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authorNicolas Bock <nicolasbock@gmail.com>2013-09-14 06:43:13 -0600
committerNicolas Bock <nicolasbock@gmail.com>2013-09-14 06:43:13 -0600
commitcee802e35ee7fda5e437b1e2d08e8526d2d67ccd (patch)
tree077d634161ff92ab6692fb47c72eaef14661193a
parentsys-cluster/charm-6.5.1: Small fix in patch to make printing less verbose. (diff)
parentSupport at least when user passes USE='gnutls -ssl -openssl' but what we real... (diff)
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Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-rw-r--r--sci-biology/ncbi-tools++/ChangeLog81
-rw-r--r--sci-biology/ncbi-tools++/Manifest1
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch1864
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch213
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch19
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch11
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch10
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch2
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch10
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch10
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch10
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch10
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild311
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild33
14 files changed, 2581 insertions, 4 deletions
diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 270521cab..3da37d966 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,87 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ncbi-tools++-9.0.0-r1.ebuild:
+ Support at least when user passes USE="gnutls -ssl -openssl" but what we
+ really want is to prefer gnutls over openssl if both are available on the
+ system.
+
+ 14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ncbi-tools++-9.0.0-r1.ebuild,
+ +files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch:
+ Add upstream ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch with
+ line
+ offset changes.
+
+ 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild,
+ +files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch,
+ +files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch:
+ Fix URL to point to a public SVN repository (an upstream patch from email
+ list):
+
+ Date: Sun, 28 Jul 2013 22:05:34 -0400
+ CC: <cpp@ncbi.nlm.nih.gov>
+ Subject: Re: [C++] new project startup example needed
+
+ 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ncbi-tools++-12.0.0.ebuild,
+ files/ncbi-tools++-9.0.0-fix-creaders-linking.patch,
+ +files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch,
+ files/ncbi-tools++-12.0.0-fix-creaders-linking.patch:
+ Added an upstream patch from:
+
+ Date: Wed, 28 Aug 2013 10:50:29 -0400
+ List cpp <cpp@ncbi.nlm.nih.gov>
+ Subject: Re: [C++] error building ncbi toolkit v.12.0.0
+
+ Fixed line offsets in the ncbi-tools++-12.0.0-fix-creaders-linking.patch
+ file.
+
+ Fixed file path in ncbi-tools++-9.0.0-fix-creaders-linking.patch header.
+
+ The patches copied blindly from ncbi-tools++-9.0.0-r1 under 12.0.0 need to be
+ adjusted still to have correct line numbers. They do NOT apply cleanly at the
+ moment.
+
+ 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild,
+ files/ncbi-tools++-9.0.0-as-needed.patch,
+ +files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.
+ patch, files/ncbi-tools++-12.0.0-as-needed.patch:
+ files/ncbi-tools++-12.0.0-as-needed.patch
+ files/ncbi-tools++-9.0.0-as-needed.patch
+
+ Remove redundant connect per message from Aaron Ucko <ucko@ncbi.nlm.nih.gov>:
+
+ > +DLL_LIB = xncbi xutil seqset connect xconnect xnetblast
+ Then simply remove connect, which is redundant with xconnect. (connect
+ consists of code shared with NCBI's C Toolkit; xconnect adds a C++
+ layer.)
+
+
+ 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ncbi-tools++-12.0.0.ebuild,
+ +files/ncbi-tools++-12.0.0-fix-creaders-linking.patch:
+ No, the fix-creaders-linking is needed for 12.0.0 as well.
+
+*ncbi-tools++-12.0.0 (13 Sep 2013)
+
+ 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +ncbi-tools++-12.0.0.ebuild, +files/ncbi-tools++-12.0.0-as-needed.patch,
+ +files/ncbi-tools++-12.0.0-conf-opts.patch:
+ Latest release which needs so far only the two Gentoo patches. Would
+ be better to drop ${PV} from their filename to avoid their duplication
+ I think.
+
+ 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ncbi-tools++-9.0.0-r1.ebuild,
+ +files/ncbi-tools++-9.0.0-fix-creaders-linking.patch:
+ add glew to dependencies inferrred via mesa
+ fix lib/libxobjread.so: undefined reference to 'AlignmentFileFree' message by
+ upstream patch
+
12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
Drop empty line
diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
index 48b9d939a..88fdd5a5e 100644
--- a/sci-biology/ncbi-tools++/Manifest
+++ b/sci-biology/ncbi-tools++/Manifest
@@ -1 +1,2 @@
+DIST ncbi_cxx--12_0_0.tar.gz 37925914 SHA256 432d5c72cc02dad263f1b2f1ab875e04e60b1ded0c5537ed54e8095b50554d20 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed WHIRLPOOL 16f0b6de7e0d898bca7a2a46a64a4aa0795f99673d4715a21cca2dc5aa728143b56f02ad9c108543195a8f86f4267777d2be9428dcf52f5495083a63961ad867
DIST ncbi_cxx--9_0_0.tar.gz 33815259 SHA256 f561eb6de12dc7a1e3325d6fc1f76ca097099a31116fb407fa52e54174757fc7 SHA512 b8ce298d4e180915c86ea94cd0cba44cabe8ae1173525a7af3038736572427b4cb25191c6b8ad0fcde14c2677a03fbc675ab22dc64d496dd4a21d70b978c2fab WHIRLPOOL 1c5569c5fc73f67850eb6b35eece0e719a97fee5368f43cca9733b6d2a308dc0c66d2814da15e7b64a400ab7df130ab77e9fc6f3412778cc7c003684a1f6b594
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch
new file mode 100644
index 000000000..821380023
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch
@@ -0,0 +1,1864 @@
+ src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib | 2 ++
+ src/algo/align/ngalign/Makefile.xngalign.lib | 2 ++
+ src/algo/align/nw/Makefile.xalgoalignnw.lib | 2 ++
+ src/algo/align/prosplign/Makefile.prosplign.lib | 2 ++
+ src/algo/align/splign/Makefile.xalgoalignsplign.lib | 2 ++
+ src/algo/blast/api/Makefile.xblast.lib | 2 +-
+ src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +-
+ src/algo/blast/core/Makefile.blast.lib | 2 ++
+ src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib | 2 ++
+ src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib | 2 ++
+ src/algo/blast/format/Makefile.xblastformat.lib | 2 +-
+ src/algo/blast/gumbel_params/Makefile.gumbelparams.lib | 1 +
+ src/algo/cobalt/Makefile.cobalt.lib | 2 ++
+ src/algo/dustmask/Makefile.xalgodustmask.lib | 1 +
+ src/algo/gnomon/Makefile.gnomon.lib | 2 +-
+ src/algo/ms/formats/pepxml/Makefile.pepXML.lib | 2 ++
+ src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++
+ src/algo/phy_tree/Makefile.xalgophytree.lib | 2 +-
+ src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib | 2 ++
+ src/algo/segmask/Makefile.xalgosegmask.lib | 1 +
+ src/algo/seqqa/Makefile.xalgoseqqa.lib | 2 ++
+ src/algo/sequence/Makefile.xalgoseq.lib | 2 ++
+ src/algo/structure/bma_refine/Makefile.xbma_refiner.lib | 3 +++
+ src/algo/structure/cd_utils/Makefile.xcd_utils.lib | 2 +-
+ src/algo/structure/struct_dp/Makefile.xstruct_dp.lib | 2 ++
+ src/algo/structure/struct_util/Makefile.xstruct_util.lib | 2 ++
+ src/algo/structure/threader/Makefile.xstruct_thread.lib | 2 ++
+ src/algo/text/Makefile.xalgotext.lib | 2 ++
+ src/algo/volume_merge/Makefile.xalgovmerge.lib | 2 ++
+ src/algo/winmask/Makefile.xalgowinmask.lib | 2 ++
+ 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/misc/cgi_redirect/Makefile.cgi_redirect.lib | 2 ++
+ src/misc/grid_cgi/Makefile.xgridcgi.lib | 2 ++
+ src/objects/access/Makefile.access.lib | 1 +
+ src/objects/biblio/Makefile.biblio.lib | 2 ++
+ src/objects/biotree/Makefile.biotree.lib | 2 ++
+ src/objects/blast/Makefile.blast.lib | 2 ++
+ src/objects/blast/Makefile.xnetblastcli.lib | 2 ++
+ src/objects/blastdb/Makefile.blastdb.lib | 2 ++
+ src/objects/blastxml/Makefile.blastxml.lib | 2 ++
+ src/objects/cdd/Makefile.cdd.lib | 2 ++
+ src/objects/cn3d/Makefile.cn3d.lib | 2 ++
+ src/objects/docsum/Makefile.docsum.lib | 2 ++
+ src/objects/entrez2/Makefile.entrez2.lib | 2 ++
+ src/objects/entrez2/Makefile.entrez2cli.lib | 2 ++
+ src/objects/entrezgene/Makefile.entrezgene.lib | 2 ++
+ src/objects/featdef/Makefile.featdef.lib | 2 ++
+ src/objects/gbseq/Makefile.gbseq.lib | 2 ++
+ src/objects/general/Makefile.general.lib | 2 ++
+ src/objects/genomecoll/Makefile.genome_collection.lib | 2 ++
+ src/objects/homologene/Makefile.homologene.lib | 2 ++
+ src/objects/id1/Makefile.id1.lib | 2 ++
+ src/objects/id1/Makefile.id1cli.lib | 2 ++
+ src/objects/id2/Makefile.id2.lib | 2 ++
+ src/objects/id2/Makefile.id2cli.lib | 2 ++
+ src/objects/insdseq/Makefile.insdseq.lib | 2 ++
+ src/objects/macro/Makefile.macro.lib | 2 ++
+ src/objects/medlars/Makefile.medlars.lib | 2 ++
+ src/objects/medline/Makefile.medline.lib | 2 ++
+ src/objects/mim/Makefile.mim.lib | 2 ++
+ src/objects/mla/Makefile.mla.lib | 2 ++
+ src/objects/mla/Makefile.mlacli.lib | 2 ++
+ src/objects/mmdb/Makefile.mmdb.lib | 2 ++
+ src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++
+ src/objects/objprt/Makefile.objprt.lib | 2 ++
+ src/objects/omssa/Makefile.omssa.lib | 2 ++
+ src/objects/pcassay/Makefile.pcassay.lib | 2 ++
+ src/objects/pcsubstance/Makefile.pcsubstance.lib | 2 ++
+ src/objects/proj/Makefile.proj.lib | 2 ++
+ src/objects/pub/Makefile.pub.lib | 2 ++
+ src/objects/pubmed/Makefile.pubmed.lib | 2 ++
+ src/objects/remap/Makefile.remap.lib | 2 ++
+ src/objects/remap/Makefile.remapcli.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/seqtest/Makefile.seqtest.lib | 2 ++
+ src/objects/submit/Makefile.submit.lib | 1 +
+ src/objects/taxon1/Makefile.taxon1.lib | 2 ++
+ src/objects/taxon3/Makefile.taxon3.lib | 2 ++
+ src/objects/tinyseq/Makefile.tinyseq.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/split/Makefile.id2_split.lib | 2 +-
+ src/objmgr/util/Makefile.util.lib | 1 +
+ src/objtools/align/Makefile.xalntool.lib | 2 ++
+ src/objtools/align_format/Makefile.align_format.lib | 2 ++
+ src/objtools/alnmgr/Makefile.alnmgr.lib | 1 +
+ src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++
+ src/objtools/blast/gene_info_reader/Makefile.gene_info.lib | 2 ++
+ src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib | 2 ++
+ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++
+ src/objtools/blast/seqdb_writer/Makefile.writedb.lib | 2 ++
+ src/objtools/blast/services/Makefile.blast_services.lib | 1 +
+ src/objtools/cddalignview/Makefile.cddalignview.lib | 2 ++
+ src/objtools/cleanup/Makefile.cleanup.lib | 2 +-
+ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++
+ .../data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib | 2 ++
+ src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib | 2 ++
+ src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +-
+ src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++
+ src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib | 2 ++
+ src/objtools/data_loaders/trace/Makefile.xloader_trace.lib | 2 ++
+ src/objtools/edit/Makefile.edit.lib | 2 ++
+ src/objtools/eutils/api/Makefile.eutils.lib | 2 ++
+ src/objtools/eutils/egquery/Makefile.egquery.lib | 2 ++
+ src/objtools/eutils/ehistory/Makefile.ehistory.lib | 2 ++
+ src/objtools/eutils/einfo/Makefile.einfo.lib | 2 ++
+ src/objtools/eutils/elink/Makefile.elink.lib | 2 ++
+ src/objtools/eutils/epost/Makefile.epost.lib | 2 ++
+ src/objtools/eutils/esearch/Makefile.esearch.lib | 2 ++
+ src/objtools/eutils/espell/Makefile.espell.lib | 2 ++
+ src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++
+ src/objtools/eutils/linkout/Makefile.linkout.lib | 2 ++
+ src/objtools/eutils/uilist/Makefile.uilist.lib | 2 ++
+ src/objtools/format/Makefile.xformat.lib | 2 ++
+ src/objtools/lds/Makefile.lds.lib | 2 +-
+ src/objtools/manip/Makefile.xobjmanip.lib | 2 ++
+ src/objtools/readers/Makefile.xobjread.lib | 3 +--
+ src/objtools/readers/Makefile.xobjreadex.lib | 2 +-
+ src/objtools/seqmasks_io/Makefile.seqmasks_io.lib | 2 +-
+ src/objtools/simple/Makefile.xobjsimple.lib | 1 +
+ src/objtools/snputil/Makefile.snputil.lib | 2 ++
+ src/objtools/validator/Makefile.validator.lib | 2 ++
+ src/objtools/writers/Makefile.xobjwrite.lib | 1 +
+ src/sample/app/asn/Makefile.sample_asn.lib | 2 ++
+ src/sample/app/soap/Makefile.soap_dataobj.lib | 2 ++
+ src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib | 2 ++
+ src/sample/lib/basic/Makefile.basic_sample_lib.lib | 2 ++
+ src/sample/lib/dtd/Makefile.dtd_sample_lib.lib | 2 ++
+ src/sample/lib/xsd/Makefile.xsd_sample_lib.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/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib | 2 +-
+ src/sra/sdk/libs/align/Makefile.align-writer.lib | 2 +-
+ 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 +-
+ 167 files changed, 307 insertions(+), 23 deletions(-)
+
+diff --git a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
+index c8851d8..35ae629 100644
+--- a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
++++ b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
+@@ -10,3 +10,5 @@ LIB = xalgocontig_assembly
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = align_format blastinput dbapi_driver seq xalgoalignnw xalgodustmask xalnmgr xblast xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/align/ngalign/Makefile.xngalign.lib b/src/algo/align/ngalign/Makefile.xngalign.lib
+index d163f7c..ade88ce 100644
+--- a/src/algo/align/ngalign/Makefile.xngalign.lib
++++ b/src/algo/align/ngalign/Makefile.xngalign.lib
+@@ -15,3 +15,5 @@ LIB = xngalign
+
+ CXXFLAGS = $(FAST_CXXFLAGS) -I./.
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = seq xalgoalignutil xncbi blastinput xalgoalignnw align_format xcgi ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2
+diff --git a/src/algo/align/nw/Makefile.xalgoalignnw.lib b/src/algo/align/nw/Makefile.xalgoalignnw.lib
+index acc1ddf..acba81c 100644
+--- a/src/algo/align/nw/Makefile.xalgoalignnw.lib
++++ b/src/algo/align/nw/Makefile.xalgoalignnw.lib
+@@ -15,3 +15,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+ WATCHERS = kiryutin
++
++DLL_LIB = access align_format dbapi_driver general seq writedb xncbi xser # axf
+diff --git a/src/algo/align/prosplign/Makefile.prosplign.lib b/src/algo/align/prosplign/Makefile.prosplign.lib
+index 248ee37..73143ad 100644
+--- a/src/algo/align/prosplign/Makefile.prosplign.lib
++++ b/src/algo/align/prosplign/Makefile.prosplign.lib
+@@ -10,3 +10,5 @@ LIB = prosplign
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = align_format blastinput dbapi_driver general igblast seq xalgoalignutil xalnmgr xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/align/splign/Makefile.xalgoalignsplign.lib b/src/algo/align/splign/Makefile.xalgoalignsplign.lib
+index d67680b..3d56789 100644
+--- a/src/algo/align/splign/Makefile.xalgoalignsplign.lib
++++ b/src/algo/align/splign/Makefile.xalgoalignsplign.lib
+@@ -10,3 +10,5 @@ LIB = xalgoalignsplign
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = access align_format blastinput dbapi_driver gene_info general seq seqdb xalgoalignnw xalgoalignutil xalgoseq xblast xncbi xobjmgr xobjutil xser xutil # axf prosplign
+diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib
+index 073973b..c6a4c2c 100644
+--- a/src/algo/blast/api/Makefile.xblast.lib
++++ b/src/algo/blast/api/Makefile.xblast.lib
+@@ -78,7 +78,7 @@ SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
+
+ LIB = xblast
+
+-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
++DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xnetblastcli xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread
+
+ CFLAGS = $(FAST_CFLAGS)
+ # Strict gcc flags
+diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib
+index bfb315c..2cd809a 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 = seqdb ncbi_xloader_blastdb ncbi_xloader_blastdb_rmt align_format xalnmgr xblast xcgi xobjread xobjutil ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 xalnmgr xcgi
+
+ # should be redundant, given the above :-/
+ ASN_DEP = seqset xnetblast
+diff --git a/src/algo/blast/core/Makefile.blast.lib b/src/algo/blast/core/Makefile.blast.lib
+index 8e889a7..1326aee 100644
+--- a/src/algo/blast/core/Makefile.blast.lib
++++ b/src/algo/blast/core/Makefile.blast.lib
+@@ -23,3 +23,5 @@ LDFLAGS = $(FAST_LDFLAGS)
+
+
+ WATCHERS = coulouri maning madden camacho
++
++DLL_LIB = xutil
+diff --git a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+index fcfb9f9..0e762b4 100644
+--- a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+@@ -14,3 +14,5 @@ LDFLAGS = $(FAST_LDFLAGS)
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
++
++DLL_LIB = dbapi_driver seq seqdb seqset xncbi xobjmgr xobjread xobjutil xser xutil # axf
+diff --git a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+index e64f111..475f4a1 100644
+--- a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
++++ b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+@@ -10,3 +10,5 @@ LDFLAGS = $(FAST_LDFLAGS)
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
++
++DLL_LIB = dbapi_driver xncbi xobjmgr # axf
+diff --git a/src/algo/blast/format/Makefile.xblastformat.lib b/src/algo/blast/format/Makefile.xblastformat.lib
+index f7da067..9920332 100644
+--- a/src/algo/blast/format/Makefile.xblastformat.lib
++++ b/src/algo/blast/format/Makefile.xblastformat.lib
+@@ -7,6 +7,6 @@ SRC = blastfmtutil blastxml_format blast_format data4xmlformat build_archive vec
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+
+-DLL_LIB = blastxml xhtml xcgi
++DLL_LIB = blastxml xhtml xcgi align_format general scoremat seq seqdb xalnmgr xblast xnetblast xobjmgr xobjutil blast_services ncbi_xloader_genbank xcgi # cobalt
+
+ WATCHERS = jianye zaretska madden camacho fongah2
+diff --git a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+index 316d4fa..844de85 100644
+--- a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
++++ b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+@@ -11,3 +11,4 @@ LDFLAGS = $(FAST_LDFLAGS)
+
+ WATCHERS = boratyng madden camacho
+
++DLL_LIB = dbapi_driver xncbi xutil # axf
+diff --git a/src/algo/cobalt/Makefile.cobalt.lib b/src/algo/cobalt/Makefile.cobalt.lib
+index e618f67..b406cc5 100644
+--- a/src/algo/cobalt/Makefile.cobalt.lib
++++ b/src/algo/cobalt/Makefile.cobalt.lib
+@@ -14,3 +14,5 @@ ASN_DEP = seq seqset biotree xnetblast blastdb
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = align_format dbapi_driver general igblast seq seqdb seqset xalgoalignnw xalgophytree xblast xncbi xnetblast xobjmgr xobjutil xser fastme # axf
+diff --git a/src/algo/dustmask/Makefile.xalgodustmask.lib b/src/algo/dustmask/Makefile.xalgodustmask.lib
+index 84e2568..3632356 100644
+--- a/src/algo/dustmask/Makefile.xalgodustmask.lib
++++ b/src/algo/dustmask/Makefile.xalgodustmask.lib
+@@ -11,3 +11,4 @@ SRC = symdust
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = dbapi_driver seq xncbi xobjmgr # axf
+diff --git a/src/algo/gnomon/Makefile.gnomon.lib b/src/algo/gnomon/Makefile.gnomon.lib
+index af363c0..3235647 100644
+--- a/src/algo/gnomon/Makefile.gnomon.lib
++++ b/src/algo/gnomon/Makefile.gnomon.lib
+@@ -6,7 +6,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) \
+ gnomon_engine gnomon_objmgr score gnomon_model parse hmm gnomon_seq asn1 chainer id_handler \
+ annot select_alignments_alt
+ LIB = xalgognomon
+-DLL_LIB = xobjutil $(SOBJMGR_LIBS)
++DLL_LIB = xobjutil $(SOBJMGR_LIBS) xalgoseq
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+diff --git a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
+index 686dd70..98f57b2 100644
+--- a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
++++ b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
+@@ -2,3 +2,5 @@ WATCHERS = lewisg slottad
+
+ LIB = pepXML
+ SRC = pepXML__ pepXML___
++
++DLL_LIB = access align_format dbapi_driver xncbi xser # axf
+diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib
+index 872b92e..78261eb 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 omssa pepXML xcompress xconnect seqdb xblast xregexp
+diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib
+index 5964ef4..8163366 100644
+--- a/src/algo/phy_tree/Makefile.xalgophytree.lib
++++ b/src/algo/phy_tree/Makefile.xalgophytree.lib
+@@ -6,7 +6,7 @@ ASN_DEP = biotree
+
+ SRC = bio_tree phy_node dist_methods lex.newick newick.tab tree_to_dist_mat phytree_calc
+ LIB = xalgophytree
+-DLL_LIB = biotree
++DLL_LIB = biotree seq xalnmgr xobjutil # fastme
+
+ # The -I flag is necessary because filenames in #line directives throw
+ # off some compilers (GCC 2.95 at least). :-/
+diff --git a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
+index 15d7440..fab9207 100644
+--- a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
++++ b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
+@@ -10,3 +10,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
+ ASN_DEP = biotree seqset taxon1
+
+ WATCHERS = boratyng
++
++DLL_LIB = access align_format biotree dbapi_driver fastme gene_info seq taxon1 xalgophytree xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/segmask/Makefile.xalgosegmask.lib b/src/algo/segmask/Makefile.xalgosegmask.lib
+index bd011c1..97281ec 100644
+--- a/src/algo/segmask/Makefile.xalgosegmask.lib
++++ b/src/algo/segmask/Makefile.xalgosegmask.lib
+@@ -11,3 +11,4 @@ SRC = segmask
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = align_format xobjmgr
+diff --git a/src/algo/seqqa/Makefile.xalgoseqqa.lib b/src/algo/seqqa/Makefile.xalgoseqqa.lib
+index b1bea47..a0e5b1b 100644
+--- a/src/algo/seqqa/Makefile.xalgoseqqa.lib
++++ b/src/algo/seqqa/Makefile.xalgoseqqa.lib
+@@ -12,3 +12,5 @@ LIB = xalgoseqqa
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
++
++DLL_LIB = access align_format dbapi_driver entrez2cli gene_info general seq seqtest xalgognomon xalgoseq xalnmgr xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib
+index 51f4cd7..724e939 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 xregexp align_format seqset xobjmgr xobjutil
+diff --git a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
+index 5562f82..68d3a87 100644
+--- a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
++++ b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
+@@ -24,3 +24,6 @@ SRC = RowSelector \
+ RefinerTrial \
+ RefinerEngine \
+ Interface
++
++DLL_LIB = blastinput cdd ncbi_xcache_bdb xcd_utils xncbi xser xutil
++
+diff --git a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
+index eda71f8..8d3a96a 100644
+--- a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
++++ b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
+@@ -68,6 +68,6 @@ SRC = \
+ cuTaxTree \
+ cuUtils
+
+-DLL_LIB = xobjread
++DLL_LIB = xobjread blastdb blast_services cdd entrez2cli id1cli mmdb ncbimime scoremat taxon1 xblast xobjmgr xregexp
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+diff --git a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib b/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib
+index 676a8dd..3d3e4c9 100644
+--- a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib
++++ b/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib
+@@ -9,3 +9,5 @@ WATCHERS = thiessen
+ SRC = block_align
+
+ LIB = xstruct_dp
++
++DLL_LIB = xncbi
+diff --git a/src/algo/structure/struct_util/Makefile.xstruct_util.lib b/src/algo/structure/struct_util/Makefile.xstruct_util.lib
+index 5a38c7d..35d7077 100644
+--- a/src/algo/structure/struct_util/Makefile.xstruct_util.lib
++++ b/src/algo/structure/struct_util/Makefile.xstruct_util.lib
+@@ -17,3 +17,5 @@ SRC = aaa_dummy_pch \
+ su_block_multiple_alignment \
+ su_pssm \
+ su_sequence_set
++
++DLL_LIB = seqset seq xncbi scoremat xstruct_dp xblast
+diff --git a/src/algo/structure/threader/Makefile.xstruct_thread.lib b/src/algo/structure/threader/Makefile.xstruct_thread.lib
+index c06a2c0..9f1ff25 100644
+--- a/src/algo/structure/threader/Makefile.xstruct_thread.lib
++++ b/src/algo/structure/threader/Makefile.xstruct_thread.lib
+@@ -10,3 +10,5 @@ SRC = thrdalgs thrdatd thrdbwfi thrdcpal thrdcpll thrdcprl \
+ thrdttbi thrdzsc
+
+ LIB = xstruct_thread
++
++DLL_LIB = xutil
+diff --git a/src/algo/text/Makefile.xalgotext.lib b/src/algo/text/Makefile.xalgotext.lib
+index 81ba0e6..f25073e 100644
+--- a/src/algo/text/Makefile.xalgotext.lib
++++ b/src/algo/text/Makefile.xalgotext.lib
+@@ -10,3 +10,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+ ASN_DEP = general
++
++DLL_LIB = align_format blastinput ncbi_xcache_bdb xcompress xncbi xutil # axf
+diff --git a/src/algo/volume_merge/Makefile.xalgovmerge.lib b/src/algo/volume_merge/Makefile.xalgovmerge.lib
+index 499861a..3ffb80b 100644
+--- a/src/algo/volume_merge/Makefile.xalgovmerge.lib
++++ b/src/algo/volume_merge/Makefile.xalgovmerge.lib
+@@ -10,3 +10,5 @@ SRC = volume_merge
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++
++DLL_LIB = xncbi
+diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib
+index afaf676..ad2c1fe 100644
+--- a/src/algo/winmask/Makefile.xalgowinmask.lib
++++ b/src/algo/winmask/Makefile.xalgowinmask.lib
+@@ -21,3 +21,5 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = seqmasks_io xobjread xobjutil
++
+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..e3d6a49 100644
+--- a/src/dbapi/Makefile.dbapi.lib
++++ b/src/dbapi/Makefile.dbapi.lib
+@@ -10,3 +10,8 @@ LIB = dbapi
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE)
+
+ WATCHERS = ivanovp
++
++#ASN_DEP = driver dbapi_driver
++
++DLL_LIB = xncbi xutil # dbapi_driver$(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/misc/cgi_redirect/Makefile.cgi_redirect.lib b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
+index 6d7a4af..332e5d0 100644
+--- a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
++++ b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
+@@ -7,3 +7,5 @@ SRC = redirect
+ LIB = xcgi_redirect
+
+ WATCHERS = ivanov
++
++DLL_LIB = axf dbapi_driver xcgi xhtml xncbi
+diff --git a/src/misc/grid_cgi/Makefile.xgridcgi.lib b/src/misc/grid_cgi/Makefile.xgridcgi.lib
+index c9ef138..8e25cbe 100644
+--- a/src/misc/grid_cgi/Makefile.xgridcgi.lib
++++ b/src/misc/grid_cgi/Makefile.xgridcgi.lib
+@@ -9,3 +9,5 @@ LIB = xgridcgi
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+
+ WATCHERS = vakatov
++
++DLL_LIB = xncbi xcgi xconnserv xhtml
+diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib
+index 11421d9..e7900a1 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 xser
+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/biotree/Makefile.biotree.lib b/src/objects/biotree/Makefile.biotree.lib
+index 8019285..2c689ae 100644
+--- a/src/objects/biotree/Makefile.biotree.lib
++++ b/src/objects/biotree/Makefile.biotree.lib
+@@ -1,3 +1,5 @@
+ ASN_DEP = seq seqset
+ LIB = biotree
+ SRC = biotree__ biotree___
++
++DLL_LIB = xncbi xser
+diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib
+index 0dd0fa3..d50f29f 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 seq seqset scoremat
+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 xconnect xnetblast
+diff --git a/src/objects/blastdb/Makefile.blastdb.lib b/src/objects/blastdb/Makefile.blastdb.lib
+index be2c0d1..2884db2 100644
+--- a/src/objects/blastdb/Makefile.blastdb.lib
++++ b/src/objects/blastdb/Makefile.blastdb.lib
+@@ -1,2 +1,4 @@
+ LIB = blastdb
+ SRC = blastdb__ blastdb___
++
++DLL_LIB = xncbi xser seq
+diff --git a/src/objects/blastxml/Makefile.blastxml.lib b/src/objects/blastxml/Makefile.blastxml.lib
+index d18eb78..f90501d 100644
+--- a/src/objects/blastxml/Makefile.blastxml.lib
++++ b/src/objects/blastxml/Makefile.blastxml.lib
+@@ -1,2 +1,4 @@
+ LIB = blastxml
+ SRC = blastxml__ blastxml___
++
++DLL_LIB = xser
+diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib
+index 978cae9..24b726c 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 xser scoremat cn3d
+diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib
+index 1af5d1d..ecd31b2 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 xser
+diff --git a/src/objects/docsum/Makefile.docsum.lib b/src/objects/docsum/Makefile.docsum.lib
+index 0e68886..0bc8a1c 100644
+--- a/src/objects/docsum/Makefile.docsum.lib
++++ b/src/objects/docsum/Makefile.docsum.lib
+@@ -1,2 +1,4 @@
+ LIB = docsum
+ SRC = docsum__ docsum___
++
++DLL_LIB = xser
+diff --git a/src/objects/entrez2/Makefile.entrez2.lib b/src/objects/entrez2/Makefile.entrez2.lib
+index 4507f72..4c47ad3 100644
+--- a/src/objects/entrez2/Makefile.entrez2.lib
++++ b/src/objects/entrez2/Makefile.entrez2.lib
+@@ -2,3 +2,5 @@ WATCHERS = lavr
+
+ LIB = entrez2
+ SRC = entrez2__ entrez2___
++
++DLL_LIB = xser
+diff --git a/src/objects/entrez2/Makefile.entrez2cli.lib b/src/objects/entrez2/Makefile.entrez2cli.lib
+index 42a4649..2fdcc6f 100644
+--- a/src/objects/entrez2/Makefile.entrez2cli.lib
++++ b/src/objects/entrez2/Makefile.entrez2cli.lib
+@@ -4,3 +4,5 @@ ASN_DEP = entrez2
+
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
++
++DLL_LIB = xncbi xconnect entrez2
+diff --git a/src/objects/entrezgene/Makefile.entrezgene.lib b/src/objects/entrezgene/Makefile.entrezgene.lib
+index a1bd4f4..27319c3 100644
+--- a/src/objects/entrezgene/Makefile.entrezgene.lib
++++ b/src/objects/entrezgene/Makefile.entrezgene.lib
+@@ -1,2 +1,4 @@
+ LIB = entrezgene
+ SRC = entrezgene__ entrezgene___
++
++DLL_LIB = xser seq
+diff --git a/src/objects/featdef/Makefile.featdef.lib b/src/objects/featdef/Makefile.featdef.lib
+index 51c7c8d..e603711 100644
+--- a/src/objects/featdef/Makefile.featdef.lib
++++ b/src/objects/featdef/Makefile.featdef.lib
+@@ -1,2 +1,4 @@
+ LIB = featdef
+ SRC = featdef__ featdef___
++
++DLL_LIB = xser
+diff --git a/src/objects/gbseq/Makefile.gbseq.lib b/src/objects/gbseq/Makefile.gbseq.lib
+index 9dabdeb..4b27881 100644
+--- a/src/objects/gbseq/Makefile.gbseq.lib
++++ b/src/objects/gbseq/Makefile.gbseq.lib
+@@ -1,2 +1,4 @@
+ LIB = gbseq
+ SRC = gbseq__ gbseq___
++
++DLL_LIB = xser
+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/genomecoll/Makefile.genome_collection.lib b/src/objects/genomecoll/Makefile.genome_collection.lib
+index f039af6..f6b41a7 100644
+--- a/src/objects/genomecoll/Makefile.genome_collection.lib
++++ b/src/objects/genomecoll/Makefile.genome_collection.lib
+@@ -4,3 +4,5 @@ LIB = genome_collection
+ SRC = genome_collection__ genome_collection___
+
+ WATCHERS = dicuccio
++
++DLL_LIB = xser seq
+diff --git a/src/objects/homologene/Makefile.homologene.lib b/src/objects/homologene/Makefile.homologene.lib
+index 15d13ad..d44b2e3 100644
+--- a/src/objects/homologene/Makefile.homologene.lib
++++ b/src/objects/homologene/Makefile.homologene.lib
+@@ -4,3 +4,5 @@
+
+ LIB = homologene
+ SRC = homologene__ homologene___
++
++DLL_LIB = xser seq
+diff --git a/src/objects/id1/Makefile.id1.lib b/src/objects/id1/Makefile.id1.lib
+index d60c728..bf98427 100644
+--- a/src/objects/id1/Makefile.id1.lib
++++ b/src/objects/id1/Makefile.id1.lib
+@@ -4,3 +4,5 @@ LIB = id1
+ SRC = id1__ id1___
+
+ WATCHERS = vasilche
++
++DLL_LIB = xser seqset
+diff --git a/src/objects/id1/Makefile.id1cli.lib b/src/objects/id1/Makefile.id1cli.lib
+index e87ea83..745c5cb 100644
+--- a/src/objects/id1/Makefile.id1cli.lib
++++ b/src/objects/id1/Makefile.id1cli.lib
+@@ -4,3 +4,5 @@ LIB = id1cli
+ SRC = id1_client id1_client_
+
+ WATCHERS = vasilche
++
++DLL_LIB = id1 xconnect
+diff --git a/src/objects/id2/Makefile.id2.lib b/src/objects/id2/Makefile.id2.lib
+index 09d8b36..1e74a58 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 seq seqsplit
+diff --git a/src/objects/id2/Makefile.id2cli.lib b/src/objects/id2/Makefile.id2cli.lib
+index 5d41f23..ccec62a 100644
+--- a/src/objects/id2/Makefile.id2cli.lib
++++ b/src/objects/id2/Makefile.id2cli.lib
+@@ -4,3 +4,5 @@ LIB = id2cli
+ SRC = id2_client id2_client_
+
+ WATCHERS = vasilche
++
++DLL_LIB = id2 xconnect
+diff --git a/src/objects/insdseq/Makefile.insdseq.lib b/src/objects/insdseq/Makefile.insdseq.lib
+index fa729b7..5754057 100644
+--- a/src/objects/insdseq/Makefile.insdseq.lib
++++ b/src/objects/insdseq/Makefile.insdseq.lib
+@@ -1,2 +1,4 @@
+ LIB = insdseq
+ SRC = insdseq__ insdseq___
++
++DLL_LIB = xser
+diff --git a/src/objects/macro/Makefile.macro.lib b/src/objects/macro/Makefile.macro.lib
+index 3a0a7c0..25a3b73 100644
+--- a/src/objects/macro/Makefile.macro.lib
++++ b/src/objects/macro/Makefile.macro.lib
+@@ -2,3 +2,5 @@
+
+ LIB = macro
+ SRC = macro__ macro___
++
++DLL_LIB = xser
+diff --git a/src/objects/medlars/Makefile.medlars.lib b/src/objects/medlars/Makefile.medlars.lib
+index 3a6d0cd..5c8e00e 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 biblio
+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/mim/Makefile.mim.lib b/src/objects/mim/Makefile.mim.lib
+index c2cd50e..2fed8f4 100644
+--- a/src/objects/mim/Makefile.mim.lib
++++ b/src/objects/mim/Makefile.mim.lib
+@@ -1,2 +1,4 @@
+ LIB = mim
+ SRC = mim__ mim___
++
++DLL_LIB = xser
+diff --git a/src/objects/mla/Makefile.mla.lib b/src/objects/mla/Makefile.mla.lib
+index a748f68..5b5523a 100644
+--- a/src/objects/mla/Makefile.mla.lib
++++ b/src/objects/mla/Makefile.mla.lib
+@@ -1,2 +1,4 @@
+ LIB = mla
+ SRC = mla__ mla___
++
++DLL_LIB = xser medline pubmed pub medlars
+diff --git a/src/objects/mla/Makefile.mlacli.lib b/src/objects/mla/Makefile.mlacli.lib
+index 48af427..4cee3ac 100644
+--- a/src/objects/mla/Makefile.mlacli.lib
++++ b/src/objects/mla/Makefile.mlacli.lib
+@@ -2,3 +2,5 @@ ASN_DEP = mla
+
+ LIB = mlacli
+ SRC = mla_client mla_client_
++
++DLL_LIB = xncbi xconnect mla
+diff --git a/src/objects/mmdb/Makefile.mmdb.lib b/src/objects/mmdb/Makefile.mmdb.lib
+index 6fc8e25..5c6c100 100644
+--- a/src/objects/mmdb/Makefile.mmdb.lib
++++ b/src/objects/mmdb/Makefile.mmdb.lib
+@@ -8,3 +8,5 @@ CPPFLAGS = -I$(srcdir) -I$(top_srcdir)/src/objects/mmdb $(ORIG_CPPFLAGS)
+
+ LIB = mmdb
+ SRC = $(ASN:%=%__) $(ASN:%=%___)
++
++DLL_LIB = xser pub seq
+diff --git a/src/objects/ncbimime/Makefile.ncbimime.lib b/src/objects/ncbimime/Makefile.ncbimime.lib
+index 93cafdf..1360ade 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 cn3d seqset cdd
+diff --git a/src/objects/objprt/Makefile.objprt.lib b/src/objects/objprt/Makefile.objprt.lib
+index 40d6b09..c00e6d2 100644
+--- a/src/objects/objprt/Makefile.objprt.lib
++++ b/src/objects/objprt/Makefile.objprt.lib
+@@ -1,2 +1,4 @@
+ LIB = objprt
+ SRC = objprt__ objprt___
++
++DLL_LIB = xser
+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/pcassay/Makefile.pcassay.lib b/src/objects/pcassay/Makefile.pcassay.lib
+index 1086865..587adb5 100644
+--- a/src/objects/pcassay/Makefile.pcassay.lib
++++ b/src/objects/pcassay/Makefile.pcassay.lib
+@@ -1,2 +1,4 @@
+ LIB = pcassay
+ SRC = pcassay__ pcassay___
++
++DLL_LIB = xser pcsubstance seq
+diff --git a/src/objects/pcsubstance/Makefile.pcsubstance.lib b/src/objects/pcsubstance/Makefile.pcsubstance.lib
+index b36802e..c3f6a39 100644
+--- a/src/objects/pcsubstance/Makefile.pcsubstance.lib
++++ b/src/objects/pcsubstance/Makefile.pcsubstance.lib
+@@ -1,2 +1,4 @@
+ LIB = pcsubstance
+ SRC = pcsubstance__ pcsubstance___
++
++DLL_LIB = xser general pub
+diff --git a/src/objects/proj/Makefile.proj.lib b/src/objects/proj/Makefile.proj.lib
+index c5bb3d3..fbde99a 100644
+--- a/src/objects/proj/Makefile.proj.lib
++++ b/src/objects/proj/Makefile.proj.lib
+@@ -1,2 +1,4 @@
+ LIB = proj
+ SRC = proj__ proj___
++
++DLL_LIB = xser pubmed seqset
+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/pubmed/Makefile.pubmed.lib b/src/objects/pubmed/Makefile.pubmed.lib
+index 8b8d553..46e3125 100644
+--- a/src/objects/pubmed/Makefile.pubmed.lib
++++ b/src/objects/pubmed/Makefile.pubmed.lib
+@@ -1,2 +1,4 @@
+ LIB = pubmed
+ SRC = pubmed__ pubmed___
++
++DLL_LIB = xser medline
+diff --git a/src/objects/remap/Makefile.remap.lib b/src/objects/remap/Makefile.remap.lib
+index 9a35d90..1256648 100644
+--- a/src/objects/remap/Makefile.remap.lib
++++ b/src/objects/remap/Makefile.remap.lib
+@@ -1,2 +1,4 @@
+ LIB = remap
+ SRC = remap__ remap___
++
++DLL_LIB = xser seq
+diff --git a/src/objects/remap/Makefile.remapcli.lib b/src/objects/remap/Makefile.remapcli.lib
+index e45f34f..2751bf9 100644
+--- a/src/objects/remap/Makefile.remapcli.lib
++++ b/src/objects/remap/Makefile.remapcli.lib
+@@ -4,3 +4,5 @@ ASN_DEP = remap
+
+ LIB = remapcli
+ SRC = remap_client remap_client_
++
++DLL_LIB = xncbi xconnect remap
+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..520b0bb 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 seqset
+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..1743321 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 seq seqset
+diff --git a/src/objects/seqtest/Makefile.seqtest.lib b/src/objects/seqtest/Makefile.seqtest.lib
+index 609a12c..e3d1e4b 100644
+--- a/src/objects/seqtest/Makefile.seqtest.lib
++++ b/src/objects/seqtest/Makefile.seqtest.lib
+@@ -4,3 +4,5 @@ ASN = seqtest
+
+ LIB = seqtest
+ SRC = $(ASN:%=%__) $(ASN:%=%___)
++
++DLL_LIB = xser seq
+diff --git a/src/objects/submit/Makefile.submit.lib b/src/objects/submit/Makefile.submit.lib
+index 74798f8..c74707c 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 seq biblio seqset
+diff --git a/src/objects/taxon1/Makefile.taxon1.lib b/src/objects/taxon1/Makefile.taxon1.lib
+index 61658ab..f46db75 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 seq xconnect
+diff --git a/src/objects/taxon3/Makefile.taxon3.lib b/src/objects/taxon3/Makefile.taxon3.lib
+index 7e4c93d..00be2c0 100644
+--- a/src/objects/taxon3/Makefile.taxon3.lib
++++ b/src/objects/taxon3/Makefile.taxon3.lib
+@@ -4,3 +4,5 @@ LIB = taxon3
+ SRC = taxon3__ taxon3___ taxon3
+
+ WATCHERS = bollin
++
++DLL_LIB = connect xser xconnect seq
+diff --git a/src/objects/tinyseq/Makefile.tinyseq.lib b/src/objects/tinyseq/Makefile.tinyseq.lib
+index 1c7ccf3..e1954cc 100644
+--- a/src/objects/tinyseq/Makefile.tinyseq.lib
++++ b/src/objects/tinyseq/Makefile.tinyseq.lib
+@@ -1,2 +1,4 @@
+ LIB = tinyseq
+ SRC = tinyseq__ tinyseq___
++
++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..64226d6 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 xregexp
+diff --git a/src/objects/variation/Makefile.variation.lib b/src/objects/variation/Makefile.variation.lib
+index f21f84a..9ba5e9d 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 general seq
+diff --git a/src/objmgr/split/Makefile.id2_split.lib b/src/objmgr/split/Makefile.id2_split.lib
+index fafa70a..8a53975 100644
+--- a/src/objmgr/split/Makefile.id2_split.lib
++++ b/src/objmgr/split/Makefile.id2_split.lib
+@@ -17,6 +17,6 @@ LIB = id2_split
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+-DLL_LIB = $(SOBJMGR_LIBS)
++DLL_LIB = $(SOBJMGR_LIBS) seqsplit xcompress
+
+ WATCHERS = vasilche
+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/Makefile.xalntool.lib b/src/objtools/align/Makefile.xalntool.lib
+index cb9846d..9c2a8f9 100644
+--- a/src/objtools/align/Makefile.xalntool.lib
++++ b/src/objtools/align/Makefile.xalntool.lib
+@@ -6,3 +6,5 @@ ASN_DEP = seqset
+
+ LIB = xalntool
+ SRC = alngraphic
++
++DLL_LIB = access dbapi_driver general seq xhtml xncbi xobjmgr xobjutil xser # align_format axf blastinput
+diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib
+index 4b3e59e..c67c352 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 xser xhtml gene_info xnetblast blast_services ncbi_xloader_genbank xalnmgr xcgi xobjread xobjutil
+diff --git a/src/objtools/alnmgr/Makefile.alnmgr.lib b/src/objtools/alnmgr/Makefile.alnmgr.lib
+index e32c351..41355ff 100644
+--- a/src/objtools/alnmgr/Makefile.alnmgr.lib
++++ b/src/objtools/alnmgr/Makefile.alnmgr.lib
+@@ -12,3 +12,4 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial \
+
+ WATCHERS = todorov dicuccio grichenk
+
++DLL_LIB = tables dbapi_driver ncbi_xcache_bdb seq seqset sequtil xncbi xobjmgr xobjutil xser # align_format axf
+diff --git a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+index d8177ed..aa4d8e4 100644
+--- a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
++++ b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
+ # CXXFLAGS = $(FAST_CXXFLAGS)
+ #
+ # LIB_OR_DLL = dll
++
++DLL_LIB = xncbi xser xobjutil seq seqdb
+diff --git a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+index bf5fd1b..c32aca4 100644
+--- a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
++++ b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+@@ -4,3 +4,5 @@ WATCHERS = camacho
+
+ LIB = gene_info
+ SRC = gene_info gene_info_reader file_utils
++
++DLL_LIB = xncbi
+diff --git a/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib b/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib
+index b0a00dc..37569f8 100644
+--- a/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib
++++ b/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib
+@@ -6,3 +6,5 @@ LIB = gene_info_writer
+ SRC = gene_info_writer
+
+ ASN_DEP = blastdb
++
++DLL_LIB = gene_info xncbi seqdb
+diff --git a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+index 25898aa..0b0e478 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 xobjmgr
+diff --git a/src/objtools/blast/seqdb_writer/Makefile.writedb.lib b/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+index 7b9c8e1..6dbdbaa 100644
+--- a/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
++++ b/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+@@ -13,3 +13,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+ WATCHERS = maning camacho
++
++DLL_LIB = seq blastdb seqdb xobjmgr xobjread xutil
+diff --git a/src/objtools/blast/services/Makefile.blast_services.lib b/src/objtools/blast/services/Makefile.blast_services.lib
+index 10a878c..7a70b22 100644
+--- a/src/objtools/blast/services/Makefile.blast_services.lib
++++ b/src/objtools/blast/services/Makefile.blast_services.lib
+@@ -12,3 +12,4 @@ CFLAGS = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = xncbi xser xnetblast xnetblastcli
+diff --git a/src/objtools/cddalignview/Makefile.cddalignview.lib b/src/objtools/cddalignview/Makefile.cddalignview.lib
+index 8e39baa..f4d3a35 100644
+--- a/src/objtools/cddalignview/Makefile.cddalignview.lib
++++ b/src/objtools/cddalignview/Makefile.cddalignview.lib
+@@ -11,3 +11,5 @@ SRC = \
+ cav_seqset
+
+ LIB = xcddalignview
++
++DLL_LIB = cdd dbapi_driver general ncbimime seq seqset xncbi xser # align_format axf ncbi_xloader_bam
+diff --git a/src/objtools/cleanup/Makefile.cleanup.lib b/src/objtools/cleanup/Makefile.cleanup.lib
+index 663d755..ad7b3cf 100644
+--- a/src/objtools/cleanup/Makefile.cleanup.lib
++++ b/src/objtools/cleanup/Makefile.cleanup.lib
+@@ -10,7 +10,7 @@ SRC = autogenerated_cleanup cleanup \
+ cleanup_utils \
+ newcleanupp
+
+-DLL_LIB = xregexp $(PCRE_LIB)
++DLL_LIB = xregexp $(PCRE_LIB) access biblio general pub seq seqset sequtil submit xobjmgr xobjutil xser
+ LIB = xcleanup
+
+ LIBS = $(PCRE_LIBS)
+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/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+index 80abb48..2ddec92 100644
+--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+@@ -6,3 +6,5 @@ SRC = bdbloader_rmt remote_blastdb_adapter
+ ASN_DEP = blastdb xnetblast
+
+ WATCHERS = camacho
++
++DLL_LIB = blast_services ncbi_xloader_blastdb xobjmgr
+diff --git a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
+index a51042b..fa92fc9 100644
+--- a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
++++ b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
+@@ -9,3 +9,5 @@ LIB = ncbi_xloader_cdd
+ SRC = cdd
+
+ ASN_DEP = seqset
++
++DLL_LIB = dbapi_driver general seq seqset xconnect xncbi xobjmgr xser # align_format axf ncbi_xloader_bam
+diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+index f2b2b49..864e4b1 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 xobjmgr seqsplit xconnect id1 id2
+
+ WATCHERS = vasilche
+diff --git a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+index 0a29cbf..74c30dc 100644
+--- a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
++++ b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+@@ -15,3 +15,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
+ # DLL_LIB = xconnect ncbi_xreader$(DLL)
+
+ WATCHERS = vasilche
++
++DLL_LIB = xncbi gene_info id2 ncbi_xreader xconnect xser
+diff --git a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
+index 8d09d8c..d6040ed 100644
+--- a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
++++ b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
+@@ -7,3 +7,5 @@ ASN_DEP = seq seqset seqedit
+
+
+ WATCHERS = vasilche
++
++DLL_LIB = dbapi_driver seq seqedit seqset xncbi xobjmgr xser # axf
+diff --git a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
+index d2debd5..33fed34 100644
+--- a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
++++ b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
+@@ -9,3 +9,5 @@ LIB = ncbi_xloader_trace
+ SRC = trace_chgr
+
+ ASN_DEP = id1
++
++DLL_LIB = dbapi_driver general id1 id1cli seq xncbi xobjmgr xser # align_format axf
+diff --git a/src/objtools/edit/Makefile.edit.lib b/src/objtools/edit/Makefile.edit.lib
+index 7ce0d11..f5458c5 100644
+--- a/src/objtools/edit/Makefile.edit.lib
++++ b/src/objtools/edit/Makefile.edit.lib
+@@ -11,3 +11,5 @@ LIB = xobjedit
+ ASN_DEP = seqset
+
+ WATCHERS = bollin
++
++DLL_LIB = xncbi seq xobjutil xobjmgr
+diff --git a/src/objtools/eutils/api/Makefile.eutils.lib b/src/objtools/eutils/api/Makefile.eutils.lib
+index da71ea9..b444e72 100644
+--- a/src/objtools/eutils/api/Makefile.eutils.lib
++++ b/src/objtools/eutils/api/Makefile.eutils.lib
+@@ -10,3 +10,5 @@ ASN_DEP = einfo esearch egquery epost elink esummary espell uilist \
+ ehistory
+
+ WATCHERS = grichenk
++
++DLL_LIB = dbapi_driver xconnect xncbi xser # align_format axf ncbi_xloader_bam
+diff --git a/src/objtools/eutils/egquery/Makefile.egquery.lib b/src/objtools/eutils/egquery/Makefile.egquery.lib
+index 82b4ed0..7030a29 100644
+--- a/src/objtools/eutils/egquery/Makefile.egquery.lib
++++ b/src/objtools/eutils/egquery/Makefile.egquery.lib
+@@ -4,3 +4,5 @@ LIB = egquery
+ SRC = egquery__ egquery___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/ehistory/Makefile.ehistory.lib b/src/objtools/eutils/ehistory/Makefile.ehistory.lib
+index f99ca0f..5683a74 100644
+--- a/src/objtools/eutils/ehistory/Makefile.ehistory.lib
++++ b/src/objtools/eutils/ehistory/Makefile.ehistory.lib
+@@ -4,3 +4,5 @@ LIB = ehistory
+ SRC = ehistory__ ehistory___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/einfo/Makefile.einfo.lib b/src/objtools/eutils/einfo/Makefile.einfo.lib
+index e18413d..7eaee71 100644
+--- a/src/objtools/eutils/einfo/Makefile.einfo.lib
++++ b/src/objtools/eutils/einfo/Makefile.einfo.lib
+@@ -4,3 +4,5 @@ LIB = einfo
+ SRC = einfo__ einfo___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/elink/Makefile.elink.lib b/src/objtools/eutils/elink/Makefile.elink.lib
+index 87f352c..692835c 100644
+--- a/src/objtools/eutils/elink/Makefile.elink.lib
++++ b/src/objtools/eutils/elink/Makefile.elink.lib
+@@ -4,3 +4,5 @@ LIB = elink
+ SRC = elink__ elink___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/epost/Makefile.epost.lib b/src/objtools/eutils/epost/Makefile.epost.lib
+index 4a456ed..d73f41b 100644
+--- a/src/objtools/eutils/epost/Makefile.epost.lib
++++ b/src/objtools/eutils/epost/Makefile.epost.lib
+@@ -4,3 +4,5 @@ LIB = epost
+ SRC = epost__ epost___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/esearch/Makefile.esearch.lib b/src/objtools/eutils/esearch/Makefile.esearch.lib
+index bb5b64b..71912da 100644
+--- a/src/objtools/eutils/esearch/Makefile.esearch.lib
++++ b/src/objtools/eutils/esearch/Makefile.esearch.lib
+@@ -4,3 +4,5 @@ LIB = esearch
+ SRC = esearch__ esearch___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/espell/Makefile.espell.lib b/src/objtools/eutils/espell/Makefile.espell.lib
+index 7cf1a34..25be846 100644
+--- a/src/objtools/eutils/espell/Makefile.espell.lib
++++ b/src/objtools/eutils/espell/Makefile.espell.lib
+@@ -4,3 +4,5 @@ LIB = espell
+ SRC = espell__ espell___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/esummary/Makefile.esummary.lib b/src/objtools/eutils/esummary/Makefile.esummary.lib
+index 4d3e058..1f74c06 100644
+--- a/src/objtools/eutils/esummary/Makefile.esummary.lib
++++ b/src/objtools/eutils/esummary/Makefile.esummary.lib
+@@ -4,3 +4,5 @@ LIB = esummary
+ SRC = esummary__ esummary___
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/linkout/Makefile.linkout.lib b/src/objtools/eutils/linkout/Makefile.linkout.lib
+index 19b2b8a..77dcc3c 100644
+--- a/src/objtools/eutils/linkout/Makefile.linkout.lib
++++ b/src/objtools/eutils/linkout/Makefile.linkout.lib
+@@ -4,3 +4,5 @@ SRC = linkout__ linkout___
+ LIB = linkout
+
+ WATCHERS = grichenk
++
++DLL_LIB = xser
+diff --git a/src/objtools/eutils/uilist/Makefile.uilist.lib b/src/objtools/eutils/uilist/Makefile.uilist.lib
+index b49c3c5..2ee63f0 100644
+--- a/src/objtools/eutils/uilist/Makefile.uilist.lib
++++ b/src/objtools/eutils/uilist/Makefile.uilist.lib
+@@ -4,3 +4,5 @@ SRC = uilist__ uilist___
+ LIB = uilist
+
+ WATCHERS = grichenk
++
++DLL_LIB = access dbapi_driver xncbi xser # align_format axf
+diff --git a/src/objtools/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib
+index a4fc469..fa58b3c 100644
+--- a/src/objtools/format/Makefile.xformat.lib
++++ b/src/objtools/format/Makefile.xformat.lib
+@@ -19,3 +19,5 @@ SRC = accession_item basecount_item comment_item contig_item date_item \
+ gather_iter html_anchor_item inst_info_map
+
+ WATCHERS = ludwigf dicuccio kornbluh
++
++DLL_LIB = submit connect xncbi gbseq xobjmgr xobjutil xalnmgr xconnect
+diff --git a/src/objtools/lds/Makefile.lds.lib b/src/objtools/lds/Makefile.lds.lib
+index e371035..689cfb4 100644
+--- a/src/objtools/lds/Makefile.lds.lib
++++ b/src/objtools/lds/Makefile.lds.lib
+@@ -9,6 +9,6 @@ SRC = lds lds_reader lds_query \
+ lds_coreobjreader lds_files lds_object lds_manager
+
+ # Dependencies for shared library
+-DLL_LIB = bdb
++DLL_LIB = bdb seq xobjread xobjmgr xobjutil
+
+ WATCHERS = vasilche
+diff --git a/src/objtools/manip/Makefile.xobjmanip.lib b/src/objtools/manip/Makefile.xobjmanip.lib
+index 300ceb2..4a81ac9 100644
+--- a/src/objtools/manip/Makefile.xobjmanip.lib
++++ b/src/objtools/manip/Makefile.xobjmanip.lib
+@@ -6,3 +6,5 @@ LIB = xobjmanip
+ SRC = sage_manip
+
+ WATCHERS = dicuccio
++
++DLL_LIB = xncbi general
+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..9f317ae 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 xobjutil
+diff --git a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+index 687af1e..f48568c 100644
+--- a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+@@ -11,6 +11,6 @@ mask_writer_seqloc \
+ mask_writer_blastdb_maskinfo
+
+ ASN_DEP = seqset
+-DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb blastdb xobjread xobjutil
+
+ WATCHERS = morgulis camacho
+diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib
+index dab25d6..f676dc7 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 ncbi_xloader_genbank
+diff --git a/src/objtools/snputil/Makefile.snputil.lib b/src/objtools/snputil/Makefile.snputil.lib
+index 15abef3..5ad1560 100644
+--- a/src/objtools/snputil/Makefile.snputil.lib
++++ b/src/objtools/snputil/Makefile.snputil.lib
+@@ -9,3 +9,5 @@ SRC = snp_utils snp_bitfield \
+ ASN_DEP = seqset
+
+ WATCHERS = rudnev
++
++DLL_LIB = general seq xncbi xobjmgr xser
+diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib
+index 80a74d8..6eec94b 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 xformat taxon3 valerr valid
+diff --git a/src/objtools/writers/Makefile.xobjwrite.lib b/src/objtools/writers/Makefile.xobjwrite.lib
+index cd6596b..a7d0c01 100644
+--- a/src/objtools/writers/Makefile.xobjwrite.lib
++++ b/src/objtools/writers/Makefile.xobjwrite.lib
+@@ -15,3 +15,4 @@ SRC = agp_write \
+
+ WATCHERS = ludwigf boukn
+
++DLL_LIB = xobjutil xalnmgr
+diff --git a/src/sample/app/asn/Makefile.sample_asn.lib b/src/sample/app/asn/Makefile.sample_asn.lib
+index 0db9ebd..26e6ad9 100644
+--- a/src/sample/app/asn/Makefile.sample_asn.lib
++++ b/src/sample/app/asn/Makefile.sample_asn.lib
+@@ -10,3 +10,5 @@ LIB = sample_asn
+ ASN_DEP = general
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver general xncbi xser
+diff --git a/src/sample/app/soap/Makefile.soap_dataobj.lib b/src/sample/app/soap/Makefile.soap_dataobj.lib
+index 4b87f51..c398ded 100644
+--- a/src/sample/app/soap/Makefile.soap_dataobj.lib
++++ b/src/sample/app/soap/Makefile.soap_dataobj.lib
+@@ -2,3 +2,5 @@ LIB = soap_dataobj
+ SRC = soap_dataobj__ soap_dataobj___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
+index f9d6103..4c22831 100644
+--- a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
++++ b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = asn_sample_lib
+ SRC = asn_sample_lib__ asn_sample_lib___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/basic/Makefile.basic_sample_lib.lib b/src/sample/lib/basic/Makefile.basic_sample_lib.lib
+index a6ba11a..364d9fc 100644
+--- a/src/sample/lib/basic/Makefile.basic_sample_lib.lib
++++ b/src/sample/lib/basic/Makefile.basic_sample_lib.lib
+@@ -5,3 +5,5 @@ SRC = basic_sample_lib
+
+
+ WATCHERS = gouriano
++
++DLL_LIB = xncbi
+diff --git a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
+index d2a27ef..a63a7e8 100644
+--- a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
++++ b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = dtd_sample_lib
+ SRC = dtd_sample_lib__ dtd_sample_lib___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
+index 4b7b6e2..838e8ea 100644
+--- a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
++++ b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = xsd_sample_lib
+ SRC = xsd_sample_lib__ xsd_sample_lib___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+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/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
+index 4896661..8e2ad56 100644
+--- a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
++++ b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
+@@ -12,7 +12,7 @@ ASN_DEP = seqset seq
+
+ LIB_OR_DLL = both
+
+-DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB)
++DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB) xobjreadex
+ LIBS = $(CMPRS_LIBS) $(ORIG_LIBS)
+
+ CPPFLAGS = $(SRA_INCLUDE) -DNCBI_XLOADER_BAM_EXPORTS $(ORIG_CPPFLAGS)
+diff --git a/src/sra/sdk/libs/align/Makefile.align-writer.lib b/src/sra/sdk/libs/align/Makefile.align-writer.lib
+index f2a2f58..f61b25a 100644
+--- a/src/sra/sdk/libs/align/Makefile.align-writer.lib
++++ b/src/sra/sdk/libs/align/Makefile.align-writer.lib
+@@ -6,7 +6,7 @@ LIB = align-writer
+ SRC = dna-reverse-cmpl reader-cmn reader-refseq refseq-mgr writer-cmn \
+ writer-refseq writer-alignment writer-sequence writer-ref writer-reference
+
+-DLL_LIB = wvdb wkdb load kfg kfs klib $(Z_LIB)
++DLL_LIB = wvdb wkdb load kfg kfs klib kapp $(Z_LIB)
+ LIBS = $(Z_LIBS) $(ORIG_LIBS)
+
+ CPPFLAGS = $(SRA_INCLUDE) $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY $(ORIG_CPPFLAGS)
+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 = $(PCRE_LIBS)
+
+ WATCHERS = ivanov
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch
new file mode 100644
index 000000000..820960354
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch
@@ -0,0 +1,213 @@
+ src/build-system/configure | 34 +++++++++++++++++++++++-----------
+ src/build-system/configure.ac | 33 ++++++++++++++++++++++-----------
+ 2 files changed, 45 insertions(+), 22 deletions(-)
+
+diff --git a/src/build-system/configure b/src/build-system/configure
+index 82fc9ef..d31a4f2 100755
+--- a/src/build-system/configure
++++ b/src/build-system/configure
+@@ -924,7 +924,7 @@ Optional Packages:
+ --without-distcc do not automatically use distcc if available
+ --without-ncbi-c do not use NCBI C Toolkit
+ --without-sss do not use NCBI SSS libraries
+- --without-utils do not use NCBI SSS UTIL library
++ --without-sssutils do not use NCBI SSS UTIL library
+ --without-sssdb do not use NCBI SSS DB library
+ --with-included-sss use the in-tree copy of SSS
+ --with-z=DIR use zlib installation in DIR
+@@ -2835,12 +2835,12 @@ check ncbi-public strip pch caution ccache distcc \
+ ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
+ geo included-geo \
+ z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \
+-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \
++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \
+ bdb python jni sqlite3 icu boost boost-tag \
+ sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \
+ gif jpeg tiff png xpm magic curl 3psw \
+ local-lbsm ncbi-crypt connext \
+-serial objects dbapi app ctools gui algo internal gbench"
++serial objects dbapi app ctools gui algo internal gbench x"
+
+ x_with_list=`echo "$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++/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
new file mode 100644
index 000000000..fede70e51
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch
@@ -0,0 +1,19 @@
+--- 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
new file mode 100644
index 000000000..46c2e83fb
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch
@@ -0,0 +1,11 @@
+--- 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) $(ORIG_LIBS)
+
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch
new file mode 100644
index 000000000..8bba91f1d
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch
@@ -0,0 +1,10 @@
+--- scripts/common/new_project.sh (revision 408264)
++++ scripts/common/new_project.sh (working copy)
+@@ -6,7 +6,7 @@
+ svn_revision=`echo '$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++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
index f5d6a3d67..821380023 100644
--- 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
@@ -783,7 +783,7 @@ index 96325c4..5a72805 100644
LIB = xnetblastcli
SRC = blastclient blastclient_
+
-+DLL_LIB = xncbi xutil seqset connect xconnect xnetblast
++DLL_LIB = xncbi xutil seqset xconnect xnetblast
diff --git a/src/objects/blastdb/Makefile.blastdb.lib b/src/objects/blastdb/Makefile.blastdb.lib
index be2c0d1..2884db2 100644
--- a/src/objects/blastdb/Makefile.blastdb.lib
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch
new file mode 100644
index 000000000..b3b57975e
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch
@@ -0,0 +1,10 @@
+--- src/objtools/alnmgr/demo/Makefile.alnmrg.app (revision 413271)
++++ src/objtools/alnmgr/demo/Makefile.alnmrg.app (working copy)
+@@ -4,7 +4,7 @@
+ APP = alnmrg
+ SRC = alnmrg
+ LIB = xalnmgr xobjread ncbi_xloader_blastdb seqdb xobjutil submit blastdb \
+- tables $(OBJMGR_LIBS)
++ tables creaders $(OBJMGR_LIBS)
+
+ LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch
new file mode 100644
index 000000000..8bba91f1d
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch
@@ -0,0 +1,10 @@
+--- scripts/common/new_project.sh (revision 408264)
++++ scripts/common/new_project.sh (working copy)
+@@ -6,7 +6,7 @@
+ svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"`
+ def_builddir="$NCBI/c++/Debug/build"
+
+-repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit'
++repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1'
+ tmp_app_checkout_dir='tmp_app_sample'
+ stem='sample/app'
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
new file mode 100644
index 000000000..be496254a
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
@@ -0,0 +1,10 @@
+--- src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2013-09-13 21:58:59.420013862 +0200
++++ src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2013-09-13 21:59:56.060014010 +0200
+@@ -10,6 +10,6 @@
+ LIB_OR_DLL = both
+
+ # Dependencies for shared library
+-DLL_LIB = ncbi_xreader$(DLL)
++DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_LDEP)
+
+ WATCHERS = vasilche
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch
new file mode 100644
index 000000000..95d3f7461
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch
@@ -0,0 +1,10 @@
+--- src/connect/ncbi_gnutls.c 2013-09-14 09:49:41.260005353 +0200
++++ src/connect/ncbi_gnutls.c 2013-09-14 09:49:46.950005368 +0200
+@@ -112,7 +112,6 @@
+ 0
+ };
+ static const int kGnuTlsCompPrio[] = {
+- GNUTLS_COMP_LZO,
+ GNUTLS_COMP_ZLIB,
+ GNUTLS_COMP_NULL,
+ 0
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
new file mode 100644
index 000000000..f217ab346
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -0,0 +1,311 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic multilib 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
+
+DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+SRC_URI="
+ ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
+# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
+
+LICENSE="public-domain"
+SLOT="0"
+IUSE="
+ debug static-libs static threads pch
+ test wxwidgets odbc
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS=""
+
+# sys-libs/db should be compiled with USE=cxx
+DEPEND="
+ berkdb? ( sys-libs/db:4.3[cxx] )
+ ftds? ( dev-db/freetds )
+ boost? ( dev-libs/boost )
+ curl? ( net-misc/curl )
+ sqlite? ( dev-db/sqlite )
+ sqlite3? ( dev-db/sqlite:3 )
+ mysql? ( virtual/mysql )
+ gnutls? ( net-libs/gnutls[lzo] )
+ ssl? ( dev-libs/openssl )
+ fltk? ( x11-libs/fltk )
+ opengl? ( virtual/opengl )
+ mesa? ( media-libs/mesa
+ media-libs/glew
+ )
+ glut? ( media-libs/freeglut )
+ freetype? ( media-libs/freetype )
+ fastcgi? ( www-apache/mod_fastcgi )
+ python? ( dev-lang/python )
+ 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 )
+ gif? ( media-libs/giflib )
+ jpeg? ( virtual/jpeg )
+ png? ( media-libs/libpng )
+ tiff? ( media-libs/tiff )
+ 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
+
+
+# seems muParser is required, also glew is required. configure exitss otherwise
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+# filter-ldflags -Wl,--as-needed
+# append-ldflags -Wl,--no-undefined
+# sed -i -e 's/-print-file-name=libstdc++.a//' \
+# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+# src/build-system/configure || die
+# epatch \
+# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
+# "${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}"/${P}-conf-opts.patch
+ #"${FILESDIR}"/${P}-as-needed.patch
+ "${FILESDIR}"/${P}-fix-creaders-linking.patch
+ "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
+ "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
+ )
+ epatch ${PATCHES[@]}
+
+ tc-export CXX CC
+
+# cd src/build-system || die
+# eaclocal -I.
+# eautoconf
+}
+
+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-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-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"
+ --with-muparser="${EPREFIX}/usr"
+ --without-sybase
+ --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)
+ $(use_with static-libs static)
+ $(use_with static static-exe)
+ $(use_with threads mt)
+ $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
+ $(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")
+ $(use_with ssl openssl "${EPREFIX}/usr")
+ $(use_with ftds ftds "${EPREFIX}/usr")
+ $(use_with mysql mysql "${EPREFIX}/usr")
+ $(use_with fltk fltk "${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")
+ $(use_with odbc odbc "${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")
+ $(use_with jpeg jpeg "${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")
+ $(use_with X x)
+ )
+
+ # http://www.ncbi.nlm.nih.gov/books/NBK7167/
+ use test || myconf+=( --with-projects="${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 repalced by e.g. -O9
+
+ 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 \
+ ${myconf[@]} || die
+#--without-debug \
+# --with-bin-release \
+# --with-bincopy \
+# --without-static \
+# --with-dll \
+# --with-mt \
+# --with-lfs \
+# --prefix="${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 "${S}"_build/build
+# emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+}
+
+src_install() {
+ rm -rvf "${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
+ rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
+ mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2
+
+ echo "LDPATH=${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++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 8c190e48b..4e1ee2e3e 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
@@ -24,7 +24,7 @@ IUSE="
debug static-libs static threads pch
test wxwidgets odbc
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
KEYWORDS=""
@@ -42,7 +42,9 @@ DEPEND="
ssl? ( dev-libs/openssl )
fltk? ( x11-libs/fltk )
opengl? ( virtual/opengl )
- mesa? ( media-libs/mesa )
+ mesa? ( media-libs/mesa
+ media-libs/glew
+ )
glut? ( media-libs/freeglut )
freetype? ( media-libs/freetype )
fastcgi? ( www-apache/mod_fastcgi )
@@ -67,6 +69,9 @@ DEPEND="
dev-libs/libpcre"
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+
+# seems muParser is required, also glew is required. configure exitss otherwise
+
RDEPEND="${DEPEND}"
S="${WORKDIR}/${MY_P}"
@@ -100,6 +105,10 @@ src_prepare() {
local PATCHES=(
"${FILESDIR}"/${P}-conf-opts.patch
"${FILESDIR}"/${P}-as-needed.patch
+ "${FILESDIR}"/${P}-fix-creaders-linking.patch
+ "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
+ "${FILESDIR}"/${P}-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
+ "${FILESDIR}"/${P}-remove-LZO-definition-upstream.patch
)
epatch ${PATCHES[@]}
@@ -190,7 +199,17 @@ src_configure() {
--with-muparser="${EPREFIX}/usr"
--without-sybase
--with-autodep
+
+# due to \*-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
+# ./configure ... --with-flat-makefile
+# cd .../build
+# make -f Makefile.flat
+#
+ --with-flat-makefile
# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
+
+
+# TODO: should improve the ssl/openssl/gmutls logic like is in net-misc/vpnc
$(use_with debug)
$(use_with debug max-debug)
$(use_with debug symbols)
@@ -254,6 +273,7 @@ src_configure() {
--srcdir="${S}" \
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
+ ${myconf} LDFLAGS="-Wl,-rpath-link,${S}_build/lib -Wl,--no-as-needed" \
${myconf[@]} || die
#--without-debug \
# --with-bin-release \
@@ -274,7 +294,14 @@ src_compile() {
# emake all_r -C GCC*-Release*/build || die
# all_p with compile only selected/required components
# cd "${S}"_build &&\
- emake all_p -C "${S}"_build/build
+
+ # disabling this because we need to take the flat Makefile route
+ # emake all_p -C "${S}"_build/build
+
+ # take the flat Makefile route
+ emake -f Makefile.flat -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?"
}