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commit: 575b7bf60f71c08b611ee74eb25ca2b8c25d0ee4 |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Thu Jan 31 16:18:57 2013 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Thu Jan 31 16:18:57 2013 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=575b7bf6 |
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|
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Some more patching |
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|
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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--- |
13 |
.../files/ncbi-tools++-9.0.0-as-needed.patch | 380 ++++++++++++++++++-- |
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1 files changed, 357 insertions(+), 23 deletions(-) |
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|
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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 |
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index 7763361..e3110de 100644 |
18 |
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch |
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+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch |
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@@ -1,4 +1,6 @@ |
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src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +- |
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+ src/algo/blast/core/Makefile.blast.lib | 2 ++ |
23 |
+ src/algo/cobalt/Makefile.cobalt.lib | 2 ++ |
24 |
src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++ |
25 |
src/algo/sequence/Makefile.xalgoseq.lib | 2 ++ |
26 |
src/algo/winmask/Makefile.xalgowinmask.lib | 1 + |
27 |
@@ -25,14 +27,27 @@ |
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src/html/Makefile.html.lib | 2 ++ |
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src/objects/access/Makefile.access.lib | 1 + |
30 |
src/objects/biblio/Makefile.biblio.lib | 2 ++ |
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+ src/objects/biotree/Makefile.biotree.lib | 2 ++ |
32 |
src/objects/blast/Makefile.blast.lib | 2 ++ |
33 |
src/objects/blast/Makefile.xnetblastcli.lib | 2 ++ |
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+ src/objects/blastdb/Makefile.blastdb.lib | 2 ++ |
35 |
+ src/objects/blastxml/Makefile.blastxml.lib | 2 ++ |
36 |
src/objects/cdd/Makefile.cdd.lib | 2 ++ |
37 |
src/objects/cn3d/Makefile.cn3d.lib | 2 ++ |
38 |
+ src/objects/docsum/Makefile.docsum.lib | 2 ++ |
39 |
+ src/objects/entrez2/Makefile.entrez2.lib | 2 ++ |
40 |
+ src/objects/entrezgene/Makefile.entrezgene.lib | 2 ++ |
41 |
+ src/objects/featdef/Makefile.featdef.lib | 2 ++ |
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+ src/objects/gbseq/Makefile.gbseq.lib | 2 ++ |
43 |
src/objects/general/Makefile.general.lib | 2 ++ |
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+ src/objects/genomecoll/Makefile.genome_collection.lib | 2 ++ |
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+ src/objects/homologene/Makefile.homologene.lib | 2 ++ |
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+ src/objects/id1/Makefile.id1.lib | 2 ++ |
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src/objects/id2/Makefile.id2.lib | 2 ++ |
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+ src/objects/insdseq/Makefile.insdseq.lib | 2 ++ |
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src/objects/medlars/Makefile.medlars.lib | 2 ++ |
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src/objects/medline/Makefile.medline.lib | 2 ++ |
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+ src/objects/mmdb/Makefile.mmdb.lib | 2 ++ |
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src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++ |
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src/objects/omssa/Makefile.omssa.lib | 2 ++ |
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src/objects/pub/Makefile.pub.lib | 2 ++ |
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@@ -44,32 +59,48 @@ |
56 |
src/objects/seqsplit/Makefile.seqsplit.lib | 2 ++ |
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src/objects/submit/Makefile.submit.lib | 1 + |
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src/objects/taxon1/Makefile.taxon1.lib | 2 ++ |
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+ src/objects/taxon3/Makefile.taxon3.lib | 2 ++ |
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src/objects/valerr/Makefile.valerr.lib | 2 ++ |
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src/objects/valid/Makefile.valid.lib | 2 ++ |
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src/objects/variation/Makefile.variation.lib | 1 + |
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src/objmgr/util/Makefile.util.lib | 1 + |
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src/objtools/align_format/Makefile.align_format.lib | 2 ++ |
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+ src/objtools/alnmgr/Makefile.alnmgr.lib | 1 + |
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+ src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++ |
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src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++ |
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+ src/objtools/blast/services/Makefile.blast_services.lib | 1 + |
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src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++ |
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src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- |
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+ src/objtools/eutils/egquery/Makefile.egquery.lib | 2 ++ |
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+ src/objtools/eutils/ehistory/Makefile.ehistory.lib | 2 ++ |
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+ src/objtools/eutils/einfo/Makefile.einfo.lib | 2 ++ |
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+ src/objtools/eutils/elink/Makefile.elink.lib | 2 ++ |
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+ src/objtools/eutils/epost/Makefile.epost.lib | 2 ++ |
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+ src/objtools/eutils/esearch/Makefile.esearch.lib | 2 ++ |
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+ src/objtools/eutils/espell/Makefile.espell.lib | 2 ++ |
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+ src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++ |
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+ src/objtools/eutils/linkout/Makefile.linkout.lib | 2 ++ |
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+ src/objtools/format/Makefile.xformat.lib | 2 ++ |
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src/objtools/readers/Makefile.xobjread.lib | 3 +-- |
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src/objtools/readers/Makefile.xobjreadex.lib | 2 +- |
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src/objtools/simple/Makefile.xobjsimple.lib | 1 + |
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src/objtools/validator/Makefile.validator.lib | 2 ++ |
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+ src/objtools/writers/Makefile.xobjwrite.lib | 1 + |
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src/serial/Makefile.serial.lib | 2 ++ |
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src/serial/soap/Makefile.soap.lib | 2 ++ |
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src/serial/soap/Makefile.soap_server.lib | 2 ++ |
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src/serial/test/Makefile.we_cpp.lib | 1 + |
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+ src/sra/sdk/libs/align/Makefile.align-writer.lib | 2 +- |
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src/util/Makefile.util.lib | 2 ++ |
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src/util/compress/api/Makefile.compress.lib | 2 +- |
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src/util/qparse/Makefile.xqueryparse.lib | 2 ++ |
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src/util/regexp/Makefile.regexp.lib | 2 ++ |
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src/util/sequtil/Makefile.sequtil.lib | 2 ++ |
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src/util/xregexp/Makefile.xregexp.lib | 2 +- |
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- 68 files changed, 124 insertions(+), 12 deletions(-) |
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+ 99 files changed, 182 insertions(+), 13 deletions(-) |
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|
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diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib |
101 |
-index bfb315c..25873a2 100644 |
102 |
+index bfb315c..6f56c5a 100644 |
103 |
--- a/src/algo/blast/blastinput/Makefile.blastinput.lib |
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+++ b/src/algo/blast/blastinput/Makefile.blastinput.lib |
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@@ -24,7 +24,7 @@ SRC = $(SRC_CXX) |
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@@ -77,12 +108,32 @@ index bfb315c..25873a2 100644 |
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LIB = blastinput |
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|
109 |
-DLL_LIB = xblast $(OBJMGR_LIBS) |
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-+DLL_LIB = xblast seqdb $(OBJMGR_LIBS) |
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++DLL_LIB = seqdb ncbi_xloader_blastdb $(OBJMGR_LIBS) |
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|
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# should be redundant, given the above :-/ |
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ASN_DEP = seqset xnetblast |
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+diff --git a/src/algo/blast/core/Makefile.blast.lib b/src/algo/blast/core/Makefile.blast.lib |
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+index 8e889a7..1326aee 100644 |
117 |
+--- a/src/algo/blast/core/Makefile.blast.lib |
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++++ b/src/algo/blast/core/Makefile.blast.lib |
119 |
+@@ -23,3 +23,5 @@ LDFLAGS = $(FAST_LDFLAGS) |
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+ |
121 |
+ |
122 |
+ WATCHERS = coulouri maning madden camacho |
123 |
++ |
124 |
++DLL_LIB = xutil |
125 |
+diff --git a/src/algo/cobalt/Makefile.cobalt.lib b/src/algo/cobalt/Makefile.cobalt.lib |
126 |
+index e618f67..32905ca 100644 |
127 |
+--- a/src/algo/cobalt/Makefile.cobalt.lib |
128 |
++++ b/src/algo/cobalt/Makefile.cobalt.lib |
129 |
+@@ -14,3 +14,5 @@ ASN_DEP = seq seqset biotree xnetblast blastdb |
130 |
+ |
131 |
+ CXXFLAGS = $(FAST_CXXFLAGS) |
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+ LDFLAGS = $(FAST_LDFLAGS) |
133 |
++ |
134 |
++DLL_LIB = align_format |
135 |
diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib |
136 |
-index 872b92e..82cc8b6 100644 |
137 |
+index 872b92e..bb66af9 100644 |
138 |
--- a/src/algo/ms/omssa/Makefile.xomssa.lib |
139 |
+++ b/src/algo/ms/omssa/Makefile.xomssa.lib |
140 |
@@ -19,3 +19,5 @@ LIB = xomssa |
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@@ -90,7 +141,7 @@ index 872b92e..82cc8b6 100644 |
142 |
CXXFLAGS = $(FAST_CXXFLAGS) |
143 |
LDFLAGS = $(FAST_LDFLAGS) |
144 |
+ |
145 |
-+DLL_LIB = xutil |
146 |
++DLL_LIB = xutil omssa |
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diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib |
148 |
index 51f4cd7..0c20790 100644 |
149 |
--- a/src/algo/sequence/Makefile.xalgoseq.lib |
150 |
@@ -347,13 +398,13 @@ index a57c1e3..0005299 100644 |
151 |
+ |
152 |
+DLL_LIB = xncbi xutil |
153 |
diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib |
154 |
-index 11421d9..cf3a300 100644 |
155 |
+index 11421d9..e7900a1 100644 |
156 |
--- a/src/objects/access/Makefile.access.lib |
157 |
+++ b/src/objects/access/Makefile.access.lib |
158 |
@@ -1,2 +1,3 @@ |
159 |
LIB = access |
160 |
SRC = access__ access___ |
161 |
-+DLL_LIB = xncbi |
162 |
++DLL_LIB = xncbi xser |
163 |
diff --git a/src/objects/biblio/Makefile.biblio.lib b/src/objects/biblio/Makefile.biblio.lib |
164 |
index 2c7d491..cb54ba6 100644 |
165 |
--- a/src/objects/biblio/Makefile.biblio.lib |
166 |
@@ -363,6 +414,16 @@ index 2c7d491..cb54ba6 100644 |
167 |
SRC = biblio__ biblio___ citation_base |
168 |
+ |
169 |
+DLL_LIB = general xser xncbi xutil |
170 |
+diff --git a/src/objects/biotree/Makefile.biotree.lib b/src/objects/biotree/Makefile.biotree.lib |
171 |
+index 8019285..2c689ae 100644 |
172 |
+--- a/src/objects/biotree/Makefile.biotree.lib |
173 |
++++ b/src/objects/biotree/Makefile.biotree.lib |
174 |
+@@ -1,3 +1,5 @@ |
175 |
+ ASN_DEP = seq seqset |
176 |
+ LIB = biotree |
177 |
+ SRC = biotree__ biotree___ |
178 |
++ |
179 |
++DLL_LIB = xncbi xser |
180 |
diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib |
181 |
index 0dd0fa3..5ffe052 100644 |
182 |
--- a/src/objects/blast/Makefile.blast.lib |
183 |
@@ -383,17 +444,35 @@ index 96325c4..5a72805 100644 |
184 |
SRC = blastclient blastclient_ |
185 |
+ |
186 |
+DLL_LIB = xncbi xutil seqset connect xconnect xnetblast |
187 |
+diff --git a/src/objects/blastdb/Makefile.blastdb.lib b/src/objects/blastdb/Makefile.blastdb.lib |
188 |
+index be2c0d1..2884db2 100644 |
189 |
+--- a/src/objects/blastdb/Makefile.blastdb.lib |
190 |
++++ b/src/objects/blastdb/Makefile.blastdb.lib |
191 |
+@@ -1,2 +1,4 @@ |
192 |
+ LIB = blastdb |
193 |
+ SRC = blastdb__ blastdb___ |
194 |
++ |
195 |
++DLL_LIB = xncbi xser seq |
196 |
+diff --git a/src/objects/blastxml/Makefile.blastxml.lib b/src/objects/blastxml/Makefile.blastxml.lib |
197 |
+index d18eb78..f90501d 100644 |
198 |
+--- a/src/objects/blastxml/Makefile.blastxml.lib |
199 |
++++ b/src/objects/blastxml/Makefile.blastxml.lib |
200 |
+@@ -1,2 +1,4 @@ |
201 |
+ LIB = blastxml |
202 |
+ SRC = blastxml__ blastxml___ |
203 |
++ |
204 |
++DLL_LIB = xser |
205 |
diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib |
206 |
-index 978cae9..e3176b2 100644 |
207 |
+index 978cae9..35e5190 100644 |
208 |
--- a/src/objects/cdd/Makefile.cdd.lib |
209 |
+++ b/src/objects/cdd/Makefile.cdd.lib |
210 |
@@ -1,2 +1,4 @@ |
211 |
LIB = cdd |
212 |
SRC = cdd__ cdd___ |
213 |
+ |
214 |
-+DLL_LIB = mmdb |
215 |
++DLL_LIB = mmdb xser |
216 |
diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib |
217 |
-index 1af5d1d..b34a966 100644 |
218 |
+index 1af5d1d..ecd31b2 100644 |
219 |
--- a/src/objects/cn3d/Makefile.cn3d.lib |
220 |
+++ b/src/objects/cn3d/Makefile.cn3d.lib |
221 |
@@ -1,3 +1,5 @@ |
222 |
@@ -401,7 +480,53 @@ index 1af5d1d..b34a966 100644 |
223 |
LIB = cn3d |
224 |
SRC = cn3d__ cn3d___ |
225 |
+ |
226 |
-+DLL_LIB = mmdb |
227 |
++DLL_LIB = mmdb xser |
228 |
+diff --git a/src/objects/docsum/Makefile.docsum.lib b/src/objects/docsum/Makefile.docsum.lib |
229 |
+index 0e68886..0bc8a1c 100644 |
230 |
+--- a/src/objects/docsum/Makefile.docsum.lib |
231 |
++++ b/src/objects/docsum/Makefile.docsum.lib |
232 |
+@@ -1,2 +1,4 @@ |
233 |
+ LIB = docsum |
234 |
+ SRC = docsum__ docsum___ |
235 |
++ |
236 |
++DLL_LIB = xser |
237 |
+diff --git a/src/objects/entrez2/Makefile.entrez2.lib b/src/objects/entrez2/Makefile.entrez2.lib |
238 |
+index 4507f72..4c47ad3 100644 |
239 |
+--- a/src/objects/entrez2/Makefile.entrez2.lib |
240 |
++++ b/src/objects/entrez2/Makefile.entrez2.lib |
241 |
+@@ -2,3 +2,5 @@ WATCHERS = lavr |
242 |
+ |
243 |
+ LIB = entrez2 |
244 |
+ SRC = entrez2__ entrez2___ |
245 |
++ |
246 |
++DLL_LIB = xser |
247 |
+diff --git a/src/objects/entrezgene/Makefile.entrezgene.lib b/src/objects/entrezgene/Makefile.entrezgene.lib |
248 |
+index a1bd4f4..e9e8c29 100644 |
249 |
+--- a/src/objects/entrezgene/Makefile.entrezgene.lib |
250 |
++++ b/src/objects/entrezgene/Makefile.entrezgene.lib |
251 |
+@@ -1,2 +1,4 @@ |
252 |
+ LIB = entrezgene |
253 |
+ SRC = entrezgene__ entrezgene___ |
254 |
++ |
255 |
++DLL_LIB = xser |
256 |
+diff --git a/src/objects/featdef/Makefile.featdef.lib b/src/objects/featdef/Makefile.featdef.lib |
257 |
+index 51c7c8d..e603711 100644 |
258 |
+--- a/src/objects/featdef/Makefile.featdef.lib |
259 |
++++ b/src/objects/featdef/Makefile.featdef.lib |
260 |
+@@ -1,2 +1,4 @@ |
261 |
+ LIB = featdef |
262 |
+ SRC = featdef__ featdef___ |
263 |
++ |
264 |
++DLL_LIB = xser |
265 |
+diff --git a/src/objects/gbseq/Makefile.gbseq.lib b/src/objects/gbseq/Makefile.gbseq.lib |
266 |
+index 9dabdeb..4b27881 100644 |
267 |
+--- a/src/objects/gbseq/Makefile.gbseq.lib |
268 |
++++ b/src/objects/gbseq/Makefile.gbseq.lib |
269 |
+@@ -1,2 +1,4 @@ |
270 |
+ LIB = gbseq |
271 |
+ SRC = gbseq__ gbseq___ |
272 |
++ |
273 |
++DLL_LIB = xser |
274 |
diff --git a/src/objects/general/Makefile.general.lib b/src/objects/general/Makefile.general.lib |
275 |
index 951304f..3be083d 100644 |
276 |
--- a/src/objects/general/Makefile.general.lib |
277 |
@@ -411,6 +536,36 @@ index 951304f..3be083d 100644 |
278 |
SRC = general__ general___ uoconv |
279 |
+ |
280 |
+DLL_LIB = xser xncbi xutil |
281 |
+diff --git a/src/objects/genomecoll/Makefile.genome_collection.lib b/src/objects/genomecoll/Makefile.genome_collection.lib |
282 |
+index f039af6..eba769c 100644 |
283 |
+--- a/src/objects/genomecoll/Makefile.genome_collection.lib |
284 |
++++ b/src/objects/genomecoll/Makefile.genome_collection.lib |
285 |
+@@ -4,3 +4,5 @@ LIB = genome_collection |
286 |
+ SRC = genome_collection__ genome_collection___ |
287 |
+ |
288 |
+ WATCHERS = dicuccio |
289 |
++ |
290 |
++DLL_LIB = xser |
291 |
+diff --git a/src/objects/homologene/Makefile.homologene.lib b/src/objects/homologene/Makefile.homologene.lib |
292 |
+index 15d13ad..2417439 100644 |
293 |
+--- a/src/objects/homologene/Makefile.homologene.lib |
294 |
++++ b/src/objects/homologene/Makefile.homologene.lib |
295 |
+@@ -4,3 +4,5 @@ |
296 |
+ |
297 |
+ LIB = homologene |
298 |
+ SRC = homologene__ homologene___ |
299 |
++ |
300 |
++DLL_LIB = xser |
301 |
+diff --git a/src/objects/id1/Makefile.id1.lib b/src/objects/id1/Makefile.id1.lib |
302 |
+index d60c728..06b4f84 100644 |
303 |
+--- a/src/objects/id1/Makefile.id1.lib |
304 |
++++ b/src/objects/id1/Makefile.id1.lib |
305 |
+@@ -4,3 +4,5 @@ LIB = id1 |
306 |
+ SRC = id1__ id1___ |
307 |
+ |
308 |
+ WATCHERS = vasilche |
309 |
++ |
310 |
++DLL_LIB = xser |
311 |
diff --git a/src/objects/id2/Makefile.id2.lib b/src/objects/id2/Makefile.id2.lib |
312 |
index 09d8b36..b25700d 100644 |
313 |
--- a/src/objects/id2/Makefile.id2.lib |
314 |
@@ -421,6 +576,15 @@ index 09d8b36..b25700d 100644 |
315 |
WATCHERS = vasilche |
316 |
+ |
317 |
+DLL_LIB = xser |
318 |
+diff --git a/src/objects/insdseq/Makefile.insdseq.lib b/src/objects/insdseq/Makefile.insdseq.lib |
319 |
+index fa729b7..5754057 100644 |
320 |
+--- a/src/objects/insdseq/Makefile.insdseq.lib |
321 |
++++ b/src/objects/insdseq/Makefile.insdseq.lib |
322 |
+@@ -1,2 +1,4 @@ |
323 |
+ LIB = insdseq |
324 |
+ SRC = insdseq__ insdseq___ |
325 |
++ |
326 |
++DLL_LIB = xser |
327 |
diff --git a/src/objects/medlars/Makefile.medlars.lib b/src/objects/medlars/Makefile.medlars.lib |
328 |
index 3a6d0cd..5230940 100644 |
329 |
--- a/src/objects/medlars/Makefile.medlars.lib |
330 |
@@ -439,6 +603,16 @@ index ea28066..eb42aa4 100644 |
331 |
SRC = medline__ medline___ |
332 |
+ |
333 |
+DLL_LIB = general biblio |
334 |
+diff --git a/src/objects/mmdb/Makefile.mmdb.lib b/src/objects/mmdb/Makefile.mmdb.lib |
335 |
+index 6fc8e25..5c6c100 100644 |
336 |
+--- a/src/objects/mmdb/Makefile.mmdb.lib |
337 |
++++ b/src/objects/mmdb/Makefile.mmdb.lib |
338 |
+@@ -8,3 +8,5 @@ CPPFLAGS = -I$(srcdir) -I$(top_srcdir)/src/objects/mmdb $(ORIG_CPPFLAGS) |
339 |
+ |
340 |
+ LIB = mmdb |
341 |
+ SRC = $(ASN:%=%__) $(ASN:%=%___) |
342 |
++ |
343 |
++DLL_LIB = xser pub seq |
344 |
diff --git a/src/objects/ncbimime/Makefile.ncbimime.lib b/src/objects/ncbimime/Makefile.ncbimime.lib |
345 |
index 93cafdf..e5aa4eb 100644 |
346 |
--- a/src/objects/ncbimime/Makefile.ncbimime.lib |
347 |
@@ -523,13 +697,13 @@ index 87ae869..a693f50 100644 |
348 |
+ |
349 |
+DLL_LIB = xser |
350 |
diff --git a/src/objects/submit/Makefile.submit.lib b/src/objects/submit/Makefile.submit.lib |
351 |
-index 74798f8..34dd5a8 100644 |
352 |
+index 74798f8..9001a87 100644 |
353 |
--- a/src/objects/submit/Makefile.submit.lib |
354 |
+++ b/src/objects/submit/Makefile.submit.lib |
355 |
@@ -1,2 +1,3 @@ |
356 |
LIB = submit |
357 |
SRC = submit__ submit___ |
358 |
-+DLL_LIB = xser xncbi # lds |
359 |
++DLL_LIB = xser xncbi seq # lds |
360 |
diff --git a/src/objects/taxon1/Makefile.taxon1.lib b/src/objects/taxon1/Makefile.taxon1.lib |
361 |
index 61658ab..d735117 100644 |
362 |
--- a/src/objects/taxon1/Makefile.taxon1.lib |
363 |
@@ -540,6 +714,16 @@ index 61658ab..d735117 100644 |
364 |
WATCHERS = domrach |
365 |
+ |
366 |
+DLL_LIB = xser |
367 |
+diff --git a/src/objects/taxon3/Makefile.taxon3.lib b/src/objects/taxon3/Makefile.taxon3.lib |
368 |
+index 7e4c93d..5a6033e 100644 |
369 |
+--- a/src/objects/taxon3/Makefile.taxon3.lib |
370 |
++++ b/src/objects/taxon3/Makefile.taxon3.lib |
371 |
+@@ -4,3 +4,5 @@ LIB = taxon3 |
372 |
+ SRC = taxon3__ taxon3___ taxon3 |
373 |
+ |
374 |
+ WATCHERS = bollin |
375 |
++ |
376 |
++DLL_LIB = connect |
377 |
diff --git a/src/objects/valerr/Makefile.valerr.lib b/src/objects/valerr/Makefile.valerr.lib |
378 |
index b202355..9699bb2 100644 |
379 |
--- a/src/objects/valerr/Makefile.valerr.lib |
380 |
@@ -551,7 +735,7 @@ index b202355..9699bb2 100644 |
381 |
+ |
382 |
+DLL_LIB = xser |
383 |
diff --git a/src/objects/valid/Makefile.valid.lib b/src/objects/valid/Makefile.valid.lib |
384 |
-index 86a00a0..ee7402f 100644 |
385 |
+index 86a00a0..64226d6 100644 |
386 |
--- a/src/objects/valid/Makefile.valid.lib |
387 |
+++ b/src/objects/valid/Makefile.valid.lib |
388 |
@@ -1,3 +1,5 @@ |
389 |
@@ -559,7 +743,7 @@ index 86a00a0..ee7402f 100644 |
390 |
LIB = valid |
391 |
SRC = valid__ valid___ |
392 |
+ |
393 |
-+DLL_LIB = xser |
394 |
++DLL_LIB = xser xregexp |
395 |
diff --git a/src/objects/variation/Makefile.variation.lib b/src/objects/variation/Makefile.variation.lib |
396 |
index f21f84a..b08e210 100644 |
397 |
--- a/src/objects/variation/Makefile.variation.lib |
398 |
@@ -578,7 +762,7 @@ index 90eeee0..138e836 100644 |
399 |
|
400 |
+DLL_LIB = xser xobjmgr |
401 |
diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib |
402 |
-index 4b3e59e..94fc319 100644 |
403 |
+index 4b3e59e..d8e9345 100644 |
404 |
--- a/src/objtools/align_format/Makefile.align_format.lib |
405 |
+++ b/src/objtools/align_format/Makefile.align_format.lib |
406 |
@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) |
407 |
@@ -586,7 +770,26 @@ index 4b3e59e..94fc319 100644 |
408 |
|
409 |
WATCHERS = zaretska jianye madden camacho |
410 |
+ |
411 |
-+DLL_LIB = seqdb blastdb |
412 |
++DLL_LIB = seqdb blastdb xser |
413 |
+diff --git a/src/objtools/alnmgr/Makefile.alnmgr.lib b/src/objtools/alnmgr/Makefile.alnmgr.lib |
414 |
+index e32c351..1702b90 100644 |
415 |
+--- a/src/objtools/alnmgr/Makefile.alnmgr.lib |
416 |
++++ b/src/objtools/alnmgr/Makefile.alnmgr.lib |
417 |
+@@ -12,3 +12,4 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial \ |
418 |
+ |
419 |
+ WATCHERS = todorov dicuccio grichenk |
420 |
+ |
421 |
++DLL_LIB = tables |
422 |
+diff --git a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib |
423 |
+index d8177ed..f7beead 100644 |
424 |
+--- a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib |
425 |
++++ b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib |
426 |
+@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) |
427 |
+ # CXXFLAGS = $(FAST_CXXFLAGS) |
428 |
+ # |
429 |
+ # LIB_OR_DLL = dll |
430 |
++ |
431 |
++DLL_LIB = xncbi xser xobjutil seq |
432 |
diff --git a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib |
433 |
index 25898aa..92d4d59 100644 |
434 |
--- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib |
435 |
@@ -597,6 +800,15 @@ index 25898aa..92d4d59 100644 |
436 |
WATCHERS = maning camacho |
437 |
+ |
438 |
+DLL_LIB = blastdb |
439 |
+diff --git a/src/objtools/blast/services/Makefile.blast_services.lib b/src/objtools/blast/services/Makefile.blast_services.lib |
440 |
+index 10a878c..7a70b22 100644 |
441 |
+--- a/src/objtools/blast/services/Makefile.blast_services.lib |
442 |
++++ b/src/objtools/blast/services/Makefile.blast_services.lib |
443 |
+@@ -12,3 +12,4 @@ CFLAGS = $(FAST_CFLAGS) |
444 |
+ CXXFLAGS = $(FAST_CXXFLAGS) |
445 |
+ LDFLAGS = $(FAST_LDFLAGS) |
446 |
+ |
447 |
++DLL_LIB = xncbi xser xnetblast xnetblastcli |
448 |
diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib |
449 |
index 80af69f..704ed7a 100644 |
450 |
--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib |
451 |
@@ -620,6 +832,106 @@ index f2b2b49..a8ee667 100644 |
452 |
+DLL_LIB = xcompress |
453 |
|
454 |
WATCHERS = vasilche |
455 |
+diff --git a/src/objtools/eutils/egquery/Makefile.egquery.lib b/src/objtools/eutils/egquery/Makefile.egquery.lib |
456 |
+index 82b4ed0..7030a29 100644 |
457 |
+--- a/src/objtools/eutils/egquery/Makefile.egquery.lib |
458 |
++++ b/src/objtools/eutils/egquery/Makefile.egquery.lib |
459 |
+@@ -4,3 +4,5 @@ LIB = egquery |
460 |
+ SRC = egquery__ egquery___ |
461 |
+ |
462 |
+ WATCHERS = grichenk |
463 |
++ |
464 |
++DLL_LIB = xser |
465 |
+diff --git a/src/objtools/eutils/ehistory/Makefile.ehistory.lib b/src/objtools/eutils/ehistory/Makefile.ehistory.lib |
466 |
+index f99ca0f..5683a74 100644 |
467 |
+--- a/src/objtools/eutils/ehistory/Makefile.ehistory.lib |
468 |
++++ b/src/objtools/eutils/ehistory/Makefile.ehistory.lib |
469 |
+@@ -4,3 +4,5 @@ LIB = ehistory |
470 |
+ SRC = ehistory__ ehistory___ |
471 |
+ |
472 |
+ WATCHERS = grichenk |
473 |
++ |
474 |
++DLL_LIB = xser |
475 |
+diff --git a/src/objtools/eutils/einfo/Makefile.einfo.lib b/src/objtools/eutils/einfo/Makefile.einfo.lib |
476 |
+index e18413d..7eaee71 100644 |
477 |
+--- a/src/objtools/eutils/einfo/Makefile.einfo.lib |
478 |
++++ b/src/objtools/eutils/einfo/Makefile.einfo.lib |
479 |
+@@ -4,3 +4,5 @@ LIB = einfo |
480 |
+ SRC = einfo__ einfo___ |
481 |
+ |
482 |
+ WATCHERS = grichenk |
483 |
++ |
484 |
++DLL_LIB = xser |
485 |
+diff --git a/src/objtools/eutils/elink/Makefile.elink.lib b/src/objtools/eutils/elink/Makefile.elink.lib |
486 |
+index 87f352c..692835c 100644 |
487 |
+--- a/src/objtools/eutils/elink/Makefile.elink.lib |
488 |
++++ b/src/objtools/eutils/elink/Makefile.elink.lib |
489 |
+@@ -4,3 +4,5 @@ LIB = elink |
490 |
+ SRC = elink__ elink___ |
491 |
+ |
492 |
+ WATCHERS = grichenk |
493 |
++ |
494 |
++DLL_LIB = xser |
495 |
+diff --git a/src/objtools/eutils/epost/Makefile.epost.lib b/src/objtools/eutils/epost/Makefile.epost.lib |
496 |
+index 4a456ed..d73f41b 100644 |
497 |
+--- a/src/objtools/eutils/epost/Makefile.epost.lib |
498 |
++++ b/src/objtools/eutils/epost/Makefile.epost.lib |
499 |
+@@ -4,3 +4,5 @@ LIB = epost |
500 |
+ SRC = epost__ epost___ |
501 |
+ |
502 |
+ WATCHERS = grichenk |
503 |
++ |
504 |
++DLL_LIB = xser |
505 |
+diff --git a/src/objtools/eutils/esearch/Makefile.esearch.lib b/src/objtools/eutils/esearch/Makefile.esearch.lib |
506 |
+index bb5b64b..71912da 100644 |
507 |
+--- a/src/objtools/eutils/esearch/Makefile.esearch.lib |
508 |
++++ b/src/objtools/eutils/esearch/Makefile.esearch.lib |
509 |
+@@ -4,3 +4,5 @@ LIB = esearch |
510 |
+ SRC = esearch__ esearch___ |
511 |
+ |
512 |
+ WATCHERS = grichenk |
513 |
++ |
514 |
++DLL_LIB = xser |
515 |
+diff --git a/src/objtools/eutils/espell/Makefile.espell.lib b/src/objtools/eutils/espell/Makefile.espell.lib |
516 |
+index 7cf1a34..25be846 100644 |
517 |
+--- a/src/objtools/eutils/espell/Makefile.espell.lib |
518 |
++++ b/src/objtools/eutils/espell/Makefile.espell.lib |
519 |
+@@ -4,3 +4,5 @@ LIB = espell |
520 |
+ SRC = espell__ espell___ |
521 |
+ |
522 |
+ WATCHERS = grichenk |
523 |
++ |
524 |
++DLL_LIB = xser |
525 |
+diff --git a/src/objtools/eutils/esummary/Makefile.esummary.lib b/src/objtools/eutils/esummary/Makefile.esummary.lib |
526 |
+index 4d3e058..1f74c06 100644 |
527 |
+--- a/src/objtools/eutils/esummary/Makefile.esummary.lib |
528 |
++++ b/src/objtools/eutils/esummary/Makefile.esummary.lib |
529 |
+@@ -4,3 +4,5 @@ LIB = esummary |
530 |
+ SRC = esummary__ esummary___ |
531 |
+ |
532 |
+ WATCHERS = grichenk |
533 |
++ |
534 |
++DLL_LIB = xser |
535 |
+diff --git a/src/objtools/eutils/linkout/Makefile.linkout.lib b/src/objtools/eutils/linkout/Makefile.linkout.lib |
536 |
+index 19b2b8a..77dcc3c 100644 |
537 |
+--- a/src/objtools/eutils/linkout/Makefile.linkout.lib |
538 |
++++ b/src/objtools/eutils/linkout/Makefile.linkout.lib |
539 |
+@@ -4,3 +4,5 @@ SRC = linkout__ linkout___ |
540 |
+ LIB = linkout |
541 |
+ |
542 |
+ WATCHERS = grichenk |
543 |
++ |
544 |
++DLL_LIB = xser |
545 |
+diff --git a/src/objtools/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib |
546 |
+index a4fc469..3f771e6 100644 |
547 |
+--- a/src/objtools/format/Makefile.xformat.lib |
548 |
++++ b/src/objtools/format/Makefile.xformat.lib |
549 |
+@@ -19,3 +19,5 @@ SRC = accession_item basecount_item comment_item contig_item date_item \ |
550 |
+ gather_iter html_anchor_item inst_info_map |
551 |
+ |
552 |
+ WATCHERS = ludwigf dicuccio kornbluh |
553 |
++ |
554 |
++DLL_LIB = submit connect xncbi |
555 |
diff --git a/src/objtools/readers/Makefile.xobjread.lib b/src/objtools/readers/Makefile.xobjread.lib |
556 |
index 0fbffd4..4ca9fed 100644 |
557 |
--- a/src/objtools/readers/Makefile.xobjread.lib |
558 |
@@ -632,7 +944,7 @@ index 0fbffd4..4ca9fed 100644 |
559 |
- |
560 |
+DLL_LIB = creaders xncbi seq biblio seqset |
561 |
diff --git a/src/objtools/readers/Makefile.xobjreadex.lib b/src/objtools/readers/Makefile.xobjreadex.lib |
562 |
-index 85eefe2..f238782 100644 |
563 |
+index 85eefe2..9f317ae 100644 |
564 |
--- a/src/objtools/readers/Makefile.xobjreadex.lib |
565 |
+++ b/src/objtools/readers/Makefile.xobjreadex.lib |
566 |
@@ -8,4 +8,4 @@ LIB = xobjreadex |
567 |
@@ -640,18 +952,18 @@ index 85eefe2..f238782 100644 |
568 |
idmapper_database source_mod_parser_wrapper |
569 |
|
570 |
-DLL_LIB = xobjread |
571 |
-+DLL_LIB = xobjread xncbi xutil seq xobjmgr |
572 |
++DLL_LIB = xobjread xncbi xutil seq xobjmgr xobjutil |
573 |
diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib |
574 |
-index dab25d6..a29b960 100644 |
575 |
+index dab25d6..f676dc7 100644 |
576 |
--- a/src/objtools/simple/Makefile.xobjsimple.lib |
577 |
+++ b/src/objtools/simple/Makefile.xobjsimple.lib |
578 |
@@ -10,3 +10,4 @@ ASN_DEP = seqset |
579 |
LIB = xobjsimple |
580 |
SRC = simple_om |
581 |
|
582 |
-+DLL_LIB = xobjmgr |
583 |
++DLL_LIB = xobjmgr ncbi_xloader_genbank |
584 |
diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib |
585 |
-index 80a74d8..69c4ef6 100644 |
586 |
+index 80a74d8..6eec94b 100644 |
587 |
--- a/src/objtools/validator/Makefile.validator.lib |
588 |
+++ b/src/objtools/validator/Makefile.validator.lib |
589 |
@@ -19,3 +19,5 @@ NOOPT_CXX = $(CXX_WRAPPER) $(CXX) $(CXXFLAGS_ALL:-xO%=) |
590 |
@@ -659,7 +971,16 @@ index 80a74d8..69c4ef6 100644 |
591 |
lat_lon_country_map.o: $(srcdir)/lat_lon_country_map.cpp |
592 |
$(NOOPT_CXX) $(srcdir)/lat_lon_country_map.cpp -o $@ $(CXX_FILTER) |
593 |
+ |
594 |
-+DLL_LIB = xncbi xobjutil xalnmgr |
595 |
++DLL_LIB = xncbi xobjutil xalnmgr xformat taxon3 valerr valid |
596 |
+diff --git a/src/objtools/writers/Makefile.xobjwrite.lib b/src/objtools/writers/Makefile.xobjwrite.lib |
597 |
+index cd6596b..b0d97b1 100644 |
598 |
+--- a/src/objtools/writers/Makefile.xobjwrite.lib |
599 |
++++ b/src/objtools/writers/Makefile.xobjwrite.lib |
600 |
+@@ -15,3 +15,4 @@ SRC = agp_write \ |
601 |
+ |
602 |
+ WATCHERS = ludwigf boukn |
603 |
+ |
604 |
++DLL_LIB = xobjutil |
605 |
diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib |
606 |
index 2563b5f..efad054 100644 |
607 |
--- a/src/serial/Makefile.serial.lib |
608 |
@@ -699,6 +1020,19 @@ index 9877691..599ef5d 100644 |
609 |
WATCHERS = gouriano |
610 |
|
611 |
+DLL_LIB = xncbi xutil xser |
612 |
+diff --git a/src/sra/sdk/libs/align/Makefile.align-writer.lib b/src/sra/sdk/libs/align/Makefile.align-writer.lib |
613 |
+index f2a2f58..f61b25a 100644 |
614 |
+--- a/src/sra/sdk/libs/align/Makefile.align-writer.lib |
615 |
++++ b/src/sra/sdk/libs/align/Makefile.align-writer.lib |
616 |
+@@ -6,7 +6,7 @@ LIB = align-writer |
617 |
+ SRC = dna-reverse-cmpl reader-cmn reader-refseq refseq-mgr writer-cmn \ |
618 |
+ writer-refseq writer-alignment writer-sequence writer-ref writer-reference |
619 |
+ |
620 |
+-DLL_LIB = wvdb wkdb load kfg kfs klib $(Z_LIB) |
621 |
++DLL_LIB = wvdb wkdb load kfg kfs klib kapp $(Z_LIB) |
622 |
+ LIBS = $(Z_LIBS) $(ORIG_LIBS) |
623 |
+ |
624 |
+ CPPFLAGS = $(SRA_INCLUDE) $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY $(ORIG_CPPFLAGS) |
625 |
diff --git a/src/util/Makefile.util.lib b/src/util/Makefile.util.lib |
626 |
index f103ff1..829a71c 100644 |
627 |
--- a/src/util/Makefile.util.lib |