[med-svn] r18512 - in trunk/packages/ncbi-blast+/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Sat Nov 22 14:32:05 UTC 2014
Author: osallou
Date: 2014-11-22 14:32:04 +0000 (Sat, 22 Nov 2014)
New Revision: 18512
Modified:
trunk/packages/ncbi-blast+/trunk/debian/changelog
trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath
trunk/packages/ncbi-blast+/trunk/debian/patches/series
trunk/packages/ncbi-blast+/trunk/debian/patches/use_pie_for_apps
Log:
adapt patches to new release
Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2014-11-21 17:36:05 UTC (rev 18511)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog 2014-11-22 14:32:04 UTC (rev 18512)
@@ -2,7 +2,8 @@
* New upstream release
* d/control: switch to Standards 3.9.6
- [TODO] updates patches to new release
+ [TODO] fix missing Makefile.flat
+ [DONE] updates patches to new release
-- Olivier Sallou <osallou at debian.org> Fri, 21 Nov 2014 18:21:26 +0100
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2014-11-21 17:36:05 UTC (rev 18511)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2014-11-22 14:32:04 UTC (rev 18512)
@@ -13,13 +13,14 @@
Last-Update: 2011-08-28
--- a/c++/src/algo/blast/core/Makefile.blast.lib
+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,5 +21,6 @@
+@@ -21,6 +21,7 @@
CFLAGS = $(FAST_CFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
+DLL_LIB = composition_adjustment xconnect tables
- WATCHERS = maning madden camacho
+ WATCHERS = madden camacho
+
--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
@@ -11,6 +11,8 @@
@@ -33,22 +34,27 @@
WATCHERS = morgulis
--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,6 +7,7 @@
+@@ -7,7 +7,8 @@
CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
--DLL_LIB = align_format blastxml xhtml xcgi
+-DLL_LIB = align_format blastxml blastxml2 xhtml xcgi
+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi
++ seq general xser tables xncbi blastxml2
WATCHERS = jianye zaretska madden camacho fongah2
+
--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,3 +21,4 @@
+@@ -21,7 +21,7 @@
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
+-
+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
+
+ USES_LIBRARIES = \
+ seqmasks_io
--- a/c++/src/cgi/Makefile.cgi.lib
+++ b/c++/src/cgi/Makefile.cgi.lib
@@ -9,6 +9,8 @@
@@ -62,21 +68,25 @@
WATCHERS = vakatov
--- a/c++/src/html/Makefile.html.lib
+++ b/c++/src/html/Makefile.html.lib
-@@ -7,4 +7,6 @@
+@@ -7,6 +7,8 @@
commentdiag indentstream html_exception writer_htmlenc
LIB = xhtml
+DLL_LIB = xncbi
+
WATCHERS = ivanov
+
+
--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -2,3 +2,5 @@
-
+@@ -3,6 +3,7 @@
LIB = xnetblastcli
SRC = blastclient blastclient_
-+
+
+DLL_LIB = xnetblast xser xconnect xutil xncbi
+
+ USES_LIBRARIES = \
+ xconnect xnetblast
--- a/c++/src/objtools/align_format/Makefile.align_format.lib
+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
@@ -13,6 +13,10 @@
@@ -92,24 +102,29 @@
# CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -12,3 +12,5 @@
+@@ -12,7 +12,7 @@
WATCHERS = todorov dicuccio grichenk
+-
+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-+
+
+ USES_LIBRARIES = \
+ tables xobjutil
--- a/c++/src/objtools/readers/Makefile.xobjread.lib
+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -20,5 +20,5 @@
+@@ -21,7 +21,7 @@
message_listener line_error
-DLL_LIB = creaders
+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi
+
+
--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -12,6 +12,6 @@
+@@ -12,7 +12,7 @@
mask_writer_blastdb_maskinfo
ASN_DEP = seqset
@@ -117,6 +132,7 @@
+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
WATCHERS = morgulis camacho
+
--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
@@ -7,6 +7,8 @@
@@ -141,13 +157,15 @@
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -7,4 +7,6 @@
+@@ -7,6 +7,8 @@
ASN_DEP = blastdb seqset
+DLL_LIB = seqdb xobjmgr seqset seq xncbi
+
WATCHERS = camacho
+
+
--- 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
@@ -5,6 +5,8 @@
@@ -159,14 +177,6 @@
ASN_DEP = blastdb xnetblast
WATCHERS = camacho
---- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-@@ -5,3 +5,5 @@
- CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG_CPPFLAGS)
- LIB = gene_info
- SRC = gene_info gene_info_reader file_utils
-+
-+DLL_LIB = xncbi
--- a/c++/src/algo/blast/api/Makefile.xblast.lib
+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
@@ -74,14 +74,15 @@
@@ -224,70 +234,73 @@
WATCHERS = lavr
--- a/c++/src/connect/ext/Makefile.xconnext.lib
+++ b/c++/src/connect/ext/Makefile.xconnext.lib
-@@ -6,4 +6,6 @@
+@@ -6,6 +6,8 @@
LIB = xconnext
+DLL_LIB = xconnect xncbi
+
WATCHERS = lavr
+
+
--- a/c++/src/objects/blast/Makefile.blast.lib
+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -1,4 +1,6 @@
+@@ -1,6 +1,8 @@
LIB = xnetblast
SRC = blast__ blast___ names
+DLL_LIB = scoremat seqset seq xser xncbi
+
WATCHERS = camacho
+
+
--- a/c++/src/objects/blastxml/Makefile.blastxml.lib
+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = blastxml
SRC = blastxml__ blastxml___
-+
+
+DLL_LIB = xser xncbi
---- a/c++/src/objects/entrez2/Makefile.entrez2.lib
-+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
-@@ -2,3 +2,5 @@
-
- LIB = entrez2
- SRC = entrez2__ entrez2___
+
-+DLL_LIB = xser xncbi
---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-@@ -4,3 +4,5 @@
- LIB = entrez2cli
- SRC = entrez2_client entrez2_client_
-+
-+DLL_LIB = entrez2 xser xconnect xutil xncbi
+ USES_LIBRARIES = \
+ xser
--- a/c++/src/objects/scoremat/Makefile.scoremat.lib
+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = scoremat
SRC = scoremat__ scoremat___
+
++DLL_LIB = seqset seq general xser xncbi
+
-+DLL_LIB = seqset seq general xser xncbi
+
+ USES_LIBRARIES = \
+ seqset
--- a/c++/src/objects/seqedit/Makefile.seqedit.lib
+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
-@@ -1,3 +1,4 @@
+@@ -1,6 +1,7 @@
LIB = seqedit
SRC = seqedit__ seqedit___
-
+
+DLL_LIB = seqset seq general xser xncbi
+
+
+ USES_LIBRARIES = \
--- a/c++/src/objects/submit/Makefile.submit.lib
+++ b/c++/src/objects/submit/Makefile.submit.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = submit
SRC = submit__ submit___
+
++DLL_LIB = seqset seq biblio general xser xncbi
+
-+DLL_LIB = seqset seq biblio general xser xncbi
+
+ USES_LIBRARIES = \
+ seqset
--- a/c++/src/objmgr/util/Makefile.util.lib
+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,5 +8,7 @@
+@@ -8,6 +8,8 @@
SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
LIB = xobjutil
@@ -295,6 +308,7 @@
+
WATCHERS = ucko vasilche kornbluh
+
--- 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 @@
@@ -318,7 +332,7 @@
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,4 +12,7 @@
+@@ -12,6 +12,9 @@
# Dependencies for shared library
DLL_LIB = ncbi_xreader$(DLL)
@@ -326,9 +340,11 @@
+ xobjmgr seq xutil xncbi
+
WATCHERS = vasilche
+
+
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -15,4 +15,7 @@
+@@ -15,6 +15,9 @@
DLL_LIB =
DLL_DLIB = $(GENBANK_READER_LDEP)
@@ -336,6 +352,8 @@
+ xser xconnect xcompress xutil xncbi
+
WATCHERS = vasilche
+
+
--- 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 @@
@@ -360,7 +378,7 @@
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
-@@ -12,6 +12,9 @@
+@@ -12,7 +12,10 @@
CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
# Dependencies for shared library (disabled due to problems on Darwin)
@@ -371,6 +389,7 @@
+
WATCHERS = vasilche
+
--- a/c++/src/util/compress/api/Makefile.compress.lib
+++ b/c++/src/util/compress/api/Makefile.compress.lib
@@ -7,7 +7,7 @@
@@ -384,17 +403,19 @@
WATCHERS = ivanov
--- a/c++/src/util/sequtil/Makefile.sequtil.lib
+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
-@@ -3,4 +3,6 @@
+@@ -3,6 +3,8 @@
LIB = sequtil
SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
+DLL_LIB = xncbi
+
WATCHERS = shomrat
+
+
--- a/c++/src/corelib/Makefile.test_boost.lib
+++ b/c++/src/corelib/Makefile.test_boost.lib
@@ -3,6 +3,8 @@
- SRC = test_boost
+ SRC = test_boost teamcity_messages
LIB = test_boost
+DLL_LIB = xncbi
@@ -415,15 +436,19 @@
USE_PCH = no
--- a/c++/src/objects/biblio/Makefile.biblio.lib
+++ b/c++/src/objects/biblio/Makefile.biblio.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = biblio
SRC = biblio__ biblio___ citation_base
+
++DLL_LIB = general xser xncbi
+
-+DLL_LIB = general xser xncbi
+
+ USES_LIBRARIES = \
+ general
--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
@@ -1,5 +1,7 @@
- # $Id: Makefile.blastdb.lib 395653 2013-04-12 14:33:22Z vakatov $
+ # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $
+
+DLL_LIB = seq xser xncbi
@@ -432,93 +457,125 @@
--- a/c++/src/objects/general/Makefile.general.lib
+++ b/c++/src/objects/general/Makefile.general.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = general
SRC = general__ general___ uoconv
+
++DLL_LIB = xser xncbi
+
-+DLL_LIB = xser xncbi
+
+ USES_LIBRARIES = \
+ xser
--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-@@ -3,4 +3,6 @@
+@@ -3,6 +3,8 @@
LIB = genome_collection
SRC = genome_collection__ genome_collection___
+DLL_LIB = seq general xser xncbi
+
WATCHERS = dicuccio
+
+
--- a/c++/src/objects/id1/Makefile.id1.lib
+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,4 +3,6 @@
+@@ -3,6 +3,8 @@
LIB = id1
SRC = id1__ id1___
+DLL_LIB = seqset seq xser xncbi
+
WATCHERS = vasilche
+
+
--- a/c++/src/objects/id2/Makefile.id2.lib
+++ b/c++/src/objects/id2/Makefile.id2.lib
-@@ -1,4 +1,6 @@
+@@ -1,6 +1,8 @@
LIB = id2
SRC = id2__ id2___
+DLL_LIB = seqsplit seq xser xncbi
+
WATCHERS = vasilche
+
+
--- a/c++/src/objects/medline/Makefile.medline.lib
+++ b/c++/src/objects/medline/Makefile.medline.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = medline
SRC = medline__ medline___
+
++DLL_LIB = biblio general xser xncbi
+
-+DLL_LIB = biblio general xser xncbi
+
+ USES_LIBRARIES = \
+ biblio
--- a/c++/src/objects/pub/Makefile.pub.lib
+++ b/c++/src/objects/pub/Makefile.pub.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = pub
SRC = pub__ pub___
+
++DLL_LIB = medline biblio xser xncbi
+
-+DLL_LIB = medline biblio xser xncbi
+
+ USES_LIBRARIES = \
+ medline
--- a/c++/src/objects/seq/Makefile.seq.lib
+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,4 +12,6 @@
+@@ -12,6 +12,8 @@
seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
seq_loc_from_string seq_loc_reverse_complementer
+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
+
WATCHERS = vasilche grichenk
+
+
--- a/c++/src/objects/seqcode/Makefile.seqcode.lib
+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = seqcode
SRC = seqcode__ seqcode___
+
++DLL_LIB = xser xncbi
+
-+DLL_LIB = xser xncbi
+
+ USES_LIBRARIES = \
+ xser
--- a/c++/src/objects/seqset/Makefile.seqset.lib
+++ b/c++/src/objects/seqset/Makefile.seqset.lib
-@@ -1,2 +1,4 @@
+@@ -1,6 +1,8 @@
LIB = seqset
SRC = seqset__ seqset___ gb_release_file
+
++DLL_LIB = seq general xser xncbi
+
-+DLL_LIB = seq general xser xncbi
+
+ USES_LIBRARIES = \
+ $(SEQ_LIBS) pub
--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-@@ -1,4 +1,6 @@
+@@ -1,6 +1,8 @@
LIB = seqsplit
SRC = seqsplit__ seqsplit___
+DLL_LIB = seqset seq xser xncbi
+
WATCHERS = vasilche
+
+
--- a/c++/src/serial/Makefile.serial.lib
+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,4 +18,6 @@
+@@ -18,6 +18,8 @@
LIB = xser
+DLL_LIB = xutil xncbi
+
WATCHERS = gouriano
+
+
--- a/c++/src/util/Makefile.util.lib
+++ b/c++/src/util/Makefile.util.lib
@@ -12,6 +12,7 @@
@@ -553,7 +610,7 @@
--- a/c++/src/objmgr/split/Makefile.id2_split.lib
+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,6 +17,6 @@
+@@ -17,7 +17,7 @@
CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -561,6 +618,7 @@
+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
WATCHERS = vasilche
+
--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
@@ -8,6 +8,9 @@
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath 2014-11-21 17:36:05 UTC (rev 18511)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath 2014-11-22 14:32:04 UTC (rev 18512)
@@ -10,7 +10,7 @@
Last-Update: 2011-08-28
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -5923,7 +5923,7 @@
+@@ -7479,7 +7479,7 @@
break
;;
/* )
@@ -21,7 +21,7 @@
esac
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -1620,7 +1620,7 @@
+@@ -1836,7 +1836,7 @@
break
;;
/* )
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2014-11-21 17:36:05 UTC (rev 18511)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series 2014-11-22 14:32:04 UTC (rev 18512)
@@ -6,4 +6,3 @@
use_pie_for_apps
skip_services_unit_test
fix_configure
-include_typeinfo
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/use_pie_for_apps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/use_pie_for_apps 2014-11-21 17:36:05 UTC (rev 18511)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/use_pie_for_apps 2014-11-22 14:32:04 UTC (rev 18512)
@@ -18,9 +18,9 @@
SOURCES = @UNIX_SRC@ $(SRC)
### Standard application build rules
-@@ -122,7 +122,7 @@
+@@ -133,7 +133,7 @@
else
- $(XAPP): $(XOBJ) $(XLIBDEP)
+ $(XAPP): $(XOBJ) $(XOBJ2) $(XLIBDEP)
@-$(RM) .$(XAPP).stamp
- $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
+ $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
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