From de7706fa8dab9c1d4868d1a4202d5f9188e6cad3 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Mon, 4 Feb 2013 18:19:16 +0100 Subject: Next couple of fixes Signed-off-by: Justin Lecher --- .../files/ncbi-tools++-9.0.0-as-needed.patch | 395 +++++++++++++++++++-- 1 file changed, 356 insertions(+), 39 deletions(-) (limited to 'sci-biology/ncbi-tools++/files') 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 4c17bb0cd..610ee24ab 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 @@ -1,8 +1,13 @@ + src/algo/align/ngalign/Makefile.xngalign.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/cobalt/Makefile.cobalt.lib | 2 ++ src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++ src/algo/sequence/Makefile.xalgoseq.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/winmask/Makefile.xalgowinmask.lib | 1 + src/cgi/Makefile.cgi.lib | 2 ++ src/cgi/Makefile.fcgi.lib | 2 ++ @@ -36,6 +41,7 @@ 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 ++ @@ -43,34 +49,55 @@ 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_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/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++ src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- + src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++ + src/objtools/edit/Makefile.edit.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 ++ @@ -81,6 +108,8 @@ src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++ src/objtools/eutils/linkout/Makefile.linkout.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/simple/Makefile.xobjsimple.lib | 1 + @@ -97,8 +126,31 @@ src/util/regexp/Makefile.regexp.lib | 2 ++ src/util/sequtil/Makefile.sequtil.lib | 2 ++ src/util/xregexp/Makefile.xregexp.lib | 2 +- - 99 files changed, 182 insertions(+), 13 deletions(-) + 128 files changed, 237 insertions(+), 16 deletions(-) +diff --git a/src/algo/align/ngalign/Makefile.xngalign.lib b/src/algo/align/ngalign/Makefile.xngalign.lib +index d163f7c..f9c79ba 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 +diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib +index 073973b..3be07ae 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 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..6f56c5a 100644 --- a/src/algo/blast/blastinput/Makefile.blastinput.lib @@ -133,7 +185,7 @@ index e618f67..32905ca 100644 + +DLL_LIB = align_format diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib -index 872b92e..bb66af9 100644 +index 872b92e..24fcff3 100644 --- a/src/algo/ms/omssa/Makefile.xomssa.lib +++ b/src/algo/ms/omssa/Makefile.xomssa.lib @@ -19,3 +19,5 @@ LIB = xomssa @@ -141,7 +193,7 @@ index 872b92e..bb66af9 100644 CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) + -+DLL_LIB = xutil omssa ++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib index 51f4cd7..0c20790 100644 --- a/src/algo/sequence/Makefile.xalgoseq.lib @@ -152,6 +204,36 @@ index 51f4cd7..0c20790 100644 WATCHERS = dicuccio + +DLL_LIB = taxon1 xalnmgr +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/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib index afaf676..7344871 100644 --- a/src/algo/winmask/Makefile.xalgowinmask.lib @@ -463,14 +545,14 @@ index d18eb78..f90501d 100644 + +DLL_LIB = xser diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib -index 978cae9..35e5190 100644 +index 978cae9..2365261 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 ++DLL_LIB = mmdb xser scoremat 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 @@ -500,15 +582,25 @@ index 4507f72..4c47ad3 100644 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..e9e8c29 100644 +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 ++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 @@ -537,7 +629,7 @@ index 951304f..3be083d 100644 + +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..eba769c 100644 +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 @@ -545,9 +637,9 @@ index f039af6..eba769c 100644 WATCHERS = dicuccio + -+DLL_LIB = xser ++DLL_LIB = xser seq diff --git a/src/objects/homologene/Makefile.homologene.lib b/src/objects/homologene/Makefile.homologene.lib -index 15d13ad..2417439 100644 +index 15d13ad..d44b2e3 100644 --- a/src/objects/homologene/Makefile.homologene.lib +++ b/src/objects/homologene/Makefile.homologene.lib @@ -4,3 +4,5 @@ @@ -555,9 +647,9 @@ index 15d13ad..2417439 100644 LIB = homologene SRC = homologene__ homologene___ + -+DLL_LIB = xser ++DLL_LIB = xser seq diff --git a/src/objects/id1/Makefile.id1.lib b/src/objects/id1/Makefile.id1.lib -index d60c728..06b4f84 100644 +index d60c728..bf98427 100644 --- a/src/objects/id1/Makefile.id1.lib +++ b/src/objects/id1/Makefile.id1.lib @@ -4,3 +4,5 @@ LIB = id1 @@ -565,9 +657,19 @@ index d60c728..06b4f84 100644 WATCHERS = vasilche + -+DLL_LIB = xser ++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..b25700d 100644 +index 09d8b36..1e74a58 100644 --- a/src/objects/id2/Makefile.id2.lib +++ b/src/objects/id2/Makefile.id2.lib @@ -2,3 +2,5 @@ LIB = id2 @@ -575,7 +677,17 @@ index 09d8b36..b25700d 100644 WATCHERS = vasilche + -+DLL_LIB = xser ++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 @@ -585,15 +697,25 @@ index fa729b7..5754057 100644 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..5230940 100644 +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 ++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 @@ -603,6 +725,34 @@ index ea28066..eb42aa4 100644 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 @@ -614,14 +764,23 @@ index 6fc8e25..5c6c100 100644 + +DLL_LIB = xser pub seq diff --git a/src/objects/ncbimime/Makefile.ncbimime.lib b/src/objects/ncbimime/Makefile.ncbimime.lib -index 93cafdf..e5aa4eb 100644 +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 ++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 @@ -632,6 +791,33 @@ index b79617f..e1d4a9e 100644 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 @@ -641,6 +827,34 @@ index 78c12e1..9baa08d 100644 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 @@ -670,14 +884,14 @@ index dc9d60e..dabd95b 100644 + +DLL_LIB = xncbi xser diff --git a/src/objects/seqedit/Makefile.seqedit.lib b/src/objects/seqedit/Makefile.seqedit.lib -index 283a9b7..80724b1 100644 +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 ++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 @@ -687,7 +901,7 @@ index 87f16d0..febce67 100644 SRC = seqset__ seqset___ gb_release_file +DLL_LIB = xser seq diff --git a/src/objects/seqsplit/Makefile.seqsplit.lib b/src/objects/seqsplit/Makefile.seqsplit.lib -index 87ae869..a693f50 100644 +index 87ae869..1743321 100644 --- a/src/objects/seqsplit/Makefile.seqsplit.lib +++ b/src/objects/seqsplit/Makefile.seqsplit.lib @@ -2,3 +2,5 @@ LIB = seqsplit @@ -695,17 +909,27 @@ index 87ae869..a693f50 100644 WATCHERS = vasilche + -+DLL_LIB = xser ++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..9001a87 100644 +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 # lds ++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..d735117 100644 +index 61658ab..f46db75 100644 --- a/src/objects/taxon1/Makefile.taxon1.lib +++ b/src/objects/taxon1/Makefile.taxon1.lib @@ -3,3 +3,5 @@ LIB = taxon1 @@ -713,9 +937,9 @@ index 61658ab..d735117 100644 WATCHERS = domrach + -+DLL_LIB = xser ++DLL_LIB = xser seq xconnect diff --git a/src/objects/taxon3/Makefile.taxon3.lib b/src/objects/taxon3/Makefile.taxon3.lib -index 7e4c93d..5a6033e 100644 +index 7e4c93d..00be2c0 100644 --- a/src/objects/taxon3/Makefile.taxon3.lib +++ b/src/objects/taxon3/Makefile.taxon3.lib @@ -4,3 +4,5 @@ LIB = taxon3 @@ -723,7 +947,16 @@ index 7e4c93d..5a6033e 100644 WATCHERS = bollin + -+DLL_LIB = connect ++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 @@ -745,13 +978,25 @@ index 86a00a0..64226d6 100644 + +DLL_LIB = xser xregexp diff --git a/src/objects/variation/Makefile.variation.lib b/src/objects/variation/Makefile.variation.lib -index f21f84a..b08e210 100644 +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 ++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 @@ -790,8 +1035,28 @@ index d8177ed..f7beead 100644 # LIB_OR_DLL = dll + +DLL_LIB = xncbi xser xobjutil seq +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..92d4d59 100644 +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) @@ -799,7 +1064,17 @@ index 25898aa..92d4d59 100644 WATCHERS = maning camacho + -+DLL_LIB = blastdb ++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 @@ -821,7 +1096,7 @@ index 80af69f..704ed7a 100644 +DLL_LIB = seqdb + diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib -index f2b2b49..a8ee667 100644 +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 @@ -829,9 +1104,29 @@ index f2b2b49..a8ee667 100644 # Dependencies for shared library -DLL_LIB = -+DLL_LIB = xcompress ++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..015ac93 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 +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/egquery/Makefile.egquery.lib b/src/objtools/eutils/egquery/Makefile.egquery.lib index 82b4ed0..7030a29 100644 --- a/src/objtools/eutils/egquery/Makefile.egquery.lib @@ -923,7 +1218,7 @@ index 19b2b8a..77dcc3c 100644 + +DLL_LIB = xser diff --git a/src/objtools/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib -index a4fc469..3f771e6 100644 +index a4fc469..0203fea 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 \ @@ -931,7 +1226,29 @@ index a4fc469..3f771e6 100644 WATCHERS = ludwigf dicuccio kornbluh + -+DLL_LIB = submit connect xncbi ++DLL_LIB = submit connect xncbi gbseq xobjmgr +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 @@ -973,14 +1290,14 @@ index 80a74d8..6eec94b 100644 + +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..b0d97b1 100644 +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 ++DLL_LIB = xobjutil xalnmgr diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib index 2563b5f..efad054 100644 --- a/src/serial/Makefile.serial.lib -- cgit v1.2.3-65-gdbad