From 1aca3e5aae88192ca717e47c5a947ef806b69b2e Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Wed, 25 Jun 2014 22:58:36 +0200 Subject: sci-biology/ncbi-tools++-12.0.0: first compile-able ebuild, wow, huge thanks to Aaron Ucko from NCBI developers on the cpp@ mailing list --- .../files/ncbi-tools++-12.0.0-as-needed.patch | 2 +- ...cbi-tools++-12.0.0-linkage-tuneups-addons.patch | 13 + .../ncbi-tools++-12.0.0-linkage-tuneups.patch | 421 +++++++++++++++++++++ .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 14 +- 4 files changed, 444 insertions(+), 6 deletions(-) create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch create mode 100644 sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch index e97c77f58..a9d166e2d 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch @@ -344,7 +344,7 @@ index 872b92e..78261eb 100644 CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) + -+DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast xregexp ++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb blast xregexp diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib index c7e2778..51ebe9d 100644 --- a/src/algo/phy_tree/Makefile.xalgophytree.lib diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch new file mode 100644 index 000000000..553e41d29 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch @@ -0,0 +1,13 @@ +--- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori (revision 439078) ++++ ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app (working copy) +@@ -7,8 +7,8 @@ + SRC = agpconvert + + LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ +- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) +-LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++ tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) ++LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) 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 new file mode 100644 index 000000000..86e96b865 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch @@ -0,0 +1,421 @@ +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 = $(SRA_SDK_SYSLIBS) ++ + LIB_OR_DLL = both diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index ecb94f0f8..8ee3f1615 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -108,14 +108,18 @@ src_prepare() { # The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers local PATCHES=( "${FILESDIR}"/${P}-conf-opts.patch - "${FILESDIR}"/${P}-as-needed.patch - "${FILESDIR}"/${P}-fix-creaders-linking.patch "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch - "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch + "${FILESDIR}"/${P}-linkage-tuneups.patch "${FILESDIR}"/${P}-more-patches.patch - "${FILESDIR}"/${P}-linking.patch - "${FILESDIR}"/${P}-linking2.patch + "${FILESDIR}"/${P}-linkage-tuneups-addons.patch ) +# "${FILESDIR}"/${P}-as-needed.patch +# "${FILESDIR}"/${P}-fix-creaders-linking.patch +# "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch +# replaced by -linkage-tuneups.patch +# "${FILESDIR}"/${P}-linking.patch +# "${FILESDIR}"/${P}-linking2.patch +# ) # "${FILESDIR}"/${P}-support-autoconf-2.60.patch # "${FILESDIR}"/${P}-configure.patch epatch ${PATCHES[@]} -- cgit v1.2.3-65-gdbad