* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2013-01-31 16:19 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2013-01-31 16:19 UTC (permalink / raw
To: gentoo-commits
commit: 575b7bf60f71c08b611ee74eb25ca2b8c25d0ee4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 31 16:18:57 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 31 16:18:57 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=575b7bf6
Some more patching
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
.../files/ncbi-tools++-9.0.0-as-needed.patch | 380 ++++++++++++++++++--
1 files changed, 357 insertions(+), 23 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
index 7763361..e3110de 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
@@ -1,4 +1,6 @@
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/winmask/Makefile.xalgowinmask.lib | 1 +
@@ -25,14 +27,27 @@
src/html/Makefile.html.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/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/id2/Makefile.id2.lib | 2 ++
+ src/objects/insdseq/Makefile.insdseq.lib | 2 ++
src/objects/medlars/Makefile.medlars.lib | 2 ++
src/objects/medline/Makefile.medline.lib | 2 ++
+ src/objects/mmdb/Makefile.mmdb.lib | 2 ++
src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++
src/objects/omssa/Makefile.omssa.lib | 2 ++
src/objects/pub/Makefile.pub.lib | 2 ++
@@ -44,32 +59,48 @@
src/objects/seqsplit/Makefile.seqsplit.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/valerr/Makefile.valerr.lib | 2 ++
src/objects/valid/Makefile.valid.lib | 2 ++
src/objects/variation/Makefile.variation.lib | 1 +
src/objmgr/util/Makefile.util.lib | 1 +
src/objtools/align_format/Makefile.align_format.lib | 2 ++
+ src/objtools/alnmgr/Makefile.alnmgr.lib | 1 +
+ src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++
src/objtools/blast/seqdb_reader/Makefile.seqdb.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/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/format/Makefile.xformat.lib | 2 ++
src/objtools/readers/Makefile.xobjread.lib | 3 +--
src/objtools/readers/Makefile.xobjreadex.lib | 2 +-
src/objtools/simple/Makefile.xobjsimple.lib | 1 +
src/objtools/validator/Makefile.validator.lib | 2 ++
+ src/objtools/writers/Makefile.xobjwrite.lib | 1 +
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/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 +-
- 68 files changed, 124 insertions(+), 12 deletions(-)
+ 99 files changed, 182 insertions(+), 13 deletions(-)
diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib
-index bfb315c..25873a2 100644
+index bfb315c..6f56c5a 100644
--- a/src/algo/blast/blastinput/Makefile.blastinput.lib
+++ b/src/algo/blast/blastinput/Makefile.blastinput.lib
@@ -24,7 +24,7 @@ SRC = $(SRC_CXX)
@@ -77,12 +108,32 @@ index bfb315c..25873a2 100644
LIB = blastinput
-DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = xblast seqdb $(OBJMGR_LIBS)
++DLL_LIB = seqdb ncbi_xloader_blastdb $(OBJMGR_LIBS)
# 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/cobalt/Makefile.cobalt.lib b/src/algo/cobalt/Makefile.cobalt.lib
+index e618f67..32905ca 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
diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib
-index 872b92e..82cc8b6 100644
+index 872b92e..bb66af9 100644
--- a/src/algo/ms/omssa/Makefile.xomssa.lib
+++ b/src/algo/ms/omssa/Makefile.xomssa.lib
@@ -19,3 +19,5 @@ LIB = xomssa
@@ -90,7 +141,7 @@ index 872b92e..82cc8b6 100644
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
+
-+DLL_LIB = xutil
++DLL_LIB = xutil omssa
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
@@ -347,13 +398,13 @@ index a57c1e3..0005299 100644
+
+DLL_LIB = xncbi xutil
diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib
-index 11421d9..cf3a300 100644
+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
++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
@@ -363,6 +414,16 @@ index 2c7d491..cb54ba6 100644
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..5ffe052 100644
--- a/src/objects/blast/Makefile.blast.lib
@@ -383,17 +444,35 @@ index 96325c4..5a72805 100644
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..e3176b2 100644
+index 978cae9..35e5190 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
++DLL_LIB = mmdb xser
diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib
-index 1af5d1d..b34a966 100644
+index 1af5d1d..ecd31b2 100644
--- a/src/objects/cn3d/Makefile.cn3d.lib
+++ b/src/objects/cn3d/Makefile.cn3d.lib
@@ -1,3 +1,5 @@
@@ -401,7 +480,53 @@ index 1af5d1d..b34a966 100644
LIB = cn3d
SRC = cn3d__ cn3d___
+
-+DLL_LIB = mmdb
++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/entrezgene/Makefile.entrezgene.lib b/src/objects/entrezgene/Makefile.entrezgene.lib
+index a1bd4f4..e9e8c29 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
+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
@@ -411,6 +536,36 @@ index 951304f..3be083d 100644
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..eba769c 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
+diff --git a/src/objects/homologene/Makefile.homologene.lib b/src/objects/homologene/Makefile.homologene.lib
+index 15d13ad..2417439 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
+diff --git a/src/objects/id1/Makefile.id1.lib b/src/objects/id1/Makefile.id1.lib
+index d60c728..06b4f84 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
diff --git a/src/objects/id2/Makefile.id2.lib b/src/objects/id2/Makefile.id2.lib
index 09d8b36..b25700d 100644
--- a/src/objects/id2/Makefile.id2.lib
@@ -421,6 +576,15 @@ index 09d8b36..b25700d 100644
WATCHERS = vasilche
+
+DLL_LIB = xser
+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/medlars/Makefile.medlars.lib b/src/objects/medlars/Makefile.medlars.lib
index 3a6d0cd..5230940 100644
--- a/src/objects/medlars/Makefile.medlars.lib
@@ -439,6 +603,16 @@ index ea28066..eb42aa4 100644
SRC = medline__ medline___
+
+DLL_LIB = general biblio
+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..e5aa4eb 100644
--- a/src/objects/ncbimime/Makefile.ncbimime.lib
@@ -523,13 +697,13 @@ index 87ae869..a693f50 100644
+
+DLL_LIB = xser
diff --git a/src/objects/submit/Makefile.submit.lib b/src/objects/submit/Makefile.submit.lib
-index 74798f8..34dd5a8 100644
+index 74798f8..9001a87 100644
--- a/src/objects/submit/Makefile.submit.lib
+++ b/src/objects/submit/Makefile.submit.lib
@@ -1,2 +1,3 @@
LIB = submit
SRC = submit__ submit___
-+DLL_LIB = xser xncbi # lds
++DLL_LIB = xser xncbi seq # lds
diff --git a/src/objects/taxon1/Makefile.taxon1.lib b/src/objects/taxon1/Makefile.taxon1.lib
index 61658ab..d735117 100644
--- a/src/objects/taxon1/Makefile.taxon1.lib
@@ -540,6 +714,16 @@ index 61658ab..d735117 100644
WATCHERS = domrach
+
+DLL_LIB = xser
+diff --git a/src/objects/taxon3/Makefile.taxon3.lib b/src/objects/taxon3/Makefile.taxon3.lib
+index 7e4c93d..5a6033e 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
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
@@ -551,7 +735,7 @@ index b202355..9699bb2 100644
+
+DLL_LIB = xser
diff --git a/src/objects/valid/Makefile.valid.lib b/src/objects/valid/Makefile.valid.lib
-index 86a00a0..ee7402f 100644
+index 86a00a0..64226d6 100644
--- a/src/objects/valid/Makefile.valid.lib
+++ b/src/objects/valid/Makefile.valid.lib
@@ -1,3 +1,5 @@
@@ -559,7 +743,7 @@ index 86a00a0..ee7402f 100644
LIB = valid
SRC = valid__ valid___
+
-+DLL_LIB = xser
++DLL_LIB = xser xregexp
diff --git a/src/objects/variation/Makefile.variation.lib b/src/objects/variation/Makefile.variation.lib
index f21f84a..b08e210 100644
--- a/src/objects/variation/Makefile.variation.lib
@@ -578,7 +762,7 @@ index 90eeee0..138e836 100644
+DLL_LIB = xser xobjmgr
diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib
-index 4b3e59e..94fc319 100644
+index 4b3e59e..d8e9345 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)
@@ -586,7 +770,26 @@ index 4b3e59e..94fc319 100644
WATCHERS = zaretska jianye madden camacho
+
-+DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb blastdb xser
+diff --git a/src/objtools/alnmgr/Makefile.alnmgr.lib b/src/objtools/alnmgr/Makefile.alnmgr.lib
+index e32c351..1702b90 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
+diff --git a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+index d8177ed..f7beead 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
diff --git a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
index 25898aa..92d4d59 100644
--- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
@@ -597,6 +800,15 @@ index 25898aa..92d4d59 100644
WATCHERS = maning camacho
+
+DLL_LIB = blastdb
+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/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
@@ -620,6 +832,106 @@ index f2b2b49..a8ee667 100644
+DLL_LIB = xcompress
WATCHERS = vasilche
+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/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib
+index a4fc469..3f771e6 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
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
@@ -632,7 +944,7 @@ index 0fbffd4..4ca9fed 100644
-
+DLL_LIB = creaders xncbi seq biblio seqset
diff --git a/src/objtools/readers/Makefile.xobjreadex.lib b/src/objtools/readers/Makefile.xobjreadex.lib
-index 85eefe2..f238782 100644
+index 85eefe2..9f317ae 100644
--- a/src/objtools/readers/Makefile.xobjreadex.lib
+++ b/src/objtools/readers/Makefile.xobjreadex.lib
@@ -8,4 +8,4 @@ LIB = xobjreadex
@@ -640,18 +952,18 @@ index 85eefe2..f238782 100644
idmapper_database source_mod_parser_wrapper
-DLL_LIB = xobjread
-+DLL_LIB = xobjread xncbi xutil seq xobjmgr
++DLL_LIB = xobjread xncbi xutil seq xobjmgr xobjutil
diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib
-index dab25d6..a29b960 100644
+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
++DLL_LIB = xobjmgr ncbi_xloader_genbank
diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib
-index 80a74d8..69c4ef6 100644
+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%=)
@@ -659,7 +971,16 @@ index 80a74d8..69c4ef6 100644
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
++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
+--- 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
diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib
index 2563b5f..efad054 100644
--- a/src/serial/Makefile.serial.lib
@@ -699,6 +1020,19 @@ index 9877691..599ef5d 100644
WATCHERS = gouriano
+DLL_LIB = xncbi xutil xser
+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
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2013-02-03 19:12 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2013-02-03 19:12 UTC (permalink / raw
To: gentoo-commits
commit: 5ea1a4083bccc5fba615a8172113f0fee0381df6
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 3 19:12:45 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 3 19:12:45 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5ea1a408
And another step forward
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
.../files/ncbi-tools++-9.0.0-as-needed.patch | 8 ++++----
1 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
index e3110de..4c17bb0 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
@@ -333,7 +333,7 @@ index cecfd16..c01668b 100644
+DLL_LIB = xncbi xutil
+LIBS = $(SQLITE3_LIBS)
diff --git a/src/dbapi/Makefile.dbapi.lib b/src/dbapi/Makefile.dbapi.lib
-index 6e3ad4c..4475a78 100644
+index 6e3ad4c..e3d6a49 100644
--- a/src/dbapi/Makefile.dbapi.lib
+++ b/src/dbapi/Makefile.dbapi.lib
@@ -10,3 +10,8 @@ LIB = dbapi
@@ -341,7 +341,7 @@ index 6e3ad4c..4475a78 100644
WATCHERS = ivanovp
+
-+#ASN_DEP = driver
++#ASN_DEP = driver dbapi_driver
+
+DLL_LIB = xncbi xutil # dbapi_driver$(DLL)
+LIBS = $(PYTHON_LIBS)
@@ -425,7 +425,7 @@ index 8019285..2c689ae 100644
+
+DLL_LIB = xncbi xser
diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib
-index 0dd0fa3..5ffe052 100644
+index 0dd0fa3..d50f29f 100644
--- a/src/objects/blast/Makefile.blast.lib
+++ b/src/objects/blast/Makefile.blast.lib
@@ -2,3 +2,5 @@ LIB = xnetblast
@@ -433,7 +433,7 @@ index 0dd0fa3..5ffe052 100644
WATCHERS = camacho
+
-+DLL_LIB = xncbi xutil xser
++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
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2013-02-21 22:56 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2013-02-21 22:56 UTC (permalink / raw
To: gentoo-commits
commit: ae3e6180c230a13dc94e8d8599316d55ceab3d39
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 21 22:56:39 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Feb 21 22:56:39 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae3e6180
First working patch
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
.../files/ncbi-tools++-9.0.0-as-needed.patch | 758 ++++++++++++++++----
1 files changed, 602 insertions(+), 156 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
index 610ee24..f5d6a3d 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
@@ -1,135 +1,184 @@
- 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 ++
- src/connect/Makefile.connssl.lib | 2 ++
- src/connect/Makefile.xconnect.lib | 4 ++++
- src/connect/Makefile.xthrserv.lib | 2 +-
- src/connect/Makefile.xxconnect.lib | 2 ++
- src/connect/services/Makefile.ncbi_xcache_netcache.lib | 2 +-
- src/connect/services/Makefile.xconnserv.lib | 2 +-
- src/connect/test/Makefile.conntest.lib | 2 ++
- src/corelib/Makefile.test_boost.lib | 2 ++
- src/corelib/Makefile.test_mt.lib | 2 ++
- src/corelib/test/Makefile.pbacktest.lib | 2 ++
- src/db/bdb/Makefile.bdb.lib | 4 ++++
- src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +-
- src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++
- src/dbapi/Makefile.dbapi.lib | 5 +++++
- src/dbapi/driver/Makefile.dbapi_driver.lib | 2 ++
- src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib | 2 ++
- src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib | 2 +-
- src/dbapi/simple/Makefile.sdbapi.lib | 1 +
- src/html/Makefile.html.lib | 2 ++
- src/objects/access/Makefile.access.lib | 1 +
- src/objects/biblio/Makefile.biblio.lib | 2 ++
- src/objects/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_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 ++
- 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/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 +
- src/objtools/validator/Makefile.validator.lib | 2 ++
- src/objtools/writers/Makefile.xobjwrite.lib | 1 +
- 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/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 +-
- 128 files changed, 237 insertions(+), 16 deletions(-)
+ 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..f9c79ba 100644
+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
@@ -137,9 +186,39 @@ index d163f7c..f9c79ba 100644
CXXFLAGS = $(FAST_CXXFLAGS) -I./.
LDFLAGS = $(FAST_LDFLAGS)
+
-+DLL_LIB = seq xalgoalignutil xncbi blastinput
++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..3be07ae 100644
+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)
@@ -147,12 +226,12 @@ index 073973b..3be07ae 100644
LIB = xblast
-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread
++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..6f56c5a 100644
+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)
@@ -160,7 +239,7 @@ index bfb315c..6f56c5a 100644
LIB = blastinput
-DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = seqdb ncbi_xloader_blastdb $(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
@@ -174,8 +253,49 @@ index 8e889a7..1326aee 100644
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..32905ca 100644
+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
@@ -183,9 +303,41 @@ index e618f67..32905ca 100644
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
+
-+DLL_LIB = align_format
++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..24fcff3 100644
+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
@@ -193,9 +345,51 @@ index 872b92e..24fcff3 100644
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
+
-+DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast
++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..0c20790 100644
+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)
@@ -203,7 +397,30 @@ index 51f4cd7..0c20790 100644
WATCHERS = dicuccio
+
-+DLL_LIB = taxon1 xalnmgr
++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
@@ -234,15 +451,36 @@ index c06a2c0..9f1ff25 100644
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..7344871 100644
+index afaf676..ad2c1fe 100644
--- a/src/algo/winmask/Makefile.xalgowinmask.lib
+++ b/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
+@@ -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
++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
@@ -479,6 +717,26 @@ index a57c1e3..0005299 100644
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
@@ -545,14 +803,14 @@ 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..2365261 100644
+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
++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
@@ -1006,8 +1264,18 @@ index 90eeee0..138e836 100644
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..d8e9345 100644
+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)
@@ -1015,18 +1283,18 @@ index 4b3e59e..d8e9345 100644
WATCHERS = zaretska jianye madden camacho
+
-+DLL_LIB = seqdb blastdb xser
++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..1702b90 100644
+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
++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..f7beead 100644
+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)
@@ -1034,7 +1302,7 @@ index d8177ed..f7beead 100644
#
# LIB_OR_DLL = dll
+
-+DLL_LIB = xncbi xser xobjutil seq
++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
@@ -1084,6 +1352,29 @@ index 10a878c..7a70b22 100644
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
@@ -1095,6 +1386,26 @@ index 80af69f..704ed7a 100644
+
+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
@@ -1108,7 +1419,7 @@ index f2b2b49..864e4b1 100644
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
+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)
@@ -1116,7 +1427,27 @@ index 0a29cbf..015ac93 100644
WATCHERS = vasilche
+
-+DLL_LIB = xncbi
++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
@@ -1127,6 +1458,16 @@ index 7ce0d11..f5458c5 100644
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
@@ -1217,8 +1558,18 @@ index 19b2b8a..77dcc3c 100644
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..0203fea 100644
+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 \
@@ -1226,7 +1577,7 @@ index a4fc469..0203fea 100644
WATCHERS = ludwigf dicuccio kornbluh
+
-+DLL_LIB = submit connect xncbi gbseq xobjmgr
++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
@@ -1270,6 +1621,18 @@ index 85eefe2..9f317ae 100644
-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
@@ -1279,6 +1642,16 @@ index dab25d6..f676dc7 100644
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
@@ -1298,6 +1671,66 @@ index cd6596b..a7d0c01 100644
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
@@ -1337,6 +1770,19 @@ index 9877691..599ef5d 100644
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
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2013-09-13 20:12 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-09-13 20:12 UTC (permalink / raw
To: gentoo-commits
commit: fc2c3ad28c32659d2b55076c7f7d4d2f0da0aa00
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Sep 13 20:14:16 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Sep 13 20:14:16 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fc2c3ad2
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 f5d6a3d..8213800 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 f5d6a3d..8213800 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
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2014-06-23 20:38 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-06-23 20:38 UTC (permalink / raw
To: gentoo-commits
commit: cb7af5375a7fbfdfaeddf149fed723aa81e1827e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 23 20:38:29 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 23 20:38:29 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cb7af537
dropped the duplicate part from the patch
---
.../files/ncbi-tools++-12.0.0-configure.patch | 1660 --------------------
1 file changed, 1660 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
index 0d4bd39..4c77991 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch
@@ -1,1663 +1,3 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014-06-23 17:35:47.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014-06-23 17:36:41.000000000 +0200
-@@ -1,5 +1,5 @@
- #############################################################################
--# $Id: configure.ac 398256 2013-05-03 19:14:07Z rafanovi $
-+# $Id$
- # Derived from configure.in version 1.173.
- # ==========================================================================
- #
-@@ -38,7 +38,7 @@
- #
- #############################################################################
-
--AC_PREREQ(2.59)
-+AC_PREREQ(2.60)
-
- dnl Early setup, most crucially for locking. The diversion magic lets
- dnl this occur before AC_INIT, which already interferes with other
-@@ -71,7 +71,7 @@
- python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat,
- sablot, libxml, libxslt, libexslt, xerces, xalan, zorba,
- oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm,
-- magic, curl],
-+ magic, curl, gsoap, mongodb],
- [if test "${[with_]X-no}" != "no"; then
- AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw])
- else
-@@ -143,6 +143,8 @@
- [ --with-bin-release build executables suitable for public release])
- AC_ARG_WITH(mt,
- [ --with-mt compile in a MultiThread-safe manner])
-+AC_ARG_WITH(openmp,
-+ [ --with-openmp enable OpenMP extensions for all projects])
- AC_ARG_WITH(64,
- [ --with-64 compile to 64-bit code])
- AC_ARG_WITH(universal,
-@@ -220,11 +222,15 @@
-
- ## NCBI packages
- AC_ARG_WITH(ncbi-c,
-+ [ --with-ncbi-c=DIR use NCBI C Toolkit installation in DIR])
-+AC_ARG_WITH(ncbi-c2,
- [ --without-ncbi-c do not use NCBI C Toolkit])
- AC_ARG_WITH(sss,
-+ [ --with-sss=DIR use NCBI SSS installation in DIR])
-+AC_ARG_WITH(sss2,
- [ --without-sss do not use NCBI SSS libraries])
- AC_ARG_WITH(sssutils,
-- [ --without-sssutils do not use NCBI SSS UTIL library])
-+ [ --without-utils 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,
-@@ -439,6 +445,14 @@
- [ --with-mimetic=DIR use libmimetic installation in DIR])
- AC_ARG_WITH(mimetic2,
- [ --without-mimetic do not use libmimetic])
-+AC_ARG_WITH(gsoap,
-+ [ --with-gsoap=DIR use gSOAP++ installation in DIR])
-+AC_ARG_WITH(gsoap2,
-+ [ --without-gsoap do not use gSOAP++])
-+AC_ARG_WITH(mongodb,
-+ [ --with-mongodb=DIR use MongoDB installation in DIR])
-+AC_ARG_WITH(mongodb2,
-+ [ --without-mongodb do not use MongoDB])
- AC_ARG_WITH(3psw,
- [ --with-3psw=std:netopt favor standard (system) builds of the above pkgs.])
- AC_ARG_WITH(3psw2,
-@@ -479,24 +493,28 @@
- [***** See also HTML documentation in ./doc/index.html *****])
-
-
-+AC_DIVERT_PUSH(PARSE_ARGS)
-+dnl As of Autoconf 2.60, this needs to run too early for config.log,
-+dnl to which AC_MSG_ERROR normally copies its output, to be available.
-+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
- #### Check the passed arguments against the list of available ones
- x_with_list="\
- debug max-debug symbols optimization profiling tcheck dll static static-exe \
- plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \
--lfs limited-linker \
-+lfs limited-linker openmp \
- autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
- deactivation makefile-auto-update projects flat-makefile configure-dialog \
- 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 gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
- bdb python perl jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt libexslt xerces xalan zorba \
- oechem sge muparser hdf5 \
--gif jpeg tiff png xpm magic curl mimetic 3psw \
-+gif jpeg tiff png xpm magic curl mimetic gsoap mongodb 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench x"
-+serial objects dbapi app ctools gui algo internal gbench"
-
- changequote(, )dnl
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-@@ -522,7 +540,6 @@
- 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])
- ;;
-@@ -533,12 +550,11 @@
- | --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=* \
-+ | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
- | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* \
-- | --with-krb5=* | --with-curl=* \
-+ | --with-krb5=* | --with-curl=* | --with-gsoap=* | --with-mongodb=* \
- | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \
- | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \
- | --with-sqlite3=* | --with-expat=* | --with-sablot=* \
-@@ -552,7 +568,7 @@
- | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
- | --x-includes=* | --x-libraries=* | --with-3psw=* \
- | --target=* | --with-runpath=* | --with-relative-runpath=* \
-- | --no-create | --no-recursion)
-+ | --help | --no-create | --no-recursion)
- ;;
-
- * )
-@@ -560,6 +576,8 @@
- ;;
- esac
- done
-+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
-+AC_DIVERT_POP
-
-
- if test "$with_gbench" = "yes" ; then
-@@ -604,6 +622,13 @@
- : ${with_optimization=no}
- fi
-
-+if test "$with_openmp" = yes; then
-+ if test "$with_mt" = no; then
-+ AC_MSG_ERROR([incompatible options: --without-mt but --with-openmp])
-+ fi
-+ : ${with_mt=yes}
-+fi
-+
- #### Check for special options
- if test "$with_extra_action" = "yes" ; then
- AC_MSG_ERROR([--with-extra-action must have a value after =])
-@@ -649,15 +674,10 @@
- *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
- esac
- fi
--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
-+# Generally save any originally specified flags.
-+USER_CFLAGS=$CFLAGS
-+USER_CXXFLAGS=$CXXFLAGS
-+USER_LDFLAGS=$LDFLAGS
-
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
-@@ -675,6 +695,23 @@
- #### Make some provisions for traditional operation
- AC_PROG_INSTALL
-
-+#### Point ICC at a suitable GCC version ASAP.
-+case "/$CXX" in
-+ */icpc )
-+ if test -d /usr/local/gcc; then
-+ case "`$CXX -dumpversion`:$host_cpu" in
-+ *:i?86) v=4.4.5 ;;
-+ ?.* | 1[[01]].* ) v=4.0.1 ;;
-+ *) v=4.4.2 ;;
-+ esac
-+ gcc=/usr/local/gcc/$v/bin/gcc
-+ if test -x $gcc; then
-+ CC="$CC -gcc-name=$gcc"
-+ CXX="$CXX -gcc-name=$gcc"
-+ fi
-+ fi
-+ ;;
-+esac
-
- #### C and C++ compilers
- AC_LANG(C++)
-@@ -987,6 +1024,30 @@
- ;;
- * ) NCBIATOMIC_LIB=xncbi ;;
- esac
-+ case "$compiler" in
-+ GCC )
-+ if $CC -v | grep clang >/dev/null; then
-+ :
-+ # Will allegedly support -openmp at some point, but as of 3.4,
-+ # just parses it as specifying an output filename: -o penmp.
-+ else
-+ case "$compiler_version" in
-+ [[123]]?? | 4[[01]]? ) ;;
-+ * ) : ${OPENMP_FLAGS=-fopenmp} ;;
-+ esac
-+ fi
-+ ;;
-+ ICC )
-+ : ${OPENMP_FLAGS=-openmp}
-+ ;;
-+ WorkShop* )
-+ : ${OPENMP_FLAGS=-xopenmp=parallel}
-+ ;;
-+ esac
-+ if test "$with_openmp" = yes; then
-+ MT_FLAG="$MT_FLAG $OPENMP_FLAGS"
-+ OPENMP_FLAGS=
-+ fi
- mt_sfx="MT"
- NCBI_FEATURE(MT)
- else
-@@ -994,6 +1055,7 @@
- MT_FLAG=
- THREAD_LIBS=
- NCBIATOMIC_LIB=
-+ OPENMP_FLAGS=
- mt_sfx=""
- fi
- MT_SFX="${mt_sfx}"
-@@ -1006,6 +1068,9 @@
- APP_LDFLAGS=
- DLL_LDFLAGS=
-
-+### Should go before any test compiler runs
-+AC_GNU_SOURCE
-+
- case "$host_os:$compiler" in
- darwin*:GCC )
- AC_CACHE_CHECK([whether $CC supports -Wl,-rpath],
-@@ -1047,6 +1112,47 @@
- ;;
- esac
-
-+case "$compiler:$compiler_version" in
-+ GCC:4[[0-6]]? | ICC:1[[01]]?? )
-+ ncbi_cv_prog_cxx_11=no
-+ ncbi_cv_prog_c_99=no
-+ ;;
-+ ICC:* )
-+ ncbi_cv_prog_c_99='-std=gnu99 -fgnu89-inline'
-+ ;;
-+esac
-+
-+AC_CACHE_CHECK([how to enable C++ '11 features in $CXX],
-+ ncbi_cv_prog_cxx_11,
-+ [orig_CXX=$CXX
-+ ncbi_cv_prog_cxx_11=no
-+ for x in -std=gnu++11 -std=gnu++0x; do
-+ CXX="$orig_CXX $x"
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+ [ncbi_cv_prog_cxx_11=$x])
-+ test "x$ncbi_cv_prog_cxx_11" = "xno" || break
-+ done
-+ CXX=$orig_CXX])
-+test "$ncbi_cv_prog_cxx_11" = no || CXX="$CXX $ncbi_cv_prog_cxx_11"
-+
-+AC_LANG_PUSH(C)
-+AC_CACHE_CHECK([how to enable C '11 or at least '99 features in $CC],
-+ ncbi_cv_prog_c_99,
-+ [orig_CC=$CC
-+ ncbi_cv_prog_c_99=no
-+ for x in -xc99=all "-std=gnu11 -fgnu89-inline" \
-+ "-std=gnu1x -fgnu89-inline" \
-+ "-std=gnu99 -fgnu89-inline" \
-+ "-std=gnu9x -fgnu89-inline"; do
-+ CC="$orig_CC $x"
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+ [ncbi_cv_prog_c_99=$x])
-+ test "x$ncbi_cv_prog_c_99" = "xno" || break
-+ done
-+ CC=$orig_CC])
-+AC_LANG_POP(C)
-+test "$ncbi_cv_prog_c_99" = no || CC="$CC $ncbi_cv_prog_c_99"
-+
- #### Provide default environment setup for known platforms/compilers
- DEPFLAGS="-M"
- DEPFLAGS_POST="" # Needed for VisualAge
-@@ -1059,7 +1165,15 @@
- ;;
-
- solaris*:GCC )
-- CPPFLAGS="-D_XOPEN_SOURCE=500 $CPPFLAGS"
-+ # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only
-+ # in C++ mode. Set it for C code as well to ensure consistent
-+ # header behavior, taking care to match the C standard version
-+ # (as enforced by <sys/feature_tests.h>).
-+ case "$ncbi_cv_prog_c_99" in
-+ no) CC="$CC -D_XOPEN_SOURCE=500" ;;
-+ *) CC="$CC -D_XOPEN_SOURCE=600" ;;
-+ esac
-+
- STRIP="@:"
- ;;
-
-@@ -1202,11 +1316,19 @@
- LDFLAGS="-flat_namespace $LDFLAGS"
-
- if test "$with_ncbi_public" = yes; then
-+ sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk'
-+ case "$host_os" in
-+ darwin?.* | darwin10.* ) # Mac OS X 10.6.x or older
- TARGET='-mmacosx-version-min=10.5'
-- sdks='/Developer/SDKs/MacOSX10.6.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk'
-+ sdks="/Developer/SDKs/MacOSX10.6.sdk"
- if test "$with_64:${with_universal-no}" != "yes:no"; then
- sdks="/Developer/SDKs/MacOSX10.5.sdk $sdks"
- fi
-+ ;;
-+ * )
-+ TARGET='-mmacosx-version-min=10.7'
-+ ;;
-+ esac
- for sdk in $sdks; do
- if test -d "$sdk"; then
- TARGET="-isysroot $sdk $TARGET"
-@@ -1487,8 +1609,8 @@
- ;;
- GCC:* )
- DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"
-- case "$host_os" in
-- freebsd* ) ;;
-+ case "$host_os:$host_cpu:$compiler_version" in
-+ freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;;
- * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
- esac
- if test "$with_profiling" != "yes"; then
-@@ -1587,13 +1709,9 @@
- solaris* )
- CONF_f_runpath="-R"
- ;;
-- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
-+ linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
- CONF_f_runpath="-Wl,-rpath,"
- ;;
-- linux*:ICC )
-- # trying to use "-Wl,-rpath," here sends "ld" to endless 100% CPU loop
-- CONF_f_runpath="-Xlinker -rpath -Xlinker "
-- ;;
- irix*:* | linux*:KCC | *:Compaq )
- CONF_f_runpath="-rpath "
- ;;
-@@ -1697,8 +1815,11 @@
- LINK="$LINK -Kc++"
- ;;
- ICC:1???:* )
-- APP_LDFLAGS="-static-intel $APP_LDFLAGS"
-- DLL_LDFLAGS="-static-intel -nodefaultlibs $DLL_LDFLAGS"
-+ # Suppress "warning #10237: -lcilkrts linked in dynamically, static
-+ # library not available" which is not a problem in practice due to
-+ # as-needed linkage.
-+ APP_LDFLAGS="-static-intel -diag-disable 10237 $APP_LDFLAGS"
-+ DLL_LDFLAGS="-static-intel -diag-disable 10237 -nodefaultlibs $DLL_LDFLAGS"
- # Redundant for apps, but necessary for plugins to be adequately
- # self-contained, at least on 32-bit Linux.
- LIBS="$LIBS -lstdc++"
-@@ -1817,18 +1938,6 @@
-
- #### Intel compiler:: common flags and definitions
- if test "$compiler" = "ICC" ; then
-- if test -d /usr/local/gcc; then
-- case "$compiler_version:$HOST_CPU" in
-- *:i?86) v=4.4.5 ;;
-- ???:* | 1[[01]]??:* ) v=4.0.1 ;;
-- *) v=4.4.2 ;;
-- esac
-- gcc=/usr/local/gcc/$v/bin/gcc
-- if test -x $gcc; then
-- CC="$CC -gcc-name=$gcc"
-- CXX="$CXX -gcc-name=$gcc"
-- fi
-- fi
- if test -n "$icc_license" ; then
- icc_CC="$CC"
- icc_CXX="$CXX"
-@@ -2073,6 +2182,7 @@
- fi
-
- AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
-+dnl AC_PATH_PROG(GREP, grep)
- AC_PROG_EGREP
- AC_MSG_CHECKING([how to run $EGREP quietly])
- if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
-@@ -2086,6 +2196,16 @@
-
- AC_CHECK_PROG(VALGRIND_PATH, valgrind, valgrind)
-
-+AC_PATH_PROG(LDD, ldd)
-+if test -n "$LDD"; then
-+ AC_MSG_CHECKING([whether $LDD accepts -r])
-+ if $LDD -r /bin/ls >/dev/null 2>&1; then
-+ AC_MSG_RESULT(yes)
-+ LDD_R="$LDD -r"
-+ else
-+ AC_MSG_RESULT(no)
-+ fi
-+fi
-
- #### Check if "${build_root}" is defined; provide a default one
- if test -n "${with_build_root}" ; then
-@@ -2170,9 +2290,6 @@
- fi
-
-
--### Should go before any test compiler runs
--AC_GNU_SOURCE
--
- #### Determine whether this is implicitly a 64-bit platform
- AC_TYPE_SIZE_T
- if test "${with_universal-no}" = "no"; then
-@@ -2342,7 +2459,7 @@
- fi
- ;;
- *:ICC )
-- runpath="$runpath -Xlinker -rpath-link -Xlinker \$(libdir)"
-+ runpath="$runpath -Wl,-rpath-link,\$(libdir)"
- ;;
- esac
- elif test "$with_runpath" = "yes" -o "$with_dll" != "no" ; then
-@@ -2658,15 +2775,30 @@
- dbgrx1="$wsrx-g[^cx$wschars]*$wsrx"
- dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx"
- optrx="$wsrx-x*O[0-9s]*$wsrx"
-+ NDEB_CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ NDEB_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ NDEB_LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
- if test "$with_symbols" = "no" ; then
-- CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-- CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-- LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ CFLAGS=$NDEB_CFLAGS
-+ CXXFLAGS=$NDEB_CXXFLAGS
-+ LDFLAGS=$NDEB_LDFLAGS
- else
- echo " $CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || CFLAGS="$CFLAGS -g"
- echo " $CXXFLAGS "| $EGREP_Q "$dbgrx1|$dbgrx2" || CXXFLAGS="$CXXFLAGS -g"
- echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"
- STRIP="@:"
-+ case "$compiler:$compiler_version" in
-+ GCC:4[89]? | GCC:[5-9]? | GCC:???? )
-+ # GCC 4.8 defaults to DWARF 4, which Totalview for one
-+ # can't handle; roll back to version 3 by default.
-+ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ CFLAGS="$NDEB_CFLAGS -gdwarf-3"
-+ echo " $USER_CXXFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ CXXFLAGS="$NDEB_CXXFLAGS -gdwarf-3"
-+ echo " $USER_LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ LDFLAGS="$NDEB_LDFLAGS -gdwarf-3"
-+ ;;
-+ esac
- fi
-
- NOPT_CFLAGS=` echo " $CFLAGS " | sed "s/$optrx/ /g"`
-@@ -3024,9 +3156,9 @@
- ### Check for other standard library functions
-
- AC_FUNC_VPRINTF
--AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getpagesize \
-- getpass getpassphrase getpwuid getrusage gettimeofday \
-- getuid memrchr readpassphrase readv usleep \
-+AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getgrouplist \
-+ getpagesize getpass getpassphrase getpwuid getrusage \
-+ gettimeofday getuid memrchr readpassphrase readv usleep \
- asprintf vasprintf vsnprintf select statfs statvfs \
- strcasecmp strlcat strlcpy strdup strndup strtok_r \
- sysmp timegm utimes lutimes writev)
-@@ -3253,17 +3385,6 @@
- fi
-
-
--AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
-- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
-- [[#include <algorithm>]],
-- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
-- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
--if test "$ncbi_cv_func_is_sorted" = yes; then
-- AC_DEFINE(HAVE_IS_SORTED, 1,
-- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
--fi
--
--
-
- AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
- AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
-@@ -3400,7 +3521,7 @@
- AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
- ncbi_cv_c_restrict,
- [ncbi_cv_c_restrict=no
-- for restrict in restrict __restrict__ __restrict; do
-+ for restrict in __restrict__ __restrict restrict; do
- test "$ncbi_cv_c_restrict" = "no" || break
- AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
- [ncbi_cv_c_restrict=$restrict], [])
-@@ -3420,7 +3541,7 @@
- AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
- ncbi_cv_cxx_restrict,
- [ncbi_cv_cxx_restrict=no
-- for restrict in restrict __restrict__ __restrict; do
-+ for restrict in __restrict__ __restrict restrict; do
- test "$ncbi_cv_cxx_restrict" = "no" || break
- AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
- [ncbi_cv_cxx_restrict=$restrict], [])
-@@ -3525,14 +3646,6 @@
- unaligned addresses.])
- fi
-
--AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
-- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
-- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
--if test "$ncbi_cv_cxx_nullptr" = yes; then
-- AC_DEFINE(HAVE_NULLPTR, 1,
-- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
--fi
--
- ### Check for the availability of other packages
- ### --------------------------------------------
-
-@@ -3630,7 +3743,16 @@
- dnl NCBI_CHECK_LIBS(FUSE, fuse, fuse_loop)
- AC_SEARCH_LIBS(fuse_loop, fuse, [NCBI_PACKAGE(FUSE)])
- LIBS=$orig_LIBS
-+# Temporarily drop OpenMP flags for this test, as some toolchains count
-+# its support library's indirect use of librt when building applications
-+# but not when building shared libraries with --no-undefined.
-+orig_CXXFLAGS=$CXXFLAGS
-+orig_LDFLAGS=$LDFLAGS
-+CXXFLAGS=`echo $CXXFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
-+LDFLAGS=`echo $LDFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
- NCBI_CHECK_LIBS(RT, rt posix4, clock_gettime)
-+CXXFLAGS=$orig_CXXFLAGS
-+LDFLAGS=$orig_LDFLAGS
- NCBI_CHECK_LIBS(DEMANGLE, demangle, cplus_demangle)
- # Add to (orig_)LIBS if present for the sake of corelib and the
- # following call to AC_CHECK_FUNCS.
-@@ -3734,7 +3856,6 @@
- NCBI_PACKAGE(LocalBZ2)
- fi
-
--: ${LZO_PATH=$NCBI/lzo2}
- if test -d "$LZO_PATH"; then
- NCBI_FIX_DIR(LZO_PATH)
- fi
-@@ -3767,7 +3888,7 @@
- ## SSL/TLS libraries
- case "$with_gcrypt" in
- no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;;
-- yes | '' ) : ${GCRYPT_PATH=$NCBI/gcrypt} ;;
-+ yes | '' ) ;;
- * ) GCRYPT_PATH=$with_gcrypt ;;
- esac
- if test -d "$GCRYPT_PATH"; then
-@@ -3802,13 +3923,16 @@
-
- case "$with_gnutls" in
- no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;;
-- yes | '' ) : ${GNUTLS_PATH=$NCBI/gnutls} ;;
-+ yes | '' ) ;;
- * ) GNUTLS_PATH=$with_gnutls ;;
- esac
- if test -d "$GNUTLS_PATH"; then
- NCBI_FIX_DIR(GNUTLS_PATH)
-+ gnutls_config_path=${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin
-+else
-+ gnutls_config_path=$PATH
- fi
--AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin:$PATH])
-+AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path])
-
- if test "x$with_gnutls" != xno; then
- if test -x "$LIBGNUTLS_CONFIG"; then
-@@ -3817,7 +3941,7 @@
- test "x$p" = "x/usr" || GNUTLS_PATH=$p
- fi
- else
-- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls"
-+ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
- $LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no
- fi
- case "$LIBGNUTLS_CONFIG" in
-@@ -3846,6 +3970,10 @@
- $GNUTLS_CONFIG_LIBS $GCRYPT_LIBS)
- if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then
- NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBS, [echo $GNUTLS_CONFIG_LIBS], [$no_usr_lib])
-+ # Conservatively build against gcrypt if available even when gnutls
-+ # uses nettle instead, because gcrypt needs explicit initialization
-+ # to be thread-safe, but gnutls's headers don't indicate which
-+ # underlying crypto library it's actually using.
- case "$GNUTLS_INCLUDE" in
- *$GCRYPT_INCLUDE* ) ;;
- * ) GNUTLS_INCLUDE="$GNUTLS_INCLUDE $GCRYPT_INCLUDE" ;;
-@@ -4108,7 +4236,8 @@
- SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS"
- SYBASE_DLLS="$SYBASE_DLLLIST"
-
-- AC_CACHE_CHECK([for Sybase in $SYBASE_PATH], ncbi_cv_lib_sybase,
-+ AC_CACHE_CHECK([for Sybase${SYBASE_PATH:+ in $SYBASE_PATH}],
-+ ncbi_cv_lib_sybase,
- [CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS"
- LIBS="$SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $DL_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4216,7 +4345,8 @@
- AC_MSG_NOTICE([Using bundled FreeTDS (version $ftds_ver) from $FTDS_PATH])
- else
- FTDS_LIBS="$FTDS_CTLIBS"
-- AC_CACHE_CHECK([for FreeTDS in $FTDS_PATH], ncbi_cv_lib_freetds,
-+ AC_CACHE_CHECK([for FreeTDS${FTDS_PATH:+ in $FTDS_PATH}],
-+ ncbi_cv_lib_freetds,
- [CPPFLAGS="$FTDS_INCLUDE $orig_CPPFLAGS"
- LIBS="$FTDS_LIBS $NETWORK_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4281,7 +4411,7 @@
- # Kill off single quotes, due to later requoting
- : ${MYSQL_INCLUDE=`$mysql_config --include | tr -d \'`}
- NCBI_RPATHIFY_OUTPUT_COND(MYSQL_LIBS, $mysql_config --libs${mt_sfx:+_r},
-- [s/'//g; ])
-+ [s/'//g; $no_usr_lib])
- AC_CACHE_CHECK([whether MySQL works], ncbi_cv_lib_mysql,
- [CPPFLAGS="$MYSQL_INCLUDE $orig_CPPFLAGS"
- LIBS="$MYSQL_LIBS $orig_LIBS"
-@@ -4310,7 +4440,6 @@
- if test "$with_bdb" != "no" ; then
- case "$with_bdb" in
- yes | "" )
-- : ${BERKELEYDB_PATH:="$NCBI/BerkeleyDB"}
- ;;
- */*)
- BERKELEYDB_PATH=$with_bdb
-@@ -4351,7 +4480,8 @@
- else
- BERKELEYDB_STATIC_LIBS=${BERKELEYDB_LIBS}
- fi
-- AC_CACHE_CHECK([for Berkeley DB libraries in $BERKELEYDB_PATH],
-+ AC_CACHE_CHECK(
-+ [for Berkeley DB libraries${BERKELEYDB_PATH:+ in $BERKELEYDB_PATH}],
- ncbi_cv_lib_berkeley_db,
- [CPPFLAGS="$BERKELEYDB_INCLUDE $orig_CPPFLAGS"
- LIBS="$BERKELEYDB_LIBS $orig_LIBS"
-@@ -4450,7 +4580,8 @@
- NCBI_RPATHIFY(ODBC_LIBS, ${ODBC_LIBPATH}, [ -lodbc -lodbcinst])
- CPPFLAGS="$ODBC_INCLUDE $orig_CPPFLAGS"
- LIBS="$ODBC_LIBS $orig_LIBS"
-- AC_CACHE_CHECK([for ODBC libraries in $ODBC_PATH], ncbi_cv_lib_odbc,
-+ AC_CACHE_CHECK([for ODBC libraries${ODBC_PATH:+ in $ODBC_PATH}],
-+ ncbi_cv_lib_odbc,
- [AC_LINK_IFELSE([AC_LANG_PROGRAM(
- [[#include <sql.h>]],
- [[SQLHDBC hdbc; SQLCHAR* cp = (SQLCHAR*) "x";
-@@ -4542,7 +4673,7 @@
- AC_PATH_PROG(PERL, perl, [], [$PERL_PATH/bin:$PATH])
- if test -x "$PERL"; then
- PERL_ARCHLIB=`$PERL -MConfig -e 'print \$Config{archlibexp};'`
-- PERL_FLAGS=`$PERL -MConfig -e 'print \$Config{cppflags};'`
-+ PERL_FLAGS=`$PERL -MConfig -e 'print join " ", grep /^-[[DI]]/, split /\\s+/, \$Config{cppflags};'`
- PERL_INCLUDE="-I$PERL_ARCHLIB/CORE $PERL_FLAGS"
- PERL_DEPS=`$PERL -MConfig -e 'print \$Config{libs};'`
- NCBI_RPATHIFY(PERL_LIBS, $PERL_ARCHLIB/CORE, [ -lperl $PERL_DEPS])
-@@ -4603,9 +4734,7 @@
-
- ## Boost
- if test "$with_boost" != "no"; then
-- if test "${with_boost-yes}" = yes; then
-- : ${BOOST_PATH=$NCBI/boost}
-- else
-+ if test "${with_boost-yes}" != yes; then
- BOOST_PATH=$with_boost
- fi
- if test -d "$BOOST_PATH"; then
-@@ -4644,17 +4773,22 @@
- if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then
- BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version}
- fi
-- case "$ncbi_compiler" in
-- MIPSPRO)
-+ case "$compiler:$ncbi_compiler_ver" in
-+ MIPSpro*)
- BOOST_INCLUDE="$BOOST_INCLUDE $BOOST_INCLUDE/boost/compatibility/cpp_c_headers"
- ;;
-- WORKSHOP)
-+ WorkShop*)
- # Boost.Test's macros yield a *lot* of spurious "should not initialize
- # a non-const reference with a temporary" warnings, to the point of
- # overwhelming the compiler in some cases; turn them off altogether
- # when using Boost at all.
- BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"
- ;;
-+ GCC*:4[[7-9]]* | GCC*:5*)
-+ # Some portions of Boost also have a lot of "unused" typedefs
-+ # from concept checking.
-+ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"
-+ ;;
- esac
- case "$ncbi_cv_lib_boost_version" in
- 0_* | 1_[[0-9]] | 1_[[0-9]]_* | 1_[[0-2]][[0-9]] | 1_[[0-2]][[0-9]]_* ) ;;
-@@ -4666,7 +4800,7 @@
- fi
- with_boost=no
- ;;
-- 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-2]] | 1_5[[0-2]]_* ) ;;
-+ 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;;
- '' ) with_boost=no ;;
- * )
- AC_MSG_WARN(
-@@ -4751,7 +4885,9 @@
- BOOST_REGEX_STATIC_LIBS=$BOOST_REGEX_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.Regex in $BOOST_PATH], ncbi_cv_lib_boost_regex,
-+ in_path=${BOOST_PATH:+ in $BOOST_PATH}
-+
-+ AC_CACHE_CHECK([for Boost.Regex$in_path], ncbi_cv_lib_boost_regex,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_REGEX_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4759,7 +4895,7 @@
- [[throw boost::regex_error(boost::regex_constants::error_stack);]])],
- [ncbi_cv_lib_boost_regex=yes], [ncbi_cv_lib_boost_regex=no])])
-
-- AC_CACHE_CHECK([for Boost.Spirit in $BOOST_PATH], ncbi_cv_lib_boost_spirit,
-+ AC_CACHE_CHECK([for Boost.Spirit$in_path], ncbi_cv_lib_boost_spirit,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4774,7 +4910,7 @@
- BOOST_SYSTEM_STATIC_LIBS=$BOOST_SYSTEM_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.System in $BOOST_PATH], ncbi_cv_lib_boost_system,
-+ AC_CACHE_CHECK([for Boost.System$in_path], ncbi_cv_lib_boost_system,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_SYSTEM_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4785,6 +4921,24 @@
- BOOST_SYSTEM_LIBS=
- BOOST_SYSTEM_STATIC_LIBS=])])
-
-+ boost_fs_lib=-lboost_filesystem${BOOST_TAG}
-+ if test -f "$BOOST_LIBPATH_/libboost_filesystem${BOOST_TAG}-static.a"; then
-+ boost_fs_static_lib=-lboost_filesystem${BOOST_TAG}-static
-+ else
-+ boost_fs_static_lib=$boost_fs_lib
-+ fi
-+ BOOST_FILESYSTEM_LIBS="$boost_fs_lib $BOOST_SYSTEM_LIBS"
-+ BOOST_FILESYSTEM_STATIC_LIBS="$boost_fs_static_lib $BOOST_SYSTEM_STATIC_LIBS"
-+
-+ AC_CACHE_CHECK([for Boost.Filesystem$in_path], ncbi_cv_lib_boost_filesystem,
-+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-+ LIBS="$BOOST_LIBPATH $BOOST_FILESYSTEM_LIBS $RT_LIBS $orig_LIBS"
-+ [AC_LINK_IFELSE(
-+ [AC_LANG_PROGRAM([[#include <boost/filesystem.hpp>]],
-+ [[return boost::filesystem::portable_name("foo");]])],
-+ [ncbi_cv_lib_boost_filesystem=yes],
-+ [ncbi_cv_lib_boost_filesystem=no])])
-+
- BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}
- if test -f "$BOOST_LIBPATH_/libboost_prg_exec_monitor${BOOST_TAG}-static.a"; then
- BOOST_TEST_PEM_STATIC_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}-static
-@@ -4813,7 +4967,7 @@
- BOOST_TEST_TEM_LIBS=$BOOST_TEST_TEM_STATIC_LIBS
- BOOST_TEST_UTF_LIBS=$BOOST_TEST_UTF_STATIC_LIBS
-
-- AC_CACHE_CHECK([for Boost.Test in $BOOST_PATH], ncbi_cv_lib_boost_test,
-+ AC_CACHE_CHECK([for Boost.Test$in_path], ncbi_cv_lib_boost_test,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$RT_LIBS $orig_LIBS"
- found=
-@@ -4853,7 +5007,7 @@
- BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.Threads in $BOOST_PATH], ncbi_cv_lib_boost_thread,
-+ AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4864,12 +5018,25 @@
- BOOST_INCLUDE=
- BOOST_LIBPATH=
- BOOST_TAG=
-+ ncbi_cv_lib_boost_filesystem=no
- ncbi_cv_lib_boost_regex=no
- ncbi_cv_lib_boost_spirit=no
-+ ncbi_cv_lib_boost_system=no
- ncbi_cv_lib_boost_test=no
- ncbi_cv_lib_boost_thread=no
- fi
-
-+if test "$ncbi_cv_lib_boost_filesystem" != "no"; then
-+ dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1,
-+ dnl [Define to 1 if the `Boost.Filesystem' library is available.])
-+ NCBI_PACKAGE(Boost.Filesystem)
-+else
-+ boost_fs_lib=
-+ boost_fs_static_lib=
-+ BOOST_FILESYSTEM_LIBS=
-+ BOOST_FILESYSTEM_STATIC_LIBS=
-+fi
-+
- if test "$ncbi_cv_lib_boost_regex" != "no"; then
- AC_DEFINE(HAVE_BOOST_REGEX, 1,
- [Define to 1 if the `Boost.Regex' library is available.])
-@@ -4927,7 +5094,10 @@
-
- ## NCBI C Toolkit
- if test "$with_ncbi_c" != "no" ; then
-- NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
-+ if test "${with_ncbi_c-yes}" != yes; then
-+ NCBI_C_PATH=$with_ncbi_c
-+ fi
-+ : ${NCBI_C_PATH="$NCBI"}
- if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then
- NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc
- fi
-@@ -4949,7 +5119,8 @@
- NCBI_C_ncbi="-lncbi"
- fi
- NCBI_C_LIBPATH="-L$NCBI_C_LIBPATH"
-- AC_CACHE_CHECK([for the NCBI C toolkit in $NCBI_C_PATH], ncbi_cv_lib_ctools,
-+ AC_CACHE_CHECK([for the NCBI C toolkit${NCBI_C_PATH:+ in $NCBI_C_PATH}],
-+ ncbi_cv_lib_ctools,
- [CPPFLAGS="$NCBI_C_INCLUDE $orig_CPPFLAGS"
- LIBS="$NCBI_C_LIBPATH $NCBI_C_ncbi $NETWORK_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5000,11 +5171,7 @@
-
- ## OpenGL
- if test "$with_opengl" != "no"; then
-- if test "${with_opengl-yes}" = yes; then
-- if test -d $NCBI/MesaGL; then
-- : ${OPENGL_PATH=$NCBI/MesaGL}
-- fi
-- else
-+ if test "${with_opengl-yes}" != yes; then
- OPENGL_PATH=$with_opengl
- fi
- if test -d "$OPENGL_PATH"; then
-@@ -5101,7 +5268,6 @@
- else
- OSMESA_STATIC_LIBS=$OSMESA_LIBS
- fi
-- : ${GLUT_PATH=$NCBI/glut}
- if test "$with_glut" != "no"; then
- if test "${with_glut-yes}" != "yes"; then
- GLUT_PATH=$with_glut
-@@ -5121,7 +5287,6 @@
- NCBI_MISSING_PACKAGE(glut)
- fi
- fi
-- : ${GLEW_PATH=$NCBI/glew}
- if test "$with_glew" != "no"; then
- if test "${with_glew-yes}" != "yes"; then
- GLEW_PATH=$with_glew
-@@ -5214,7 +5379,7 @@
- : ${with_wxwidgets_ucs=no}
- if test "$with_wxwidgets" != "no" ; then
- case "$with_wxwidgets" in
-- yes | "" ) : ${WXWIDGETS_PATH=$NCBI/wxwidgets} ;;
-+ yes | "" ) ;;
- * ) WXWIDGETS_PATH=$with_wxwidgets ;;
- esac
- if test -d "$WXWIDGETS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-@@ -5283,12 +5448,13 @@
- libsed=$basesed
- ;;
- esac
-- AC_CACHE_CHECK([for wxWidgets in $WXWIDGETS_ARCH_PATH],
-+ AC_CACHE_CHECK(
-+ [for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}],
- ncbi_cv_lib_wxwidgets,
- [if test -x "$wxconf" ; then
- WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
- NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs],
-- [$libsed; ])
-+ [$libsed; s/ -lm / /g;])
-
- CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS"
- LIBS="$WXWIDGETS_LIBS $orig_LIBS"
-@@ -5315,12 +5481,12 @@
- else
- NCBI_PACKAGE(wxWidgets)
- case "`"$wxconf" $wxcfflags --version`" in
-- 2.[[89]].* | 2.[[0-9]][[0-9]]* )
-- NCBI_PACKAGE(wx2.8)
-- wxlibs=std,richtext,aui
-+ 1.* | 2.[[0-7]].*)
-+ wxlibs=std
- ;;
- *)
-- wxlibs=std
-+ NCBI_PACKAGE(wx2.8)
-+ wxlibs=std,richtext,aui,propgrid
- ;;
- esac
- # The "yes" may have been cached; get the actual settings again if needed
-@@ -5328,9 +5494,9 @@
- WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
- fi
- NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, [$wxconf $wxcfflags --libs $wxlibs],
-- [$libsed; ])
-+ [$libsed; s/ -lm / /g;])
- WXWIDGETS_STATIC_LIBS=`"$wxconf" $wxcfflags --libs --static $wxlibs \
-- 2>/dev/null | sed -e "$basesed"`
-+ 2>/dev/null | sed -e "$basesed; s/ -lm / /g;"`
- if test -n "$WXWIDGETS_STATIC_LIBS"; then
- # Allow direct use of underlying libraries with strict linkers
- WXWIDGETS_LIBS="$WXWIDGETS_LIBS `echo $WXWIDGETS_STATIC_LIBS | sed -e 's/.*\.a *//'`"
-@@ -5350,7 +5516,7 @@
- ## In-house Fast-CGI library
- if test "$with_fastcgi" != "no" ; then
- case "$with_fastcgi" in
-- yes | "" ) : ${FASTCGI_PATH:="$NCBI/fcgi-current"} ;;
-+ yes | "" ) ;;
- */* ) FASTCGI_PATH=$with_fastcgi ;;
- * ) FASTCGI_PATH=$NCBI/fcgi-${with_fastcgi} ;;
- esac
-@@ -5366,7 +5532,8 @@
- NCBI_RPATHIFY(FASTCGI_LIBS, $FASTCGI_LIBDIR, [ -lfcgi $NETWORK_LIBS])
- FASTCGI_OBJS="fcgibuf"
- LIBS="$FASTCGI_LIBS $orig_LIBS"
-- AC_CACHE_CHECK([for FastCGI libraries in $FASTCGI_PATH], ncbi_cv_lib_fcgi,
-+ AC_CACHE_CHECK([for FastCGI libraries${FASTCGI_PATH:+ in $FASTCGI_PATH}],
-+ ncbi_cv_lib_fcgi,
- [CPPFLAGS="$FASTCGI_INCLUDE $orig_CPPFLAGS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
- [[#include <fcgiapp.h>]],
-@@ -5416,7 +5583,11 @@
- else
- with_included_sss=no
- fi
-+ if test "${with_sss-yes}" = yes; then
- NCBI_SSS_PATH=${NCBI_SSS_PATH:="$NCBI/sss/BUILD"}
-+ else
-+ NCBI_SSS_PATH=$with_sss
-+ fi
- NCBI_SSS_INCLUDE=${NCBI_SSS_INCLUDE:="$NCBI_SSS_PATH/include"}
- if test -z "$NCBI_SSS_LIBPATH" ; then
- NCBI_SSS_LIBPATH="${NCBI_SSS_PATH}/lib/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}"
-@@ -5424,7 +5595,8 @@
- NCBI_SSS_LIBPATH="${NCBI_SSS_LIBPATH}mt"
- fi
- fi
-- AC_MSG_CHECKING([for NCBI SSS directories in $NCBI_SSS_PATH])
-+ AC_MSG_CHECKING(
-+ [for NCBI SSS directories${NCBI_SSS_PATH:+ in $NCBI_SSS_PATH}])
- if test "$with_included_sss" = "yes"; then
- AC_MSG_RESULT([yes]) # duh
- elif test ! -d "${NCBI_SSS_LIBPATH}" -o ! -d "${NCBI_SSS_INCLUDE}" ; then
-@@ -5510,7 +5682,6 @@
-
- # SP
- if test "$with_sp" != "no" ; then
-- SP_PATH=${SP_PATH:="$NCBI/SP"}
- if test -n "$SP_INCLUDE"; then
- SP_GENERIC="$SP_INCLUDE/../generic"
- else
-@@ -5520,7 +5691,7 @@
- if test -z "$SP_LIBPATH" ; then
- SP_LIBPATH="${SP_PATH}/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}"
- fi
-- AC_MSG_CHECKING([for SP directories in $SP_PATH])
-+ AC_MSG_CHECKING([for SP directories${SP_PATH:+ in $SP_PATH}])
- if test ! -d "${SP_LIBPATH}" -o ! -d "${SP_INCLUDE}" ; then
- AC_MSG_RESULT([no])
- NCBI_MISSING_PACKAGE(sp)
-@@ -5558,19 +5729,13 @@
-
-
- ## ORBacus CORBA
--if test "${with_orbacus:-yes}" = yes; then
-- if test -d $NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT; then
-- : ${ORBACUS_PATH=$NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT}
-- else
-- : ${ORBACUS_PATH=$NCBI/corba/OB-4.0.1}
-- fi
--elif test "$with_orbacus" != no; then
-+if test "$with_orbacus" != no; then
-+ if test "$with_orbacus" != yes; then
- ORBACUS_PATH=$with_orbacus
- fi
- if test -d "$ORBACUS_PATH"; then
- NCBI_FIX_DIR(ORBACUS_PATH)
- fi
--if test "$with_orbacus" != no; then
- fullpath=${ORBACUS_PATH}/${DEBUG_SFX}${mt_sfx}${bit64_sfx}
- if test -f ${fullpath}/inc/OB/Config.h ; then
- : ${ORBACUS_INCLUDE="-I$ORBACUS_PATH/include -I$fullpath/inc"}
-@@ -5594,7 +5759,8 @@
- LIBIMR=
- ;;
- esac
-- AC_CACHE_CHECK([for ORBacus in $ORBACUS_PATH], ncbi_cv_lib_orbacus,
-+ AC_CACHE_CHECK([for ORBacus${ORBACUS_PATH:+ in $ORBACUS_PATH}],
-+ ncbi_cv_lib_orbacus,
- [CPPFLAGS="$ORBACUS_INCLUDE $orig_CPPFLAGS"
- LIBS="$ORBACUS_LIBPATH $LIBOB $NETWORK_LIBS $DL_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5633,7 +5799,7 @@
-
- if test "$with_icu" != "no" ; then
- case "$with_icu" in
-- yes | "" ) : ${ICU_PATH=$NCBI/icu} ;;
-+ yes | "" ) ;;
- * ) ICU_PATH=$with_icu ;;
- esac
- if test -d "$ICU_PATH/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}${mt_sfx}/lib" \
-@@ -5648,7 +5814,8 @@
- ICU_BINPATH=${ICU_BINPATH:="$ICU_ARCH_PATH/bin"}
- ICU_LIBPATH=${ICU_LIBPATH:="$ICU_ARCH_PATH/lib"}
- ICU_INCLUDE=
-- AC_CACHE_CHECK([for ICU in $ICU_ARCH_PATH], ncbi_cv_lib_icu,
-+ AC_CACHE_CHECK([for ICU${ICU_ARCH_PATH:+ in $ICU_ARCH_PATH}],
-+ ncbi_cv_lib_icu,
- [ICU_CONFIG=`$ICU_BINPATH/icu-config --bindir 2>/dev/null`/icu-config
- if test -x "$ICU_CONFIG" ; then
- ICU_INCLUDE=`$ICU_CONFIG --cppflags-searchpath`
-@@ -5690,9 +5857,6 @@
-
-
- ### XML/XSL libraries
--if test -d "$NCBI/expat/include"; then
-- : ${EXPAT_PATH=$NCBI/expat}
--fi
- NCBI_CHECK_THIRD_PARTY_LIB(expat,
- AC_LANG_PROGRAM([#include <expat.h>],
- [XML_Parser parser = XML_ParserCreate("utf-8");]))
-@@ -5701,7 +5865,6 @@
- else
- EXPAT_STATIC_LIBS=${EXPAT_LIBS}
- fi
--: ${SABLOT_PATH=$NCBI/Sablot}
- vpath="$SABLOT_PATH/${compiler_vpfx}build"
- test -d "$vpath" && SABLOT_PATH=$vpath
- if test -d "$SABLOT_PATH"; then
-@@ -5718,7 +5881,6 @@
- SABLOT_STATIC_LIBS=${SABLOT_LIBS}
- fi
-
--: ${LIBXML_PATH=$NCBI/libxml}
- # test -d "$LIBXML_PATH" || LIBXML_PATH=`xml2-config --prefix 2>/dev/null`
- if test "$with_libxml" != "no"; then
- case "$with_libxml" in
-@@ -5813,7 +5975,6 @@
- LIBEXSLT_STATIC_LIBS=${LIBEXSLT_LIBS}
- fi
-
--: ${XERCES_PATH=$NCBI/xerces}
- if test "$with_xerces" != no; then
- if test "${with_xerces-yes}" != yes; then
- XERCES_PATH=$with_xerces
-@@ -5838,7 +5999,7 @@
- NCBI_FIX_DIR(XERCES_LIBPATH)
- fi
- fi
-- if test -d $XERCES_PATH; then
-+ if test -d "$XERCES_PATH"; then
- in_path=" in $XERCES_PATH"
- : ${XERCES_INCLUDE=-I$XERCES_PATH/include}
- : ${XERCES_LIBPATH=$XERCES_PATH/lib}
-@@ -5875,7 +6036,6 @@
- XERCES_STATIC_LIBS=
- fi
-
--: ${XALAN_PATH=$NCBI/xalan}
- if test "$with_xalan" != no; then
- if test "${with_xalan-yes}" != yes; then
- XALAN_PATH=$with_xalan
-@@ -5900,7 +6060,7 @@
- NCBI_FIX_DIR(XALAN_LIBPATH)
- fi
- fi
-- if test -d $XALAN_PATH; then
-+ if test -d "$XALAN_PATH"; then
- in_path=" in $XALAN_PATH"
- : ${XALAN_INCLUDE=-I$XALAN_PATH/include}
- : ${XALAN_LIBPATH=$XALAN_PATH/lib}
-@@ -5937,7 +6097,6 @@
-
- test -d SunWS_cache && rm -r SunWS_cache
-
--: ${ZORBA_PATH=$NCBI/zorba}
- if test "$with_zorba" != no; then
- if test "${with_zorba-yes}" != yes; then
- ZORBA_PATH=$with_zorba
-@@ -5967,7 +6126,7 @@
- ZORBA_PATH=`$ZORBA_CONFIG --prefix`
- : ${ZORBA_INCLUDE=`$ZORBA_CONFIG --cppflags`}
- fi
-- if test -d $ZORBA_PATH; then
-+ if test -d "$ZORBA_PATH"; then
- in_path=" in $ZORBA_PATH"
- : ${ZORBA_INCLUDE=-I$ZORBA_PATH/include}
- : ${ZORBA_LIBPATH=$ZORBA_PATH/lib}
-@@ -6010,7 +6169,7 @@
-
- ### SQLite
- case "$with_sqlite3" in
-- yes | '' ) : ${SQLITE3_PATH=$NCBI/sqlite3} ;;
-+ yes | '' ) ;;
- * ) SQLITE3_PATH=$with_sqlite3 ;;
- esac
-
-@@ -6048,7 +6207,6 @@
- ### OEChem
- # somewhat kludgish, as we now wanto to add in oeiupac and oedepict,
- # which depend on oechem....
--: ${OECHEM_PATH=$NCBI/oechem}
- NCBI_CHECK_THIRD_PARTY_LIB(oechem,
- AC_LANG_PROGRAM([#include <oechem.h>],
- [OEChem::OEMol mol; OEChem::OEConfBase* c = mol.GetActive();]),
-@@ -6091,7 +6249,7 @@
-
- ### muParser
- case "$with_muparser" in
-- yes | '' ) : ${MUPARSER_PATH=$NCBI/muParser} ;;
-+ yes | '' ) ;;
- * ) MUPARSER_PATH=$with_muparser ;;
- esac
-
-@@ -6111,7 +6269,7 @@
-
- ### hdf5
- case "$with_hdf5" in
-- yes | '' ) : ${HDF5_PATH=$NCBI/hdf5} ;;
-+ yes | '' ) ;;
- * ) HDF5_PATH=$with_hdf5 ;;
- esac
-
-@@ -6176,7 +6334,7 @@
- GIF_LIBS=$UNGIF_LIBS
- fi
-
--test -n "$x_libraries" && : ${XPM_PATH=`dirname "$x_libraries"`}
-+case "$x_libraries" in */*) : ${XPM_PATH=`dirname "$x_libraries"`} ;; esac
- NCBI_CHECK_THIRD_PARTY_LIB(Xpm,
- AC_LANG_PROGRAM([#include <X11/xpm.h>],
- [XpmImage image; XpmInfo info;
-@@ -6241,7 +6399,7 @@
- fi
-
- case "$with_ftgl" in
-- yes | '' ) : ${FTGL_PATH=$NCBI/ftgl} ;;
-+ yes | '' ) ;;
- * ) FTGL_PATH=$with_ftgl ;;
- esac
-
-@@ -6268,7 +6426,7 @@
-
- # Mimetic
- case "$with_mimetic" in
-- yes | '' ) : ${MIMETIC_PATH=$NCBI/mimetic} ;;
-+ yes | '' ) ;;
- * ) MIMETIC_PATH=$with_mimetic ;;
- esac
- if test -d "$MIMETIC_PATH"; then
-@@ -6293,6 +6451,88 @@
- [mimetic::MimeEntity me;])])
-
-
-+# gSOAP++
-+case "$with_gsoap" in
-+ yes | '' ) ;;
-+ * ) GSOAP_PATH=$with_gsoap ;;
-+esac
-+if test -d "$GSOAP_PATH"; then
-+ NCBI_FIX_DIR(GSOAP_PATH)
-+fi
-+for d in "$GSOAP_LIBDIR" \
-+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+ "$GSOAP_PATH/lib${bit64_sfx}" \
-+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+ "$GSOAP_PATH/lib"; do
-+ if test -d "$d"; then
-+ GSOAP_LIBDIR=$d
-+ NCBI_FIX_DIR(GSOAP_LIBDIR)
-+ break
-+ fi
-+done
-+NCBI_RPATHIFY(GSOAP_LIBPATH, $GSOAP_LIBDIR)
-+
-+: ${GSOAP_BINDIR=`dirname "$GSOAP_LIBDIR"`/bin}
-+AC_PATH_PROG(GSOAP_SOAPCPP2, soapcpp2, [], $GSOAP_BINDIR:$PATH)
-+AC_PATH_PROG(GSOAP_WSDL2H, wsdl2h, [], $GSOAP_BINDIR:$PATH)
-+
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(gsoap, GSOAP, gsoapssl++,
-+ [AC_LANG_PROGRAM([#include <stdsoap2.h>
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultsubcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultstring(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultdetail(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultsubcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultdetail(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap*) { }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap*) { return 0; }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap*) { return 0; }
-+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap*) { }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap*) { return 0; }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap*) { return 0; }],
-+ [soap s;])],
-+ $OPENSSL_LIBS $Z_LIBS)
-+
-+case "$with_sqlite3" in
-+ yes | '' ) ;;
-+ * ) SQLITE3_PATH=$with_sqlite3 ;;
-+esac
-+
-+
-+# MongoDB
-+if test -d "$MONGODB_PATH"; then
-+ NCBI_FIX_DIR(MONGODB_PATH)
-+fi
-+if test -d $MONGODB_PATH/lib${bit64_sfx}; then
-+ MONGODB_LIBDIR=$MONGODB_PATH/lib${bit64_sfx}
-+else
-+ MONGODB_LIBDIR=$MONGODB_PATH/lib
-+fi
-+# need Boost rpath
-+NCBI_RPATHIFY(MONGODB_LIBPATH, $MONGODB_LIBDIR)
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient,
-+ [AC_LANG_PROGRAM([#include <mongo/client/dbclient.h>],
-+ [std::vector<mongo::HostAndPort> v;
-+ mongo::DBClientReplicaSet client("foo", v);
-+ client.connect();])],
-+ [$BOOST_LIBPATH $boost_fs_lib $BOOST_THREAD_LIBS], [],
-+ [$BOOST_INCLUDE])
-+# MongoDB's own library is normally static, but its supporting Boost
-+# libraries might not be by default.
-+if test -n "$MONGODB_LIBS"; then
-+ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_THREAD_STATIC_LIBS"
-+else
-+ MONGODB_STATIC_LIBS=
-+fi
-+
- ### Restore original compiler/linker flags
- LIBS="$orig_LIBS"
- CPPFLAGS="$orig_CPPFLAGS"
-@@ -6499,16 +6739,6 @@
- fi
-
-
--## Sequence Read Archive SDK, which may be attached on either the
--## public or the internal side
--
--if test -f "${real_srcdir}/src/sra/sdk/Makefile.sra_macros.mk"; then
-- sra=sra
--else
-- sra=
--fi
--
--
- ## `internal' project cluster
-
- if test "$with_internal" = "no" \
-@@ -6781,6 +7011,7 @@
- AC_SUBST(C_LINK)
- AC_SUBST(TAIL_N)
- AC_SUBST(EGREP_Q)
-+AC_SUBST(LDD_R)
-
- AC_SUBST(CFLAGS)
- AC_SUBST(FAST_CFLAGS)
-@@ -6829,7 +7060,6 @@
- AC_SUBST(algo)
- AC_SUBST(app)
- AC_SUBST(internal)
--AC_SUBST(sra)
-
- AC_SUBST(check)
- AC_SUBST(CHECK_ARG)
-@@ -6865,6 +7095,7 @@
-
- AC_SUBST(THREAD_LIBS)
- AC_SUBST(NCBIATOMIC_LIB)
-+AC_SUBST(OPENMP_FLAGS)
- AC_SUBST(NETWORK_LIBS)
- AC_SUBST(NETWORK_PURE_LIBS)
- AC_SUBST(RESOLVER_LIBS)
-@@ -6902,6 +7133,8 @@
- AC_SUBST(BOOST_INCLUDE)
- AC_SUBST(BOOST_LIBPATH)
- AC_SUBST(BOOST_TAG)
-+AC_SUBST(BOOST_FILESYSTEM_LIBS)
-+AC_SUBST(BOOST_FILESYSTEM_STATIC_LIBS)
- AC_SUBST(BOOST_REGEX_LIBS)
- AC_SUBST(BOOST_REGEX_STATIC_LIBS)
- AC_SUBST(BOOST_SYSTEM_LIBS)
-@@ -6968,6 +7201,8 @@
- AC_SUBST(SQLITE3_STATIC_LIBS)
- AC_SUBST(FREETYPE_INCLUDE)
- AC_SUBST(FREETYPE_LIBS)
-+AC_SUBST(GSOAP_PATH)
-+AC_SUBST(MONGODB_STATIC_LIBS)
- AC_SUBST(ncbi_xreader_pubseqos)
- AC_SUBST(ncbi_xreader_pubseqos2)
- AC_SUBST(UNLESS_PUBSEQOS)
-@@ -7194,7 +7429,9 @@
-
- cat << EOCONF
- ===============================================================================
--NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running
-+NCBI C++ Toolkit documentation:
-+ Online: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/
-+ Local: ./doc/public/index.html
- For the available configuration flags run: ./configure --help
-
- CFLAGS = $CFLAGS
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014-06-23 17:36:18.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014-06-23 17:36:59.000000000 +0200
-@@ -1,126 +1,45 @@
--# Hacked up in various ways, since Autoconf's version doesn't quite
--# suit our (unusual) conventions. (Originally from status.m4)
--m4_define([_AC_SRCPATHS],
--[#ac_builddir=. # Useless!
--ac_builddir=$builddir
--dnl Base source directories on path to *input* file.
--if test -n "$ac_file_in"; then
-- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])`
-+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS)
-+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly.
-+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS])
-+m4_define([_AC_SRCDIRS],
-+[# Base source directories on path to *input* file.
-+if test -n "$ac_f"; then
-+ ac_dir_in=`AS_DIRNAME(["$ac_f"])`
- else
- ac_dir_in=$1
- fi
-
--if test $ac_dir_in != .; then
-- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'`
-- # A "../" for each directory in $ac_dir_suffix.
-- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'`
--else
-- ac_dir_suffix= ac_top_builddir=
--fi
-+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
-
--case $srcdir in
-- .) # No --srcdir option. We are building in place.
-- ac_srcdir=.
-- if test -z "$ac_top_builddir"; then
-- ac_top_srcdir=.
-- else
-- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
-- fi ;;
-- [[\\/]]* | ?:[[\\/]]* ) # Absolute path.
-- ac_srcdir=$srcdir/$ac_dir_suffix;
-- ac_top_srcdir=$srcdir ;;
-- *) # Relative path.
-- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix
-- ac_top_srcdir=$ac_top_builddir$srcdir ;;
--esac
--# Do not use `cd foo && pwd` to compute absolute paths, because
--# the directories may not exist.
--AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1])
--AS_SET_CATFILE([ac_abs_top_builddir],
-- [$ac_abs_builddir], [${ac_top_builddir}.])
- AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
--AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix])
--])# _AC_SRCPATHS
--
-+ac_builddir=$builddir
-+])
-
--# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a
--# last resort due to issues with sourcing .bashrc.
--m4_define([_AS_LINENO_PREPARE],
--[_AS_LINENO_WORKS || {
-- # Find who we are. Look in the path if we contain no path at all
-- # relative or not.
-- case $[0] in
-- *[[\\/]]* ) as_myself=$[0] ;;
-- *) _AS_PATH_WALK([],
-- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break])
-- ;;
-- esac
-- # We did not find ourselves, most probably we were run as `sh COMMAND'
-- # in which case we are not to be found in the path.
-- if test "x$as_myself" = x; then
-- as_myself=$[0]
-- fi
-- if test ! -f "$as_myself"; then
-- AS_ERROR([cannot find myself; rerun with an absolute path])
-- fi
-- case $CONFIG_SHELL in
-- '')
-- AS_UNSET(ZSH_VERSION)
-- for as_base in sh ksh sh5 bash; do
-- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH],
-- [case $as_dir in
-- /*)
-- if ("$as_dir/$as_base" -c \
-- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null
-- then
-- AS_UNSET(BASH_ENV)
-- AS_UNSET(ENV)
-- CONFIG_SHELL=$as_dir/$as_base
-- export CONFIG_SHELL
-- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"}
-- fi;;
-- esac
-- done]);;
-- esac
-
-- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
-- # uniformly replaced by the line number. The first 'sed' inserts a
-- # line-number line before each line; the second 'sed' does the real
-- # work. The second script uses 'N' to pair each line-number line
-- # with the numbered line, and appends trailing '-' during
-- # substitution so that $LINENO is not a special case at line end.
-- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
-- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-)
-- sed '=' <$as_myself |
-- sed '
-- N
-- s,$,-,
-- : loop
-- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3,
-- t loop
-- s,-$,,
-- s,^[['$as_cr_digits']]*\n,,
-- ' >$as_me.lineno &&
-- chmod +x $as_me.lineno ||
-- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell])
--
-- # Don't try to exec as it changes $[0], causing all sort of problems
-- # (the dirname of $[0] is not the place where we might find the
-- # original and so on. Autoconf is especially sensible to this).
-- . ./$as_me.lineno
-- # Exit status is that of the last command.
-- exit
--}
--])# _AS_LINENO_PREPARE
-+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
-+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
-+# bash a last resort due to issues with sourcing .bashrc while entirely
-+# avoiding zsh, which passes itself off as ksh on some systems but runs
-+# parent shells' exit handlers from subshells, resulting in premature
-+# cleanup of temporary files (notably confdefs.h).
-+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL])
-+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN])
-+
-+m4_define([_AS_DETECT_BETTER_SHELL],
-+ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]),
-+ [sh bash ksh sh5], [sh ksh sh5 bash])])
-+m4_define([_AS_RUN],
-+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl
-+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])])
-
-
- # One more hack: suppress PACKAGE_*, as we don't use them and some
- # third-party libraries expose their corresponding settings, leading
- # to preprocessor warnings.
--m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED]))
-+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED])
- m4_define([AC_DEFINE_UNQUOTED],
- [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [],
-- [NCBI_ORIG_ACDU($@)])])
-+ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])])
-
-
- AC_DEFUN(NCBI_FIX_DIR,
-@@ -158,7 +77,7 @@
- AC_MSG_WARN([Proceeding without questions per --without-caution]) ;;
- * )
- echo "$1 [[y/N]]"
-- read answer
-+ read answer <& AS_ORIGINAL_STDIN_FD
- case "$answer" in
- [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;;
- * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;;
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014-06-23 17:38:56.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014-06-23 17:39:04.000000000 +0200
-@@ -98,6 +98,9 @@
- /* Define to 1 if you have the `getaddrinfo' function. */
- #undef HAVE_GETADDRINFO
-
-+/* Define to 1 if you have the `getgrouplist' function. */
-+#undef HAVE_GETGROUPLIST
-+
- /* If you have the `gethostbyaddr_r' function, define to the number of
- arguments it takes (normally 7 or 8). */
- #undef HAVE_GETHOSTBYADDR_R
-@@ -176,9 +179,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #undef HAVE_IOS_REGISTER_CALLBACK
-
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--#undef HAVE_IS_SORTED
--
- /* Define to 1 if you have the `lchown' function. */
- #undef HAVE_LCHOWN
-
-@@ -234,6 +234,9 @@
- /* Define to 1 if libgnutls is available. */
- #undef HAVE_LIBGNUTLS
-
-+/* Define to 1 if libgsoapssl++ is available. */
-+#undef HAVE_LIBGSOAP
-+
- /* Define to 1 if libhdf5_cpp is available. */
- #undef HAVE_LIBHDF5
-
-@@ -260,6 +263,9 @@
- /* Define to 1 if libmimetic is available. */
- #undef HAVE_LIBMIMETIC
-
-+/* Define to 1 if libmongoclient is available. */
-+#undef HAVE_LIBMONGODB
-+
- /* Define to 1 if libmuparser is available. */
- #undef HAVE_LIBMUPARSER
-
-@@ -382,9 +388,6 @@
- /* Define to 1 if `min'/`max' templates are not implemented. */
- #undef HAVE_NO_MINMAX_TEMPLATE
-
--/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
--#undef HAVE_NULLPTR
--
- /* Define to 1 if ODBC libraries are available. */
- #undef HAVE_ODBC
-
-@@ -799,37 +802,37 @@
- by a signal. */
- #undef SELECT_UPDATES_TIMEOUT
-
--/* The size of a `char', as computed by sizeof. */
-+/* The size of `char', as computed by sizeof. */
- #undef SIZEOF_CHAR
-
--/* The size of a `double', as computed by sizeof. */
-+/* The size of `double', as computed by sizeof. */
- #undef SIZEOF_DOUBLE
-
--/* The size of a `float', as computed by sizeof. */
-+/* The size of `float', as computed by sizeof. */
- #undef SIZEOF_FLOAT
-
--/* The size of a `int', as computed by sizeof. */
-+/* The size of `int', as computed by sizeof. */
- #undef SIZEOF_INT
-
--/* The size of a `long', as computed by sizeof. */
-+/* The size of `long', as computed by sizeof. */
- #undef SIZEOF_LONG
-
--/* The size of a `long double', as computed by sizeof. */
-+/* The size of `long double', as computed by sizeof. */
- #undef SIZEOF_LONG_DOUBLE
-
--/* The size of a `long long', as computed by sizeof. */
-+/* The size of `long long', as computed by sizeof. */
- #undef SIZEOF_LONG_LONG
-
--/* The size of a `short', as computed by sizeof. */
-+/* The size of `short', as computed by sizeof. */
- #undef SIZEOF_SHORT
-
--/* The size of a `size_t', as computed by sizeof. */
-+/* The size of `size_t', as computed by sizeof. */
- #undef SIZEOF_SIZE_T
-
--/* The size of a `void*', as computed by sizeof. */
-+/* The size of `void*', as computed by sizeof. */
- #undef SIZEOF_VOIDP
-
--/* The size of a `__int64', as computed by sizeof. */
-+/* The size of `__int64', as computed by sizeof. */
- #undef SIZEOF___INT64
-
- /* Define to 1 if the stack grows down. */
-@@ -870,5 +873,5 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- #undef const
-
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- #undef size_t
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014-06-23 17:40:40.000000000 +0200
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014-06-23 17:40:57.000000000 +0200
-@@ -1,4 +1,4 @@
--/* $Id: ncbiconf_xcode.h 361821 2012-05-04 14:28:13Z ucko $
-+/* $Id$
- * By Vlad Lebedev, NCBI (lebedev@ncbi.nlm.nih.gov)
- *
- * Mac OS X - xCode Build
-@@ -258,9 +258,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #define HAVE_IOS_REGISTER_CALLBACK 1
-
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--/* #undef HAVE_IS_SORTED */
--
- /* Define to 1 if you have the `lchown' function. */
- /* #undef HAVE_LCHOWN */
-
-@@ -358,6 +355,9 @@
- /* Define to 1 if you have the `lutimes' function. */
- /* #undef HAVE_LUTIMES */
-
-+/* Define to 1 if you have the `madvise' function. */
-+#define HAVE_MADVISE 1
-+
- /* Define to 1 if you have the <malloc.h> header file. */
- /* #undef HAVE_MALLOC_H */
-
-@@ -589,15 +589,15 @@
- /* Define to 1 if you have the <windows.h> header file. */
- /* #undef HAVE_WINDOWS_H */
-
-+/* Define to 1 if you have the `writev' function. */
-+#define HAVE_WRITEV 1
-+
- /* Define to 1 if the system has the type `wstring'. */
- #define HAVE_WSTRING 1
-
- /* Define to 1 if wxWidgets is available. */
- /* #undef HAVE_WXWIDGETS */
-
--/* Define to 1 if nullptr keyword is available. */
--/* #undef HAVE_NULLPTR */
--
- /* Define as const if the declaration of iconv() needs const. */
- #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
- # define ICONV_CONST
-@@ -694,7 +694,7 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- /* #undef const */
-
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- /* #undef size_t */
-
- /*
--- ncbi_cxx--12_0_0/src/build-system/configure.ori 2013-05-20 23:03:20.000000000 +0200
+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-23 22:22:50.000000000 +0200
@@ -1,19 +1,13 @@
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2014-06-25 23:25 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-06-25 23:25 UTC (permalink / raw
To: gentoo-commits
commit: 88e4dd4274fab0bd7e7a26ad618d34de95489656
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 25 23:24:59 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 25 23:24:59 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=88e4dd42
sci-biology/ncbi-tools++-12.0.0: dropped unneeded patch
---
...-tools++-12.0.0-support-autoconf-2.60.patch.bad | 1660 --------------------
1 file changed, 1660 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad
deleted file mode 100644
index 80b23e9..0000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad
+++ /dev/null
@@ -1,1660 +0,0 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014-06-23 17:35:47.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014-06-23 17:36:41.000000000 +0200
-@@ -1,5 +1,5 @@
- #############################################################################
--# $Id: configure.ac 398256 2013-05-03 19:14:07Z rafanovi $
-+# $Id$
- # Derived from configure.in version 1.173.
- # ==========================================================================
- #
-@@ -38,7 +38,7 @@
- #
- #############################################################################
-
--AC_PREREQ(2.59)
-+AC_PREREQ(2.60)
-
- dnl Early setup, most crucially for locking. The diversion magic lets
- dnl this occur before AC_INIT, which already interferes with other
-@@ -71,7 +71,7 @@
- python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat,
- sablot, libxml, libxslt, libexslt, xerces, xalan, zorba,
- oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm,
-- magic, curl],
-+ magic, curl, gsoap, mongodb],
- [if test "${[with_]X-no}" != "no"; then
- AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw])
- else
-@@ -143,6 +143,8 @@
- [ --with-bin-release build executables suitable for public release])
- AC_ARG_WITH(mt,
- [ --with-mt compile in a MultiThread-safe manner])
-+AC_ARG_WITH(openmp,
-+ [ --with-openmp enable OpenMP extensions for all projects])
- AC_ARG_WITH(64,
- [ --with-64 compile to 64-bit code])
- AC_ARG_WITH(universal,
-@@ -220,11 +222,15 @@
-
- ## NCBI packages
- AC_ARG_WITH(ncbi-c,
-+ [ --with-ncbi-c=DIR use NCBI C Toolkit installation in DIR])
-+AC_ARG_WITH(ncbi-c2,
- [ --without-ncbi-c do not use NCBI C Toolkit])
- AC_ARG_WITH(sss,
-+ [ --with-sss=DIR use NCBI SSS installation in DIR])
-+AC_ARG_WITH(sss2,
- [ --without-sss do not use NCBI SSS libraries])
- AC_ARG_WITH(sssutils,
-- [ --without-sssutils do not use NCBI SSS UTIL library])
-+ [ --without-utils 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,
-@@ -439,6 +445,14 @@
- [ --with-mimetic=DIR use libmimetic installation in DIR])
- AC_ARG_WITH(mimetic2,
- [ --without-mimetic do not use libmimetic])
-+AC_ARG_WITH(gsoap,
-+ [ --with-gsoap=DIR use gSOAP++ installation in DIR])
-+AC_ARG_WITH(gsoap2,
-+ [ --without-gsoap do not use gSOAP++])
-+AC_ARG_WITH(mongodb,
-+ [ --with-mongodb=DIR use MongoDB installation in DIR])
-+AC_ARG_WITH(mongodb2,
-+ [ --without-mongodb do not use MongoDB])
- AC_ARG_WITH(3psw,
- [ --with-3psw=std:netopt favor standard (system) builds of the above pkgs.])
- AC_ARG_WITH(3psw2,
-@@ -479,24 +493,28 @@
- [***** See also HTML documentation in ./doc/index.html *****])
-
-
-+AC_DIVERT_PUSH(PARSE_ARGS)
-+dnl As of Autoconf 2.60, this needs to run too early for config.log,
-+dnl to which AC_MSG_ERROR normally copies its output, to be available.
-+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
- #### Check the passed arguments against the list of available ones
- x_with_list="\
- debug max-debug symbols optimization profiling tcheck dll static static-exe \
- plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \
--lfs limited-linker \
-+lfs limited-linker openmp \
- autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
- deactivation makefile-auto-update projects flat-makefile configure-dialog \
- 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 gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
- bdb python perl jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt libexslt xerces xalan zorba \
- oechem sge muparser hdf5 \
--gif jpeg tiff png xpm magic curl mimetic 3psw \
-+gif jpeg tiff png xpm magic curl mimetic gsoap mongodb 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench x"
-+serial objects dbapi app ctools gui algo internal gbench"
-
- changequote(, )dnl
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-@@ -522,7 +540,6 @@
- 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])
- ;;
-@@ -533,12 +550,11 @@
- | --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=* \
-+ | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
- | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* \
-- | --with-krb5=* | --with-curl=* \
-+ | --with-krb5=* | --with-curl=* | --with-gsoap=* | --with-mongodb=* \
- | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \
- | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \
- | --with-sqlite3=* | --with-expat=* | --with-sablot=* \
-@@ -552,7 +568,7 @@
- | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
- | --x-includes=* | --x-libraries=* | --with-3psw=* \
- | --target=* | --with-runpath=* | --with-relative-runpath=* \
-- | --no-create | --no-recursion)
-+ | --help | --no-create | --no-recursion)
- ;;
-
- * )
-@@ -560,6 +576,8 @@
- ;;
- esac
- done
-+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
-+AC_DIVERT_POP
-
-
- if test "$with_gbench" = "yes" ; then
-@@ -604,6 +622,13 @@
- : ${with_optimization=no}
- fi
-
-+if test "$with_openmp" = yes; then
-+ if test "$with_mt" = no; then
-+ AC_MSG_ERROR([incompatible options: --without-mt but --with-openmp])
-+ fi
-+ : ${with_mt=yes}
-+fi
-+
- #### Check for special options
- if test "$with_extra_action" = "yes" ; then
- AC_MSG_ERROR([--with-extra-action must have a value after =])
-@@ -649,15 +674,10 @@
- *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
- esac
- fi
--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
-+# Generally save any originally specified flags.
-+USER_CFLAGS=$CFLAGS
-+USER_CXXFLAGS=$CXXFLAGS
-+USER_LDFLAGS=$LDFLAGS
-
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
-@@ -675,6 +695,23 @@
- #### Make some provisions for traditional operation
- AC_PROG_INSTALL
-
-+#### Point ICC at a suitable GCC version ASAP.
-+case "/$CXX" in
-+ */icpc )
-+ if test -d /usr/local/gcc; then
-+ case "`$CXX -dumpversion`:$host_cpu" in
-+ *:i?86) v=4.4.5 ;;
-+ ?.* | 1[[01]].* ) v=4.0.1 ;;
-+ *) v=4.4.2 ;;
-+ esac
-+ gcc=/usr/local/gcc/$v/bin/gcc
-+ if test -x $gcc; then
-+ CC="$CC -gcc-name=$gcc"
-+ CXX="$CXX -gcc-name=$gcc"
-+ fi
-+ fi
-+ ;;
-+esac
-
- #### C and C++ compilers
- AC_LANG(C++)
-@@ -987,6 +1024,30 @@
- ;;
- * ) NCBIATOMIC_LIB=xncbi ;;
- esac
-+ case "$compiler" in
-+ GCC )
-+ if $CC -v | grep clang >/dev/null; then
-+ :
-+ # Will allegedly support -openmp at some point, but as of 3.4,
-+ # just parses it as specifying an output filename: -o penmp.
-+ else
-+ case "$compiler_version" in
-+ [[123]]?? | 4[[01]]? ) ;;
-+ * ) : ${OPENMP_FLAGS=-fopenmp} ;;
-+ esac
-+ fi
-+ ;;
-+ ICC )
-+ : ${OPENMP_FLAGS=-openmp}
-+ ;;
-+ WorkShop* )
-+ : ${OPENMP_FLAGS=-xopenmp=parallel}
-+ ;;
-+ esac
-+ if test "$with_openmp" = yes; then
-+ MT_FLAG="$MT_FLAG $OPENMP_FLAGS"
-+ OPENMP_FLAGS=
-+ fi
- mt_sfx="MT"
- NCBI_FEATURE(MT)
- else
-@@ -994,6 +1055,7 @@
- MT_FLAG=
- THREAD_LIBS=
- NCBIATOMIC_LIB=
-+ OPENMP_FLAGS=
- mt_sfx=""
- fi
- MT_SFX="${mt_sfx}"
-@@ -1006,6 +1068,9 @@
- APP_LDFLAGS=
- DLL_LDFLAGS=
-
-+### Should go before any test compiler runs
-+AC_GNU_SOURCE
-+
- case "$host_os:$compiler" in
- darwin*:GCC )
- AC_CACHE_CHECK([whether $CC supports -Wl,-rpath],
-@@ -1047,6 +1112,47 @@
- ;;
- esac
-
-+case "$compiler:$compiler_version" in
-+ GCC:4[[0-6]]? | ICC:1[[01]]?? )
-+ ncbi_cv_prog_cxx_11=no
-+ ncbi_cv_prog_c_99=no
-+ ;;
-+ ICC:* )
-+ ncbi_cv_prog_c_99='-std=gnu99 -fgnu89-inline'
-+ ;;
-+esac
-+
-+AC_CACHE_CHECK([how to enable C++ '11 features in $CXX],
-+ ncbi_cv_prog_cxx_11,
-+ [orig_CXX=$CXX
-+ ncbi_cv_prog_cxx_11=no
-+ for x in -std=gnu++11 -std=gnu++0x; do
-+ CXX="$orig_CXX $x"
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+ [ncbi_cv_prog_cxx_11=$x])
-+ test "x$ncbi_cv_prog_cxx_11" = "xno" || break
-+ done
-+ CXX=$orig_CXX])
-+test "$ncbi_cv_prog_cxx_11" = no || CXX="$CXX $ncbi_cv_prog_cxx_11"
-+
-+AC_LANG_PUSH(C)
-+AC_CACHE_CHECK([how to enable C '11 or at least '99 features in $CC],
-+ ncbi_cv_prog_c_99,
-+ [orig_CC=$CC
-+ ncbi_cv_prog_c_99=no
-+ for x in -xc99=all "-std=gnu11 -fgnu89-inline" \
-+ "-std=gnu1x -fgnu89-inline" \
-+ "-std=gnu99 -fgnu89-inline" \
-+ "-std=gnu9x -fgnu89-inline"; do
-+ CC="$orig_CC $x"
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+ [ncbi_cv_prog_c_99=$x])
-+ test "x$ncbi_cv_prog_c_99" = "xno" || break
-+ done
-+ CC=$orig_CC])
-+AC_LANG_POP(C)
-+test "$ncbi_cv_prog_c_99" = no || CC="$CC $ncbi_cv_prog_c_99"
-+
- #### Provide default environment setup for known platforms/compilers
- DEPFLAGS="-M"
- DEPFLAGS_POST="" # Needed for VisualAge
-@@ -1059,7 +1165,15 @@
- ;;
-
- solaris*:GCC )
-- CPPFLAGS="-D_XOPEN_SOURCE=500 $CPPFLAGS"
-+ # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only
-+ # in C++ mode. Set it for C code as well to ensure consistent
-+ # header behavior, taking care to match the C standard version
-+ # (as enforced by <sys/feature_tests.h>).
-+ case "$ncbi_cv_prog_c_99" in
-+ no) CC="$CC -D_XOPEN_SOURCE=500" ;;
-+ *) CC="$CC -D_XOPEN_SOURCE=600" ;;
-+ esac
-+
- STRIP="@:"
- ;;
-
-@@ -1202,11 +1316,19 @@
- LDFLAGS="-flat_namespace $LDFLAGS"
-
- if test "$with_ncbi_public" = yes; then
-+ sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk'
-+ case "$host_os" in
-+ darwin?.* | darwin10.* ) # Mac OS X 10.6.x or older
- TARGET='-mmacosx-version-min=10.5'
-- sdks='/Developer/SDKs/MacOSX10.6.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk'
-+ sdks="/Developer/SDKs/MacOSX10.6.sdk"
- if test "$with_64:${with_universal-no}" != "yes:no"; then
- sdks="/Developer/SDKs/MacOSX10.5.sdk $sdks"
- fi
-+ ;;
-+ * )
-+ TARGET='-mmacosx-version-min=10.7'
-+ ;;
-+ esac
- for sdk in $sdks; do
- if test -d "$sdk"; then
- TARGET="-isysroot $sdk $TARGET"
-@@ -1487,8 +1609,8 @@
- ;;
- GCC:* )
- DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"
-- case "$host_os" in
-- freebsd* ) ;;
-+ case "$host_os:$host_cpu:$compiler_version" in
-+ freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;;
- * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
- esac
- if test "$with_profiling" != "yes"; then
-@@ -1587,13 +1709,9 @@
- solaris* )
- CONF_f_runpath="-R"
- ;;
-- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
-+ linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
- CONF_f_runpath="-Wl,-rpath,"
- ;;
-- linux*:ICC )
-- # trying to use "-Wl,-rpath," here sends "ld" to endless 100% CPU loop
-- CONF_f_runpath="-Xlinker -rpath -Xlinker "
-- ;;
- irix*:* | linux*:KCC | *:Compaq )
- CONF_f_runpath="-rpath "
- ;;
-@@ -1697,8 +1815,11 @@
- LINK="$LINK -Kc++"
- ;;
- ICC:1???:* )
-- APP_LDFLAGS="-static-intel $APP_LDFLAGS"
-- DLL_LDFLAGS="-static-intel -nodefaultlibs $DLL_LDFLAGS"
-+ # Suppress "warning #10237: -lcilkrts linked in dynamically, static
-+ # library not available" which is not a problem in practice due to
-+ # as-needed linkage.
-+ APP_LDFLAGS="-static-intel -diag-disable 10237 $APP_LDFLAGS"
-+ DLL_LDFLAGS="-static-intel -diag-disable 10237 -nodefaultlibs $DLL_LDFLAGS"
- # Redundant for apps, but necessary for plugins to be adequately
- # self-contained, at least on 32-bit Linux.
- LIBS="$LIBS -lstdc++"
-@@ -1817,18 +1938,6 @@
-
- #### Intel compiler:: common flags and definitions
- if test "$compiler" = "ICC" ; then
-- if test -d /usr/local/gcc; then
-- case "$compiler_version:$HOST_CPU" in
-- *:i?86) v=4.4.5 ;;
-- ???:* | 1[[01]]??:* ) v=4.0.1 ;;
-- *) v=4.4.2 ;;
-- esac
-- gcc=/usr/local/gcc/$v/bin/gcc
-- if test -x $gcc; then
-- CC="$CC -gcc-name=$gcc"
-- CXX="$CXX -gcc-name=$gcc"
-- fi
-- fi
- if test -n "$icc_license" ; then
- icc_CC="$CC"
- icc_CXX="$CXX"
-@@ -2073,6 +2182,7 @@
- fi
-
- AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
-+dnl AC_PATH_PROG(GREP, grep)
- AC_PROG_EGREP
- AC_MSG_CHECKING([how to run $EGREP quietly])
- if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
-@@ -2086,6 +2196,16 @@
-
- AC_CHECK_PROG(VALGRIND_PATH, valgrind, valgrind)
-
-+AC_PATH_PROG(LDD, ldd)
-+if test -n "$LDD"; then
-+ AC_MSG_CHECKING([whether $LDD accepts -r])
-+ if $LDD -r /bin/ls >/dev/null 2>&1; then
-+ AC_MSG_RESULT(yes)
-+ LDD_R="$LDD -r"
-+ else
-+ AC_MSG_RESULT(no)
-+ fi
-+fi
-
- #### Check if "${build_root}" is defined; provide a default one
- if test -n "${with_build_root}" ; then
-@@ -2170,9 +2290,6 @@
- fi
-
-
--### Should go before any test compiler runs
--AC_GNU_SOURCE
--
- #### Determine whether this is implicitly a 64-bit platform
- AC_TYPE_SIZE_T
- if test "${with_universal-no}" = "no"; then
-@@ -2342,7 +2459,7 @@
- fi
- ;;
- *:ICC )
-- runpath="$runpath -Xlinker -rpath-link -Xlinker \$(libdir)"
-+ runpath="$runpath -Wl,-rpath-link,\$(libdir)"
- ;;
- esac
- elif test "$with_runpath" = "yes" -o "$with_dll" != "no" ; then
-@@ -2658,15 +2775,30 @@
- dbgrx1="$wsrx-g[^cx$wschars]*$wsrx"
- dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx"
- optrx="$wsrx-x*O[0-9s]*$wsrx"
-+ NDEB_CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ NDEB_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ NDEB_LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
- if test "$with_symbols" = "no" ; then
-- CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-- CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-- LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ CFLAGS=$NDEB_CFLAGS
-+ CXXFLAGS=$NDEB_CXXFLAGS
-+ LDFLAGS=$NDEB_LDFLAGS
- else
- echo " $CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || CFLAGS="$CFLAGS -g"
- echo " $CXXFLAGS "| $EGREP_Q "$dbgrx1|$dbgrx2" || CXXFLAGS="$CXXFLAGS -g"
- echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"
- STRIP="@:"
-+ case "$compiler:$compiler_version" in
-+ GCC:4[89]? | GCC:[5-9]? | GCC:???? )
-+ # GCC 4.8 defaults to DWARF 4, which Totalview for one
-+ # can't handle; roll back to version 3 by default.
-+ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ CFLAGS="$NDEB_CFLAGS -gdwarf-3"
-+ echo " $USER_CXXFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ CXXFLAGS="$NDEB_CXXFLAGS -gdwarf-3"
-+ echo " $USER_LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ LDFLAGS="$NDEB_LDFLAGS -gdwarf-3"
-+ ;;
-+ esac
- fi
-
- NOPT_CFLAGS=` echo " $CFLAGS " | sed "s/$optrx/ /g"`
-@@ -3024,9 +3156,9 @@
- ### Check for other standard library functions
-
- AC_FUNC_VPRINTF
--AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getpagesize \
-- getpass getpassphrase getpwuid getrusage gettimeofday \
-- getuid memrchr readpassphrase readv usleep \
-+AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getgrouplist \
-+ getpagesize getpass getpassphrase getpwuid getrusage \
-+ gettimeofday getuid memrchr readpassphrase readv usleep \
- asprintf vasprintf vsnprintf select statfs statvfs \
- strcasecmp strlcat strlcpy strdup strndup strtok_r \
- sysmp timegm utimes lutimes writev)
-@@ -3253,17 +3385,6 @@
- fi
-
-
--AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
-- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
-- [[#include <algorithm>]],
-- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
-- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
--if test "$ncbi_cv_func_is_sorted" = yes; then
-- AC_DEFINE(HAVE_IS_SORTED, 1,
-- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
--fi
--
--
-
- AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
- AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
-@@ -3400,7 +3521,7 @@
- AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
- ncbi_cv_c_restrict,
- [ncbi_cv_c_restrict=no
-- for restrict in restrict __restrict__ __restrict; do
-+ for restrict in __restrict__ __restrict restrict; do
- test "$ncbi_cv_c_restrict" = "no" || break
- AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
- [ncbi_cv_c_restrict=$restrict], [])
-@@ -3420,7 +3541,7 @@
- AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
- ncbi_cv_cxx_restrict,
- [ncbi_cv_cxx_restrict=no
-- for restrict in restrict __restrict__ __restrict; do
-+ for restrict in __restrict__ __restrict restrict; do
- test "$ncbi_cv_cxx_restrict" = "no" || break
- AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
- [ncbi_cv_cxx_restrict=$restrict], [])
-@@ -3525,14 +3646,6 @@
- unaligned addresses.])
- fi
-
--AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
-- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
-- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
--if test "$ncbi_cv_cxx_nullptr" = yes; then
-- AC_DEFINE(HAVE_NULLPTR, 1,
-- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
--fi
--
- ### Check for the availability of other packages
- ### --------------------------------------------
-
-@@ -3630,7 +3743,16 @@
- dnl NCBI_CHECK_LIBS(FUSE, fuse, fuse_loop)
- AC_SEARCH_LIBS(fuse_loop, fuse, [NCBI_PACKAGE(FUSE)])
- LIBS=$orig_LIBS
-+# Temporarily drop OpenMP flags for this test, as some toolchains count
-+# its support library's indirect use of librt when building applications
-+# but not when building shared libraries with --no-undefined.
-+orig_CXXFLAGS=$CXXFLAGS
-+orig_LDFLAGS=$LDFLAGS
-+CXXFLAGS=`echo $CXXFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
-+LDFLAGS=`echo $LDFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
- NCBI_CHECK_LIBS(RT, rt posix4, clock_gettime)
-+CXXFLAGS=$orig_CXXFLAGS
-+LDFLAGS=$orig_LDFLAGS
- NCBI_CHECK_LIBS(DEMANGLE, demangle, cplus_demangle)
- # Add to (orig_)LIBS if present for the sake of corelib and the
- # following call to AC_CHECK_FUNCS.
-@@ -3734,7 +3856,6 @@
- NCBI_PACKAGE(LocalBZ2)
- fi
-
--: ${LZO_PATH=$NCBI/lzo2}
- if test -d "$LZO_PATH"; then
- NCBI_FIX_DIR(LZO_PATH)
- fi
-@@ -3767,7 +3888,7 @@
- ## SSL/TLS libraries
- case "$with_gcrypt" in
- no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;;
-- yes | '' ) : ${GCRYPT_PATH=$NCBI/gcrypt} ;;
-+ yes | '' ) ;;
- * ) GCRYPT_PATH=$with_gcrypt ;;
- esac
- if test -d "$GCRYPT_PATH"; then
-@@ -3802,13 +3923,16 @@
-
- case "$with_gnutls" in
- no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;;
-- yes | '' ) : ${GNUTLS_PATH=$NCBI/gnutls} ;;
-+ yes | '' ) ;;
- * ) GNUTLS_PATH=$with_gnutls ;;
- esac
- if test -d "$GNUTLS_PATH"; then
- NCBI_FIX_DIR(GNUTLS_PATH)
-+ gnutls_config_path=${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin
-+else
-+ gnutls_config_path=$PATH
- fi
--AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin:$PATH])
-+AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path])
-
- if test "x$with_gnutls" != xno; then
- if test -x "$LIBGNUTLS_CONFIG"; then
-@@ -3817,7 +3941,7 @@
- test "x$p" = "x/usr" || GNUTLS_PATH=$p
- fi
- else
-- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls"
-+ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
- $LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no
- fi
- case "$LIBGNUTLS_CONFIG" in
-@@ -3846,6 +3970,10 @@
- $GNUTLS_CONFIG_LIBS $GCRYPT_LIBS)
- if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then
- NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBS, [echo $GNUTLS_CONFIG_LIBS], [$no_usr_lib])
-+ # Conservatively build against gcrypt if available even when gnutls
-+ # uses nettle instead, because gcrypt needs explicit initialization
-+ # to be thread-safe, but gnutls's headers don't indicate which
-+ # underlying crypto library it's actually using.
- case "$GNUTLS_INCLUDE" in
- *$GCRYPT_INCLUDE* ) ;;
- * ) GNUTLS_INCLUDE="$GNUTLS_INCLUDE $GCRYPT_INCLUDE" ;;
-@@ -4108,7 +4236,8 @@
- SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS"
- SYBASE_DLLS="$SYBASE_DLLLIST"
-
-- AC_CACHE_CHECK([for Sybase in $SYBASE_PATH], ncbi_cv_lib_sybase,
-+ AC_CACHE_CHECK([for Sybase${SYBASE_PATH:+ in $SYBASE_PATH}],
-+ ncbi_cv_lib_sybase,
- [CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS"
- LIBS="$SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $DL_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4216,7 +4345,8 @@
- AC_MSG_NOTICE([Using bundled FreeTDS (version $ftds_ver) from $FTDS_PATH])
- else
- FTDS_LIBS="$FTDS_CTLIBS"
-- AC_CACHE_CHECK([for FreeTDS in $FTDS_PATH], ncbi_cv_lib_freetds,
-+ AC_CACHE_CHECK([for FreeTDS${FTDS_PATH:+ in $FTDS_PATH}],
-+ ncbi_cv_lib_freetds,
- [CPPFLAGS="$FTDS_INCLUDE $orig_CPPFLAGS"
- LIBS="$FTDS_LIBS $NETWORK_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4281,7 +4411,7 @@
- # Kill off single quotes, due to later requoting
- : ${MYSQL_INCLUDE=`$mysql_config --include | tr -d \'`}
- NCBI_RPATHIFY_OUTPUT_COND(MYSQL_LIBS, $mysql_config --libs${mt_sfx:+_r},
-- [s/'//g; ])
-+ [s/'//g; $no_usr_lib])
- AC_CACHE_CHECK([whether MySQL works], ncbi_cv_lib_mysql,
- [CPPFLAGS="$MYSQL_INCLUDE $orig_CPPFLAGS"
- LIBS="$MYSQL_LIBS $orig_LIBS"
-@@ -4310,7 +4440,6 @@
- if test "$with_bdb" != "no" ; then
- case "$with_bdb" in
- yes | "" )
-- : ${BERKELEYDB_PATH:="$NCBI/BerkeleyDB"}
- ;;
- */*)
- BERKELEYDB_PATH=$with_bdb
-@@ -4351,7 +4480,8 @@
- else
- BERKELEYDB_STATIC_LIBS=${BERKELEYDB_LIBS}
- fi
-- AC_CACHE_CHECK([for Berkeley DB libraries in $BERKELEYDB_PATH],
-+ AC_CACHE_CHECK(
-+ [for Berkeley DB libraries${BERKELEYDB_PATH:+ in $BERKELEYDB_PATH}],
- ncbi_cv_lib_berkeley_db,
- [CPPFLAGS="$BERKELEYDB_INCLUDE $orig_CPPFLAGS"
- LIBS="$BERKELEYDB_LIBS $orig_LIBS"
-@@ -4450,7 +4580,8 @@
- NCBI_RPATHIFY(ODBC_LIBS, ${ODBC_LIBPATH}, [ -lodbc -lodbcinst])
- CPPFLAGS="$ODBC_INCLUDE $orig_CPPFLAGS"
- LIBS="$ODBC_LIBS $orig_LIBS"
-- AC_CACHE_CHECK([for ODBC libraries in $ODBC_PATH], ncbi_cv_lib_odbc,
-+ AC_CACHE_CHECK([for ODBC libraries${ODBC_PATH:+ in $ODBC_PATH}],
-+ ncbi_cv_lib_odbc,
- [AC_LINK_IFELSE([AC_LANG_PROGRAM(
- [[#include <sql.h>]],
- [[SQLHDBC hdbc; SQLCHAR* cp = (SQLCHAR*) "x";
-@@ -4542,7 +4673,7 @@
- AC_PATH_PROG(PERL, perl, [], [$PERL_PATH/bin:$PATH])
- if test -x "$PERL"; then
- PERL_ARCHLIB=`$PERL -MConfig -e 'print \$Config{archlibexp};'`
-- PERL_FLAGS=`$PERL -MConfig -e 'print \$Config{cppflags};'`
-+ PERL_FLAGS=`$PERL -MConfig -e 'print join " ", grep /^-[[DI]]/, split /\\s+/, \$Config{cppflags};'`
- PERL_INCLUDE="-I$PERL_ARCHLIB/CORE $PERL_FLAGS"
- PERL_DEPS=`$PERL -MConfig -e 'print \$Config{libs};'`
- NCBI_RPATHIFY(PERL_LIBS, $PERL_ARCHLIB/CORE, [ -lperl $PERL_DEPS])
-@@ -4603,9 +4734,7 @@
-
- ## Boost
- if test "$with_boost" != "no"; then
-- if test "${with_boost-yes}" = yes; then
-- : ${BOOST_PATH=$NCBI/boost}
-- else
-+ if test "${with_boost-yes}" != yes; then
- BOOST_PATH=$with_boost
- fi
- if test -d "$BOOST_PATH"; then
-@@ -4644,17 +4773,22 @@
- if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then
- BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version}
- fi
-- case "$ncbi_compiler" in
-- MIPSPRO)
-+ case "$compiler:$ncbi_compiler_ver" in
-+ MIPSpro*)
- BOOST_INCLUDE="$BOOST_INCLUDE $BOOST_INCLUDE/boost/compatibility/cpp_c_headers"
- ;;
-- WORKSHOP)
-+ WorkShop*)
- # Boost.Test's macros yield a *lot* of spurious "should not initialize
- # a non-const reference with a temporary" warnings, to the point of
- # overwhelming the compiler in some cases; turn them off altogether
- # when using Boost at all.
- BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"
- ;;
-+ GCC*:4[[7-9]]* | GCC*:5*)
-+ # Some portions of Boost also have a lot of "unused" typedefs
-+ # from concept checking.
-+ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"
-+ ;;
- esac
- case "$ncbi_cv_lib_boost_version" in
- 0_* | 1_[[0-9]] | 1_[[0-9]]_* | 1_[[0-2]][[0-9]] | 1_[[0-2]][[0-9]]_* ) ;;
-@@ -4666,7 +4800,7 @@
- fi
- with_boost=no
- ;;
-- 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-2]] | 1_5[[0-2]]_* ) ;;
-+ 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;;
- '' ) with_boost=no ;;
- * )
- AC_MSG_WARN(
-@@ -4751,7 +4885,9 @@
- BOOST_REGEX_STATIC_LIBS=$BOOST_REGEX_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.Regex in $BOOST_PATH], ncbi_cv_lib_boost_regex,
-+ in_path=${BOOST_PATH:+ in $BOOST_PATH}
-+
-+ AC_CACHE_CHECK([for Boost.Regex$in_path], ncbi_cv_lib_boost_regex,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_REGEX_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4759,7 +4895,7 @@
- [[throw boost::regex_error(boost::regex_constants::error_stack);]])],
- [ncbi_cv_lib_boost_regex=yes], [ncbi_cv_lib_boost_regex=no])])
-
-- AC_CACHE_CHECK([for Boost.Spirit in $BOOST_PATH], ncbi_cv_lib_boost_spirit,
-+ AC_CACHE_CHECK([for Boost.Spirit$in_path], ncbi_cv_lib_boost_spirit,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4774,7 +4910,7 @@
- BOOST_SYSTEM_STATIC_LIBS=$BOOST_SYSTEM_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.System in $BOOST_PATH], ncbi_cv_lib_boost_system,
-+ AC_CACHE_CHECK([for Boost.System$in_path], ncbi_cv_lib_boost_system,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_SYSTEM_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4785,6 +4921,24 @@
- BOOST_SYSTEM_LIBS=
- BOOST_SYSTEM_STATIC_LIBS=])])
-
-+ boost_fs_lib=-lboost_filesystem${BOOST_TAG}
-+ if test -f "$BOOST_LIBPATH_/libboost_filesystem${BOOST_TAG}-static.a"; then
-+ boost_fs_static_lib=-lboost_filesystem${BOOST_TAG}-static
-+ else
-+ boost_fs_static_lib=$boost_fs_lib
-+ fi
-+ BOOST_FILESYSTEM_LIBS="$boost_fs_lib $BOOST_SYSTEM_LIBS"
-+ BOOST_FILESYSTEM_STATIC_LIBS="$boost_fs_static_lib $BOOST_SYSTEM_STATIC_LIBS"
-+
-+ AC_CACHE_CHECK([for Boost.Filesystem$in_path], ncbi_cv_lib_boost_filesystem,
-+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-+ LIBS="$BOOST_LIBPATH $BOOST_FILESYSTEM_LIBS $RT_LIBS $orig_LIBS"
-+ [AC_LINK_IFELSE(
-+ [AC_LANG_PROGRAM([[#include <boost/filesystem.hpp>]],
-+ [[return boost::filesystem::portable_name("foo");]])],
-+ [ncbi_cv_lib_boost_filesystem=yes],
-+ [ncbi_cv_lib_boost_filesystem=no])])
-+
- BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}
- if test -f "$BOOST_LIBPATH_/libboost_prg_exec_monitor${BOOST_TAG}-static.a"; then
- BOOST_TEST_PEM_STATIC_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}-static
-@@ -4813,7 +4967,7 @@
- BOOST_TEST_TEM_LIBS=$BOOST_TEST_TEM_STATIC_LIBS
- BOOST_TEST_UTF_LIBS=$BOOST_TEST_UTF_STATIC_LIBS
-
-- AC_CACHE_CHECK([for Boost.Test in $BOOST_PATH], ncbi_cv_lib_boost_test,
-+ AC_CACHE_CHECK([for Boost.Test$in_path], ncbi_cv_lib_boost_test,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$RT_LIBS $orig_LIBS"
- found=
-@@ -4853,7 +5007,7 @@
- BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.Threads in $BOOST_PATH], ncbi_cv_lib_boost_thread,
-+ AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4864,12 +5018,25 @@
- BOOST_INCLUDE=
- BOOST_LIBPATH=
- BOOST_TAG=
-+ ncbi_cv_lib_boost_filesystem=no
- ncbi_cv_lib_boost_regex=no
- ncbi_cv_lib_boost_spirit=no
-+ ncbi_cv_lib_boost_system=no
- ncbi_cv_lib_boost_test=no
- ncbi_cv_lib_boost_thread=no
- fi
-
-+if test "$ncbi_cv_lib_boost_filesystem" != "no"; then
-+ dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1,
-+ dnl [Define to 1 if the `Boost.Filesystem' library is available.])
-+ NCBI_PACKAGE(Boost.Filesystem)
-+else
-+ boost_fs_lib=
-+ boost_fs_static_lib=
-+ BOOST_FILESYSTEM_LIBS=
-+ BOOST_FILESYSTEM_STATIC_LIBS=
-+fi
-+
- if test "$ncbi_cv_lib_boost_regex" != "no"; then
- AC_DEFINE(HAVE_BOOST_REGEX, 1,
- [Define to 1 if the `Boost.Regex' library is available.])
-@@ -4927,7 +5094,10 @@
-
- ## NCBI C Toolkit
- if test "$with_ncbi_c" != "no" ; then
-- NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
-+ if test "${with_ncbi_c-yes}" != yes; then
-+ NCBI_C_PATH=$with_ncbi_c
-+ fi
-+ : ${NCBI_C_PATH="$NCBI"}
- if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then
- NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc
- fi
-@@ -4949,7 +5119,8 @@
- NCBI_C_ncbi="-lncbi"
- fi
- NCBI_C_LIBPATH="-L$NCBI_C_LIBPATH"
-- AC_CACHE_CHECK([for the NCBI C toolkit in $NCBI_C_PATH], ncbi_cv_lib_ctools,
-+ AC_CACHE_CHECK([for the NCBI C toolkit${NCBI_C_PATH:+ in $NCBI_C_PATH}],
-+ ncbi_cv_lib_ctools,
- [CPPFLAGS="$NCBI_C_INCLUDE $orig_CPPFLAGS"
- LIBS="$NCBI_C_LIBPATH $NCBI_C_ncbi $NETWORK_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5000,11 +5171,7 @@
-
- ## OpenGL
- if test "$with_opengl" != "no"; then
-- if test "${with_opengl-yes}" = yes; then
-- if test -d $NCBI/MesaGL; then
-- : ${OPENGL_PATH=$NCBI/MesaGL}
-- fi
-- else
-+ if test "${with_opengl-yes}" != yes; then
- OPENGL_PATH=$with_opengl
- fi
- if test -d "$OPENGL_PATH"; then
-@@ -5101,7 +5268,6 @@
- else
- OSMESA_STATIC_LIBS=$OSMESA_LIBS
- fi
-- : ${GLUT_PATH=$NCBI/glut}
- if test "$with_glut" != "no"; then
- if test "${with_glut-yes}" != "yes"; then
- GLUT_PATH=$with_glut
-@@ -5121,7 +5287,6 @@
- NCBI_MISSING_PACKAGE(glut)
- fi
- fi
-- : ${GLEW_PATH=$NCBI/glew}
- if test "$with_glew" != "no"; then
- if test "${with_glew-yes}" != "yes"; then
- GLEW_PATH=$with_glew
-@@ -5214,7 +5379,7 @@
- : ${with_wxwidgets_ucs=no}
- if test "$with_wxwidgets" != "no" ; then
- case "$with_wxwidgets" in
-- yes | "" ) : ${WXWIDGETS_PATH=$NCBI/wxwidgets} ;;
-+ yes | "" ) ;;
- * ) WXWIDGETS_PATH=$with_wxwidgets ;;
- esac
- if test -d "$WXWIDGETS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-@@ -5283,12 +5448,13 @@
- libsed=$basesed
- ;;
- esac
-- AC_CACHE_CHECK([for wxWidgets in $WXWIDGETS_ARCH_PATH],
-+ AC_CACHE_CHECK(
-+ [for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}],
- ncbi_cv_lib_wxwidgets,
- [if test -x "$wxconf" ; then
- WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
- NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs],
-- [$libsed; ])
-+ [$libsed; s/ -lm / /g;])
-
- CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS"
- LIBS="$WXWIDGETS_LIBS $orig_LIBS"
-@@ -5315,12 +5481,12 @@
- else
- NCBI_PACKAGE(wxWidgets)
- case "`"$wxconf" $wxcfflags --version`" in
-- 2.[[89]].* | 2.[[0-9]][[0-9]]* )
-- NCBI_PACKAGE(wx2.8)
-- wxlibs=std,richtext,aui
-+ 1.* | 2.[[0-7]].*)
-+ wxlibs=std
- ;;
- *)
-- wxlibs=std
-+ NCBI_PACKAGE(wx2.8)
-+ wxlibs=std,richtext,aui,propgrid
- ;;
- esac
- # The "yes" may have been cached; get the actual settings again if needed
-@@ -5328,9 +5494,9 @@
- WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
- fi
- NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, [$wxconf $wxcfflags --libs $wxlibs],
-- [$libsed; ])
-+ [$libsed; s/ -lm / /g;])
- WXWIDGETS_STATIC_LIBS=`"$wxconf" $wxcfflags --libs --static $wxlibs \
-- 2>/dev/null | sed -e "$basesed"`
-+ 2>/dev/null | sed -e "$basesed; s/ -lm / /g;"`
- if test -n "$WXWIDGETS_STATIC_LIBS"; then
- # Allow direct use of underlying libraries with strict linkers
- WXWIDGETS_LIBS="$WXWIDGETS_LIBS `echo $WXWIDGETS_STATIC_LIBS | sed -e 's/.*\.a *//'`"
-@@ -5350,7 +5516,7 @@
- ## In-house Fast-CGI library
- if test "$with_fastcgi" != "no" ; then
- case "$with_fastcgi" in
-- yes | "" ) : ${FASTCGI_PATH:="$NCBI/fcgi-current"} ;;
-+ yes | "" ) ;;
- */* ) FASTCGI_PATH=$with_fastcgi ;;
- * ) FASTCGI_PATH=$NCBI/fcgi-${with_fastcgi} ;;
- esac
-@@ -5366,7 +5532,8 @@
- NCBI_RPATHIFY(FASTCGI_LIBS, $FASTCGI_LIBDIR, [ -lfcgi $NETWORK_LIBS])
- FASTCGI_OBJS="fcgibuf"
- LIBS="$FASTCGI_LIBS $orig_LIBS"
-- AC_CACHE_CHECK([for FastCGI libraries in $FASTCGI_PATH], ncbi_cv_lib_fcgi,
-+ AC_CACHE_CHECK([for FastCGI libraries${FASTCGI_PATH:+ in $FASTCGI_PATH}],
-+ ncbi_cv_lib_fcgi,
- [CPPFLAGS="$FASTCGI_INCLUDE $orig_CPPFLAGS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
- [[#include <fcgiapp.h>]],
-@@ -5416,7 +5583,11 @@
- else
- with_included_sss=no
- fi
-+ if test "${with_sss-yes}" = yes; then
- NCBI_SSS_PATH=${NCBI_SSS_PATH:="$NCBI/sss/BUILD"}
-+ else
-+ NCBI_SSS_PATH=$with_sss
-+ fi
- NCBI_SSS_INCLUDE=${NCBI_SSS_INCLUDE:="$NCBI_SSS_PATH/include"}
- if test -z "$NCBI_SSS_LIBPATH" ; then
- NCBI_SSS_LIBPATH="${NCBI_SSS_PATH}/lib/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}"
-@@ -5424,7 +5595,8 @@
- NCBI_SSS_LIBPATH="${NCBI_SSS_LIBPATH}mt"
- fi
- fi
-- AC_MSG_CHECKING([for NCBI SSS directories in $NCBI_SSS_PATH])
-+ AC_MSG_CHECKING(
-+ [for NCBI SSS directories${NCBI_SSS_PATH:+ in $NCBI_SSS_PATH}])
- if test "$with_included_sss" = "yes"; then
- AC_MSG_RESULT([yes]) # duh
- elif test ! -d "${NCBI_SSS_LIBPATH}" -o ! -d "${NCBI_SSS_INCLUDE}" ; then
-@@ -5510,7 +5682,6 @@
-
- # SP
- if test "$with_sp" != "no" ; then
-- SP_PATH=${SP_PATH:="$NCBI/SP"}
- if test -n "$SP_INCLUDE"; then
- SP_GENERIC="$SP_INCLUDE/../generic"
- else
-@@ -5520,7 +5691,7 @@
- if test -z "$SP_LIBPATH" ; then
- SP_LIBPATH="${SP_PATH}/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}"
- fi
-- AC_MSG_CHECKING([for SP directories in $SP_PATH])
-+ AC_MSG_CHECKING([for SP directories${SP_PATH:+ in $SP_PATH}])
- if test ! -d "${SP_LIBPATH}" -o ! -d "${SP_INCLUDE}" ; then
- AC_MSG_RESULT([no])
- NCBI_MISSING_PACKAGE(sp)
-@@ -5558,19 +5729,13 @@
-
-
- ## ORBacus CORBA
--if test "${with_orbacus:-yes}" = yes; then
-- if test -d $NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT; then
-- : ${ORBACUS_PATH=$NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT}
-- else
-- : ${ORBACUS_PATH=$NCBI/corba/OB-4.0.1}
-- fi
--elif test "$with_orbacus" != no; then
-+if test "$with_orbacus" != no; then
-+ if test "$with_orbacus" != yes; then
- ORBACUS_PATH=$with_orbacus
- fi
- if test -d "$ORBACUS_PATH"; then
- NCBI_FIX_DIR(ORBACUS_PATH)
- fi
--if test "$with_orbacus" != no; then
- fullpath=${ORBACUS_PATH}/${DEBUG_SFX}${mt_sfx}${bit64_sfx}
- if test -f ${fullpath}/inc/OB/Config.h ; then
- : ${ORBACUS_INCLUDE="-I$ORBACUS_PATH/include -I$fullpath/inc"}
-@@ -5594,7 +5759,8 @@
- LIBIMR=
- ;;
- esac
-- AC_CACHE_CHECK([for ORBacus in $ORBACUS_PATH], ncbi_cv_lib_orbacus,
-+ AC_CACHE_CHECK([for ORBacus${ORBACUS_PATH:+ in $ORBACUS_PATH}],
-+ ncbi_cv_lib_orbacus,
- [CPPFLAGS="$ORBACUS_INCLUDE $orig_CPPFLAGS"
- LIBS="$ORBACUS_LIBPATH $LIBOB $NETWORK_LIBS $DL_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5633,7 +5799,7 @@
-
- if test "$with_icu" != "no" ; then
- case "$with_icu" in
-- yes | "" ) : ${ICU_PATH=$NCBI/icu} ;;
-+ yes | "" ) ;;
- * ) ICU_PATH=$with_icu ;;
- esac
- if test -d "$ICU_PATH/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}${mt_sfx}/lib" \
-@@ -5648,7 +5814,8 @@
- ICU_BINPATH=${ICU_BINPATH:="$ICU_ARCH_PATH/bin"}
- ICU_LIBPATH=${ICU_LIBPATH:="$ICU_ARCH_PATH/lib"}
- ICU_INCLUDE=
-- AC_CACHE_CHECK([for ICU in $ICU_ARCH_PATH], ncbi_cv_lib_icu,
-+ AC_CACHE_CHECK([for ICU${ICU_ARCH_PATH:+ in $ICU_ARCH_PATH}],
-+ ncbi_cv_lib_icu,
- [ICU_CONFIG=`$ICU_BINPATH/icu-config --bindir 2>/dev/null`/icu-config
- if test -x "$ICU_CONFIG" ; then
- ICU_INCLUDE=`$ICU_CONFIG --cppflags-searchpath`
-@@ -5690,9 +5857,6 @@
-
-
- ### XML/XSL libraries
--if test -d "$NCBI/expat/include"; then
-- : ${EXPAT_PATH=$NCBI/expat}
--fi
- NCBI_CHECK_THIRD_PARTY_LIB(expat,
- AC_LANG_PROGRAM([#include <expat.h>],
- [XML_Parser parser = XML_ParserCreate("utf-8");]))
-@@ -5701,7 +5865,6 @@
- else
- EXPAT_STATIC_LIBS=${EXPAT_LIBS}
- fi
--: ${SABLOT_PATH=$NCBI/Sablot}
- vpath="$SABLOT_PATH/${compiler_vpfx}build"
- test -d "$vpath" && SABLOT_PATH=$vpath
- if test -d "$SABLOT_PATH"; then
-@@ -5718,7 +5881,6 @@
- SABLOT_STATIC_LIBS=${SABLOT_LIBS}
- fi
-
--: ${LIBXML_PATH=$NCBI/libxml}
- # test -d "$LIBXML_PATH" || LIBXML_PATH=`xml2-config --prefix 2>/dev/null`
- if test "$with_libxml" != "no"; then
- case "$with_libxml" in
-@@ -5813,7 +5975,6 @@
- LIBEXSLT_STATIC_LIBS=${LIBEXSLT_LIBS}
- fi
-
--: ${XERCES_PATH=$NCBI/xerces}
- if test "$with_xerces" != no; then
- if test "${with_xerces-yes}" != yes; then
- XERCES_PATH=$with_xerces
-@@ -5838,7 +5999,7 @@
- NCBI_FIX_DIR(XERCES_LIBPATH)
- fi
- fi
-- if test -d $XERCES_PATH; then
-+ if test -d "$XERCES_PATH"; then
- in_path=" in $XERCES_PATH"
- : ${XERCES_INCLUDE=-I$XERCES_PATH/include}
- : ${XERCES_LIBPATH=$XERCES_PATH/lib}
-@@ -5875,7 +6036,6 @@
- XERCES_STATIC_LIBS=
- fi
-
--: ${XALAN_PATH=$NCBI/xalan}
- if test "$with_xalan" != no; then
- if test "${with_xalan-yes}" != yes; then
- XALAN_PATH=$with_xalan
-@@ -5900,7 +6060,7 @@
- NCBI_FIX_DIR(XALAN_LIBPATH)
- fi
- fi
-- if test -d $XALAN_PATH; then
-+ if test -d "$XALAN_PATH"; then
- in_path=" in $XALAN_PATH"
- : ${XALAN_INCLUDE=-I$XALAN_PATH/include}
- : ${XALAN_LIBPATH=$XALAN_PATH/lib}
-@@ -5937,7 +6097,6 @@
-
- test -d SunWS_cache && rm -r SunWS_cache
-
--: ${ZORBA_PATH=$NCBI/zorba}
- if test "$with_zorba" != no; then
- if test "${with_zorba-yes}" != yes; then
- ZORBA_PATH=$with_zorba
-@@ -5967,7 +6126,7 @@
- ZORBA_PATH=`$ZORBA_CONFIG --prefix`
- : ${ZORBA_INCLUDE=`$ZORBA_CONFIG --cppflags`}
- fi
-- if test -d $ZORBA_PATH; then
-+ if test -d "$ZORBA_PATH"; then
- in_path=" in $ZORBA_PATH"
- : ${ZORBA_INCLUDE=-I$ZORBA_PATH/include}
- : ${ZORBA_LIBPATH=$ZORBA_PATH/lib}
-@@ -6010,7 +6169,7 @@
-
- ### SQLite
- case "$with_sqlite3" in
-- yes | '' ) : ${SQLITE3_PATH=$NCBI/sqlite3} ;;
-+ yes | '' ) ;;
- * ) SQLITE3_PATH=$with_sqlite3 ;;
- esac
-
-@@ -6048,7 +6207,6 @@
- ### OEChem
- # somewhat kludgish, as we now wanto to add in oeiupac and oedepict,
- # which depend on oechem....
--: ${OECHEM_PATH=$NCBI/oechem}
- NCBI_CHECK_THIRD_PARTY_LIB(oechem,
- AC_LANG_PROGRAM([#include <oechem.h>],
- [OEChem::OEMol mol; OEChem::OEConfBase* c = mol.GetActive();]),
-@@ -6091,7 +6249,7 @@
-
- ### muParser
- case "$with_muparser" in
-- yes | '' ) : ${MUPARSER_PATH=$NCBI/muParser} ;;
-+ yes | '' ) ;;
- * ) MUPARSER_PATH=$with_muparser ;;
- esac
-
-@@ -6111,7 +6269,7 @@
-
- ### hdf5
- case "$with_hdf5" in
-- yes | '' ) : ${HDF5_PATH=$NCBI/hdf5} ;;
-+ yes | '' ) ;;
- * ) HDF5_PATH=$with_hdf5 ;;
- esac
-
-@@ -6176,7 +6334,7 @@
- GIF_LIBS=$UNGIF_LIBS
- fi
-
--test -n "$x_libraries" && : ${XPM_PATH=`dirname "$x_libraries"`}
-+case "$x_libraries" in */*) : ${XPM_PATH=`dirname "$x_libraries"`} ;; esac
- NCBI_CHECK_THIRD_PARTY_LIB(Xpm,
- AC_LANG_PROGRAM([#include <X11/xpm.h>],
- [XpmImage image; XpmInfo info;
-@@ -6241,7 +6399,7 @@
- fi
-
- case "$with_ftgl" in
-- yes | '' ) : ${FTGL_PATH=$NCBI/ftgl} ;;
-+ yes | '' ) ;;
- * ) FTGL_PATH=$with_ftgl ;;
- esac
-
-@@ -6268,7 +6426,7 @@
-
- # Mimetic
- case "$with_mimetic" in
-- yes | '' ) : ${MIMETIC_PATH=$NCBI/mimetic} ;;
-+ yes | '' ) ;;
- * ) MIMETIC_PATH=$with_mimetic ;;
- esac
- if test -d "$MIMETIC_PATH"; then
-@@ -6293,6 +6451,88 @@
- [mimetic::MimeEntity me;])])
-
-
-+# gSOAP++
-+case "$with_gsoap" in
-+ yes | '' ) ;;
-+ * ) GSOAP_PATH=$with_gsoap ;;
-+esac
-+if test -d "$GSOAP_PATH"; then
-+ NCBI_FIX_DIR(GSOAP_PATH)
-+fi
-+for d in "$GSOAP_LIBDIR" \
-+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+ "$GSOAP_PATH/lib${bit64_sfx}" \
-+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+ "$GSOAP_PATH/lib"; do
-+ if test -d "$d"; then
-+ GSOAP_LIBDIR=$d
-+ NCBI_FIX_DIR(GSOAP_LIBDIR)
-+ break
-+ fi
-+done
-+NCBI_RPATHIFY(GSOAP_LIBPATH, $GSOAP_LIBDIR)
-+
-+: ${GSOAP_BINDIR=`dirname "$GSOAP_LIBDIR"`/bin}
-+AC_PATH_PROG(GSOAP_SOAPCPP2, soapcpp2, [], $GSOAP_BINDIR:$PATH)
-+AC_PATH_PROG(GSOAP_WSDL2H, wsdl2h, [], $GSOAP_BINDIR:$PATH)
-+
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(gsoap, GSOAP, gsoapssl++,
-+ [AC_LANG_PROGRAM([#include <stdsoap2.h>
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultsubcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultstring(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultdetail(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultsubcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultdetail(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap*) { }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap*) { return 0; }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap*) { return 0; }
-+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap*) { }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap*) { return 0; }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap*) { return 0; }],
-+ [soap s;])],
-+ $OPENSSL_LIBS $Z_LIBS)
-+
-+case "$with_sqlite3" in
-+ yes | '' ) ;;
-+ * ) SQLITE3_PATH=$with_sqlite3 ;;
-+esac
-+
-+
-+# MongoDB
-+if test -d "$MONGODB_PATH"; then
-+ NCBI_FIX_DIR(MONGODB_PATH)
-+fi
-+if test -d $MONGODB_PATH/lib${bit64_sfx}; then
-+ MONGODB_LIBDIR=$MONGODB_PATH/lib${bit64_sfx}
-+else
-+ MONGODB_LIBDIR=$MONGODB_PATH/lib
-+fi
-+# need Boost rpath
-+NCBI_RPATHIFY(MONGODB_LIBPATH, $MONGODB_LIBDIR)
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient,
-+ [AC_LANG_PROGRAM([#include <mongo/client/dbclient.h>],
-+ [std::vector<mongo::HostAndPort> v;
-+ mongo::DBClientReplicaSet client("foo", v);
-+ client.connect();])],
-+ [$BOOST_LIBPATH $boost_fs_lib $BOOST_THREAD_LIBS], [],
-+ [$BOOST_INCLUDE])
-+# MongoDB's own library is normally static, but its supporting Boost
-+# libraries might not be by default.
-+if test -n "$MONGODB_LIBS"; then
-+ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_THREAD_STATIC_LIBS"
-+else
-+ MONGODB_STATIC_LIBS=
-+fi
-+
- ### Restore original compiler/linker flags
- LIBS="$orig_LIBS"
- CPPFLAGS="$orig_CPPFLAGS"
-@@ -6499,16 +6739,6 @@
- fi
-
-
--## Sequence Read Archive SDK, which may be attached on either the
--## public or the internal side
--
--if test -f "${real_srcdir}/src/sra/sdk/Makefile.sra_macros.mk"; then
-- sra=sra
--else
-- sra=
--fi
--
--
- ## `internal' project cluster
-
- if test "$with_internal" = "no" \
-@@ -6781,6 +7011,7 @@
- AC_SUBST(C_LINK)
- AC_SUBST(TAIL_N)
- AC_SUBST(EGREP_Q)
-+AC_SUBST(LDD_R)
-
- AC_SUBST(CFLAGS)
- AC_SUBST(FAST_CFLAGS)
-@@ -6829,7 +7060,6 @@
- AC_SUBST(algo)
- AC_SUBST(app)
- AC_SUBST(internal)
--AC_SUBST(sra)
-
- AC_SUBST(check)
- AC_SUBST(CHECK_ARG)
-@@ -6865,6 +7095,7 @@
-
- AC_SUBST(THREAD_LIBS)
- AC_SUBST(NCBIATOMIC_LIB)
-+AC_SUBST(OPENMP_FLAGS)
- AC_SUBST(NETWORK_LIBS)
- AC_SUBST(NETWORK_PURE_LIBS)
- AC_SUBST(RESOLVER_LIBS)
-@@ -6902,6 +7133,8 @@
- AC_SUBST(BOOST_INCLUDE)
- AC_SUBST(BOOST_LIBPATH)
- AC_SUBST(BOOST_TAG)
-+AC_SUBST(BOOST_FILESYSTEM_LIBS)
-+AC_SUBST(BOOST_FILESYSTEM_STATIC_LIBS)
- AC_SUBST(BOOST_REGEX_LIBS)
- AC_SUBST(BOOST_REGEX_STATIC_LIBS)
- AC_SUBST(BOOST_SYSTEM_LIBS)
-@@ -6968,6 +7201,8 @@
- AC_SUBST(SQLITE3_STATIC_LIBS)
- AC_SUBST(FREETYPE_INCLUDE)
- AC_SUBST(FREETYPE_LIBS)
-+AC_SUBST(GSOAP_PATH)
-+AC_SUBST(MONGODB_STATIC_LIBS)
- AC_SUBST(ncbi_xreader_pubseqos)
- AC_SUBST(ncbi_xreader_pubseqos2)
- AC_SUBST(UNLESS_PUBSEQOS)
-@@ -7194,7 +7429,9 @@
-
- cat << EOCONF
- ===============================================================================
--NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running
-+NCBI C++ Toolkit documentation:
-+ Online: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/
-+ Local: ./doc/public/index.html
- For the available configuration flags run: ./configure --help
-
- CFLAGS = $CFLAGS
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014-06-23 17:36:18.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014-06-23 17:36:59.000000000 +0200
-@@ -1,126 +1,45 @@
--# Hacked up in various ways, since Autoconf's version doesn't quite
--# suit our (unusual) conventions. (Originally from status.m4)
--m4_define([_AC_SRCPATHS],
--[#ac_builddir=. # Useless!
--ac_builddir=$builddir
--dnl Base source directories on path to *input* file.
--if test -n "$ac_file_in"; then
-- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])`
-+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS)
-+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly.
-+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS])
-+m4_define([_AC_SRCDIRS],
-+[# Base source directories on path to *input* file.
-+if test -n "$ac_f"; then
-+ ac_dir_in=`AS_DIRNAME(["$ac_f"])`
- else
- ac_dir_in=$1
- fi
-
--if test $ac_dir_in != .; then
-- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'`
-- # A "../" for each directory in $ac_dir_suffix.
-- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'`
--else
-- ac_dir_suffix= ac_top_builddir=
--fi
-+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
-
--case $srcdir in
-- .) # No --srcdir option. We are building in place.
-- ac_srcdir=.
-- if test -z "$ac_top_builddir"; then
-- ac_top_srcdir=.
-- else
-- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
-- fi ;;
-- [[\\/]]* | ?:[[\\/]]* ) # Absolute path.
-- ac_srcdir=$srcdir/$ac_dir_suffix;
-- ac_top_srcdir=$srcdir ;;
-- *) # Relative path.
-- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix
-- ac_top_srcdir=$ac_top_builddir$srcdir ;;
--esac
--# Do not use `cd foo && pwd` to compute absolute paths, because
--# the directories may not exist.
--AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1])
--AS_SET_CATFILE([ac_abs_top_builddir],
-- [$ac_abs_builddir], [${ac_top_builddir}.])
- AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
--AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix])
--])# _AC_SRCPATHS
--
-+ac_builddir=$builddir
-+])
-
--# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a
--# last resort due to issues with sourcing .bashrc.
--m4_define([_AS_LINENO_PREPARE],
--[_AS_LINENO_WORKS || {
-- # Find who we are. Look in the path if we contain no path at all
-- # relative or not.
-- case $[0] in
-- *[[\\/]]* ) as_myself=$[0] ;;
-- *) _AS_PATH_WALK([],
-- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break])
-- ;;
-- esac
-- # We did not find ourselves, most probably we were run as `sh COMMAND'
-- # in which case we are not to be found in the path.
-- if test "x$as_myself" = x; then
-- as_myself=$[0]
-- fi
-- if test ! -f "$as_myself"; then
-- AS_ERROR([cannot find myself; rerun with an absolute path])
-- fi
-- case $CONFIG_SHELL in
-- '')
-- AS_UNSET(ZSH_VERSION)
-- for as_base in sh ksh sh5 bash; do
-- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH],
-- [case $as_dir in
-- /*)
-- if ("$as_dir/$as_base" -c \
-- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null
-- then
-- AS_UNSET(BASH_ENV)
-- AS_UNSET(ENV)
-- CONFIG_SHELL=$as_dir/$as_base
-- export CONFIG_SHELL
-- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"}
-- fi;;
-- esac
-- done]);;
-- esac
-
-- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
-- # uniformly replaced by the line number. The first 'sed' inserts a
-- # line-number line before each line; the second 'sed' does the real
-- # work. The second script uses 'N' to pair each line-number line
-- # with the numbered line, and appends trailing '-' during
-- # substitution so that $LINENO is not a special case at line end.
-- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
-- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-)
-- sed '=' <$as_myself |
-- sed '
-- N
-- s,$,-,
-- : loop
-- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3,
-- t loop
-- s,-$,,
-- s,^[['$as_cr_digits']]*\n,,
-- ' >$as_me.lineno &&
-- chmod +x $as_me.lineno ||
-- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell])
--
-- # Don't try to exec as it changes $[0], causing all sort of problems
-- # (the dirname of $[0] is not the place where we might find the
-- # original and so on. Autoconf is especially sensible to this).
-- . ./$as_me.lineno
-- # Exit status is that of the last command.
-- exit
--}
--])# _AS_LINENO_PREPARE
-+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
-+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
-+# bash a last resort due to issues with sourcing .bashrc while entirely
-+# avoiding zsh, which passes itself off as ksh on some systems but runs
-+# parent shells' exit handlers from subshells, resulting in premature
-+# cleanup of temporary files (notably confdefs.h).
-+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL])
-+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN])
-+
-+m4_define([_AS_DETECT_BETTER_SHELL],
-+ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]),
-+ [sh bash ksh sh5], [sh ksh sh5 bash])])
-+m4_define([_AS_RUN],
-+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl
-+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])])
-
-
- # One more hack: suppress PACKAGE_*, as we don't use them and some
- # third-party libraries expose their corresponding settings, leading
- # to preprocessor warnings.
--m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED]))
-+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED])
- m4_define([AC_DEFINE_UNQUOTED],
- [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [],
-- [NCBI_ORIG_ACDU($@)])])
-+ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])])
-
-
- AC_DEFUN(NCBI_FIX_DIR,
-@@ -158,7 +77,7 @@
- AC_MSG_WARN([Proceeding without questions per --without-caution]) ;;
- * )
- echo "$1 [[y/N]]"
-- read answer
-+ read answer <& AS_ORIGINAL_STDIN_FD
- case "$answer" in
- [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;;
- * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;;
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014-06-23 17:38:56.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014-06-23 17:39:04.000000000 +0200
-@@ -98,6 +98,9 @@
- /* Define to 1 if you have the `getaddrinfo' function. */
- #undef HAVE_GETADDRINFO
-
-+/* Define to 1 if you have the `getgrouplist' function. */
-+#undef HAVE_GETGROUPLIST
-+
- /* If you have the `gethostbyaddr_r' function, define to the number of
- arguments it takes (normally 7 or 8). */
- #undef HAVE_GETHOSTBYADDR_R
-@@ -176,9 +179,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #undef HAVE_IOS_REGISTER_CALLBACK
-
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--#undef HAVE_IS_SORTED
--
- /* Define to 1 if you have the `lchown' function. */
- #undef HAVE_LCHOWN
-
-@@ -234,6 +234,9 @@
- /* Define to 1 if libgnutls is available. */
- #undef HAVE_LIBGNUTLS
-
-+/* Define to 1 if libgsoapssl++ is available. */
-+#undef HAVE_LIBGSOAP
-+
- /* Define to 1 if libhdf5_cpp is available. */
- #undef HAVE_LIBHDF5
-
-@@ -260,6 +263,9 @@
- /* Define to 1 if libmimetic is available. */
- #undef HAVE_LIBMIMETIC
-
-+/* Define to 1 if libmongoclient is available. */
-+#undef HAVE_LIBMONGODB
-+
- /* Define to 1 if libmuparser is available. */
- #undef HAVE_LIBMUPARSER
-
-@@ -382,9 +388,6 @@
- /* Define to 1 if `min'/`max' templates are not implemented. */
- #undef HAVE_NO_MINMAX_TEMPLATE
-
--/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
--#undef HAVE_NULLPTR
--
- /* Define to 1 if ODBC libraries are available. */
- #undef HAVE_ODBC
-
-@@ -799,37 +802,37 @@
- by a signal. */
- #undef SELECT_UPDATES_TIMEOUT
-
--/* The size of a `char', as computed by sizeof. */
-+/* The size of `char', as computed by sizeof. */
- #undef SIZEOF_CHAR
-
--/* The size of a `double', as computed by sizeof. */
-+/* The size of `double', as computed by sizeof. */
- #undef SIZEOF_DOUBLE
-
--/* The size of a `float', as computed by sizeof. */
-+/* The size of `float', as computed by sizeof. */
- #undef SIZEOF_FLOAT
-
--/* The size of a `int', as computed by sizeof. */
-+/* The size of `int', as computed by sizeof. */
- #undef SIZEOF_INT
-
--/* The size of a `long', as computed by sizeof. */
-+/* The size of `long', as computed by sizeof. */
- #undef SIZEOF_LONG
-
--/* The size of a `long double', as computed by sizeof. */
-+/* The size of `long double', as computed by sizeof. */
- #undef SIZEOF_LONG_DOUBLE
-
--/* The size of a `long long', as computed by sizeof. */
-+/* The size of `long long', as computed by sizeof. */
- #undef SIZEOF_LONG_LONG
-
--/* The size of a `short', as computed by sizeof. */
-+/* The size of `short', as computed by sizeof. */
- #undef SIZEOF_SHORT
-
--/* The size of a `size_t', as computed by sizeof. */
-+/* The size of `size_t', as computed by sizeof. */
- #undef SIZEOF_SIZE_T
-
--/* The size of a `void*', as computed by sizeof. */
-+/* The size of `void*', as computed by sizeof. */
- #undef SIZEOF_VOIDP
-
--/* The size of a `__int64', as computed by sizeof. */
-+/* The size of `__int64', as computed by sizeof. */
- #undef SIZEOF___INT64
-
- /* Define to 1 if the stack grows down. */
-@@ -870,5 +873,5 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- #undef const
-
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- #undef size_t
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014-06-23 17:40:40.000000000 +0200
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014-06-23 17:40:57.000000000 +0200
-@@ -1,4 +1,4 @@
--/* $Id: ncbiconf_xcode.h 361821 2012-05-04 14:28:13Z ucko $
-+/* $Id$
- * By Vlad Lebedev, NCBI (lebedev@ncbi.nlm.nih.gov)
- *
- * Mac OS X - xCode Build
-@@ -258,9 +258,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #define HAVE_IOS_REGISTER_CALLBACK 1
-
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--/* #undef HAVE_IS_SORTED */
--
- /* Define to 1 if you have the `lchown' function. */
- /* #undef HAVE_LCHOWN */
-
-@@ -358,6 +355,9 @@
- /* Define to 1 if you have the `lutimes' function. */
- /* #undef HAVE_LUTIMES */
-
-+/* Define to 1 if you have the `madvise' function. */
-+#define HAVE_MADVISE 1
-+
- /* Define to 1 if you have the <malloc.h> header file. */
- /* #undef HAVE_MALLOC_H */
-
-@@ -589,15 +589,15 @@
- /* Define to 1 if you have the <windows.h> header file. */
- /* #undef HAVE_WINDOWS_H */
-
-+/* Define to 1 if you have the `writev' function. */
-+#define HAVE_WRITEV 1
-+
- /* Define to 1 if the system has the type `wstring'. */
- #define HAVE_WSTRING 1
-
- /* Define to 1 if wxWidgets is available. */
- /* #undef HAVE_WXWIDGETS */
-
--/* Define to 1 if nullptr keyword is available. */
--/* #undef HAVE_NULLPTR */
--
- /* Define as const if the declaration of iconv() needs const. */
- #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
- # define ICONV_CONST
-@@ -694,7 +694,7 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- /* #undef const */
-
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- /* #undef size_t */
-
- /*
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2014-06-26 15:11 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-06-26 15:11 UTC (permalink / raw
To: gentoo-commits
commit: c9cc902bf22b5154a8dcc82a937da0fd7ebae446
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 15:10:53 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 15:10:53 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c9cc902b
sci-biology/ncbi-tools++-12.0.0: added the patch istelf dropping :%=% from LIB settings
---
.../ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
new file mode 100644
index 0000000..2b94208
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
@@ -0,0 +1,22 @@
+--- ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2014-06-26 16:46:27.000000000 +0200
++++ ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app 2014-06-26 16:47:26.000000000 +0200
+@@ -9,7 +9,7 @@
+ APP = speedtest
+ SRC = speedtest
+ LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \
+- xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
++ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+
+ LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+--- ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app.ori 2014-06-26 16:47:53.000000000 +0200
++++ ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app 2014-06-26 16:48:07.000000000 +0200
+@@ -7,7 +7,7 @@
+
+ LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \
+ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \
+- $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC))
++ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS)
+
+ LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2014-06-26 15:53 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-06-26 15:53 UTC (permalink / raw
To: gentoo-commits
commit: a9c97c981e04e280b2d1b21a54d178f680f0dba4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 15:52:27 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 15:52:27 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a9c97c98
sci-biology/ncbi-tools++-12.0.0: more entries to ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
---
.../ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
index 2b94208..44b16ae 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
@@ -19,4 +19,26 @@
+ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS)
LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+
+--- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app.ori 2014-06-26 17:45:11.000000000 +0200
++++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app 2014-06-26 17:48:26.000000000 +0200
+@@ -3,7 +3,7 @@
+ APP = igblastp
+ SRC = igblastp_app
+ LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+-LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
++LIB = blast_app_util igblast $(LIB_)
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+ CFLAGS = $(FAST_CFLAGS:ppc=i386)
+--- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app.ori 2014-06-26 17:47:53.000000000 +0200
++++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app 2014-06-26 17:49:31.000000000 +0200
+@@ -3,7 +3,7 @@
+ APP = igblastn
+ SRC = igblastn_app
+ LIB_ = $(BLAST_INPUT_LIBS) xalgoalignutil xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS)
+-LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
++LIB = blast_app_util igblast $(LIB_)
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+ CFLAGS = $(FAST_CFLAGS:ppc=i386)
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2014-06-26 16:56 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-06-26 16:56 UTC (permalink / raw
To: gentoo-commits
commit: a28e615a1579b782b069ac9f6224c1d24b986788
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 16:56:12 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 16:56:12 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a28e615a
sci-biology/ncbi-tools++-12.0.0: more places where to drop ':%=%'
---
.../ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
index 44b16ae..fad02c3 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch
@@ -16,7 +16,7 @@
LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \
taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \
- $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC))
-+ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS)
++ $(BLAST_LIBS) $(OBJMGR_LIBS)
LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2014-06-26 20:53 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-06-26 20:53 UTC (permalink / raw
To: gentoo-commits
commit: 5bdca751bc342372b06bcaa65796885de3a1d513
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 20:52:38 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 20:52:38 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5bdca751
sci-biology/ncbi-tools++: reworked patch
---
.../ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
index 8d53ebe..97e845f 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
@@ -1,11 +1,11 @@
---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori (revision 439078)
-+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top (working copy)
+--- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.000000000 +0200
++++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.000000000 +0200
@@ -48,7 +48,7 @@
- for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
- cd $(includedir0) && find * -name CVS -prune -o -print |\
+ for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
+ cd $(includedir0) && find * -name CVS -prune -o -print |\
cpio -pd $(pincludedir)
-- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
-+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
+- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
++ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
## set up appropriate build and status directories somewhere under $(libdir)?
install-gbench:
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2017-07-28 20:48 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:48 UTC (permalink / raw
To: gentoo-commits
commit: 6ad973f70eefbffeebb8ff400d57572d5059cf37
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 20:19:40 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:19:40 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ad973f7
sci-biology/ncbi-tools++: resolving my 'stash pop' with an empty change
Sorry for noise.
Package-Manager: Portage-2.3.6, Repoman-2.3.3
.../ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
index 49a4adb4e..bc62bd658 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
@@ -11,5 +11,8 @@ Index: c++.18.0.0/src/app/srcchk/Makefile.srcchk.app
+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
@ 2017-07-28 20:51 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:51 UTC (permalink / raw
To: gentoo-commits
commit: 0eb19cf5891c22bab171539902ba6dac381a8ba2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 20:50:56 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:50:56 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0eb19cf5
sci-biology/ncbi-tools++: re-adding the patch with PCRE_LIBS added
Package-Manager: Portage-2.3.6, Repoman-2.3.3
.../ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
index bc62bd658..49a4adb4e 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
@@ -11,8 +11,5 @@ Index: c++.18.0.0/src/app/srcchk/Makefile.srcchk.app
+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
--LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-+LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
-
- REQUIRES = objects -Cygwin
+ LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
^ permalink raw reply related [flat|nested] 12+ messages in thread
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