From: Olivier Sallou Date: Sun, 11 Feb 2018 09:21:27 +0000 (+0000) Subject: update patches to new release X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~179^2^2~2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=b762cc31b4784331a8613273855a2e0cdc6ea494;p=ncbi-blast%2B.git update patches to new release --- diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 0692cafe..9182e5b8 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -14,26 +14,6 @@ Subject: ensure that all libraries link against all direct dependencies Debian-Bug: 633567. Author: Aaron M. Ucko Last-Update: 2016-12-05 ---- a/c++/src/algo/blast/api/Makefile.xblast.lib -+++ b/c++/src/algo/blast/api/Makefile.xblast.lib -@@ -76,14 +76,15 @@ - magicblast_options \ - magicblast - --SRC = $(SRC_C:%=.core_%) $(SRC_CXX) -+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%) - - LIB = xblast - - DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \ - xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \ - blastdb xnetblastcli xnetblast scoremat xconnect tables \ -- $(SOBJMGR_LIBS) -+ $(SOBJMGR_LIBS) blast seqdb seqset seq general \ -+ xser xconnect sequtil tables xutil xncbi - - CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS) --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib @@ -27,7 +27,9 @@ @@ -114,7 +94,7 @@ Last-Update: 2016-12-05 seqmasks_io --- a/c++/src/build-system/library_relations.txt +++ b/c++/src/build-system/library_relations.txt -@@ -1287,7 +1287,7 @@ +@@ -1308,7 +1308,7 @@ xbiosample_util needs $(XFORMAT_LIBS) xbiosample_util needs xalnmgr xbiosample_util needs xmlwrapp @@ -134,17 +114,6 @@ Last-Update: 2016-12-05 CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) WATCHERS = vakatov ---- a/c++/src/connect/Makefile.xconnect.lib -+++ b/c++/src/connect/Makefile.xconnect.lib -@@ -14,6 +14,8 @@ - LIB = xconnect - PROJ_TAG = core - -+DLL_LIB = xncbi -+ - LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) - - WATCHERS = lavr elisovdn --- a/c++/src/corelib/Makefile.test_boost.lib +++ b/c++/src/corelib/Makefile.test_boost.lib @@ -3,6 +3,8 @@ @@ -233,17 +202,6 @@ Last-Update: 2016-12-05 WATCHERS = vasilche ---- a/c++/src/objects/seq/Makefile.seq.lib -+++ b/c++/src/objects/seq/Makefile.seq.lib -@@ -14,6 +14,8 @@ - - DLL_LIB = seqcode pub general xser sequtil - -+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 @@ -1,6 +1,8 @@ @@ -266,17 +224,6 @@ Last-Update: 2016-12-05 USES_LIBRARIES = \ ---- a/c++/src/objects/seqset/Makefile.seqset.lib -+++ b/c++/src/objects/seqset/Makefile.seqset.lib -@@ -1,6 +1,8 @@ - LIB = seqset - SRC = seqset__ seqset___ gb_release_file - -+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 @@ -1,6 +1,8 @@ @@ -312,9 +259,9 @@ Last-Update: 2016-12-05 --- a/c++/src/objmgr/util/Makefile.util.lib +++ b/c++/src/objmgr/util/Makefile.util.lib -@@ -11,6 +11,8 @@ +@@ -14,6 +14,8 @@ - DLL_LIB = $(SOBJMGR_LIBS) + DLL_LIB = submit $(SOBJMGR_LIBS) +DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi + @@ -367,7 +314,7 @@ Last-Update: 2016-12-05 CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib -@@ -8,6 +8,9 @@ +@@ -11,6 +11,9 @@ LIB = writedb @@ -449,7 +396,7 @@ Last-Update: 2016-12-05 +++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib @@ -12,6 +12,8 @@ # Dependencies for shared library - DLL_LIB = xconnect ncbi_xreader$(DLL) + DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_READER_LDEP) +DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi + @@ -622,16 +569,6 @@ Last-Update: 2016-12-05 USES_LIBRARIES = \ xser ---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib -+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib -@@ -5,6 +5,7 @@ - LIB = entrez2cli - SRC = entrez2_client entrez2_client_ - -+DLL_LIB = entrez2 xconnect xser xutil xncbi - - USES_LIBRARIES = \ - entrez2 xconnect --- a/c++/src/objects/gbseq/Makefile.gbseq.lib +++ b/c++/src/objects/gbseq/Makefile.gbseq.lib @@ -1,6 +1,7 @@ @@ -704,7 +641,7 @@ Last-Update: 2016-12-05 $(SEQ_LIBS) pub xconnect --- a/c++/src/objects/taxon3/Makefile.taxon3.lib +++ b/c++/src/objects/taxon3/Makefile.taxon3.lib -@@ -7,6 +7,7 @@ +@@ -8,6 +8,7 @@ WATCHERS = bollin holmesbr @@ -795,14 +732,63 @@ Last-Update: 2016-12-05 USES_LIBRARIES = \ xregexp $(PCRE_LIB) $(PCRE_LIBS) xncbi ---- a/c++/src/algo/blast/Makefile.blast_macros.mk -+++ b/c++/src/algo/blast/Makefile.blast_macros.mk -@@ -18,7 +18,7 @@ - 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 composition_adjustment blast \ - xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \ - xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables - # 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 +@@ -77,11 +77,11 @@ + magicblast_options \ + magicblast + +-SRC = $(SRC_C:%=.core_%) $(SRC_CXX) ++SRC = $(SRC_CXX) + + LIB = xblast + +-DLL_LIB = $(BLAST_LDEP) $(SOBJMGR_LIBS) ++DLL_LIB = $(BLAST_LDEP) $(SOBJMGR_LIBS) blast seqdb seqset seq general xser xconnect sequtil tables xutil xncbi + + CFLAGS = $(FAST_CFLAGS) + CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS) +--- a/c++/src/connect/Makefile.xconnect.lib ++++ b/c++/src/connect/Makefile.xconnect.lib +@@ -14,6 +14,8 @@ + LIB = xconnect + PROJ_TAG = core + ++DLL_LIB = xncbi ++ + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr mcelhany +--- a/c++/src/objects/seq/Makefile.seq.lib ++++ b/c++/src/objects/seq/Makefile.seq.lib +@@ -12,7 +12,7 @@ + seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map so_map \ + seq_loc_from_string seq_loc_reverse_complementer + +-DLL_LIB = seqcode pub general xser sequtil ++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi + + WATCHERS = vasilche grichenk bollin ludwigf + +--- a/c++/src/objects/seqset/Makefile.seqset.lib ++++ b/c++/src/objects/seqset/Makefile.seqset.lib +@@ -1,7 +1,7 @@ + LIB = seqset + SRC = seqset__ seqset___ gb_release_file + +-DLL_LIB = $(SEQ_LIBS) ++DLL_LIB = $(SEQ_LIBS) xser xncbi + + USES_LIBRARIES = \ + $(SEQ_LIBS) pub +--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib ++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib +@@ -5,7 +5,7 @@ + LIB = entrez2cli + SRC = entrez2_client entrez2_client_ + +-DLL_LIB = entrez2 xconnect ++DLL_LIB = entrez2 xconnect xser xutil xncbi + + USES_LIBRARIES = \ + entrez2 xconnect diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes index 13d20726..c664ef2a 100644 --- a/debian/patches/hurd_fixes +++ b/debian/patches/hurd_fixes @@ -9,7 +9,7 @@ Author: Aaron M. Ucko Last-Update: 2011-06-10 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -9157,7 +9157,7 @@ +@@ -9716,7 +9716,7 @@ 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 -@@ -1939,7 +1939,7 @@ +@@ -2081,7 +2081,7 @@ solaris* ) CONF_f_runpath="-R" ;; diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index 15cd5e30..a5601282 100644 --- a/debian/patches/no_multiarch_rpath +++ b/debian/patches/no_multiarch_rpath @@ -10,7 +10,7 @@ Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -9285,7 +9285,7 @@ +@@ -9823,7 +9823,7 @@ 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 -@@ -2006,7 +2006,7 @@ +@@ -2148,7 +2148,7 @@ break ;; /* ) diff --git a/debian/patches/suppress_gnutls_version_check b/debian/patches/suppress_gnutls_version_check index 7dca5fc0..3794f6c1 100644 --- a/debian/patches/suppress_gnutls_version_check +++ b/debian/patches/suppress_gnutls_version_check @@ -1,6 +1,6 @@ --- a/c++/src/connect/ncbi_gnutls.c +++ b/c++/src/connect/ncbi_gnutls.c -@@ -585,6 +585,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull +@@ -661,6 +661,7 @@ assert(!s_GnuTlsCredAnon); @@ -8,11 +8,11 @@ version = gnutls_check_version(0); if (strcasecmp(GNUTLS_VERSION, version) != 0) { CORE_LOGF(eLOG_Critical, -@@ -592,6 +593,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull +@@ -668,6 +669,7 @@ GNUTLS_VERSION, version)); assert(0); } +#endif - val = ConnNetInfo_GetValue(0, "GNUTLS_LOGLEVEL", buf, sizeof(buf), 0); - CORE_LOCK_READ; + if (!pull || !push) + return eIO_InvalidArg; diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps index b43c7b4f..89bc7d7d 100644 --- a/debian/patches/use_pie_for_apps +++ b/debian/patches/use_pie_for_apps @@ -7,7 +7,7 @@ Author: Aaron M. Ucko Last-Update: 2012-05-10 --- a/c++/src/build-system/Makefile.app.in +++ b/c++/src/build-system/Makefile.app.in -@@ -24,8 +24,8 @@ default_rule: all +@@ -24,8 +24,8 @@ ### C/C++ source file compilation setup @@ -18,12 +18,12 @@ Last-Update: 2012-05-10 SOURCES = @UNIX_SRC@ $(SRC) ### Standard application build rules -@@ -53,7 +53,7 @@ ifneq "" "$(wildcard Makefile.$(TMPL).ap - endif - endif +@@ -56,7 +56,7 @@ + include $(builddir)/Makefile.$(Rules) --CMD_BASE = $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) -+CMD_BASE = $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) + CMD_BASE = $(LINK_WRAPPER) $(LINK) +-CMD_BASEARGS = $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) ++CMD_BASEARGS = $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) CMD_TAIL = @f_outexe@$(XAPP) $(LINK_FILTER) - CMD = $(CMD_BASE) $(XLIB) $(XAPP_LIBS) $(CMD_TAIL) - CMD2 = $(CMD_BASE) $(XLIB2) $(XAPP_LIBS2) $(CMD_TAIL) + CMD_ARGS = $(CMD_BASEARGS) $(XLIB) $(XAPP_LIBS) + CMD_ARGS2 = $(CMD_BASEARGS) $(XLIB2) $(XAPP_LIBS2)