NCBI_ORIG_ACDU($@)])])
-+       [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])])
- 
- 
- AC_DEFUN(NCBI_FIX_DIR,
-@@ -158,7 +76,7 @@
-        AC_MSG_WARN([Proceeding without questions per --without-caution]) ;;
-     * )
-        echo "$1 [[y/N]]"
--       read answer
-+       read answer <& AS_ORIGINAL_STDIN_FD
-        case "$answer" in
-          [[Yy]]* )  AC_MSG_WARN([Proceeding at your own risk...]) ;;
-          *       )  AC_MSG_ERROR([Configuration has been canceled by user.]) ;;
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori     2014/05/05 12:38:59     62744
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac     2014/05/05 13:59:33     62745
-@@ -38,7 +38,7 @@
- #
- #############################################################################
- 
--AC_PREREQ(2.59)
-+AC_PREREQ(2.60)
- 
- dnl Early setup, most crucially for locking.  The diversion magic lets
- dnl this occur before AC_INIT, which already interferes with other
-@@ -493,6 +493,10 @@
-    [***** See also HTML documentation in ./doc/index.html *****])
- 
- 
-+AC_DIVERT_PUSH(PARSE_ARGS)
-+dnl As of Autoconf 2.60, this needs to run too early for config.log,
-+dnl to which AC_MSG_ERROR normally copies its output, to be available.
-+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
- #### Check the passed arguments against the list of available ones
- x_with_list="\
- debug max-debug symbols optimization profiling tcheck dll static static-exe \
-@@ -564,7 +568,7 @@
-       | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
-       | --x-includes=* | --x-libraries=* | --with-3psw=* \
-       | --target=* | --with-runpath=* | --with-relative-runpath=* \
--      | --no-create | --no-recursion)
-+      | --help | --no-create | --no-recursion)
-       ;;
- 
-       * )
-@@ -572,6 +576,8 @@
-       ;;
-    esac
- done
-+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
-+AC_DIVERT_POP
- 
- 
- if test "$with_gbench" = "yes" ; then
-@@ -2176,7 +2182,7 @@
- fi
- 
- AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
--AC_PATH_PROG(GREP, grep)
-+dnl AC_PATH_PROG(GREP, grep)
- AC_PROG_EGREP
- AC_MSG_CHECKING([how to run $EGREP quietly])
- if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori    2014/05/05 14:10:55     62749
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h    2014/05/05 14:23:49     62750
-@@ -694,7 +694,7 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- /* #undef const */
- 
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- /* #undef size_t */
- 
- /*
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori      2014/05/05 14:10:55     62749
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in      2014/05/05 14:23:49     62750
-@@ -802,37 +802,37 @@
-    by a signal. */
- #undef SELECT_UPDATES_TIMEOUT
- 
--/* The size of a `char', as computed by sizeof. */
-+/* The size of `char', as computed by sizeof. */
- #undef SIZEOF_CHAR
- 
--/* The size of a `double', as computed by sizeof. */
-+/* The size of `double', as computed by sizeof. */
- #undef SIZEOF_DOUBLE
- 
--/* The size of a `float', as computed by sizeof. */
-+/* The size of `float', as computed by sizeof. */
- #undef SIZEOF_FLOAT
- 
--/* The size of a `int', as computed by sizeof. */
-+/* The size of `int', as computed by sizeof. */
- #undef SIZEOF_INT
- 
--/* The size of a `long', as computed by sizeof. */
-+/* The size of `long', as computed by sizeof. */
- #undef SIZEOF_LONG
- 
--/* The size of a `long double', as computed by sizeof. */
-+/* The size of `long double', as computed by sizeof. */
- #undef SIZEOF_LONG_DOUBLE
- 
--/* The size of a `long long', as computed by sizeof. */
-+/* The size of `long long', as computed by sizeof. */
- #undef SIZEOF_LONG_LONG
- 
--/* The size of a `short', as computed by sizeof. */
-+/* The size of `short', as computed by sizeof. */
- #undef SIZEOF_SHORT
- 
--/* The size of a `size_t', as computed by sizeof. */
-+/* The size of `size_t', as computed by sizeof. */
- #undef SIZEOF_SIZE_T
- 
--/* The size of a `void*', as computed by sizeof. */
-+/* The size of `void*', as computed by sizeof. */
- #undef SIZEOF_VOIDP
- 
--/* The size of a `__int64', as computed by sizeof. */
-+/* The size of `__int64', as computed by sizeof. */
- #undef SIZEOF___INT64
- 
- /* Define to 1 if the stack grows down. */
-@@ -873,5 +873,5 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- #undef const
- 
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- #undef size_t
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori       2014/05/06 13:12:18     62759
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4       2014/05/06 13:42:48     62760
-@@ -11,6 +11,7 @@
- 
- NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
- 
-+AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
- ac_builddir=$builddir
- ])
- 
-

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch
deleted file mode 100644
index b2d887c92..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ori	2014-06-25 23:47:05.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure	2014-06-25 23:52:35.000000000 +0200
-@@ -3201,6 +3203,17 @@
-       *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-    esac
- fi
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5
-+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;}
-+   { (exit 1); exit 1; }; }
-+fi
- 
- #### Always define this
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch
deleted file mode 100644
index c9428084d..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Index: c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app
-===================================================================
---- c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app	(revision 523253)
-+++ c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app	(working copy)
-@@ -8,8 +8,8 @@
- 
- APP = annotwriter
- SRC = annotwriter
--LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \
--      gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS)
-+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
-+      xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch
deleted file mode 100644
index 7a158dc5c..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Index: c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app
-===================================================================
---- c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app	(revision 523253)
-+++ c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app	(working copy)
-@@ -12,7 +12,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB_ = xobjsimple $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xobjsimple $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
-Index: c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app
-===================================================================
---- c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app	(revision 523253)
-+++ c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app	(working copy)
-@@ -12,7 +12,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch
deleted file mode 100644
index 749c2e57f..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Index: c++.18.0.0/src/app/compart/Makefile.compart.app
-===================================================================
---- c++.18.0.0/src/app/compart/Makefile.compart.app	(revision 523253)
-+++ c++.18.0.0/src/app/compart/Makefile.compart.app	(working copy)
-@@ -5,8 +5,8 @@
- APP = compart
- SRC = compart
- 
--LIB =  xalgoalignsplign xalgoalignutil xalgoalignnw xqueryparse \
--       $(BLAST_LIBS:%=%$(STATIC)) \
-+LIB =  xalgoalignsplign xalgoalignutil xalgoalignnw xalgoseq taxon1 \
-+       $(BLAST_LIBS:%=%$(STATIC)) xqueryparse xregexp $(PCRE_LIB) \
-        $(OBJMGR_LIBS:%=%$(STATIC))
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-Index: c++.18.0.0/src/app/compart/Makefile.compartp.app
-===================================================================
---- c++.18.0.0/src/app/compart/Makefile.compartp.app	(revision 523253)
-+++ c++.18.0.0/src/app/compart/Makefile.compartp.app	(working copy)
-@@ -5,7 +5,8 @@
- APP = compartp
- SRC = compartp
- 
--LIB = prosplign  xalgoalignutil $(BLAST_LIBS)  xqueryparse $(OBJMGR_LIBS)
-+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \
-+      xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch
deleted file mode 100644
index e495c9645..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app.ori	2017-03-23 19:24:31.534280319 +0100
-+++ ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app	2017-03-23 19:25:14.395360214 +0100
-@@ -2,7 +2,7 @@
- 
- APP = convert_seq
- SRC = convert_seq
--LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite \
-+LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite variation_utils \
-       $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil tables xregexp \
-       $(PCRE_LIB) $(OBJMGR_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch
deleted file mode 100644
index 63bbcc45a..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Index: c++.18.0.0/src/app/hfilter/Makefile.hfilter.app
-===================================================================
---- c++.18.0.0/src/app/hfilter/Makefile.hfilter.app	(revision 523253)
-+++ c++.18.0.0/src/app/hfilter/Makefile.hfilter.app	(working copy)
-@@ -5,7 +5,8 @@
- APP = hfilter
- SRC = hitfilter_app
- 
--LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS)
-+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \
-+	xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch
deleted file mode 100644
index ffd3f897f..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Index: c++.18.0.0/src/app/igblast/Makefile.igblastn.app
-===================================================================
---- c++.18.0.0/src/app/igblast/Makefile.igblastn.app	(revision 523253)
-+++ c++.18.0.0/src/app/igblast/Makefile.igblastn.app	(working copy)
-@@ -2,7 +2,8 @@
- 
- APP = igblastn
- SRC = igblastn_app
--LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \
-+	xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/igblast/Makefile.igblastp.app
-===================================================================
---- c++.18.0.0/src/app/igblast/Makefile.igblastp.app	(revision 523253)
-+++ c++.18.0.0/src/app/igblast/Makefile.igblastp.app	(working copy)
-@@ -2,7 +2,8 @@
- 
- APP = igblastp
- SRC = igblastp_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \
-+	xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
deleted file mode 100644
index fce7263b2..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app.ori	2017-03-26 18:49:50.431994978 +0200
-+++ ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app	2017-03-26 18:50:11.222552131 +0200
-@@ -2,7 +2,7 @@
- 
- APP = rmblastn
- SRC = rmblastn_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch
deleted file mode 100644
index 222cb2c06..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app.ori	2017-03-27 00:41:58.742206850 +0200
-+++ ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app	2017-03-27 00:43:13.142206236 +0200
-@@ -12,8 +12,8 @@
- 
- LIB  = xdiscrepancy xalgophytree fastme prosplign xalgoalignutil xalgoseq xmlwrapp \
-        xvalidate xobjwrite xobjreadex valerr biotree macro \
--       $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) id2cli \
--       xregexp $(PCRE_LIB) $(SRAREAD_LIBS) $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS)
-+       $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) taxon1 id2cli \
-+       xregexp $(PCRE_LIB) xqueryparse $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(LIBXSLT_LIBS) $(DATA_LOADERS_UTIL_LIBS) $(LIBXML_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) \
-        $(SRA_SDK_SYSLIBS) \

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
deleted file mode 100644
index 541dc2514..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app.ori	2017-03-27 02:33:36.312151540 +0200
-+++ ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app	2017-03-27 02:34:19.372151184 +0200
-@@ -10,7 +10,7 @@
- SRC = tls
- 
- LIB = $(OBJEDIT_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil \
--       xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
-+       xregexp $(PCRE_LIB) tables $(OBJMGR_LIBS)
- 
- LIBS = $(PCRE_LIBS) \
-        $(NETWORK_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS)

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
deleted file mode 100644
index 898e3a70b..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app
-===================================================================
---- c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app	(revision 523253)
-+++ c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = vecscreen
- SRC = vecscreen_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- # FIXME: do we need blast_app_util
- #LIB = blast_app_util $(LIB_:%=%$(STATIC))

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
deleted file mode 100644
index e9dd1f710..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
+++ /dev/null
@@ -1,130 +0,0 @@
-Index: c++.18.0.0/src/app/blast/Makefile.blast_formatter.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.blast_formatter.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.blast_formatter.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = blast_formatter
- SRC = blast_formatter
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.blastp.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.blastp.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.blastp.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = blastp
- SRC = blastp_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.blastx.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.blastx.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.blastx.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = blastx
- SRC = blastx_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.deltablast.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.deltablast.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.deltablast.app	(working copy)
-@@ -1,7 +1,7 @@
- 
- APP = deltablast
- SRC = deltablast_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.psiblast.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.psiblast.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.psiblast.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = psiblast
- SRC = psiblast_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.rpsblast.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.rpsblast.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.rpsblast.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = rpsblast
- SRC = rpsblast_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.rpstblastn.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.rpstblastn.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.rpstblastn.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = rpstblastn
- SRC = rpstblastn_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.seedtop.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.seedtop.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.seedtop.app	(working copy)
-@@ -2,7 +2,7 @@
- 
- APP = seedtop
- SRC = seedtop_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.tblastn.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.tblastn.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.tblastn.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = tblastn
- SRC = tblastn_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation
-Index: c++.18.0.0/src/app/blast/Makefile.tblastx.app
-===================================================================
---- c++.18.0.0/src/app/blast/Makefile.tblastx.app	(revision 523253)
-+++ c++.18.0.0/src/app/blast/Makefile.tblastx.app	(working copy)
-@@ -4,7 +4,7 @@
- 
- APP = tblastx
- SRC = tblastx_app
--LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
-+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIB = blast_app_util $(LIB_:%=%$(STATIC))
- 
- # De-universalize Mac builds to work around a PPC toolchain limitation

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch
deleted file mode 100644
index 97e845fdb..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori	2014-06-26 22:49:49.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top	2014-06-26 22:50:57.000000000 +0200
-@@ -48,7 +48,7 @@
- 	    for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
- 	cd $(includedir0) && find * -name CVS -prune -o -print |\
-             cpio -pd $(pincludedir)
--	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)
-+	$(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
- ## set up appropriate build and status directories somewhere under $(libdir)?
- 
- install-gbench:

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch
deleted file mode 100644
index aacb20a6c..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app.ori	2017-03-23 21:12:52.028724998 +0100
-+++ ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app	2017-03-23 21:13:30.079737366 +0100
-@@ -5,7 +5,7 @@
- APP = ncfetch.cgi
- SRC = ncfetch
- 
--LIB = xcgi xconnserv xconnect xutil xncbi
-+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 
- WATCHERS = sadyrovr

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch
deleted file mode 100644
index e074046cf..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori	2017-03-23 21:16:18.824226906 +0100
-+++ ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app	2017-03-23 21:16:50.085058615 +0100
-@@ -4,7 +4,7 @@
- SRC = netcache_cgi_sample
- 
- ### BEGIN COPIED SETTINGS
--LIB = xconnserv xconnect xcgi xhtml xutil xncbi
-+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- ### END COPIED SETTINGS

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch
deleted file mode 100644
index f237a86d8..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app.ori	2017-03-23 21:22:14.463688886 +0100
-+++ ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app	2017-03-23 21:22:48.854603873 +0100
-@@ -10,7 +10,7 @@
- REQUIRES = MT Linux
- 
- 
--LIB =  netstorage ncbi_xcache_netcache xconnserv \
-+LIB =  netstorage ncbi_xcache_netcache xconnserv xthrserv \
-        $(SDBAPI_LIB) xconnect connssl xutil xncbi
- LIBS = $(SDBAPI_LIBS) $(NETWORK_LIBS) $(GNUTLS_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch
deleted file mode 100644
index c45d4ad96..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori	2017-03-22 23:52:58.984696074 +0100
-+++ ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app	2017-03-22 23:53:54.746258126 +0100
-@@ -11,7 +11,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
-+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch
deleted file mode 100644
index 9435e8b6a..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app.ori	2017-03-23 21:41:31.084603405 +0100
-+++ ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app	2017-03-23 21:45:47.601428174 +0100
-@@ -8,7 +8,7 @@
- 
- APP = speedtest
- SRC = speedtest
--LIB = prosplign xalgoalignutil xcleanup taxon3 valid valerr $(BLAST_LIBS) \
-+LIB = prosplign xalgoalignutil taxon1 xalgoseq xcleanup taxon3 valid valerr $(BLAST_LIBS) \
-       xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch
deleted file mode 100644
index 56f213f08..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app.ori	2017-03-23 22:08:16.937327984 +0100
-+++ ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app	2017-03-23 22:09:19.208984755 +0100
-@@ -12,7 +12,7 @@
- LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \
-       $(BLAST_DB_DATA_LOADER_LIBS) \
-       ncbi_xloader_lds2 lds2 sqlitewrapp \
--      xqueryparse xalgoseq $(PCRE_LIB) \
-+      xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \
-       $(BLAST_LIBS:%=%$(STATIC)) \
-       $(OBJMGR_LIBS:%=%$(STATIC))
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
deleted file mode 100644
index 49a4adb4e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Index: c++.18.0.0/src/app/srcchk/Makefile.srcchk.app
-===================================================================
---- c++.18.0.0/src/app/srcchk/Makefile.srcchk.app	(revision 523253)
-+++ c++.18.0.0/src/app/srcchk/Makefile.srcchk.app	(working copy)
-@@ -8,8 +8,8 @@
- 
- APP = srcchk
- SRC = srcchk
--LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \
--      gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS)
-+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
-+      xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- 
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
deleted file mode 100644
index f0a27d85a..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- work/ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib.ori	2017-03-17 22:33:51.569635396 +0100
-+++ ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib	2017-03-17 22:33:58.349811199 +0100
-@@ -4,6 +4,6 @@
- LIB      = xthrserv
- PROJ_TAG = core
- LIBS     = $(NETWORK_LIBS)
--DLL_LIB  = xutil xconnect
-+DLL_LIB  = xncbi xutil xconnect
- 
- WATCHERS = vakatov

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch
deleted file mode 100644
index 3c1cb0a9e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app.ori	2016-06-24 16:55:25.000000000 +0200
-+++ ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app	2017-03-21 14:07:31.070364301 +0100
-@@ -9,7 +9,7 @@
- APP = asn2fasta
- SRC = asn2fasta
- LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) \
--          xobjwrite xobjread $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \
-+          xobjwrite variation_utils $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \
- 	  ncbi_xdbapi_ftds dbapi $(ncbi_xreader_pubseqos2) $(FTDS_LIB) \
- 	  entrez2cli entrez2 tables $(OBJMGR_LIBS) $(PCRE_LIB)
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch
deleted file mode 100644
index 68baea046..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori	2016-12-01 20:28:33.239758102 +0100
-+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in	2016-12-01 20:28:46.330110659 +0100
-@@ -7,7 +7,7 @@
- #################################
- 
- USR_PROJ = precompile
--LIB_PROJ = corelib test_mt test_boost
-+LIB_PROJ = corelib test_mt
- SUB_PROJ = test
- PROJ_TAG = core
- 

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
deleted file mode 100644
index 098a9ad1e..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in.old	2017-03-26 19:01:58.101495278 +0200
-+++ ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in	2017-03-26 19:02:16.581990522 +0200
-@@ -13,6 +13,7 @@
- 	     -a ! -d $(libdir)/64 ]; then \
- 	    cd $(libdir)  &&  $(LN_S) . 64; \
- 	fi
-+	$(RM) $(LINK)
- 	cd $(libdir)  &&  $(LN_S) libpython_ncbi_dbapi$(loadable_ext) $(LINK)
- 
- clean:;

diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch
deleted file mode 100644
index 41240c330..000000000
--- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch
+++ /dev/null
@@ -1,64 +0,0 @@
---- trunk/c++/src/build-system/configure.ac     2012/12/27 15:43:29     56694
-+++ trunk/c++/src/build-system/configure.ac     2013/01/03 03:16:14     56754
-@@ -605,7 +605,8 @@
- fi
- 
- case "$with_projects" in
-- "") if test -r projects; then
-+ ""|yes)
-+     if test -r projects; then
-         AC_MSG_NOTICE([using default projects file "projects".])
-         with_projects=projects
-         AC_SUBST(PROJECTS, "\$(top_srcdir)/projects")
-@@ -623,6 +624,16 @@
-  * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;;
- esac
- 
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
-+fi
-+
- # Check for custom optimization flags before potentially going with defaults.
- skip_fast_flags=no
- if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-@@ -6379,7 +6390,7 @@
-      sep=", "
-    fi
-    if test -n "$reason" -a "$with_internal" = "yes"; then
--      if test -z "$with_projects"  -o  "$with_projects" = "no"; then
-+      if test -z "$with_projects"; then
-          AC_MSG_ERROR([--with-internal:  Cannot build INTERNAL projects: missing $reason])
-       else
-          AC_MSG_WARN([--with-internal:  Cannot build all INTERNAL projects: missing $reason])
-@@ -6982,11 +6993,9 @@
-    else
-       cfm_flags='-remoteptb'
-    fi
--   case "$with_projects" in
--      yes     ) cfm_flags="$cfm_flags -p projects" ;;
--      no | '' ) ;;
--      *       ) cfm_flags="$cfm_flags -p $with_projects" ;;
--   esac
-+   if test -n "$with_projects"; then
-+      cfm_flags="$cfm_flags -p $with_projects"
-+   fi
-    if test "$with_configure_dialog" = yes; then
-       cfm_flags="$cfm_flags -cfg"
-    fi
-@@ -7029,7 +7038,8 @@
- esac
- 
- if test -n "$with_projects"; then
--    build_proj="To build selected projects:  cd $builddir && make all_p"
-+    build_proj="To build selected projects (as listed in \"$with_projects\"):
-+  cd $builddir && make all_p"
- fi
- 
- cat << EOCONF
-

diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch
deleted file mode 100644
index 0c1b2d227..000000000
--- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch
+++ /dev/null
@@ -1,66 +0,0 @@
--- trunk/c++/src/build-system/configure 2012/12/27 15:43:29     56694
-+++ trunk/c++/src/build-system/configure        2013/01/03 03:16:14     56754
-@@ -3125,7 +3125,8 @@
- fi
- 
- case "$with_projects" in
-- "") if test -r projects; then
-+ ""|yes)
-+     if test -r projects; then
-         { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5
- echo "$as_me: using default projects file \"projects\"." >&6;}
-         with_projects=projects
-@@ -3151,6 +3152,18 @@
-  ;;
- esac
- 
-+if test -n "$with_projects"; then
-+   case "$with_projects" in
-+      /* ) abs_projects=$with_projects         ;;
-+      yes) abs_projects=$srcdir/projects       ;;
-+      *  ) abs_projects=$srcdir/$with_projects ;;
-+   esac
-+   test -r "$abs_projects"  ||  \
-+      { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5
-+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;}
-+   { (exit 1); exit 1; }; }
-+fi
-+
- # Check for custom optimization flags before potentially going with defaults.
- skip_fast_flags=no
- if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-@@ -33825,7 +33838,7 @@
-      sep=", "
-    fi
-    if test -n "$reason" -a "$with_internal" = "yes"; then
--      if test -z "$with_projects"  -o  "$with_projects" = "no"; then
-+      if test -z "$with_projects"; then
-          { { echo "$as_me:$LINENO: error: --with-internal:  Cannot build INTERNAL projects: missing $reason" >&5
- echo "$as_me: error: --with-internal:  Cannot build INTERNAL projects: missing $reason" >&2;}
-    { (exit 1); exit 1; }; }
-@@ -36062,11 +36075,9 @@
-    else
-       cfm_flags='-remoteptb'
-    fi
--   case "$with_projects" in
--      yes     ) cfm_flags="$cfm_flags -p projects" ;;
--      no | '' ) ;;
--      *       ) cfm_flags="$cfm_flags -p $with_projects" ;;
--   esac
-+   if test -n "$with_projects"; then
-+      cfm_flags="$cfm_flags -p $with_projects"
-+   fi
-    if test "$with_configure_dialog" = yes; then
-       cfm_flags="$cfm_flags -cfg"
-    fi
-@@ -36110,7 +36121,8 @@
- esac
- 
- if test -n "$with_projects"; then
--    build_proj="To build selected projects:  cd $builddir && make all_p"
-+    build_proj="To build selected projects (as listed in \"$with_projects\"):
-+  cd $builddir && make all_p"
- fi
- 
- cat << EOCONF
-

diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch
deleted file mode 100644
index 89dae23ad..000000000
--- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- trunk/c++/src/build-system/configure.ac     2012/12/21 15:12:14     56664
-+++ trunk/c++/src/build-system/configure.ac     2012/12/27 15:43:29     56694
-@@ -623,6 +623,13 @@
-  * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;;
- esac
- 
-+# Check for custom optimization flags before potentially going with defaults.
-+skip_fast_flags=no
-+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-+   case " $CFLAGS $CXXFLAGS" in
-+      *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-+   esac
-+fi
- 
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
-@@ -1431,7 +1438,7 @@
- wsrx="[[$wschars]]"
- 
- #### Flags to enable (potentially unsafe) extra optimization.
--if test -z "$DEF_FAST_FLAGS"  -o  -z "$FAST_CXXFLAGS" ; then
-+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
-    case "$compiler:$compiler_version" in
-       GCC:2* | GCC:344 )
-         # GCC 2.9x sometimes experiences internal errors at high optimization;
-@@ -1502,8 +1509,6 @@
-         DEF_FAST_FLAGS="-O"
-         ;;
-    esac
--else
--   DEF_FAST_FLAGS="-O"
- fi
- 
- : ${FAST_CFLAGS="$DEF_FAST_FLAGS"}
-@@ -2608,9 +2613,15 @@
-          CXXFLAGS="$CXXFLAGS -O" ; fi
-       if echo " $LDFLAGS "  | grep -v "$optrx" >/dev/null ; then
-          LDFLAGS="$LDFLAGS -O" ; fi
--      FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
--      FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
--      FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      if test "$skip_fast_flags" = yes ; then
-+         FAST_CFLAGS="$CFLAGS"
-+         FAST_CXXFLAGS="$CXXFLAGS"
-+         FAST_LDFLAGS="$LDFLAGS"
-+      else
-+         FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
-+         FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
-+         FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      fi
-    fi
- changequote([, ])dnl
- fi
-

diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch
deleted file mode 100644
index 669b31722..000000000
--- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- trunk/c++/src/build-system/configure        2012/12/21 15:12:14     56664
-+++ trunk/c++/src/build-system/configure        2012/12/27 15:43:29     56694
-@@ -3151,6 +3151,13 @@
-  ;;
- esac
- 
-+# Check for custom optimization flags before potentially going with defaults.
-+skip_fast_flags=no
-+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
-+   case " $CFLAGS $CXXFLAGS" in
-+      *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
-+   esac
-+fi
- 
- #### Always define this
- 
-@@ -5715,7 +5722,7 @@
- wsrx="[$wschars]"
- 
- #### Flags to enable (potentially unsafe) extra optimization.
--if test -z "$DEF_FAST_FLAGS"  -o  -z "$FAST_CXXFLAGS" ; then
-+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
-    case "$compiler:$compiler_version" in
-       GCC:2* | GCC:344 )
-         # GCC 2.9x sometimes experiences internal errors at high optimization;
-@@ -5786,8 +5793,6 @@
-         DEF_FAST_FLAGS="-O"
-         ;;
-    esac
--else
--   DEF_FAST_FLAGS="-O"
- fi
- 
- : ${FAST_CFLAGS="$DEF_FAST_FLAGS"}
-@@ -8936,9 +8941,15 @@
-          CXXFLAGS="$CXXFLAGS -O" ; fi
-       if echo " $LDFLAGS "  | grep -v "$optrx" >/dev/null ; then
-          LDFLAGS="$LDFLAGS -O" ; fi
--      FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
--      FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
--      FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      if test "$skip_fast_flags" = yes ; then
-+         FAST_CFLAGS="$CFLAGS"
-+         FAST_CXXFLAGS="$CXXFLAGS"
-+         FAST_LDFLAGS="$LDFLAGS"
-+      else
-+         FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
-+         FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
-+         FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
-+      fi
-    fi
- fi
- 

diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
deleted file mode 100644
index fbf79d9b7..000000000
--- a/sci-biology/ncbi-tools++/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="boost">Undocumented USE</flag>
-		<flag name="cppunit">Undocumented USE</flag>
-		<flag name="freetype">Undocumented USE</flag>
-		<flag name="mesa">Undocumented USE</flag>
-		<flag name="muparser">Undocumented USE</flag>
-		<flag name="sablotron">Undocumented USE</flag>
-		<flag name="xerces">Undocumented USE</flag>
-		<flag name="xalan">Undocumented USE</flag>
-		<flag name="xslt">Undocumented USE</flag>
-	</use>
-</pkgmetadata>

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
deleted file mode 100644
index 009085d15..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ /dev/null
@@ -1,364 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_TAG="Jun_15_2010"
-MY_Y="${MY_TAG/*_/}"
-MY_PV="12_0_0"
-MY_P="ncbi_cxx--${MY_PV}"
-#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
-# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
-
-# sys-libs/db should be compiled with USE=cxx
-# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
-DEPEND="
-	<sys-devel/gcc-10:=
-	app-arch/cpio
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost[tools] )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-		"${FILESDIR}"/${P}-conf-opts.patch
-		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-		"${FILESDIR}"/${P}-linkage-tuneups.patch
-		"${FILESDIR}"/${P}-more-patches.patch
-		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-		"${FILESDIR}"/${P}-configure.patch
-		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-		"${FILESDIR}"/${P}-fix-install.patch
-		"${FILESDIR}"/${P}-bdb6.patch
-		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		)
-
-src_prepare() {
-	default
-#	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}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${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)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-#       "${FILESDIR}"/${P}-as-needed.patch
-#       "${FILESDIR}"/${P}-fix-creaders-linking.patch
-#       "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
-#		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	# --without-downloaded-vdb is not available in 12.0.0 release yet
-	# preventing executing git to checkout during configure phase ncbi-vdb sources
-	# resulting in 'checking for ncbi-vdb... no' and
-	# '^PACKAGES:'
-	# '^  disabled: ... VDB'
-	# --without-downloaded-vdb
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
-	$(use_with berkdb bdb "${EPREFIX}/usr")
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	# is python2
-	--without-python
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-	#
-	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
-	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	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.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
deleted file mode 100644
index 604c9c638..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ /dev/null
@@ -1,383 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-single-r1 toolchain-funcs
-
-MY_TAG="Jun_15_2010"
-MY_Y="${MY_TAG/*_/}"
-MY_PV="18_0_0"
-MY_P="ncbi_cxx--${MY_PV}"
-#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
-# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
-DEPEND="
-	<sys-devel/gcc-10:=
-	app-arch/cpio
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost[tools] )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-		"${FILESDIR}"/${P}-configure.patch
-		"${FILESDIR}"/${P}-fix-install.patch
-		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
-		"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
-		"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
-		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
-		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
-		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
-		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
-		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
-		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
-		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
-		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
-		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
-		"${FILESDIR}"/${P}-fix-splign-linking.patch
-		"${FILESDIR}"/${P}-fix-srcchk-linking.patch
-		"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
-		"${FILESDIR}"/${P}-remove-old-symlinks.patch
-		"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
-		"${FILESDIR}"/${P}-fix-app-tls-linking.patch
-		"${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
-		"${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
-		)
-
-src_prepare() {
-	default
-#	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}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${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}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-	#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	# --without-downloaded-vdb is not available in 12.0.0 release yet
-	# preventing executing git to checkout during configure phase ncbi-vdb sources
-	# resulting in 'checking for ncbi-vdb... no' and
-	# '^PACKAGES:'
-	# '^  disabled: ... VDB'
-	--without-downloaded-vdb
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
-	$(use_with berkdb bdb "${EPREFIX}/usr")
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-	#
-	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
-	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-	#
-	# idfetch collides with idfetch from ncbi-tools-2.2.26
-	# Although the two idfetch implementations do deliberately have several
-	# options in common, the C++ version is not yet a full drop-in replacement
-	# for the C version (and will never entirely be, due to fundamental
-	# differences between the two toolkits' argument-parsing conventions).
-	mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0
-
-	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.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
deleted file mode 100644
index 4d0d6363e..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ /dev/null
@@ -1,388 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-single-r1 toolchain-funcs
-
-MY_TAG="Mar_28_2019"
-MY_Y="${MY_TAG/*_/}"
-MY_PV="22_0_0"
-MY_P="ncbi_cxx--${MY_PV}"
-
-# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-# https://ncbi.github.io/cxx-toolkit/pages/release_notes
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
-DEPEND="
-	<sys-devel/gcc-10:=
-	app-arch/cpio
-	berkdb? ( sys-libs/db:=[cxx(-)] )
-	boost? ( dev-libs/boost[tools] )
-	curl? ( net-misc/curl )
-	sqlite? ( >=dev-db/sqlite-3.6.6:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( >=dev-libs/libxslt-1.1.14 )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/libjpeg-turbo:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	>=dev-libs/lzo-2.0
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	default
-#	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}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${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)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-#	local PATCHES=(
-#		"${FILESDIR}"/${P}-configure.patch
-#		"${FILESDIR}"/${P}-fix-install.patch
-#		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-#		"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
-#		"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
-#		"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
-#		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
-#		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
-#		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
-#		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
-#		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
-#		"${FILESDIR}"/${P}-fix-splign-linking.patch
-#		"${FILESDIR}"/${P}-fix-srcchk-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
-#		"${FILESDIR}"/${P}-remove-old-symlinks.patch
-#		"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-tls-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
-#		"${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
-#		)
-	#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
-#	epatch ${PATCHES[@]}
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	# --without-downloaded-vdb is not available in 12.0.0 release yet
-	# preventing executing git to checkout during configure phase ncbi-vdb sources
-	# resulting in 'checking for ncbi-vdb... no' and
-	# '^PACKAGES:'
-	# '^  disabled: ... VDB'
-	--without-downloaded-vdb
-	$(use_with debug)
-#	$(use_with debug max-debug) # broken in 22.0.0 as it triggers need for https://github.com/google/sanitizers/wiki/AddressSanitizer
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-#	$(use_with opengl glew-mx) can't find this with any version of media-libs/glew installed: explicitly specified, but no usable version found.
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
-	$(use_with berkdb bdb "${EPREFIX}/usr")
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib emake -C "${S}"_build/build -f Makefile.flat
-	#
-	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
-	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-	#
-	#if [ ! use static-libs -a ! use static ]; then
-	#	rm -f "${ED}/usr/$(get_libdir)/${PN}"/*.a \
-	#		"${ED}/usr/$(get_libdir)/${PN}"/*-static.a || die
-	#fi
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-	#
-	# idfetch collides with idfetch from ncbi-tools-2.2.26
-	# Although the two idfetch implementations do deliberately have several
-	# options in common, the C++ version is not yet a full drop-in replacement
-	# for the C version (and will never entirely be, due to fundamental
-	# differences between the two toolkits' argument-parsing conventions).
-	mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0
-
-	echo "LDPATH=${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.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}

next             reply	other threads:[~2023-05-02 12:15 UTC|newest]

Thread overview: 30+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2023-05-02 12:15 Andrew Ammerlaan [this message]
  -- strict thread matches above, loose matches on Subject: below --
2019-04-05 15:27 [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/ Martin Mokrejs
2017-03-27  0:44 Martin Mokrejs
2017-03-26 22:48 Martin Mokrejs
2017-03-26 20:37 Martin Mokrejs
2017-03-23 21:28 Martin Mokrejs
2017-03-23 18:28 Martin Mokrejs
2017-03-23 17:17 Martin Mokrejs
2017-03-22 22:36 Martin Mokrejs
2016-12-02 23:28 Martin Mokrejs
2014-09-16  4:07 Christoph Junghans
2014-06-26 20:42 Martin Mokrejs
2014-06-25 23:24 Martin Mokrejs
2014-06-25 21:57 Martin Mokrejs
2014-06-25 20:59 Martin Mokrejs
2014-06-25 15:00 Martin Mokrejs
2014-06-23 20:34 Martin Mokrejs
2014-06-23 16:10 Martin Mokrejs
2014-01-25 16:25 Justin Lecher
2013-09-14  8:17 Martin Mokrejs
2013-09-13 22:17 Martin Mokrejs
2013-09-13 22:05 Martin Mokrejs
2013-09-13 21:27 Martin Mokrejs
2013-09-13 16:51 Martin Mokrejs
2013-09-13 16:45 Martin Mokrejs
2013-09-13 16:08 Martin Mokrejs
2013-01-30 17:08 Justin Lecher
2013-01-07 22:13 Martin Mokrejs
2013-01-07 17:09 Martin Mokrejs
2012-12-28 19:19 Martin Mokrejs

find likely ancestor, descendant, or conflicting patches for this message:
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dfblob:4d0d6363 )
 OR (
bs:"[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/" )
	(help)

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