From 2936a6fec14426e76f9e3f095b82e25eddcc1072 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 18:09:46 +0200 Subject: add glew to dependencies inferrred via mesa; fix lib/libxobjread.so: undefined reference to 'AlignmentFileFree' message by upstream patch --- sci-biology/ncbi-tools++/ChangeLog | 7 +++++++ .../files/ncbi-tools++-9.0.0-fix-creaders-linking.patch | 10 ++++++++++ sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 10 ++++++++-- 3 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 270521cab..711ef6c7a 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Sep 2013; Martin Mokrejs + 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 ncbi-tools++-9.0.0-r1.ebuild: Drop empty line 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..1380764f1 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch @@ -0,0 +1,10 @@ +--- ncbi_cxx--9_0_0/src/objtools/alnmgr/demo/Makefile.alnmrg.app (revision 413271) ++++ ncbi_cxx--9_0_0/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) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild index 8c190e48b..33ee6fb9e 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild @@ -38,11 +38,13 @@ DEPEND=" sqlite? ( dev-db/sqlite ) sqlite3? ( dev-db/sqlite:3 ) mysql? ( virtual/mysql ) - gnutls? ( net-libs/gnutls ) + gnutls? ( net-libs/gnutls[lzo] ) ssl? ( dev-libs/openssl ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl ) - mesa? ( media-libs/mesa ) + mesa? ( media-libs/mesa + media-libs/glew + ) glut? ( media-libs/freeglut ) freetype? ( media-libs/freetype ) fastcgi? ( www-apache/mod_fastcgi ) @@ -67,6 +69,9 @@ DEPEND=" dev-libs/libpcre" # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge + +# seems muParser is required, also glew is required. configure exitss otherwise + RDEPEND="${DEPEND}" S="${WORKDIR}/${MY_P}" @@ -100,6 +105,7 @@ src_prepare() { local PATCHES=( "${FILESDIR}"/${P}-conf-opts.patch "${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-fix-creaders-linking.patch ) epatch ${PATCHES[@]} -- cgit v1.2.3-65-gdbad From 1f50f92899961b2c6522f8a071184138ff5aa94e Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 18:46:50 +0200 Subject: Latest release which needs so far only the two Gentoo patches. Would be better to drop from their filename to avoid their duplication I think. --- .../files/ncbi-tools++-12.0.0-as-needed.patch | 1864 ++++++++++++++++++++ .../files/ncbi-tools++-12.0.0-conf-opts.patch | 213 +++ .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 306 ++++ 3 files changed, 2383 insertions(+) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch create mode 100644 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild 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..f5d6a3d67 --- /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 connect 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++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild new file mode 100644 index 000000000..8121a798e --- /dev/null +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -0,0 +1,306 @@ +# 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="${MY_TAG/*_/}" +MY_PV="9_0_0" +MY_P="ncbi_cxx--${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)/${PN}" + + local PATCHES=( + "${FILESDIR}"/${P}-conf-opts.patch + "${FILESDIR}"/${P}-as-needed.patch + ) + epatch ${PATCHES[@]} + + tc-export CXX CC + +# cd src/build-system || die +# eaclocal -I. +# eautoconf +} + +src_configure() { + 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/' +} -- cgit v1.2.3-65-gdbad From 58b3cd84dbafc6fb04a305a29889b3332d9890e5 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 18:53:33 +0200 Subject: No, the fix-creaders-linking is needed for 12.0.0 as well. --- sci-biology/ncbi-tools++/ChangeLog | 14 ++++++++++++++ .../files/ncbi-tools++-12.0.0-fix-creaders-linking.patch | 10 ++++++++++ sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 + 3 files changed, 25 insertions(+) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 711ef6c7a..2e245b383 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,20 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Sep 2013; Martin Mokrejs + 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 + +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 ncbi-tools++-9.0.0-r1.ebuild, +files/ncbi-tools++-9.0.0-fix-creaders-linking.patch: 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..1380764f1 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch @@ -0,0 +1,10 @@ +--- ncbi_cxx--9_0_0/src/objtools/alnmgr/demo/Makefile.alnmrg.app (revision 413271) ++++ ncbi_cxx--9_0_0/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) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 8121a798e..33ee6fb9e 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -105,6 +105,7 @@ src_prepare() { local PATCHES=( "${FILESDIR}"/${P}-conf-opts.patch "${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-fix-creaders-linking.patch ) epatch ${PATCHES[@]} -- cgit v1.2.3-65-gdbad From fc2c3ad28c32659d2b55076c7f7d4d2f0da0aa00 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 22:14:16 +0200 Subject: Remove redundant connect from DLL_LIB lines. --- sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch | 2 +- sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 index f5d6a3d67..821380023 100644 --- 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 @@ -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-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 -- cgit v1.2.3-65-gdbad From 16bbfdefcf0e1b35ba1502f6c8948d6d60c9e5ed Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 22:23:24 +0200 Subject: Remove redundant connect from DLL_LIB lines. --- sci-biology/ncbi-tools++/ChangeLog | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 2e245b383..b73708196 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,22 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Sep 2013; Martin Mokrejs + 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 : + + > +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 ncbi-tools++-12.0.0.ebuild, +files/ncbi-tools++-12.0.0-fix-creaders-linking.patch: -- cgit v1.2.3-65-gdbad From a7ae3afe2de608896ea47fa540b1d61e9f5cb6a1 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 22:23:27 +0200 Subject: Remove redundant connect from DLL_LIB lines. --- sci-biology/ncbi-tools++/Manifest | 1 + 1 file changed, 1 insertion(+) diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest index 48b9d939a..33144be75 100644 --- a/sci-biology/ncbi-tools++/Manifest +++ b/sci-biology/ncbi-tools++/Manifest @@ -1 +1,2 @@ +DIST ncbi_cxx--12_0_0.tar.gz 385648 SHA256 0500192648d84e564de1cba01044039b6c1801d0af67355f1b6b54085fabae24 SHA512 e93683f3d1673699788ed21b235ffb468e43003a67eb46941d49215da4fe4c522e550e320b6633d215f92d3e01bb0775a0cf637a925ac9af2ce4dc4dcf239b43 WHIRLPOOL ded3d15e8065fbec7a62643b30b13eeb97d614fafe47112b0ce856b90b06a67db616ba02e30216a8e84d197f44d1120ec35befbd6ee2f8ef044097f25a778d1c DIST ncbi_cxx--9_0_0.tar.gz 33815259 SHA256 f561eb6de12dc7a1e3325d6fc1f76ca097099a31116fb407fa52e54174757fc7 SHA512 b8ce298d4e180915c86ea94cd0cba44cabe8ae1173525a7af3038736572427b4cb25191c6b8ad0fcde14c2677a03fbc675ab22dc64d496dd4a21d70b978c2fab WHIRLPOOL 1c5569c5fc73f67850eb6b35eece0e719a97fee5368f43cca9733b6d2a308dc0c66d2814da15e7b64a400ab7df130ab77e9fc6f3412778cc7c003684a1f6b594 -- cgit v1.2.3-65-gdbad From cbacda12d70dc97ab35fe390abf09d44502b1c3d Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 22:24:36 +0200 Subject: fix version number in the ebuild --- sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 33ee6fb9e..0549445e7 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -8,7 +8,7 @@ inherit eutils flag-o-matic multilib toolchain-funcs MY_TAG="Jun_15_2010" MY_Y="${MY_TAG/*_/}" -MY_PV="9_0_0" +MY_PV="12_0_0" MY_P="ncbi_cxx--${MY_PV}" #ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz -- cgit v1.2.3-65-gdbad From a42ec1c56c4d2691ac3adbff76c5d9ec4f686aa6 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Sep 2013 23:28:39 +0200 Subject: add ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch; get around a bug in the C++ Toolkit's handling of --without-runpath with certain linker versions by running configure with -Wl,-rpath-link,_build/lib in LDFLAGS (assuming _build is an absolute path; otherwise, prepend /home/mmokrejs/proj/sci/sci-biology/ncbi-tools++/) [from Aaron Ucko]. --- sci-biology/ncbi-tools++/Manifest | 2 +- ...ndef-reference-to-GenBankReaders_Register_Id1.patch | 10 ++++++++++ sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 18 +++++++++++++++++- 3 files changed, 28 insertions(+), 2 deletions(-) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest index 33144be75..88fdd5a5e 100644 --- a/sci-biology/ncbi-tools++/Manifest +++ b/sci-biology/ncbi-tools++/Manifest @@ -1,2 +1,2 @@ -DIST ncbi_cxx--12_0_0.tar.gz 385648 SHA256 0500192648d84e564de1cba01044039b6c1801d0af67355f1b6b54085fabae24 SHA512 e93683f3d1673699788ed21b235ffb468e43003a67eb46941d49215da4fe4c522e550e320b6633d215f92d3e01bb0775a0cf637a925ac9af2ce4dc4dcf239b43 WHIRLPOOL ded3d15e8065fbec7a62643b30b13eeb97d614fafe47112b0ce856b90b06a67db616ba02e30216a8e84d197f44d1120ec35befbd6ee2f8ef044097f25a778d1c +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++-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) $(GENBANK_LDEP) + + WATCHERS = vasilche diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild index 33ee6fb9e..a43dfefba 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild @@ -106,6 +106,7 @@ src_prepare() { "${FILESDIR}"/${P}-conf-opts.patch "${FILESDIR}"/${P}-as-needed.patch "${FILESDIR}"/${P}-fix-creaders-linking.patch + "${FILESDIR}"/${P}-fix-undef-reference-to-GenBankReaders_Register_Id1.patch ) epatch ${PATCHES[@]} @@ -196,6 +197,13 @@ src_configure() { --with-muparser="${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 $(use_with debug) $(use_with debug max-debug) @@ -260,6 +268,7 @@ src_configure() { --srcdir="${S}" \ --prefix="${EPREFIX}/usr" \ --libdir=/usr/lib64 \ + ${myconf} LDFLAGS="-Wl,-rpath-link,${S}_build/lib -Wl,--no-as-needed" \ ${myconf[@]} || die #--without-debug \ # --with-bin-release \ @@ -280,7 +289,14 @@ src_compile() { # emake all_r -C GCC*-Release*/build || die # all_p with compile only selected/required components # cd "${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?" } -- cgit v1.2.3-65-gdbad From db3890c80a85542d3c14254c20a03bf72a2caae0 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Sat, 14 Sep 2013 00:06:41 +0200 Subject: more 12.0.0 cleanup, still not working --- sci-biology/ncbi-tools++/ChangeLog | 20 ++++++++++++++++++++ .../ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch | 19 +++++++++++++++++++ .../ncbi-tools++-12.0.0-fix-creaders-linking.patch | 11 ++++++----- .../ncbi-tools++-9.0.0-fix-creaders-linking.patch | 4 ++-- sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 3 +++ 5 files changed, 50 insertions(+), 7 deletions(-) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index b73708196..b4a234b98 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,26 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Sep 2013; Martin Mokrejs + 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 + 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 ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild, files/ncbi-tools++-9.0.0-as-needed.patch, 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 index 1380764f1..46c2e83fb 100644 --- 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 @@ -1,10 +1,11 @@ ---- ncbi_cxx--9_0_0/src/objtools/alnmgr/demo/Makefile.alnmrg.app (revision 413271) -+++ ncbi_cxx--9_0_0/src/objtools/alnmgr/demo/Makefile.alnmrg.app (working copy) -@@ -4,7 +4,7 @@ - APP = alnmrg +--- 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 xobjread ncbi_xloader_blastdb seqdb xobjutil submit blastdb \ + + 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) $(ORIG_LIBS) + diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch index 1380764f1..b3b57975e 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch @@ -1,5 +1,5 @@ ---- ncbi_cxx--9_0_0/src/objtools/alnmgr/demo/Makefile.alnmrg.app (revision 413271) -+++ ncbi_cxx--9_0_0/src/objtools/alnmgr/demo/Makefile.alnmrg.app (working copy) +--- src/objtools/alnmgr/demo/Makefile.alnmrg.app (revision 413271) ++++ src/objtools/alnmgr/demo/Makefile.alnmrg.app (working copy) @@ -4,7 +4,7 @@ APP = alnmrg SRC = alnmrg diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 0549445e7..7415d8ff1 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -102,10 +102,13 @@ src_prepare() { # use prefix && append-ldflags -Wl,-rpath,"${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-FreeTDS-upstream.patch ) epatch ${PATCHES[@]} -- cgit v1.2.3-65-gdbad From 51dbd486d1fb08026b4f366e33c2a1395f49b16e Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Sat, 14 Sep 2013 00:18:50 +0200 Subject: Fix URL to point to a public SVN repository --- sci-biology/ncbi-tools++/ChangeLog | 11 +++++++++++ .../files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch | 10 ++++++++++ .../files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch | 10 ++++++++++ sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 +++-- sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 1 + 5 files changed, 35 insertions(+), 2 deletions(-) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index b4a234b98..6b670ef3e 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,17 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Sep 2013; Martin Mokrejs + 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: + Subject: Re: [C++] new project startup example needed + 13 Sep 2013; Martin Mokrejs ncbi-tools++-12.0.0.ebuild, files/ncbi-tools++-9.0.0-fix-creaders-linking.patch, 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="$NCBI/c++/Debug/build" + +-repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit' ++repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1' + tmp_app_checkout_dir='tmp_app_sample' + stem='sample/app' diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch new file mode 100644 index 000000000..8bba91f1d --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch @@ -0,0 +1,10 @@ +--- scripts/common/new_project.sh (revision 408264) ++++ scripts/common/new_project.sh (working copy) +@@ -6,7 +6,7 @@ + svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"` + def_builddir="$NCBI/c++/Debug/build" + +-repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit' ++repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1' + tmp_app_checkout_dir='tmp_app_sample' + stem='sample/app' diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 7415d8ff1..f217ab346 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -105,9 +105,10 @@ src_prepare() { # The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers local PATCHES=( - "${FILESDIR}"/${P}-conf-opts.patch - "${FILESDIR}"/${P}-as-needed.patch + #"${FILESDIR}"/${P}-conf-opts.patch + #"${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 ${PATCHES[@]} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild index a43dfefba..24f92be32 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild @@ -106,6 +106,7 @@ src_prepare() { "${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 ) epatch ${PATCHES[@]} -- cgit v1.2.3-65-gdbad From 2159e8e3583f47d97226803cd59fa3e715979c01 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Sat, 14 Sep 2013 10:18:58 +0200 Subject: Add upstream ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch with line offset changes. --- sci-biology/ncbi-tools++/ChangeLog | 7 +++++++ .../ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch | 10 ++++++++++ sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 7 +++---- 3 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 6b670ef3e..7f9450200 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 14 Sep 2013; Martin Mokrejs + 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 ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild, +files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch, 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++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild index 24f92be32..1a34f3554 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 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="" @@ -38,7 +38,7 @@ DEPEND=" sqlite? ( dev-db/sqlite ) sqlite3? ( dev-db/sqlite:3 ) mysql? ( virtual/mysql ) - gnutls? ( net-libs/gnutls[lzo] ) + gnutls? ( net-libs/gnutls ) ssl? ( dev-libs/openssl ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl ) @@ -64,7 +64,6 @@ DEPEND=" 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 @@ -108,6 +107,7 @@ src_prepare() { "${FILESDIR}"/${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[@]} @@ -215,7 +215,6 @@ src_configure() { $(use_with prefix runpath "${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") -- cgit v1.2.3-65-gdbad From 5c30b638891d5120f4a6757229945f6103dffa43 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Sat, 14 Sep 2013 10:46:29 +0200 Subject: 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. --- sci-biology/ncbi-tools++/ChangeLog | 6 ++++++ sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 7 ++++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 7f9450200..3da37d966 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 14 Sep 2013; Martin Mokrejs + 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 ncbi-tools++-9.0.0-r1.ebuild, +files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch: 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 1a34f3554..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 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="" @@ -64,6 +64,7 @@ DEPEND=" 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 @@ -206,6 +207,9 @@ src_configure() { # --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) @@ -215,6 +219,7 @@ src_configure() { $(use_with prefix runpath "${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") -- cgit v1.2.3-65-gdbad