diff options
Diffstat (limited to 'sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch')
| -rw-r--r-- | sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch | 421 |
1 files changed, 0 insertions, 421 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch deleted file mode 100644 index 86e96b865..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch +++ /dev/null @@ -1,421 +0,0 @@ -Index: src/algo/blast/format/Makefile.xblastformat.lib -=================================================================== ---- src/algo/blast/format/Makefile.xblastformat.lib (revision 439078) -+++ src/algo/blast/format/Makefile.xblastformat.lib (working copy) -@@ -7,6 +7,6 @@ - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - --DLL_LIB = align_format blastxml xhtml xcgi -+DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi - - WATCHERS = jianye zaretska madden camacho fongah2 -Index: src/app/compart/Makefile.compart.app -=================================================================== ---- src/app/compart/Makefile.compart.app (revision 439078) -+++ src/app/compart/Makefile.compart.app (working copy) -@@ -5,11 +5,11 @@ - APP = compart - SRC = compart - --LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \ -- $(BLAST_LIBS:%=%$(STATIC)) \ -- $(OBJMGR_LIBS:%=%$(STATIC)) -+LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ -+ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ -+ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/compart/Makefile.compartp.app -=================================================================== ---- src/app/compart/Makefile.compartp.app (revision 439078) -+++ src/app/compart/Makefile.compartp.app (working copy) -@@ -5,7 +5,8 @@ - APP = compartp - SRC = compartp - --LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/app/grid/util/Makefile.ncfetch.app -=================================================================== ---- src/app/grid/util/Makefile.ncfetch.app (revision 439078) -+++ src/app/grid/util/Makefile.ncfetch.app (working copy) -@@ -5,7 +5,7 @@ - APP = ncfetch.cgi - SRC = ncfetch - --LIB = xcgi xconnserv xconnect xutil xncbi -+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - WATCHERS = kazimird -Index: src/app/hfilter/Makefile.hfilter.app -=================================================================== ---- src/app/hfilter/Makefile.hfilter.app (revision 439078) -+++ src/app/hfilter/Makefile.hfilter.app (working copy) -@@ -5,9 +5,10 @@ - APP = hfilter - SRC = hitfilter_app - --LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/speedtest/Makefile.speedtest.app -=================================================================== ---- src/app/speedtest/Makefile.speedtest.app (revision 439078) -+++ src/app/speedtest/Makefile.speedtest.app (working copy) -@@ -8,7 +8,7 @@ - - APP = speedtest - SRC = speedtest --LIB = prosplign xalgoalignutil xcleanup submit $(BLAST_LIBS) \ -+LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ - xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) -Index: src/app/splign/Makefile.splign.app -=================================================================== ---- src/app/splign/Makefile.splign.app (revision 439078) -+++ src/app/splign/Makefile.splign.app (working copy) -@@ -12,7 +12,7 @@ - LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ - $(BLAST_DB_DATA_LOADER_LIBS) \ - ncbi_xloader_lds2 lds2 sqlitewrapp \ -- xqueryparse xalgoseq $(PCRE_LIB) \ -+ xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) submit \ - $(OBJMGR_LIBS:%=%$(STATIC)) - -Index: src/connect/services/test/Makefile.test_nsstorage.app -=================================================================== ---- src/connect/services/test/Makefile.test_nsstorage.app (revision 439078) -+++ src/connect/services/test/Makefile.test_nsstorage.app (working copy) -@@ -2,7 +2,7 @@ - - APP = test_nsstorage - SRC = test_nsstorage --LIB = xconnserv xconnect xutil xncbi -+LIB = xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/misc/hgvs/test/Makefile.hgvs2variation.app -=================================================================== ---- src/misc/hgvs/test/Makefile.hgvs2variation.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.hgvs2variation.app (working copy) -@@ -6,7 +6,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation \ -+LIB_ = hgvs objcoords variation \ - entrez2cli entrez2 xregexp $(PCRE_LIB) xobjutil $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - -Index: src/misc/hgvs/test/Makefile.test_hgvs_parser.app -=================================================================== ---- src/misc/hgvs/test/Makefile.test_hgvs_parser.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.test_hgvs_parser.app (working copy) -@@ -5,7 +5,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation test_boost xregexp $(PCRE_LIB) xobjutil \ -+LIB_ = hgvs objcoords variation test_boost xregexp $(PCRE_LIB) xobjutil \ - entrez2cli entrez2 $(OBJMGR_LIBS) - - LIB = $(LIB_:%=%$(STATIC)) -Index: src/objects/biblio/Makefile.biblio.lib -=================================================================== ---- src/objects/biblio/Makefile.biblio.lib (revision 439078) -+++ src/objects/biblio/Makefile.biblio.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = biblio - SRC = biblio__ biblio___ citation_base -+ -+DLL_LIB = general -Index: src/objects/blast/Makefile.blast.lib -=================================================================== ---- src/objects/blast/Makefile.blast.lib (revision 439078) -+++ src/objects/blast/Makefile.blast.lib (working copy) -@@ -1,4 +1,6 @@ - LIB = xnetblast - SRC = blast__ blast___ names - -+DLL_LIB = scoremat seqset -+ - WATCHERS = camacho -Index: src/objects/blast/Makefile.xnetblastcli.lib -=================================================================== ---- src/objects/blast/Makefile.xnetblastcli.lib (revision 439078) -+++ src/objects/blast/Makefile.xnetblastcli.lib (working copy) -@@ -2,3 +2,5 @@ - - LIB = xnetblastcli - SRC = blastclient blastclient_ -+ -+DLL_LIB = xnetblast xconnect -Index: src/objects/blastdb/Makefile.blastdb.lib -=================================================================== ---- src/objects/blastdb/Makefile.blastdb.lib (revision 439078) -+++ src/objects/blastdb/Makefile.blastdb.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = blastdb - SRC = blastdb__ blastdb___ -+ -+DLL_LIB = seq -Index: src/objects/general/Makefile.general.lib -=================================================================== ---- src/objects/general/Makefile.general.lib (revision 439078) -+++ src/objects/general/Makefile.general.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = general - SRC = general__ general___ uoconv -+ -+DLL_LIB = xser -Index: src/objects/medline/Makefile.medline.lib -=================================================================== ---- src/objects/medline/Makefile.medline.lib (revision 439078) -+++ src/objects/medline/Makefile.medline.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = medline - SRC = medline__ medline___ -+ -+DLL_LIB = biblio general -Index: src/objects/pub/Makefile.pub.lib -=================================================================== ---- src/objects/pub/Makefile.pub.lib (revision 439078) -+++ src/objects/pub/Makefile.pub.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = pub - SRC = pub__ pub___ -+ -+DLL_LIB = medline biblio -Index: src/objects/scoremat/Makefile.scoremat.lib -=================================================================== ---- src/objects/scoremat/Makefile.scoremat.lib (revision 439078) -+++ src/objects/scoremat/Makefile.scoremat.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = scoremat - SRC = scoremat__ scoremat___ -+ -+DLL_LIB = seqset -Index: src/objects/seq/Makefile.seq.lib -=================================================================== ---- src/objects/seq/Makefile.seq.lib (revision 439078) -+++ src/objects/seq/Makefile.seq.lib (working copy) -@@ -13,3 +13,5 @@ - seq_loc_from_string seq_loc_reverse_complementer - - WATCHERS = vasilche grichenk -+ -+DLL_LIB = seqcode pub biblio general xser sequtil -Index: src/objects/seqset/Makefile.seqset.lib -=================================================================== ---- src/objects/seqset/Makefile.seqset.lib (revision 439078) -+++ src/objects/seqset/Makefile.seqset.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = seqset - SRC = seqset__ seqset___ gb_release_file -+ -+DLL_LIB = xser -Index: src/objects/taxon1/Makefile.taxon1.lib -=================================================================== ---- src/objects/taxon1/Makefile.taxon1.lib (revision 439078) -+++ src/objects/taxon1/Makefile.taxon1.lib (working copy) -@@ -3,4 +3,6 @@ - LIB = taxon1 - SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont - -+DLL_LIB = xconnect -+ - WATCHERS = domrach -Index: src/objmgr/util/Makefile.util.lib -=================================================================== ---- src/objmgr/util/Makefile.util.lib (revision 439078) -+++ src/objmgr/util/Makefile.util.lib (working copy) -@@ -8,5 +8,7 @@ - SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util - LIB = xobjutil - -+DLL_LIB = xobjmgr -+ - WATCHERS = ucko vasilche - -Index: src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -=================================================================== ---- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (revision 439078) -+++ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (working copy) -@@ -29,4 +29,6 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xobjmgr blastdb -+ - WATCHERS = maning camacho -Index: src/objtools/blast/services/Makefile.blast_services.lib -=================================================================== ---- src/objtools/blast/services/Makefile.blast_services.lib (revision 439078) -+++ src/objtools/blast/services/Makefile.blast_services.lib (working copy) -@@ -13,3 +13,4 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xnetblastcli xconnect -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb seqset - -+DLL_LIB = seqdb -+ - WATCHERS = camacho -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb xnetblast - -+DLL_LIB = blast_services -+ - WATCHERS = camacho -Index: src/objtools/lds2/Makefile.lds2.lib -=================================================================== ---- src/objtools/lds2/Makefile.lds2.lib (revision 439078) -+++ src/objtools/lds2/Makefile.lds2.lib (working copy) -@@ -8,9 +8,9 @@ - SRC = lds2 lds2_db lds2_handlers - - # Dependencies for shared library --#DLL_LIB = sqlitewrapp -+DLL_LIB = sqlitewrapp $(COMPRESS_LIBS) - --LIBS = $(CMPRS_LIBS) $(ORIG_LIBS) -+LIBS = $(SQLITE3_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) - - CPPFLAGS = $(SQLITE3_INCLUDE) $(CMPRS_INCLUDE) $(ORIG_CPPFLAGS) - -Index: src/objtools/readers/Makefile.xobjread.lib -=================================================================== ---- src/objtools/readers/Makefile.xobjread.lib (revision 439078) -+++ src/objtools/readers/Makefile.xobjread.lib (working copy) -@@ -19,5 +19,6 @@ - best_feat_finder source_mod_parser fasta_exception - - --DLL_LIB = creaders -+DLL_LIB = seqset $(SEQ_LIBS) pub general creaders xutil - -+ -Index: src/sample/app/cgi/Makefile.cgi_session_sample.app -=================================================================== ---- src/sample/app/cgi/Makefile.cgi_session_sample.app (revision 439078) -+++ src/sample/app/cgi/Makefile.cgi_session_sample.app (working copy) -@@ -11,7 +11,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi -+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/sample/app/netcache/Makefile.netcache_cgi_sample.app -=================================================================== ---- src/sample/app/netcache/Makefile.netcache_cgi_sample.app (revision 439078) -+++ src/sample/app/netcache/Makefile.netcache_cgi_sample.app (working copy) -@@ -4,7 +4,7 @@ - SRC = netcache_cgi_sample - - ### BEGIN COPIED SETTINGS --LIB = xconnserv xconnect xcgi xhtml xutil xncbi -+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ### END COPIED SETTINGS -Index: src/serial/Makefile.serial.lib -=================================================================== ---- src/serial/Makefile.serial.lib (revision 439078) -+++ src/serial/Makefile.serial.lib (working copy) -@@ -19,3 +19,5 @@ - LIB = xser - - WATCHERS = gouriano -+ -+DLL_LIB = xutil xncbi -Index: src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app -=================================================================== ---- src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (revision 439078) -+++ src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (working copy) -@@ -7,7 +7,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_bam bamread $(BAM_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_bam bamread $(BAM_LIBS) \ -+ xobjreadex $(OBJREAD_LIBS) xobjutil test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app -=================================================================== ---- src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (revision 439078) -+++ src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (working copy) -@@ -5,7 +5,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil \ -+ test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/readers/bam/test/Makefile.bam_test.app -=================================================================== ---- src/sra/readers/bam/test/Makefile.bam_test.app (revision 439078) -+++ src/sra/readers/bam/test/Makefile.bam_test.app (working copy) -@@ -9,7 +9,8 @@ - APP = bam_test - SRC = bam_test - --LIB = bamread xobjreadex xobjutil xobjsimple $(OBJMGR_LIBS) $(BAM_LIBS) -+LIB = bamread $(BAM_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil xobjsimple \ -+ $(OBJMGR_LIBS) - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - - REQUIRES = objects -Index: src/sra/sdk/libs/vfs/Makefile.vfs.lib -=================================================================== ---- src/sra/sdk/libs/vfs/Makefile.vfs.lib (revision 16076) -+++ src/sra/sdk/libs/vfs/Makefile.vfs.lib (working copy) -@@ -8,6 +8,9 @@ - CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \ - $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS) - --DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) -+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) \ -+ krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) - -+LIBS = $(SRA_SDK_SYSLIBS) -+ - LIB_OR_DLL = both |