[med-svn] [ncbi-blast+] 03/03: new upstream release 2.5.0, update patches to match release
Olivier Sallou
osallou at debian.org
Fri Dec 2 08:55:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository ncbi-blast+.
commit 87072b8536628e3b55bed49026ae73ce749cfeb4
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Thu Dec 1 15:42:13 2016 +0100
new upstream release 2.5.0, update patches to match release
---
debian/changelog | 6 +
debian/patches/fix_lib_deps | 136 +++++++++----------
debian/patches/fix_version_extraction | 89 ------------
debian/patches/hurd_fixes | 4 +-
debian/patches/no_multiarch_rpath | 4 +-
debian/patches/series | 4 +-
debian/patches/support_recent_boost | 249 ----------------------------------
debian/patches/support_x32 | 2 +-
8 files changed, 75 insertions(+), 419 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index da01b5c..d4b1cf9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+ncbi-blast+ (2.5.0-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 01 Dec 2016 14:40:17 +0100
+
ncbi-blast+ (2.4.0-3) unstable; urgency=medium
* debian/rules:
diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index f333f81..57cbc8c 100644
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -13,22 +13,11 @@ Subject: ensure that all libraries link against all direct dependencies
Debian-Bug: 633567.
Author: Aaron M. Ucko <ucko at debian.org>
Last-Update: 2014-12-02
---- a/c++/src/algo/blast/Makefile.blast_macros.mk
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \
- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
-
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
- xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
--- a/c++/src/algo/blast/api/Makefile.xblast.lib
+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,14 +74,15 @@ cdd_pssm_input \
- deltablast_options \
- deltablast
+@@ -76,14 +76,15 @@
+ magicblast_options \
+ magicblast
-SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
@@ -46,7 +35,7 @@ Last-Update: 2014-12-02
CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -24,7 +24,9 @@ SRC = $(SRC_CXX)
+@@ -26,7 +26,9 @@
LIB = blastinput
@@ -59,8 +48,8 @@ Last-Update: 2014-12-02
ASN_DEP = seqset xnetblast
--- a/c++/src/algo/blast/core/Makefile.blast.lib
+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -23,6 +23,7 @@ LDFLAGS = $(FAST_LDFLAGS)
-
+@@ -23,6 +23,7 @@
+ LDFLAGS = $(FAST_LDFLAGS)
WATCHERS = madden camacho fongah2
+DLL_LIB = composition_adjustment xconnect tables
@@ -69,7 +58,7 @@ Last-Update: 2014-12-02
composition_adjustment connect tables
--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
+@@ -11,6 +11,8 @@
CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
@@ -80,7 +69,7 @@ Last-Update: 2014-12-02
WATCHERS = morgulis
--- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-@@ -2,7 +2,7 @@ APP = makembindex
+@@ -2,7 +2,7 @@
SRC = main mkindex_app
LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
@@ -91,7 +80,7 @@ Last-Update: 2014-12-02
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgodustmask
+@@ -8,6 +8,8 @@
SRC = symdust
@@ -102,7 +91,7 @@ Last-Update: 2014-12-02
--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgosegmask
+@@ -8,6 +8,8 @@
SRC = segmask
@@ -113,7 +102,7 @@ Last-Update: 2014-12-02
--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s
+@@ -21,7 +21,7 @@
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
@@ -124,7 +113,7 @@ Last-Update: 2014-12-02
seqmasks_io
--- a/c++/src/build-system/library_relations.txt
+++ b/c++/src/build-system/library_relations.txt
-@@ -1331,7 +1331,7 @@ xbiosample_util needs $(OBJEDIT_LIBS)
+@@ -1287,7 +1287,7 @@
xbiosample_util needs $(XFORMAT_LIBS)
xbiosample_util needs xalnmgr
xbiosample_util needs xmlwrapp
@@ -135,7 +124,7 @@ Last-Update: 2014-12-02
xblast needs xalgowinmask
--- a/c++/src/cgi/Makefile.cgi.lib
+++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb
+@@ -9,6 +9,8 @@
user_agent
LIB = xcgi
@@ -146,7 +135,7 @@ Last-Update: 2014-12-02
WATCHERS = vakatov
--- a/c++/src/connect/Makefile.xconnect.lib
+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
+@@ -14,6 +14,8 @@
LIB = xconnect
PROJ_TAG = core
@@ -179,7 +168,7 @@ Last-Update: 2014-12-02
USE_PCH = no
--- a/c++/src/html/Makefile.html.lib
+++ b/c++/src/html/Makefile.html.lib
-@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se
+@@ -7,6 +7,8 @@
commentdiag indentstream html_exception writer_htmlenc
LIB = xhtml
@@ -190,7 +179,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objects/blast/Makefile.blast.lib
+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -3,6 +3,8 @@ SRC = blast__ blast___ names
+@@ -3,6 +3,8 @@
DLL_LIB = seqset scoremat
@@ -201,7 +190,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -5,6 +5,8 @@ SRC = blastdb__ blastdb___
+@@ -5,6 +5,8 @@
DLL_LIB = xser
@@ -223,7 +212,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/id1/Makefile.id1.lib
+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -5,6 +5,8 @@ SRC = id1__ id1___
+@@ -5,6 +5,8 @@
DLL_LIB = seqset
@@ -245,7 +234,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objects/seq/Makefile.seq.lib
+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -14,6 +14,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
+@@ -14,6 +14,8 @@
DLL_LIB = seqcode pub general xser sequtil
@@ -311,7 +300,7 @@ Last-Update: 2014-12-02
seqset
--- a/c++/src/objmgr/split/Makefile.id2_split.lib
+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,7 +17,7 @@ LIB = id2_split
+@@ -17,7 +17,7 @@
CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -322,18 +311,18 @@ Last-Update: 2014-12-02
--- a/c++/src/objmgr/util/Makefile.util.lib
+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -11,6 +11,8 @@ LIB = xobjutil
+@@ -11,6 +11,8 @@
DLL_LIB = $(SOBJMGR_LIBS)
+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
+
- WATCHERS = ucko vasilche kornbluh
+ WATCHERS = ucko vasilche
--- a/c++/src/objtools/align_format/Makefile.align_format.lib
+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho
+@@ -13,6 +13,10 @@
CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
@@ -346,18 +335,17 @@ Last-Update: 2014-12-02
# CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -14,7 +14,7 @@ DLL_LIB = tables
+@@ -14,6 +14,7 @@
- WATCHERS = todorov dicuccio grichenk
+ WATCHERS = grichenk
--
+DLL_LIB = xobjutil xobjmgr seqset seq xser tables xncbi
USES_LIBRARIES = \
tables xobjutil
--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla
+@@ -11,6 +11,7 @@
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
@@ -367,7 +355,7 @@ Last-Update: 2014-12-02
# CFLAGS = $(FAST_CFLAGS)
--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -25,6 +25,8 @@ seqdbobj
+@@ -25,6 +25,8 @@
LIB = seqdb
DLL_LIB = blastdb $(SOBJMGR_LIBS)
@@ -378,7 +366,7 @@ Last-Update: 2014-12-02
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum
+@@ -8,6 +8,9 @@
LIB = writedb
@@ -390,18 +378,18 @@ Last-Update: 2014-12-02
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-@@ -10,6 +10,8 @@ LIB = blast_services
+@@ -10,6 +10,8 @@
DLL_LIB = xnetblastcli xnetblast
+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
+
CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
+ # -DNCBI_MODULE=NETBLAST moved to blast_services.*pp to avoid misnamed modules in DLL configurations
+ CPPFLAGS = $(ORIG_CPPFLAGS)
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -9,6 +9,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_
+@@ -9,6 +9,8 @@
ASN_DEP = blastdb seqset
@@ -412,7 +400,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -7,6 +7,8 @@ DLL_LIB = blast_services
+@@ -7,6 +7,8 @@
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
@@ -423,7 +411,7 @@ Last-Update: 2014-12-02
WATCHERS = camacho
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@ LIB_OR_DLL = both
+@@ -12,6 +12,9 @@
# Dependencies for shared library
DLL_LIB = ncbi_xreader$(DLL)
@@ -435,9 +423,9 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -14,6 +14,9 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = $(GENBANK_READER_LDEP)
+@@ -16,6 +16,9 @@
+
+ LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
+ xser xconnect xcompress xutil xncbi
@@ -447,7 +435,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
+@@ -12,6 +12,8 @@
# Dependencies for shared library
DLL_LIB = ncbi_xreader$(DLL)
@@ -458,7 +446,7 @@ Last-Update: 2014-12-02
WATCHERS = vasilche
--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
+@@ -12,6 +12,8 @@
# Dependencies for shared library
DLL_LIB = xconnect ncbi_xreader$(DLL)
@@ -469,7 +457,7 @@ Last-Update: 2014-12-02
WATCHERS = vasilche
--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-@@ -12,7 +12,10 @@ LIB_OR_DLL = both
+@@ -12,7 +12,10 @@
CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
# Dependencies for shared library (disabled due to problems on Darwin)
@@ -483,7 +471,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -12,7 +12,7 @@ mask_writer_seqloc \
+@@ -12,7 +12,7 @@
mask_writer_blastdb_maskinfo
ASN_DEP = seqset
@@ -494,7 +482,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@ WATCHERS = jcherry
+@@ -7,6 +7,8 @@
ASN_DEP = seqset
@@ -505,7 +493,7 @@ Last-Update: 2014-12-02
--- a/c++/src/serial/Makefile.serial.lib
+++ b/c++/src/serial/Makefile.serial.lib
-@@ -20,6 +20,8 @@ LIB = xser
+@@ -20,6 +20,8 @@
DLL_LIB = xutil
@@ -516,17 +504,17 @@ Last-Update: 2014-12-02
--- a/c++/src/util/Makefile.util.lib
+++ b/c++/src/util/Makefile.util.lib
-@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s
+@@ -12,6 +12,7 @@
LIB = xutil
PROJ_TAG = core
+DLL_LIB = xncbi
LIBS = $(ORIG_LIBS)
- WATCHERS = vakatov kornbluh
+ WATCHERS = vakatov
--- a/c++/src/util/compress/api/Makefile.compress.lib
+++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -7,7 +7,7 @@ LIB = xcompress
+@@ -7,7 +7,7 @@
CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -537,7 +525,7 @@ Last-Update: 2014-12-02
WATCHERS = ivanov
--- a/c++/src/util/xregexp/Makefile.xregexp.lib
+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -5,7 +5,7 @@ LIB = xregexp
+@@ -5,7 +5,7 @@
CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
@@ -548,7 +536,7 @@ Last-Update: 2014-12-02
USES_LIBRARIES = \
--- a/c++/src/objtools/readers/Makefile.xobjread.lib
+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -20,8 +20,7 @@ SRC = read_util format_guess_ex \
+@@ -20,8 +20,7 @@
ucscregion_reader \
message_listener line_error
@@ -625,7 +613,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/entrez2/Makefile.entrez2.lib
+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
-@@ -3,6 +3,7 @@ WATCHERS = lavr
+@@ -3,6 +3,7 @@
LIB = entrez2
SRC = entrez2__ entrez2___
@@ -635,7 +623,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-@@ -5,6 +5,7 @@ ASN_DEP = entrez2
+@@ -5,6 +5,7 @@
LIB = entrez2cli
SRC = entrez2_client entrez2_client_
@@ -655,7 +643,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-@@ -6,6 +6,7 @@ CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG
+@@ -6,6 +6,7 @@
LIB = gene_info
SRC = gene_info gene_info_reader file_utils
@@ -685,7 +673,7 @@ Last-Update: 2014-12-02
medlars pub pubmed
--- a/c++/src/objects/mla/Makefile.mlacli.lib
+++ b/c++/src/objects/mla/Makefile.mlacli.lib
-@@ -5,5 +5,7 @@ SRC = mla_client mla_client_
+@@ -5,5 +5,7 @@
DLL_LIB = xconnect
@@ -705,7 +693,7 @@ Last-Update: 2014-12-02
medline
--- a/c++/src/objects/taxon1/Makefile.taxon1.lib
+++ b/c++/src/objects/taxon1/Makefile.taxon1.lib
-@@ -7,6 +7,7 @@ DLL_LIB = xconnect
+@@ -7,6 +7,7 @@
WATCHERS = domrach
@@ -715,7 +703,7 @@ Last-Update: 2014-12-02
$(SEQ_LIBS) pub xconnect
--- a/c++/src/objects/taxon3/Makefile.taxon3.lib
+++ b/c++/src/objects/taxon3/Makefile.taxon3.lib
-@@ -7,6 +7,7 @@ DLL_LIB = xconnect
+@@ -7,6 +7,7 @@
WATCHERS = bollin holmesbr
@@ -725,7 +713,7 @@ Last-Update: 2014-12-02
$(SEQ_LIBS) pub xconnect
--- a/c++/src/objects/valerr/Makefile.valerr.lib
+++ b/c++/src/objects/valerr/Makefile.valerr.lib
-@@ -3,6 +3,7 @@ SRC = valerr__ valerr___
+@@ -3,6 +3,7 @@
ASN_DEP = seqset
@@ -735,7 +723,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/valid/Makefile.valid.lib
+++ b/c++/src/objects/valid/Makefile.valid.lib
-@@ -4,5 +4,7 @@ SRC = valid__ valid___
+@@ -4,5 +4,7 @@
ASN_DEP = general
@@ -755,7 +743,7 @@ Last-Update: 2014-12-02
$(SEQ_LIBS) pub
--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -11,6 +11,8 @@ DLL_LIB = $(BLAST_LIBS) align_format bla
+@@ -11,6 +11,8 @@
WATCHERS = jianye zaretska madden camacho fongah2
@@ -766,7 +754,7 @@ Last-Update: 2014-12-02
$(BLAST_LIBS) align_format blastxml blastxml2
--- a/c++/src/objtools/cleanup/Makefile.cleanup.lib
+++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib
-@@ -15,6 +15,7 @@ LIB = xcleanup
+@@ -15,6 +15,7 @@
LIBS = $(PCRE_LIBS)
@@ -776,9 +764,9 @@ Last-Update: 2014-12-02
submit valid xobjutil
--- a/c++/src/objtools/format/Makefile.xformat.lib
+++ b/c++/src/objtools/format/Makefile.xformat.lib
-@@ -22,6 +22,8 @@ DLL_LIB = xalnmgr xconnect
+@@ -22,6 +22,8 @@
- WATCHERS = ludwigf dicuccio kornbluh
+ WATCHERS = ludwigf dicuccio
+DLL_LIB = xcleanup valid gbseq mlacli mla medlars pubmed submit xalnmgr \
+ xobjutil taxon3 $(SOBJMGR_LIBS)
@@ -787,7 +775,7 @@ Last-Update: 2014-12-02
gbseq mlacli xalnmgr xcleanup
--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -5,5 +5,7 @@ SRC = blastclient blastclient_
+@@ -5,5 +5,7 @@
DLL_LIB = xconnect
@@ -797,7 +785,7 @@ Last-Update: 2014-12-02
xconnect xnetblast
--- a/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib
+++ b/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib
-@@ -6,6 +6,8 @@ LIB = xregexp_template_tester
+@@ -6,6 +6,8 @@
DLL_LIB = $(PCRE_LIB)
LIBS = $(PCRE_LIBS)
diff --git a/debian/patches/fix_version_extraction b/debian/patches/fix_version_extraction
index 14951cc..650370e 100644
--- a/debian/patches/fix_version_extraction
+++ b/debian/patches/fix_version_extraction
@@ -1,94 +1,5 @@
---- a/c++/src/build-system/configure
-+++ b/c++/src/build-system/configure
-@@ -31352,15 +31352,21 @@ cat confdefs.h >>conftest.$ac_ext
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h. */
-
-+cat >/dev/null <<_NCBI_EOF
- #include <db.h>
--ncbi_cv_lib_berkeley_db_version=DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH
-+_NCBI_EOF
-+get_DB_VERSION() {
-+ grep '^[^#]' <<_NCBI_EOF
-+DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH
-+_NCBI_EOF
-+}
-+ncbi_cv_lib_berkeley_db_version=\`get_DB_VERSION | tr -cd 0123456789.\`
-
- _ACEOF
-- eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" \
-- 2>&5 | grep '^ncbi_cv_' \
-- | tr -d "$wschars" > conftest.sh
-+ eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" > conftest.sh \
-+ 2>&5
- . ./conftest.sh
-- rm -f contest*
-+ rm -f conftest*
-
- fi
- { echo "$as_me:$LINENO: result: $ncbi_cv_lib_berkeley_db_version" >&5
-@@ -33569,16 +33575,27 @@ cat confdefs.h >>conftest.$ac_ext
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h. */
-
-+cat >/dev/null <<_NCBI_EOF
- #include <boost/version.hpp>
--ncbi_cv_lib_boost_version_num=BOOST_VERSION
--ncbi_cv_lib_boost_version=BOOST_LIB_VERSION
-+_NCBI_EOF
-+get_BOOST_VERSION() {
-+ grep '^[^#]' <<_NCBI_EOF
-+BOOST_VERSION
-+_NCBI_EOF
-+}
-+get_BOOST_LIB_VERSION() {
-+ grep '^[^#]' <<_NCBI_EOF
-+BOOST_LIB_VERSION
-+_NCBI_EOF
-+}
-+ncbi_cv_lib_boost_version_num=\`get_BOOST_VERSION\`
-+ncbi_cv_lib_boost_version=\`get_BOOST_LIB_VERSION | tr -d '"'\`
-
- _ACEOF
-- eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" \
-- 2>&5 | grep '^ncbi_cv_' \
-- | tr -d "$wschars" > conftest.sh
-+ eval "$ac_cpp $BOOST_INCLUDE conftest.$ac_ext" > conftest.sh \
-+ 2>&5
- . ./conftest.sh
-- rm -f contest*
-+ rm -f conftest*
-
- fi
- { echo "$as_me:$LINENO: result: $ncbi_cv_lib_boost_version" >&5
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -4905,14 +4905,20 @@ if test "$with_bdb" != "no" ; then
- AC_CACHE_CHECK([Berkeley DB version (4.3 or newer required)],
- ncbi_cv_lib_berkeley_db_version,
- [AC_LANG_CONFTEST([AC_LANG_SOURCE([[
-+cat >/dev/null <<_NCBI_EOF
- #include <db.h>
--ncbi_cv_lib_berkeley_db_version=DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH
-+_NCBI_EOF
-+get_DB_VERSION() {
-+ grep '^[^#]' <<_NCBI_EOF
-+DB_VERSION_MAJOR.DB_VERSION_MINOR.DB_VERSION_PATCH
-+_NCBI_EOF
-+}
-+ncbi_cv_lib_berkeley_db_version=\`get_DB_VERSION | tr -cd 0123456789.\`
- ]])])
-- eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" \
-- 2>&AS_MESSAGE_LOG_FD | grep '^ncbi_cv_' \
-- | tr -d "$wschars" > conftest.sh
-+ eval "$ac_cpp $BERKELEYDB_INCLUDE conftest.$ac_ext" > conftest.sh \
-+ 2>&AS_MESSAGE_LOG_FD
- . ./conftest.sh
-- rm -f contest*
-+ rm -f conftest*
- ])
- case "$ncbi_cv_lib_berkeley_db_version" in
- 1.* | 2.* | 3.* | 4.[[0-2]].* )
@@ -5181,15 +5187,26 @@ if test "$with_boost" != "no"; then
AC_CACHE_CHECK([Boost version],
ncbi_cv_lib_boost_version,
diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes
index 6d2c913..13d2072 100644
--- a/debian/patches/hurd_fixes
+++ b/debian/patches/hurd_fixes
@@ -9,7 +9,7 @@ Author: Aaron M. Ucko <ucko at debian.org>
Last-Update: 2011-06-10
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -9000,7 +9000,7 @@ if test -z "$CONF_f_runpath" ; then
+@@ -9157,7 +9157,7 @@
solaris* )
CONF_f_runpath="-R"
;;
@@ -20,7 +20,7 @@ Last-Update: 2011-06-10
irix*:* | linux*:KCC | *:Compaq )
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -1894,7 +1894,7 @@ if test -z "$CONF_f_runpath" ; then
+@@ -1939,7 +1939,7 @@
solaris* )
CONF_f_runpath="-R"
;;
diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 70543bb..870d187 100644
--- a/debian/patches/no_multiarch_rpath
+++ b/debian/patches/no_multiarch_rpath
@@ -10,7 +10,7 @@ Author: Aaron M. Ucko <ucko at debian.org>
Last-Update: 2011-08-28
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -9107,7 +9107,7 @@ echo "$as_me: WARNING: Unable to find st
+@@ -9264,7 +9264,7 @@
break
;;
/* )
@@ -21,7 +21,7 @@ Last-Update: 2011-08-28
esac
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -1961,7 +1961,7 @@ case "$compiler:$compiler_version:$with_
+@@ -2006,7 +2006,7 @@
break
;;
/* )
diff --git a/debian/patches/series b/debian/patches/series
index 2fd0e8c..37dc548 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,6 +6,6 @@ no_multiarch_rpath
use_pie_for_apps
skip_services_unit_test
fix_configure
-fix_version_extraction
-support_recent_boost
+#fix_version_extraction
+#support_recent_boost
support_x32
diff --git a/debian/patches/support_recent_boost b/debian/patches/support_recent_boost
index 8e7bc85..d223c85 100644
--- a/debian/patches/support_recent_boost
+++ b/debian/patches/support_recent_boost
@@ -1,252 +1,3 @@
---- a/c++/src/corelib/teamcity_boost.cpp
-+++ b/c++/src/corelib/teamcity_boost.cpp
-@@ -1,83 +1,106 @@
- /* Copyright 2011 JetBrains s.r.o.
-- *
-+ *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
-- *
-+ *
- * http://www.apache.org/licenses/LICENSE-2.0
-- *
-+ *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
-- *
-+ *
- * $Id: teamcity_boost.cpp 488254 2015-12-29 13:56:26Z ivanov $
- */
-
- #include <sstream>
-
--#include <boost/test/unit_test_suite_impl.hpp>
- #include <boost/test/results_collector.hpp>
- #include <boost/test/utils/basic_cstring/io.hpp>
- #include <boost/test/unit_test_log.hpp>
--#include <boost/test/included/unit_test.hpp>
-+#include <boost/test/execution_monitor.hpp>
-+#include <boost/test/unit_test_log_formatter.hpp>
-+#include <boost/test/unit_test.hpp>
-+
-+// In 1.59.0, they changed the name of this enum value, so we have to this hacky thing...
-+#include <boost/version.hpp>
-+#if BOOST_VERSION >= 105900
-+ #define TUT_CASE_IDENTIFIER boost::unit_test::TUT_CASE
-+ #define CURRENT_TEST_NAME boost::unit_test_framework::framework::current_test_case().full_name()
-+#else
-+ #define TUT_CASE_IDENTIFIER boost::unit_test::tut_case
-+ #define CURRENT_TEST_NAME boost::unit_test_framework::framework::current_test_case().p_name
-+#endif
-
- #include "teamcity_messages.h"
-
--///
--// NOTE: Using namespace boost::unit_test breaks GPIPE Static build!!
--///
--//using namespace boost::unit_test;
--using namespace std;
--
--namespace JetBrains {
-+namespace jetbrains { namespace teamcity {
-+const std::string ASSERT_CTX = "Assertion occurred in a following context:";
-+const std::string FAILURE_CTX = "Failure occurred in a following context:";
-
- // Custom formatter for TeamCity messages
- class TeamcityBoostLogFormatter: public boost::unit_test::unit_test_log_formatter {
- TeamcityMessages messages;
- std::string currentDetails;
-+ std::string currentContextDetails;
- std::string flowId;
-
- public:
- TeamcityBoostLogFormatter(const std::string &_flowId);
- TeamcityBoostLogFormatter();
-
-- void log_start(std::ostream&, boost::unit_test::counter_t test_cases_amount);
-- void log_finish(std::ostream&);
-- void log_build_info(std::ostream&);
-+ virtual ~TeamcityBoostLogFormatter() {}
-+
-+ virtual void log_start(std::ostream&, boost::unit_test::counter_t test_cases_amount);
-+ virtual void log_finish(std::ostream&);
-+ virtual void log_build_info(std::ostream&);
-
-- void test_unit_start(std::ostream&, boost::unit_test::test_unit const& tu);
-- void test_unit_finish(std::ostream&,
-+ virtual void test_unit_start(std::ostream&, boost::unit_test::test_unit const& tu);
-+ virtual void test_unit_finish(std::ostream&,
- boost::unit_test::test_unit const& tu,
- unsigned long elapsed);
-- void test_unit_skipped(std::ostream&, boost::unit_test::test_unit const& tu);
-+ virtual void test_unit_skipped(std::ostream&, boost::unit_test::test_unit const& tu);
-+ virtual void test_unit_skipped(std::ostream&,
-+ boost::unit_test::test_unit const& tu,
-+ boost::unit_test::const_string reason);
-
-- void log_exception(std::ostream&,
-+ virtual void log_exception(std::ostream&,
- boost::unit_test::log_checkpoint_data const&,
- boost::unit_test::const_string explanation);
-+ virtual void log_exception_start(std::ostream&,
-+ boost::unit_test::log_checkpoint_data const&,
-+ const boost::execution_exception&);
-+ virtual void log_exception_finish(std::ostream&);
-
-- void log_entry_start(std::ostream&,
-- boost::unit_test::log_entry_data const&,
-+ virtual void log_entry_start(std::ostream & out,
-+ boost::unit_test::log_entry_data const & entry_data,
- log_entry_types let);
-- void log_entry_value(std::ostream&, boost::unit_test::const_string value);
-- void log_entry_finish(std::ostream&);
-+ virtual void log_entry_value(std::ostream&, boost::unit_test::const_string value);
-+ virtual void log_entry_finish(std::ostream&);
-+
-+ virtual void entry_context_start(std::ostream&, boost::unit_test::log_level);
-+ virtual void log_entry_context(std::ostream&, boost::unit_test::const_string);
-+ virtual void entry_context_finish(std::ostream&);
- };
-
- // Fake fixture to register formatter
- struct TeamcityFormatterRegistrar {
- TeamcityFormatterRegistrar() {
-- if (JetBrains::underTeamcity()) {
-- boost::unit_test::unit_test_log.set_formatter(new JetBrains::TeamcityBoostLogFormatter());
-- boost::unit_test::unit_test_log.set_threshold_level(boost::unit_test::runtime_config::log_level());
-+ if (underTeamcity()) {
-+ boost::unit_test::unit_test_log.set_formatter(new TeamcityBoostLogFormatter());
-+ boost::unit_test::unit_test_log.set_threshold_level
-+ (RTCFG(but::log_level, LOG_LEVEL, log_level));
- }
- }
- };
-+
- BOOST_GLOBAL_FIXTURE(TeamcityFormatterRegistrar);
-
- // Formatter implementation
--string toString(boost::unit_test::const_string bstr) {
-- stringstream ss;
-+static std::string toString(boost::unit_test::const_string bstr) {
-+ std::stringstream ss;
-
- ss << bstr;
-
-@@ -92,19 +115,19 @@ TeamcityBoostLogFormatter::TeamcityBoost
- : flowId(getFlowIdFromEnvironment())
- {}
-
--void TeamcityBoostLogFormatter::log_start(ostream &out, boost::unit_test::counter_t test_cases_amount)
-+void TeamcityBoostLogFormatter::log_start(std::ostream &/*out*/, boost::unit_test::counter_t /*test_cases_amount*/)
- {}
-
--void TeamcityBoostLogFormatter::log_finish(ostream &out)
-+void TeamcityBoostLogFormatter::log_finish(std::ostream &/*out*/)
- {}
-
--void TeamcityBoostLogFormatter::log_build_info(ostream &out)
-+void TeamcityBoostLogFormatter::log_build_info(std::ostream &/*out*/)
- {}
-
--void TeamcityBoostLogFormatter::test_unit_start(ostream &out, boost::unit_test::test_unit const& tu) {
-+void TeamcityBoostLogFormatter::test_unit_start(std::ostream &out, boost::unit_test::test_unit const& tu) {
- messages.setOutput(out);
-
-- if (tu.p_type == boost::unit_test::tut_case) {
-+ if (tu.p_type == TUT_CASE_IDENTIFIER) {
- messages.testStarted(tu.p_name, flowId);
- } else {
- messages.suiteStarted(tu.p_name, flowId);
-@@ -113,11 +136,11 @@ void TeamcityBoostLogFormatter::test_uni
- currentDetails.clear();
- }
-
--void TeamcityBoostLogFormatter::test_unit_finish(ostream &out, boost::unit_test::test_unit const& tu, unsigned long elapsed) {
-+void TeamcityBoostLogFormatter::test_unit_finish(std::ostream &out, boost::unit_test::test_unit const& tu, unsigned long elapsed) {
- messages.setOutput(out);
-
- boost::unit_test::test_results const& tr = boost::unit_test::results_collector.results(tu.p_id);
-- if (tu.p_type == boost::unit_test::tut_case) {
-+ if (tu.p_type == TUT_CASE_IDENTIFIER) {
- if(!tr.passed()) {
- if(tr.p_skipped) {
- messages.testIgnored(tu.p_name, "ignored", flowId);
-@@ -134,27 +157,62 @@ void TeamcityBoostLogFormatter::test_uni
- }
- }
-
--void TeamcityBoostLogFormatter::test_unit_skipped(ostream &out, boost::unit_test::test_unit const& tu)
-+void TeamcityBoostLogFormatter::test_unit_skipped(std::ostream &/*out*/, boost::unit_test::test_unit const& /*tu*/)
- {}
-
--void TeamcityBoostLogFormatter::log_exception(ostream &out, boost::unit_test::log_checkpoint_data const&, boost::unit_test::const_string explanation) {
-- string what = toString(explanation);
-+void TeamcityBoostLogFormatter::test_unit_skipped(std::ostream &out, boost::unit_test::test_unit const& tu, boost::unit_test::const_string reason)
-+{
-+ messages.testIgnored(tu.p_name, toString(reason), flowId);
-+}
-+
-+void TeamcityBoostLogFormatter::log_exception(std::ostream &out, boost::unit_test::log_checkpoint_data const &, boost::unit_test::const_string explanation) {
-+ std::string what = toString(explanation);
-
-- out << what << endl;
-+ out << what << std::endl;
- currentDetails += what + "\n";
- }
-
--void TeamcityBoostLogFormatter::log_entry_start(ostream&, boost::unit_test::log_entry_data const&, log_entry_types let)
--{}
-+void TeamcityBoostLogFormatter::log_exception_start(std::ostream &out, boost::unit_test::log_checkpoint_data const &data, const boost::execution_exception& excpt) {
-+ log_exception(out, data, excpt.what());
-+}
-+
-+void TeamcityBoostLogFormatter::log_exception_finish(std::ostream &/*out*/) {}
-
--void TeamcityBoostLogFormatter::log_entry_value(ostream &out, boost::unit_test::const_string value) {
-+
-+void TeamcityBoostLogFormatter::log_entry_start(std::ostream & out, boost::unit_test::log_entry_data const & entry_data, log_entry_types /*let*/)
-+{
-+ std::stringstream ss(std::ios_base::out);
-+
-+ out << entry_data.m_file_name << "(" << entry_data.m_line_num << "): ";
-+ ss << entry_data.m_file_name << "(" << entry_data.m_line_num << "): ";
-+
-+ currentDetails += ss.str();
-+}
-+
-+void TeamcityBoostLogFormatter::log_entry_value(std::ostream &out, boost::unit_test::const_string value) {
- out << value;
- currentDetails += toString(value);
- }
-
--void TeamcityBoostLogFormatter::log_entry_finish(ostream &out) {
-- out << endl;
-+void TeamcityBoostLogFormatter::log_entry_finish(std::ostream &out) {
-+ out << std::endl;
- currentDetails += "\n";
- }
-
-+void TeamcityBoostLogFormatter::entry_context_start(std::ostream &out, boost::unit_test::log_level l) {
-+ const std::string& initial_msg = (l == boost::unit_test::log_successful_tests ? ASSERT_CTX : FAILURE_CTX);
-+ out << initial_msg;
-+ currentContextDetails = initial_msg;
- }
-+
-+void TeamcityBoostLogFormatter::log_entry_context(std::ostream &out, boost::unit_test::const_string ctx) {
-+ out << "\n " << ctx;
-+ currentContextDetails += "\n " + toString(ctx);
-+}
-+
-+void TeamcityBoostLogFormatter::entry_context_finish(std::ostream &out) {
-+ out.flush();
-+ messages.testOutput(CURRENT_TEST_NAME, currentContextDetails, flowId, TeamcityMessages::StdErr);
-+}
-+
-+}} // namespace teamcity, jetbrains
--- a/c++/src/corelib/teamcity_messages.cpp
+++ b/c++/src/corelib/teamcity_messages.cpp
@@ -15,40 +15,61 @@
diff --git a/debian/patches/support_x32 b/debian/patches/support_x32
index 8c8874f..df9fb95 100644
--- a/debian/patches/support_x32
+++ b/debian/patches/support_x32
@@ -1,6 +1,6 @@
--- a/c++/include/corelib/impl/ncbi_atomic_defs.h
+++ b/c++/include/corelib/impl/ncbi_atomic_defs.h
-@@ -117,7 +117,7 @@ extern "C" {
+@@ -117,7 +117,7 @@
((defined(__i386) || defined(__sparc) || defined(__x86_64)) && \
!defined(__GLIBCPP__) /* < 3.0 or >= 3.4 */) && \
(!defined(__GLIBCXX__) || !defined(NCBI_TCHECK)))
--
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