From f6b129e9165d07a5952f6373e0df27170c78b3cc Mon Sep 17 00:00:00 2001 From: Olivier Sallou Date: Wed, 11 Sep 2019 08:07:30 +0000 Subject: [PATCH] remove fuzz --- debian/patches/fix_lib_deps | 102 +++++++++++++++--------------- debian/patches/hurd_fixes | 4 +- debian/patches/no_multiarch_rpath | 4 +- 3 files changed, 55 insertions(+), 55 deletions(-) diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 5c4bfc11..89455233 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -16,7 +16,7 @@ Author: Aaron M. Ucko Last-Update: 2016-12-05 --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib -@@ -27,7 +27,9 @@ SRC = $(SRC_CXX) +@@ -27,7 +27,9 @@ LIB = blastinput @@ -29,7 +29,7 @@ Last-Update: 2016-12-05 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 @@ CFLAGS = $(FAST_CFLAGS) +@@ -23,6 +23,7 @@ LDFLAGS = $(FAST_LDFLAGS) WATCHERS = madden camacho fongah2 @@ -39,7 +39,7 @@ Last-Update: 2016-12-05 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) @@ -50,7 +50,7 @@ Last-Update: 2016-12-05 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 \ @@ -61,7 +61,7 @@ Last-Update: 2016-12-05 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 @@ -72,7 +72,7 @@ Last-Update: 2016-12-05 --- 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 @@ -83,7 +83,7 @@ Last-Update: 2016-12-05 --- 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) @@ -94,7 +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 -@@ -1511,7 +1511,7 @@ xbiosample_util needs mlacli +@@ -1511,7 +1511,7 @@ xbiosample_util needs valid xbiosample_util needs xmlwrapp xbiosample_util needs xobjutil @@ -105,7 +105,7 @@ Last-Update: 2016-12-05 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 @@ -138,7 +138,7 @@ Last-Update: 2016-12-05 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 @@ -149,7 +149,7 @@ Last-Update: 2016-12-05 --- 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 @@ -160,7 +160,7 @@ Last-Update: 2016-12-05 --- 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 @@ -182,7 +182,7 @@ Last-Update: 2016-12-05 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 @@ -248,7 +248,7 @@ Last-Update: 2016-12-05 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) @@ -259,7 +259,7 @@ Last-Update: 2016-12-05 --- a/c++/src/objmgr/util/Makefile.util.lib +++ b/c++/src/objmgr/util/Makefile.util.lib -@@ -14,6 +14,8 @@ LIB = xobjutil +@@ -14,6 +14,8 @@ DLL_LIB = submit $(SOBJMGR_LIBS) @@ -270,7 +270,7 @@ Last-Update: 2016-12-05 --- a/c++/src/objtools/align_format/Makefile.align_format.lib +++ b/c++/src/objtools/align_format/Makefile.align_format.lib -@@ -15,6 +15,10 @@ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(O +@@ -15,6 +15,10 @@ LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS) @@ -283,7 +283,7 @@ Last-Update: 2016-12-05 # CXXFLAGS = $(FAST_CXXFLAGS) --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib -@@ -14,6 +14,7 @@ DLL_LIB = xobjutil tables +@@ -14,6 +14,7 @@ WATCHERS = grichenk @@ -293,7 +293,7 @@ Last-Update: 2016-12-05 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) @@ -303,7 +303,7 @@ Last-Update: 2016-12-05 # CFLAGS = $(FAST_CFLAGS) --- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -@@ -29,6 +29,8 @@ LIB = seqdb +@@ -29,6 +29,8 @@ DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) LIBS = $(BLAST_THIRD_PARTY_LIBS) @@ -314,7 +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 -@@ -11,6 +11,9 @@ DLL_LIB = blastdb $(SOBJMGR_LIBS) +@@ -11,6 +11,9 @@ LIB = writedb @@ -326,7 +326,7 @@ Last-Update: 2016-12-05 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 @@ -348,7 +348,7 @@ Last-Update: 2016-12-05 --- 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 $(ORIG_CPPFLAGS) @@ -359,7 +359,7 @@ Last-Update: 2016-12-05 WATCHERS = camacho --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -@@ -12,6 +12,9 @@ LIB_OR_DLL = both +@@ -12,6 +12,9 @@ # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) @@ -371,7 +371,7 @@ Last-Update: 2016-12-05 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib -@@ -16,6 +16,9 @@ DLL_LIB = $(GENBANK_READER_LDEP) +@@ -16,6 +16,9 @@ LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) @@ -383,7 +383,7 @@ Last-Update: 2016-12-05 --- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib +++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib -@@ -12,6 +12,8 @@ LIB_OR_DLL = both +@@ -12,6 +12,8 @@ # Dependencies for shared library DLL_LIB = ncbi_xreader$(DLL) @@ -394,7 +394,7 @@ Last-Update: 2016-12-05 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 = ncbi_xreader$(DLL) $(GENBANK_READER_LDEP) @@ -405,7 +405,7 @@ Last-Update: 2016-12-05 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) @@ -419,7 +419,7 @@ Last-Update: 2016-12-05 --- 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 @@ -430,7 +430,7 @@ Last-Update: 2016-12-05 --- 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 @@ -441,7 +441,7 @@ Last-Update: 2016-12-05 --- 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 @@ -452,7 +452,7 @@ Last-Update: 2016-12-05 --- a/c++/src/util/Makefile.util.lib +++ b/c++/src/util/Makefile.util.lib -@@ -14,6 +14,7 @@ SRC = random_gen utf8 checksum checksum_ +@@ -14,6 +14,7 @@ LIB = xutil PROJ_TAG = core @@ -462,7 +462,7 @@ Last-Update: 2016-12-05 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) @@ -473,7 +473,7 @@ Last-Update: 2016-12-05 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) @@ -484,7 +484,7 @@ Last-Update: 2016-12-05 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 struct_cmt_reader \ message_listener line_error @@ -561,7 +561,7 @@ Last-Update: 2016-12-05 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___ @@ -581,7 +581,7 @@ Last-Update: 2016-12-05 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 @@ -611,7 +611,7 @@ Last-Update: 2016-12-05 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 = mla pubmed medlars xconnect @@ -631,7 +631,7 @@ Last-Update: 2016-12-05 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 @@ -641,7 +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 -@@ -8,6 +8,7 @@ DLL_LIB = xconnect +@@ -8,6 +8,7 @@ WATCHERS = bollin holmesbr @@ -651,7 +651,7 @@ Last-Update: 2016-12-05 $(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 @@ -661,7 +661,7 @@ Last-Update: 2016-12-05 xser --- a/c++/src/objects/valid/Makefile.valid.lib +++ b/c++/src/objects/valid/Makefile.valid.lib -@@ -6,5 +6,7 @@ DLL_LIB = xregexp +@@ -6,5 +6,7 @@ ASN_DEP = general @@ -681,7 +681,7 @@ Last-Update: 2016-12-05 $(SEQ_LIBS) pub --- a/c++/src/algo/blast/format/Makefile.xblastformat.lib +++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib -@@ -13,6 +13,8 @@ LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_ +@@ -13,6 +13,8 @@ WATCHERS = jianye zaretska madden camacho fongah2 @@ -692,9 +692,9 @@ Last-Update: 2016-12-05 $(BLAST_LIBS) align_format blastxml blastxml2 --- a/c++/src/objtools/cleanup/Makefile.cleanup.lib +++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib -@@ -10,11 +10,10 @@ SRC = autogenerated_cleanup autogenerate +@@ -10,11 +10,10 @@ cleanup_utils gene_qual_normalization cleanup_user_object cleanup_author \ - newcleanupp capitalization_string + cleanup_pub newcleanupp capitalization_string fix_feature_id -DLL_LIB = xregexp $(PCRE_LIB) +DLL_LIB = $(OBJEDIT_LIBS) xobjutil valid xregexp $(PCRE_LIB) $(SOBJMGR_LIBS) @@ -707,7 +707,7 @@ Last-Update: 2016-12-05 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 @@ -718,7 +718,7 @@ Last-Update: 2016-12-05 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 @@ -728,7 +728,7 @@ Last-Update: 2016-12-05 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) @@ -739,7 +739,7 @@ Last-Update: 2016-12-05 --- a/c++/src/algo/blast/api/Makefile.xblast.lib +++ b/c++/src/algo/blast/api/Makefile.xblast.lib -@@ -77,11 +77,11 @@ deltablast \ +@@ -77,11 +77,11 @@ magicblast_options \ magicblast @@ -755,7 +755,7 @@ Last-Update: 2016-12-05 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS) --- 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 @@ -766,7 +766,7 @@ Last-Update: 2016-12-05 WATCHERS = lavr mcelhany --- a/c++/src/objects/seq/Makefile.seq.lib +++ b/c++/src/objects/seq/Makefile.seq.lib -@@ -12,7 +12,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport +@@ -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 @@ -788,7 +788,7 @@ Last-Update: 2016-12-05 $(SEQ_LIBS) pub --- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib +++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib -@@ -5,7 +5,7 @@ ASN_DEP = entrez2 +@@ -5,7 +5,7 @@ LIB = entrez2cli SRC = entrez2_client entrez2_client_ diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes index 30c97128..fd29c84a 100644 --- a/debian/patches/hurd_fixes +++ b/debian/patches/hurd_fixes @@ -9,7 +9,7 @@ Author: Aaron M. Ucko Last-Update: 2011-06-10 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -9891,7 +9891,7 @@ if test -z "$CONF_f_runpath" ; then +@@ -9914,7 +9914,7 @@ 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 -@@ -2131,7 +2131,7 @@ if test -z "$CONF_f_runpath" ; then +@@ -2136,7 +2136,7 @@ solaris* ) CONF_f_runpath="-R" ;; diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index dc82958b..8b11eb4a 100644 --- a/debian/patches/no_multiarch_rpath +++ b/debian/patches/no_multiarch_rpath @@ -10,7 +10,7 @@ Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -9999,7 +9999,7 @@ echo "$as_me: error: Unable to find stat +@@ -10022,7 +10022,7 @@ 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 -@@ -2198,7 +2198,7 @@ case "$compiler:$compiler_version:$with_ +@@ -2203,7 +2203,7 @@ break ;; /* ) -- 2.30.2