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

[Justin Lecher]

commit:     18c9916513894240043fe47a76012e9a58342605
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 30 17:07:57 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 30 17:07:57 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=18c99165

More work on as-needed problems

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .../files/ncbi-tools++-9.0.0-as-needed.patch       |  767 ++++++++++++++++++++
 .../files/ncbi-tools++-9.0.0-conf-opts.patch       |  213 ++++++
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |  188 ++---
 3 files changed, 1049 insertions(+), 119 deletions(-)

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
new file mode 100644
index 0000000..7763361
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
@@ -0,0 +1,767 @@
+ src/algo/blast/blastinput/Makefile.blastinput.lib                   | 2 +-
+ src/algo/ms/omssa/Makefile.xomssa.lib                               | 2 ++
+ src/algo/sequence/Makefile.xalgoseq.lib                             | 2 ++
+ src/algo/winmask/Makefile.xalgowinmask.lib                          | 1 +
+ src/cgi/Makefile.cgi.lib                                            | 2 ++
+ src/cgi/Makefile.fcgi.lib                                           | 2 ++
+ src/connect/Makefile.connssl.lib                                    | 2 ++
+ src/connect/Makefile.xconnect.lib                                   | 4 ++++
+ src/connect/Makefile.xthrserv.lib                                   | 2 +-
+ src/connect/Makefile.xxconnect.lib                                  | 2 ++
+ src/connect/services/Makefile.ncbi_xcache_netcache.lib              | 2 +-
+ src/connect/services/Makefile.xconnserv.lib                         | 2 +-
+ src/connect/test/Makefile.conntest.lib                              | 2 ++
+ src/corelib/Makefile.test_boost.lib                                 | 2 ++
+ src/corelib/Makefile.test_mt.lib                                    | 2 ++
+ src/corelib/test/Makefile.pbacktest.lib                             | 2 ++
+ src/db/bdb/Makefile.bdb.lib                                         | 4 ++++
+ src/db/bdb/Makefile.ncbi_xcache_bdb.lib                             | 2 +-
+ src/db/sqlite/Makefile.sqlitewrapp.lib                              | 3 +++
+ src/dbapi/Makefile.dbapi.lib                                        | 5 +++++
+ src/dbapi/driver/Makefile.dbapi_driver.lib                          | 2 ++
+ src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib             | 2 ++
+ src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib           | 2 +-
+ src/dbapi/simple/Makefile.sdbapi.lib                                | 1 +
+ src/html/Makefile.html.lib                                          | 2 ++
+ src/objects/access/Makefile.access.lib                              | 1 +
+ src/objects/biblio/Makefile.biblio.lib                              | 2 ++
+ src/objects/blast/Makefile.blast.lib                                | 2 ++
+ src/objects/blast/Makefile.xnetblastcli.lib                         | 2 ++
+ src/objects/cdd/Makefile.cdd.lib                                    | 2 ++
+ src/objects/cn3d/Makefile.cn3d.lib                                  | 2 ++
+ src/objects/general/Makefile.general.lib                            | 2 ++
+ src/objects/id2/Makefile.id2.lib                                    | 2 ++
+ src/objects/medlars/Makefile.medlars.lib                            | 2 ++
+ src/objects/medline/Makefile.medline.lib                            | 2 ++
+ src/objects/ncbimime/Makefile.ncbimime.lib                          | 2 ++
+ src/objects/omssa/Makefile.omssa.lib                                | 2 ++
+ src/objects/pub/Makefile.pub.lib                                    | 2 ++
+ src/objects/scoremat/Makefile.scoremat.lib                          | 2 ++
+ src/objects/seq/Makefile.seq.lib                                    | 2 ++
+ src/objects/seqcode/Makefile.seqcode.lib                            | 2 ++
+ src/objects/seqedit/Makefile.seqedit.lib                            | 1 +
+ src/objects/seqset/Makefile.seqset.lib                              | 1 +
+ src/objects/seqsplit/Makefile.seqsplit.lib                          | 2 ++
+ src/objects/submit/Makefile.submit.lib                              | 1 +
+ src/objects/taxon1/Makefile.taxon1.lib                              | 2 ++
+ src/objects/valerr/Makefile.valerr.lib                              | 2 ++
+ src/objects/valid/Makefile.valid.lib                                | 2 ++
+ src/objects/variation/Makefile.variation.lib                        | 1 +
+ src/objmgr/util/Makefile.util.lib                                   | 1 +
+ src/objtools/align_format/Makefile.align_format.lib                 | 2 ++
+ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib                  | 2 ++
+ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++
+ src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib         | 2 +-
+ src/objtools/readers/Makefile.xobjread.lib                          | 3 +--
+ src/objtools/readers/Makefile.xobjreadex.lib                        | 2 +-
+ src/objtools/simple/Makefile.xobjsimple.lib                         | 1 +
+ src/objtools/validator/Makefile.validator.lib                       | 2 ++
+ src/serial/Makefile.serial.lib                                      | 2 ++
+ src/serial/soap/Makefile.soap.lib                                   | 2 ++
+ src/serial/soap/Makefile.soap_server.lib                            | 2 ++
+ src/serial/test/Makefile.we_cpp.lib                                 | 1 +
+ src/util/Makefile.util.lib                                          | 2 ++
+ src/util/compress/api/Makefile.compress.lib                         | 2 +-
+ src/util/qparse/Makefile.xqueryparse.lib                            | 2 ++
+ src/util/regexp/Makefile.regexp.lib                                 | 2 ++
+ src/util/sequtil/Makefile.sequtil.lib                               | 2 ++
+ src/util/xregexp/Makefile.xregexp.lib                               | 2 +-
+ 68 files changed, 124 insertions(+), 12 deletions(-)
+
+diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib
+index bfb315c..25873a2 100644
+--- a/src/algo/blast/blastinput/Makefile.blastinput.lib
++++ b/src/algo/blast/blastinput/Makefile.blastinput.lib
+@@ -24,7 +24,7 @@ SRC  = $(SRC_CXX)
+ 
+ LIB = blastinput
+ 
+-DLL_LIB = xblast $(OBJMGR_LIBS)
++DLL_LIB = xblast seqdb $(OBJMGR_LIBS)
+ 
+ # should be redundant, given the above :-/
+ ASN_DEP = seqset xnetblast
+diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib
+index 872b92e..82cc8b6 100644
+--- a/src/algo/ms/omssa/Makefile.xomssa.lib
++++ b/src/algo/ms/omssa/Makefile.xomssa.lib
+@@ -19,3 +19,5 @@ LIB = xomssa
+ CFLAGS   = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
++
++DLL_LIB = xutil
+diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib
+index 51f4cd7..0c20790 100644
+--- a/src/algo/sequence/Makefile.xalgoseq.lib
++++ b/src/algo/sequence/Makefile.xalgoseq.lib
+@@ -13,3 +13,5 @@ LDFLAGS  = $(FAST_LDFLAGS)
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+ 
+ WATCHERS = dicuccio
++
++DLL_LIB = taxon1 xalnmgr
+diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib
+index afaf676..7344871 100644
+--- a/src/algo/winmask/Makefile.xalgowinmask.lib
++++ b/src/algo/winmask/Makefile.xalgowinmask.lib
+@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++DLL_LIB = seqmasks_io
+diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib
+index a990390..edf40aa 100644
+--- a/src/cgi/Makefile.cgi.lib
++++ b/src/cgi/Makefile.cgi.lib
+@@ -11,3 +11,5 @@ LIB = xcgi
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+ 
+ WATCHERS = vakatov
++
++DLL_LIB  = xncbi xutil
+diff --git a/src/cgi/Makefile.fcgi.lib b/src/cgi/Makefile.fcgi.lib
+index 2569b41..6b85780 100644
+--- a/src/cgi/Makefile.fcgi.lib
++++ b/src/cgi/Makefile.fcgi.lib
+@@ -12,3 +12,5 @@ LIB = xfcgi
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) -DNCBI_XFCGI_EXPORTS
+ 
+ WATCHERS = vakatov
++
++DLL_LIB  = xncbi xutil
+diff --git a/src/connect/Makefile.connssl.lib b/src/connect/Makefile.connssl.lib
+index b400ca2..8756320 100644
+--- a/src/connect/Makefile.connssl.lib
++++ b/src/connect/Makefile.connssl.lib
+@@ -8,3 +8,5 @@ CPPFLAGS = $(GNUTLS_INCLUDE) $(ORIG_CPPFLAGS)
+ LIBS     = $(GNUTLS_LIBS) $(ORIG_LIBS)
+ 
+ WATCHERS = lavr
++
++DLL_LIB = connect
+diff --git a/src/connect/Makefile.xconnect.lib b/src/connect/Makefile.xconnect.lib
+index 473bb0b..88dae10 100644
+--- a/src/connect/Makefile.xconnect.lib
++++ b/src/connect/Makefile.xconnect.lib
+@@ -11,9 +11,13 @@ include $(srcdir)/Makefile.xxconnect.lib
+ SRC  = $(SRC_C) $(SRC_CXX)
+ UNIX_SRC = $(LOCAL_LBSM)
+ 
++DLL_LIB = xncbi
++
+ LIB  = xconnect
+ PROJ_TAG = core
+ 
+ LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
+ 
+ WATCHERS = lavr
++
++DLL_LIB = xncbi xutil
+diff --git a/src/connect/Makefile.xthrserv.lib b/src/connect/Makefile.xthrserv.lib
+index 1e5b857..0833a78 100644
+--- a/src/connect/Makefile.xthrserv.lib
++++ b/src/connect/Makefile.xthrserv.lib
+@@ -4,6 +4,6 @@ SRC      = threaded_server server server_monitor connection_pool
+ LIB      = xthrserv
+ PROJ_TAG = core
+ LIBS     = $(NETWORK_LIBS)
+-DLL_LIB  = xutil xconnect
++DLL_LIB  = xncbi xutil xconnect
+ 
+ WATCHERS = ivanovp
+diff --git a/src/connect/Makefile.xxconnect.lib b/src/connect/Makefile.xxconnect.lib
+index d7ba751..8e27819 100644
+--- a/src/connect/Makefile.xxconnect.lib
++++ b/src/connect/Makefile.xxconnect.lib
+@@ -16,3 +16,5 @@ PROJ_TAG = core
+ LIBS     = $(NETWORK_LIBS) $(ORIG_LIBS)
+ 
+ WATCHERS = lavr
++
++DLL_LIB = xncbi xutil connect
+diff --git a/src/connect/services/Makefile.ncbi_xcache_netcache.lib b/src/connect/services/Makefile.ncbi_xcache_netcache.lib
+index 606f4f1..e6cfdac 100644
+--- a/src/connect/services/Makefile.ncbi_xcache_netcache.lib
++++ b/src/connect/services/Makefile.ncbi_xcache_netcache.lib
+@@ -6,7 +6,7 @@ SRC = neticache_client
+ LIB = ncbi_xcache_netcache
+ 
+ LIB_OR_DLL = both
+-DLL_LIB = xconnserv xconnect xutil
++DLL_LIB = xconnserv xconnect xutil xncbi
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+ LIBS = $(ORIG_LIBS)
+diff --git a/src/connect/services/Makefile.xconnserv.lib b/src/connect/services/Makefile.xconnserv.lib
+index 4b8f21f..04fcbf8 100644
+--- a/src/connect/services/Makefile.xconnserv.lib
++++ b/src/connect/services/Makefile.xconnserv.lib
+@@ -15,6 +15,6 @@ LIB     = xconnserv
+ PROJ_TAG = core
+ LIBS    = $(NETWORK_LIBS)
+ 
+-DLL_LIB = xthrserv xconnect xutil
++DLL_LIB = xthrserv xconnect xutil xncbi
+ 
+ WATCHERS = kazimird
+diff --git a/src/connect/test/Makefile.conntest.lib b/src/connect/test/Makefile.conntest.lib
+index 58a2fa5..3d9876c 100644
+--- a/src/connect/test/Makefile.conntest.lib
++++ b/src/connect/test/Makefile.conntest.lib
+@@ -4,3 +4,5 @@ SRC = ncbi_conntest
+ LIB = xconntest
+ 
+ WATCHERS = lavr
++
++DLL_LIB = xncbi xutil connect
+diff --git a/src/corelib/Makefile.test_boost.lib b/src/corelib/Makefile.test_boost.lib
+index e8fa174..f90441d 100644
+--- a/src/corelib/Makefile.test_boost.lib
++++ b/src/corelib/Makefile.test_boost.lib
+@@ -9,3 +9,5 @@ REQUIRES = Boost.Test.Included
+ 
+ WATCHERS = ivanovp
+ PROJ_TAG = test
++
++DLL_LIB = xncbi
+diff --git a/src/corelib/Makefile.test_mt.lib b/src/corelib/Makefile.test_mt.lib
+index 6153eab..f64c3a2 100644
+--- a/src/corelib/Makefile.test_mt.lib
++++ b/src/corelib/Makefile.test_mt.lib
+@@ -8,3 +8,5 @@ LIB    = test_mt
+ USE_PCH = no
+ WATCHERS = grichenk
+ PROJ_TAG = test
++
++DLL_LIB = xncbi
+diff --git a/src/corelib/test/Makefile.pbacktest.lib b/src/corelib/test/Makefile.pbacktest.lib
+index da0c616..c4c62ab 100644
+--- a/src/corelib/test/Makefile.pbacktest.lib
++++ b/src/corelib/test/Makefile.pbacktest.lib
+@@ -4,3 +4,5 @@ SRC = pbacktest
+ LIB = xpbacktest
+ 
+ WATCHERS = lavr
++
++DLL_LIB = xncbi
+diff --git a/src/db/bdb/Makefile.bdb.lib b/src/db/bdb/Makefile.bdb.lib
+index 3729707..cd2827c 100644
+--- a/src/db/bdb/Makefile.bdb.lib
++++ b/src/db/bdb/Makefile.bdb.lib
+@@ -14,3 +14,7 @@ LIB = bdb
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE)
+ 
+ WATCHERS = kuznets
++
++DLL_LIB = xncbi xutil
++LIBS = $(BERKELEYDB_LIBS)
++
+diff --git a/src/db/bdb/Makefile.ncbi_xcache_bdb.lib b/src/db/bdb/Makefile.ncbi_xcache_bdb.lib
+index 7e97a26..8f54efc 100644
+--- a/src/db/bdb/Makefile.ncbi_xcache_bdb.lib
++++ b/src/db/bdb/Makefile.ncbi_xcache_bdb.lib
+@@ -8,7 +8,7 @@ SRC = bdb_blobcache
+ LIB = ncbi_xcache_bdb
+ 
+ LIB_OR_DLL = both
+-DLL_LIB = bdb xutil
++DLL_LIB = bdb xutil xncbi
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE)
+ LIBS = $(BERKELEYDB_LIBS) $(ORIG_LIBS)
+diff --git a/src/db/sqlite/Makefile.sqlitewrapp.lib b/src/db/sqlite/Makefile.sqlitewrapp.lib
+index cecfd16..c01668b 100644
+--- a/src/db/sqlite/Makefile.sqlitewrapp.lib
++++ b/src/db/sqlite/Makefile.sqlitewrapp.lib
+@@ -8,3 +8,6 @@ CPPFLAGS= $(ORIG_CPPFLAGS) $(SQLITE3_INCLUDE)
+ REQUIRES = SQLITE3
+ 
+ WATCHERS = ivanovp
++
++DLL_LIB = xncbi xutil
++LIBS = $(SQLITE3_LIBS)
+diff --git a/src/dbapi/Makefile.dbapi.lib b/src/dbapi/Makefile.dbapi.lib
+index 6e3ad4c..4475a78 100644
+--- a/src/dbapi/Makefile.dbapi.lib
++++ b/src/dbapi/Makefile.dbapi.lib
+@@ -10,3 +10,8 @@ LIB    = dbapi
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE)
+ 
+ WATCHERS = ivanovp
++
++#ASN_DEP = driver
++
++DLL_LIB = xncbi xutil # dbapi_driver$(DLL)
++LIBS   = $(PYTHON_LIBS)
+diff --git a/src/dbapi/driver/Makefile.dbapi_driver.lib b/src/dbapi/driver/Makefile.dbapi_driver.lib
+index dfeac5a..bc113ed 100644
+--- a/src/dbapi/driver/Makefile.dbapi_driver.lib
++++ b/src/dbapi/driver/Makefile.dbapi_driver.lib
+@@ -22,3 +22,5 @@ CXXFLAGS_darwin = -fno-inline
+ CXXFLAGS = $(ORIG_CXXFLAGS) $(CXXFLAGS_$(OSTYPE))
+ 
+ WATCHERS = ivanovp
++
++DLL_LIB = xncbi xutil
+diff --git a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib
+index 941ccd6..f1f872c 100644
+--- a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib
++++ b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib
+@@ -6,3 +6,5 @@ LIB = dbapi_sample_base
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE)
+ 
+ WATCHERS = ivanovp
++
++DLL_LIB = xncbi xutil dbapi_driver
+diff --git a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib
+index ebe08c4..86ecda6 100644
+--- a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib
++++ b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib
+@@ -11,7 +11,7 @@ LIB_OR_DLL = dll
+ 
+ # Dependencies for shared library
+ DLL_LIB = dbapi dbapi_driver$(DLL) $(XCONNEXT) xconnect xutil xncbi
+-LIBS    = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS)
++LIBS    = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS) $(PYTHON_LIBS)
+ # Drop other flags to build with full dependencies under ICC.
+ DLL_LDFLAGS = $(DLL_UNDEF_FLAGS)
+ 
+diff --git a/src/dbapi/simple/Makefile.sdbapi.lib b/src/dbapi/simple/Makefile.sdbapi.lib
+index 603fd1e..0d06323 100644
+--- a/src/dbapi/simple/Makefile.sdbapi.lib
++++ b/src/dbapi/simple/Makefile.sdbapi.lib
+@@ -5,3 +5,4 @@ LIB = sdbapi
+ 
+ WATCHERS = ivanovp
+ 
++DLL_LIB = xncbi xutil dbapi_driver ncbi_xdbapi_ftds xconnect xser bdb xconnserv
+diff --git a/src/html/Makefile.html.lib b/src/html/Makefile.html.lib
+index a57c1e3..0005299 100644
+--- a/src/html/Makefile.html.lib
++++ b/src/html/Makefile.html.lib
+@@ -8,3 +8,5 @@ SRC = node html htmlhelper page pager selection components \
+ LIB = xhtml
+ 
+ WATCHERS = ivanov
++
++DLL_LIB = xncbi xutil
+diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib
+index 11421d9..cf3a300 100644
+--- a/src/objects/access/Makefile.access.lib
++++ b/src/objects/access/Makefile.access.lib
+@@ -1,2 +1,3 @@
+ LIB = access
+ SRC = access__ access___
++DLL_LIB = xncbi
+diff --git a/src/objects/biblio/Makefile.biblio.lib b/src/objects/biblio/Makefile.biblio.lib
+index 2c7d491..cb54ba6 100644
+--- a/src/objects/biblio/Makefile.biblio.lib
++++ b/src/objects/biblio/Makefile.biblio.lib
+@@ -1,2 +1,4 @@
+ LIB = biblio
+ SRC = biblio__ biblio___ citation_base
++
++DLL_LIB = general xser  xncbi xutil
+diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib
+index 0dd0fa3..5ffe052 100644
+--- a/src/objects/blast/Makefile.blast.lib
++++ b/src/objects/blast/Makefile.blast.lib
+@@ -2,3 +2,5 @@ LIB = xnetblast
+ SRC = blast__ blast___ names
+ 
+ WATCHERS = camacho
++
++DLL_LIB = xncbi xutil xser
+diff --git a/src/objects/blast/Makefile.xnetblastcli.lib b/src/objects/blast/Makefile.xnetblastcli.lib
+index 96325c4..5a72805 100644
+--- a/src/objects/blast/Makefile.xnetblastcli.lib
++++ b/src/objects/blast/Makefile.xnetblastcli.lib
+@@ -2,3 +2,5 @@ ASN_DEP = xnetblast
+ 
+ LIB = xnetblastcli
+ SRC = blastclient blastclient_
++
++DLL_LIB  = xncbi xutil seqset connect xconnect xnetblast
+diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib
+index 978cae9..e3176b2 100644
+--- a/src/objects/cdd/Makefile.cdd.lib
++++ b/src/objects/cdd/Makefile.cdd.lib
+@@ -1,2 +1,4 @@
+ LIB = cdd
+ SRC = cdd__ cdd___
++
++DLL_LIB = mmdb
+diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib
+index 1af5d1d..b34a966 100644
+--- a/src/objects/cn3d/Makefile.cn3d.lib
++++ b/src/objects/cn3d/Makefile.cn3d.lib
+@@ -1,3 +1,5 @@
+ ASN_DEP = mmdb
+ LIB = cn3d
+ SRC = cn3d__ cn3d___
++
++DLL_LIB = mmdb
+diff --git a/src/objects/general/Makefile.general.lib b/src/objects/general/Makefile.general.lib
+index 951304f..3be083d 100644
+--- a/src/objects/general/Makefile.general.lib
++++ b/src/objects/general/Makefile.general.lib
+@@ -1,2 +1,4 @@
+ LIB = general
+ SRC = general__ general___ uoconv
++
++DLL_LIB = xser  xncbi xutil
+diff --git a/src/objects/id2/Makefile.id2.lib b/src/objects/id2/Makefile.id2.lib
+index 09d8b36..b25700d 100644
+--- a/src/objects/id2/Makefile.id2.lib
++++ b/src/objects/id2/Makefile.id2.lib
+@@ -2,3 +2,5 @@ LIB = id2
+ SRC = id2__ id2___
+ 
+ WATCHERS = vasilche
++
++DLL_LIB = xser
+diff --git a/src/objects/medlars/Makefile.medlars.lib b/src/objects/medlars/Makefile.medlars.lib
+index 3a6d0cd..5230940 100644
+--- a/src/objects/medlars/Makefile.medlars.lib
++++ b/src/objects/medlars/Makefile.medlars.lib
+@@ -1,2 +1,4 @@
+ LIB = medlars
+ SRC = medlars__ medlars___
++
++DLL_LIB = xser
+diff --git a/src/objects/medline/Makefile.medline.lib b/src/objects/medline/Makefile.medline.lib
+index ea28066..eb42aa4 100644
+--- a/src/objects/medline/Makefile.medline.lib
++++ b/src/objects/medline/Makefile.medline.lib
+@@ -1,2 +1,4 @@
+ LIB = medline
+ SRC = medline__ medline___
++
++DLL_LIB = general biblio
+diff --git a/src/objects/ncbimime/Makefile.ncbimime.lib b/src/objects/ncbimime/Makefile.ncbimime.lib
+index 93cafdf..e5aa4eb 100644
+--- a/src/objects/ncbimime/Makefile.ncbimime.lib
++++ b/src/objects/ncbimime/Makefile.ncbimime.lib
+@@ -1,2 +1,4 @@
+ LIB = ncbimime
+ SRC = ncbimime__ ncbimime___
++
++DLL_LIB = mmdb
+diff --git a/src/objects/omssa/Makefile.omssa.lib b/src/objects/omssa/Makefile.omssa.lib
+index b79617f..e1d4a9e 100644
+--- a/src/objects/omssa/Makefile.omssa.lib
++++ b/src/objects/omssa/Makefile.omssa.lib
+@@ -2,3 +2,5 @@ APP_DEP = seq
+ 
+ LIB = omssa
+ SRC = omssa__ omssa___
++
++DLL_LIB = seq
+diff --git a/src/objects/pub/Makefile.pub.lib b/src/objects/pub/Makefile.pub.lib
+index 78c12e1..9baa08d 100644
+--- a/src/objects/pub/Makefile.pub.lib
++++ b/src/objects/pub/Makefile.pub.lib
+@@ -1,2 +1,4 @@
+ LIB = pub
+ SRC = pub__ pub___
++
++DLL_LIB = medline biblio
+diff --git a/src/objects/scoremat/Makefile.scoremat.lib b/src/objects/scoremat/Makefile.scoremat.lib
+index 62e01f5..93bb071 100644
+--- a/src/objects/scoremat/Makefile.scoremat.lib
++++ b/src/objects/scoremat/Makefile.scoremat.lib
+@@ -1,2 +1,4 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
++
++DLL_LIB = seqset seq
+diff --git a/src/objects/seq/Makefile.seq.lib b/src/objects/seq/Makefile.seq.lib
+index 1b5edc5..30ef316 100644
+--- a/src/objects/seq/Makefile.seq.lib
++++ b/src/objects/seq/Makefile.seq.lib
+@@ -13,3 +13,5 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \
+       seq_loc_from_string seq_loc_reverse_complementer
+ 
+ WATCHERS = vasilche grichenk
++
++DLL_LIB = general seqcode pub sequtil biblio xser xncbi xutil
+diff --git a/src/objects/seqcode/Makefile.seqcode.lib b/src/objects/seqcode/Makefile.seqcode.lib
+index dc9d60e..dabd95b 100644
+--- a/src/objects/seqcode/Makefile.seqcode.lib
++++ b/src/objects/seqcode/Makefile.seqcode.lib
+@@ -1,2 +1,4 @@
+ LIB = seqcode
+ SRC = seqcode__ seqcode___
++
++DLL_LIB = xncbi xser
+diff --git a/src/objects/seqedit/Makefile.seqedit.lib b/src/objects/seqedit/Makefile.seqedit.lib
+index 283a9b7..80724b1 100644
+--- a/src/objects/seqedit/Makefile.seqedit.lib
++++ b/src/objects/seqedit/Makefile.seqedit.lib
+@@ -1,3 +1,4 @@
+ LIB = seqedit
+ SRC = seqedit__ seqedit___
+  
++DLL_LIB = xser seq
+diff --git a/src/objects/seqset/Makefile.seqset.lib b/src/objects/seqset/Makefile.seqset.lib
+index 87f16d0..febce67 100644
+--- a/src/objects/seqset/Makefile.seqset.lib
++++ b/src/objects/seqset/Makefile.seqset.lib
+@@ -1,2 +1,3 @@
+ LIB = seqset
+ SRC = seqset__ seqset___ gb_release_file
++DLL_LIB = xser seq
+diff --git a/src/objects/seqsplit/Makefile.seqsplit.lib b/src/objects/seqsplit/Makefile.seqsplit.lib
+index 87ae869..a693f50 100644
+--- a/src/objects/seqsplit/Makefile.seqsplit.lib
++++ b/src/objects/seqsplit/Makefile.seqsplit.lib
+@@ -2,3 +2,5 @@ LIB = seqsplit
+ SRC = seqsplit__ seqsplit___
+ 
+ WATCHERS = vasilche
++
++DLL_LIB = xser
+diff --git a/src/objects/submit/Makefile.submit.lib b/src/objects/submit/Makefile.submit.lib
+index 74798f8..34dd5a8 100644
+--- a/src/objects/submit/Makefile.submit.lib
++++ b/src/objects/submit/Makefile.submit.lib
+@@ -1,2 +1,3 @@
+ LIB = submit
+ SRC = submit__ submit___
++DLL_LIB = xser xncbi # lds
+diff --git a/src/objects/taxon1/Makefile.taxon1.lib b/src/objects/taxon1/Makefile.taxon1.lib
+index 61658ab..d735117 100644
+--- a/src/objects/taxon1/Makefile.taxon1.lib
++++ b/src/objects/taxon1/Makefile.taxon1.lib
+@@ -3,3 +3,5 @@ LIB = taxon1
+ SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont
+ 
+ WATCHERS = domrach
++
++DLL_LIB = xser
+diff --git a/src/objects/valerr/Makefile.valerr.lib b/src/objects/valerr/Makefile.valerr.lib
+index b202355..9699bb2 100644
+--- a/src/objects/valerr/Makefile.valerr.lib
++++ b/src/objects/valerr/Makefile.valerr.lib
+@@ -2,3 +2,5 @@ LIB = valerr
+ SRC = valerr__ valerr___
+ 
+ ASN_DEP = seqset
++
++DLL_LIB = xser
+diff --git a/src/objects/valid/Makefile.valid.lib b/src/objects/valid/Makefile.valid.lib
+index 86a00a0..ee7402f 100644
+--- a/src/objects/valid/Makefile.valid.lib
++++ b/src/objects/valid/Makefile.valid.lib
+@@ -1,3 +1,5 @@
+ # $Id: Makefile.valid.lib 156738 2009-04-07 16:35:10Z ucko $
+ LIB = valid
+ SRC = valid__ valid___
++
++DLL_LIB = xser
+diff --git a/src/objects/variation/Makefile.variation.lib b/src/objects/variation/Makefile.variation.lib
+index f21f84a..b08e210 100644
+--- a/src/objects/variation/Makefile.variation.lib
++++ b/src/objects/variation/Makefile.variation.lib
+@@ -1,2 +1,3 @@
+ LIB = variation
+ SRC = variation__ variation___
++DLL_LIB = xser
+diff --git a/src/objmgr/util/Makefile.util.lib b/src/objmgr/util/Makefile.util.lib
+index 90eeee0..138e836 100644
+--- a/src/objmgr/util/Makefile.util.lib
++++ b/src/objmgr/util/Makefile.util.lib
+@@ -10,3 +10,4 @@ LIB = xobjutil
+ 
+ WATCHERS = ucko vasilche
+ 
++DLL_LIB = xser xobjmgr
+diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib
+index 4b3e59e..94fc319 100644
+--- a/src/objtools/align_format/Makefile.align_format.lib
++++ b/src/objtools/align_format/Makefile.align_format.lib
+@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
+ # LIB_OR_DLL = dll
+ 
+ WATCHERS = zaretska jianye madden camacho
++
++DLL_LIB = seqdb blastdb
+diff --git a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+index 25898aa..92d4d59 100644
+--- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
++++ b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+@@ -29,3 +29,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+ WATCHERS = maning camacho
++
++DLL_LIB = blastdb
+diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+index 80af69f..704ed7a 100644
+--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+@@ -6,3 +6,6 @@ SRC = bdbloader cached_sequence local_blastdb_adapter
+ ASN_DEP = blastdb seqset
+ 
+ WATCHERS = camacho
++
++DLL_LIB = seqdb
++
+diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+index f2b2b49..a8ee667 100644
+--- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
++++ b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+@@ -12,6 +12,6 @@ LIB = ncbi_xreader
+ LIB_OR_DLL = both
+ 
+ # Dependencies for shared library
+-DLL_LIB = 
++DLL_LIB = xcompress
+ 
+ WATCHERS = vasilche
+diff --git a/src/objtools/readers/Makefile.xobjread.lib b/src/objtools/readers/Makefile.xobjread.lib
+index 0fbffd4..4ca9fed 100644
+--- a/src/objtools/readers/Makefile.xobjread.lib
++++ b/src/objtools/readers/Makefile.xobjread.lib
+@@ -19,5 +19,4 @@ SRC = read_util format_guess_ex \
+       best_feat_finder source_mod_parser fasta_exception
+ 
+ 
+-DLL_LIB = creaders
+-
++DLL_LIB = creaders xncbi seq biblio seqset
+diff --git a/src/objtools/readers/Makefile.xobjreadex.lib b/src/objtools/readers/Makefile.xobjreadex.lib
+index 85eefe2..f238782 100644
+--- a/src/objtools/readers/Makefile.xobjreadex.lib
++++ b/src/objtools/readers/Makefile.xobjreadex.lib
+@@ -8,4 +8,4 @@ LIB = xobjreadex
+ SRC = glimmer_reader idmapper idmapper_builtin idmapper_config \
+ 	  idmapper_database source_mod_parser_wrapper
+ 
+-DLL_LIB = xobjread
++DLL_LIB = xobjread xncbi xutil seq xobjmgr
+diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib
+index dab25d6..a29b960 100644
+--- a/src/objtools/simple/Makefile.xobjsimple.lib
++++ b/src/objtools/simple/Makefile.xobjsimple.lib
+@@ -10,3 +10,4 @@ ASN_DEP = seqset
+ LIB = xobjsimple
+ SRC = simple_om
+ 
++DLL_LIB = xobjmgr
+diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib
+index 80a74d8..69c4ef6 100644
+--- a/src/objtools/validator/Makefile.validator.lib
++++ b/src/objtools/validator/Makefile.validator.lib
+@@ -19,3 +19,5 @@ NOOPT_CXX = $(CXX_WRAPPER) $(CXX) $(CXXFLAGS_ALL:-xO%=)
+ 
+ lat_lon_country_map.o: $(srcdir)/lat_lon_country_map.cpp
+ 	$(NOOPT_CXX) $(srcdir)/lat_lon_country_map.cpp -o $@ $(CXX_FILTER)
++
++DLL_LIB = xncbi xobjutil xalnmgr
+diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib
+index 2563b5f..efad054 100644
+--- a/src/serial/Makefile.serial.lib
++++ b/src/serial/Makefile.serial.lib
+@@ -19,3 +19,5 @@ SRC = \
+ LIB    = xser
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = xncbi xutil
+diff --git a/src/serial/soap/Makefile.soap.lib b/src/serial/soap/Makefile.soap.lib
+index e77d4ee..3b28bc4 100644
+--- a/src/serial/soap/Makefile.soap.lib
++++ b/src/serial/soap/Makefile.soap.lib
+@@ -8,3 +8,5 @@ SRC = soap_message soap_readhook soap_writehook soap_client \
+ LIB = xsoap
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = xncbi xutil xser xconnect
+diff --git a/src/serial/soap/Makefile.soap_server.lib b/src/serial/soap/Makefile.soap_server.lib
+index c961496..0ccb2f0 100644
+--- a/src/serial/soap/Makefile.soap_server.lib
++++ b/src/serial/soap/Makefile.soap_server.lib
+@@ -9,3 +9,5 @@ LIB = xsoap_server
+ REQUIRES = cgi
+ 
+ WATCHERS = gouriano
++
++DLL_LIB = xncbi xutil xcgi xsoap xser
+diff --git a/src/serial/test/Makefile.we_cpp.lib b/src/serial/test/Makefile.we_cpp.lib
+index 9877691..599ef5d 100644
+--- a/src/serial/test/Makefile.we_cpp.lib
++++ b/src/serial/test/Makefile.we_cpp.lib
+@@ -3,3 +3,4 @@ SRC = we_cpp__ we_cpp___
+ 
+ WATCHERS = gouriano
+ 
++DLL_LIB = xncbi xutil xser
+diff --git a/src/util/Makefile.util.lib b/src/util/Makefile.util.lib
+index f103ff1..829a71c 100644
+--- a/src/util/Makefile.util.lib
++++ b/src/util/Makefile.util.lib
+@@ -14,3 +14,5 @@ PROJ_TAG = core
+ LIBS = $(ORIG_LIBS)
+ 
+ WATCHERS = vakatov
++
++DLL_LIB = xncbi
+diff --git a/src/util/compress/api/Makefile.compress.lib b/src/util/compress/api/Makefile.compress.lib
+index ae22234..2ce803a 100644
+--- a/src/util/compress/api/Makefile.compress.lib
++++ b/src/util/compress/api/Makefile.compress.lib
+@@ -6,7 +6,7 @@ LIB = xcompress
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+-DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB)
++DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB) xutil xncbi
+ LIBS    =  $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS)
+ 
+ WATCHERS = ivanov
+diff --git a/src/util/qparse/Makefile.xqueryparse.lib b/src/util/qparse/Makefile.xqueryparse.lib
+index a003930..0505da7 100644
+--- a/src/util/qparse/Makefile.xqueryparse.lib
++++ b/src/util/qparse/Makefile.xqueryparse.lib
+@@ -7,3 +7,5 @@ query_parser_bison.tab.c : query_parser_bison.y
+ 	bison -v -p ncbi_q_ -o query_parser_bison.tab.c query_parser_bison.y
+ 
+ WATCHERS = kuznets
++
++DLL_LIB = xncbi xutil
+diff --git a/src/util/regexp/Makefile.regexp.lib b/src/util/regexp/Makefile.regexp.lib
+index 0f8d5e8..83a82af 100644
+--- a/src/util/regexp/Makefile.regexp.lib
++++ b/src/util/regexp/Makefile.regexp.lib
+@@ -10,3 +10,5 @@ LIB = regexp
+ CPPFLAGS = -I$(includedir)/util/regexp -DHAVE_CONFIG_H $(ORIG_CPPFLAGS)
+ 
+ WATCHERS = ivanov
++
++DLL_LIB = xncbi xutil
+diff --git a/src/util/sequtil/Makefile.sequtil.lib b/src/util/sequtil/Makefile.sequtil.lib
+index c068a32..453c911 100644
+--- a/src/util/sequtil/Makefile.sequtil.lib
++++ b/src/util/sequtil/Makefile.sequtil.lib
+@@ -4,3 +4,5 @@ LIB = sequtil
+ SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
+ 
+ WATCHERS = shomrat
++
++DLL_LIB = xncbi xutil
+diff --git a/src/util/xregexp/Makefile.xregexp.lib b/src/util/xregexp/Makefile.xregexp.lib
+index 965fac4..3accea3 100644
+--- a/src/util/xregexp/Makefile.xregexp.lib
++++ b/src/util/xregexp/Makefile.xregexp.lib
+@@ -6,7 +6,7 @@ LIB = xregexp
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+ 
+-DLL_LIB = $(PCRE_LIB)
++DLL_LIB = $(PCRE_LIB) xutil xncbi
+ LIBS    = $(PCRE_LIBS)
+ 
+ WATCHERS = ivanov

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch
new file mode 100644
index 0000000..8209603
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch
@@ -0,0 +1,213 @@
+ src/build-system/configure    | 34 +++++++++++++++++++++++-----------
+ src/build-system/configure.ac | 33 ++++++++++++++++++++++-----------
+ 2 files changed, 45 insertions(+), 22 deletions(-)
+
+diff --git a/src/build-system/configure b/src/build-system/configure
+index 82fc9ef..d31a4f2 100755
+--- a/src/build-system/configure
++++ b/src/build-system/configure
+@@ -924,7 +924,7 @@ Optional Packages:
+  --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
+@@ -2835,12 +2835,12 @@ 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 gnutls openssl sybase sybase-local sybase-new \
+-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \
++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \
+ bdb python jni sqlite3 icu boost boost-tag \
+ sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \
+ gif jpeg tiff png xpm magic curl 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'`
+ 
+@@ -2864,6 +2864,7 @@ 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= )
+       { { echo "$as_me:$LINENO: error: $x_arg:  requires value;  use --help to show usage" >&5
+ echo "$as_me: error: $x_arg:  requires value;  use --help to show usage" >&2;}
+@@ -2876,6 +2877,7 @@ echo "$as_me: error: $x_arg:  requires value;  use --help to show usage" >&2;}
+       | --with-universal=* | --with-tcheck=* \
+       | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
+       | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
++      | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
+       | [A-Z]*=* \
+       | --with-z=* | --with-bz2=* | --with-lzo=* \
+       | --with-pcre=* \
+@@ -3023,7 +3025,8 @@ echo "$as_me: error: --without-extra-action is not allowed" >&2;}
+ 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
+@@ -3049,6 +3052,16 @@ echo "$as_me: WARNING: default projects file \"projects\" is a dangling link." >
+  ;;
+ esac
+ 
++if test -n "$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"  ||  \
++      as_fn_error $? "unable to read requested projects file \"$abs_projects\"." "$LINENO" 5
++fi
++
+ 
+ #### Always define this
+ 
+@@ -32712,7 +32725,7 @@ else
+      sep=", "
+    fi
+    if test -n "$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 $reason" >&2;}
+    { (exit 1); exit 1; }; }
+@@ -34949,11 +34962,9 @@ if test "$with_flat_makefile" != "no"; then
+    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="$cfm_flags -cfg"
+    fi
+@@ -34997,7 +35008,8 @@ lib)
+ esac
+ 
+ if test -n "$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 $builddir && make all_p"
+ fi
+ 
+ cat << EOCONF
+diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac
+index 7b733af..3b55bf5 100644
+--- a/src/build-system/configure.ac
++++ b/src/build-system/configure.ac
+@@ -222,7 +222,7 @@ AC_ARG_WITH(ncbi-c,
+ AC_ARG_WITH(sss,
+    [ --without-sss           do not use NCBI SSS libraries])
+ AC_ARG_WITH(sssutils,
+-   [ --without-utils         do not use NCBI SSS UTIL library])
++   [ --without-sssutils      do not use NCBI SSS UTIL library])
+ AC_ARG_WITH(sssdb,
+    [ --without-sssdb         do not use NCBI SSS DB library])
+ AC_ARG_WITH(included-sss,
+@@ -462,12 +462,12 @@ check ncbi-public strip pch caution ccache distcc \
+ ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
+ geo included-geo \
+ z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \
+-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \
++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \
+ bdb python jni sqlite3 icu boost boost-tag \
+ sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \
+ gif jpeg tiff png xpm magic curl 3psw \
+ local-lbsm ncbi-crypt connext \
+-serial objects dbapi app ctools gui algo internal gbench"
++serial objects dbapi app ctools gui algo internal gbench x"
+ 
+ changequote(, )dnl
+ x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
+@@ -493,6 +493,7 @@ 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([$x_arg:  requires value;  use --help to show usage])
+       ;;
+@@ -503,6 +504,7 @@ for x_arg in "$@" ; 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=* \
+@@ -581,7 +583,8 @@ if test "$with_extra_action" = "no" ; then
+ fi
+ 
+ case "$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")
+@@ -599,6 +602,15 @@ case "$with_projects" in
+  * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$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
+ 
+ #### Always define this
+ AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
+@@ -6198,7 +6210,7 @@ else
+      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 $reason])
+@@ -6807,11 +6819,9 @@ if test "$with_flat_makefile" != "no"; then
+    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="$cfm_flags -cfg"
+    fi
+@@ -6854,7 +6864,8 @@ lib)
+ esac
+ 
+ if test -n "$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++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 9806b41..439e917 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-inherit eutils flag-o-matic multilib toolchain-funcs
+inherit autotools eutils flag-o-matic multilib toolchain-funcs
 
 MY_TAG="Jun_15_2010"
 MY_Y="${MY_TAG/*_/}"
@@ -68,70 +68,6 @@ DEPEND="
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
 
-# configure options, may want to expose some
-#  --without-debug         build non-debug versions of libs and apps
-#  --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-dll              build all libraries as DLLs
-#  --with-static           build all libraries statically even if --with-dll
-#  --with-static-exe       build all executables as statically as possible
-#  --with-plugin-auto-load always enable the plugin manager by default
-#  --with-bin-release      build executables suitable for public release
-#  --with-mt               compile in a MultiThread-safe manner
-#  --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-runpath=         hard-code the runtime path to DLLs
-#  --with-lfs              enable large file support to the extent possible
-#  --with-extra-action=    script to call after the configuration is complete
-#  --with-autodep          automatic generation of dependencies (GNU make)
-#  --with-build-root=DIR   specify a non-default build directory name
-#  --with-fake-root=DIR    appear to have been built under DIR
-#  --without-suffix        no Release/Debug, MT or DLL sfx in the build dir name
-#  --with-hostspec         add full host specs to the build dir name
-#  --without-version       don't always include the cplr ver in the bd name
-#  --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-bincopy          populate lib and bin with copies, not hard links
-#  --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            run test suite after the build
-#  --with-check-tools=...  use the specified tools for testing
-#  --with-ncbi-public      ensure compatibility for all in-house platforms
-#  --with-strip            strip binaries at build time
-#  --with-pch              use precompiled headers if possible
-#  --with-caution          cancel configuration unconditionally when in doubt
-#  --without-caution       proceed without asking when in doubt
-#  --without-ccache        do not automatically use ccache if available
-#  --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-sssdb         do not use NCBI SSS DB library
-#  --with-included-sss     use the in-tree copy of SSS
-
-#  --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-ctools        do not build NCBI C Toolkit based projects
-#  --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
-
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${MY_P}"
@@ -162,7 +98,17 @@ src_prepare() {
 #		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
 
 #	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
+
+	local PATCHES=(
+		"${FILESDIR}"/${P}-conf-opts.patch
+		"${FILESDIR}"/${P}-as-needed.patch
+		)
+	epatch ${PATCHES[@]}
+
 	tc-export CXX CC
+#	cd src/build-system || die
+#	eaclocal -I.
+#	eautoconf
 }
 
 src_configure() {
@@ -175,54 +121,54 @@ src_configure() {
 	#--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-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-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-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
+	#--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-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)
+	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
 	#--without-ftds-renamed  do not rename Sybase DBLIB symbols in built-in FTDS
 	#--without-sp            do not use SP libraries
 	#--without-orbacus       do not use ORBacus CORBA libraries
-	# --with-orbacus=DIR      use ORBacus installation in DIR
+	#--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
+	#--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
+	#--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-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-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
+	#--with-gbench           ensure that Genome Workbench can be built
+	#--without-gbench        do not build Genome Workbench
 	myconf+=(
 	--with-dll
 	--with-lfs
@@ -234,17 +180,18 @@ src_configure() {
 	--without-strip
 	--without-ccache
 	--without-distcc
-	--with-ncbi-c
+#	--with-ncbi-c
 	--without-ctools
-	--with-sss
-	--with-utils
-	--with-sssdb
-	--with-included-sss
+#	--with-sss
+#	--with-sssutils
+#	--with-sssdb
+#	--with-included-sss
 	--with-z="${EPREFIX}"/usr
 	--with-bz2="${EPREFIX}"/usr
 	--with-muparser="${EPREFIX}"/usr
 	--without-sybase
-#	--with-3psw=std:netopt
+	--with-autodep
+#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
 	$(use_with debug)
 	$(use_with debug max-debug)
 	$(use_with debug symbols)
@@ -265,7 +212,7 @@ src_configure() {
 	$(use_with mesa mesa "${EPREFIX}"/usr)
 	$(use_with opengl glut "${EPREFIX}"/usr)
 	$(use_with opengl glew "${EPREFIX}"/usr)
-	$(use_with opengl glew-m)
+	$(use_with opengl glew-mx)
 	$(use_with wxwidgets wxwidgets "${EPREFIX}"/usr)
 	$(use_with wxwidgets wxwidgets-ucs)
 	$(use_with freetype freetype "${EPREFIX}"/usr)
@@ -277,18 +224,19 @@ src_configure() {
 	$(use_with sqlite sqlite3 "${EPREFIX}"/usr)
 	$(use_with icu icu "${EPREFIX}"/usr)
 	$(use_with expat expat "${EPREFIX}"/usr)
-	$(use_with xml libxml2 "${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)
+#	$(use_with gif gif "${EPREFIX}"/usr)
 	$(use_with jpeg jpeg "${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)
+#	$(use_with X x "${EPREFIX}"/usr)
+	$(use_with X x)
 	)
 
 	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
@@ -298,16 +246,16 @@ src_configure() {
     # 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 repalced by e.g. -O9
 
-	"${S}"/configure \
-	--prefix="${EPREFIX}"/usr \
-	--build=x86_64-pc-linux-gnu \
-	--host=x86_64-pc-linux-gnu \
-	--infodir=/usr/share/info \
-	--datadir=/usr/share \
-	--sysconfdir=/etc \
-	--localstatedir=/var/lib \
-	--libdir=/usr/lib64 \
-	${myconf[@]} || die
+	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}"/usr --libdir=/usr/lib64 ${myconf[@]}"
+
+#	bash \
+#		./src/build-system/configure \
+#	cd src/build-system || die
+	econf \
+		--srcdir="${S}" \
+		--prefix="${EPREFIX}"/usr \
+		--libdir=/usr/lib64 \
+		${myconf[@]} || die
 #--without-debug \
 #		--with-bin-release \
 #		--with-bincopy \
@@ -326,7 +274,9 @@ src_compile() {
 	# all_r would ignore the --with-projects contents and build more
 	# emake all_r -C GCC*-Release*/build || die
 	# all_p with compile only selected/required components
-	emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+#	cd "${S}"_build &&\
+	emake all_p -C "${S}"_build/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?"
 }
 
 src_install() {