commit: 90e60e2f6d4782f0dffc9996a07cc0bdcd24545b Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue May 2 12:09:35 2023 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue May 2 12:15:13 2023 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=90e60e2f
sci-biology/ncbi-blast+: treeclean Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../files/disable-testsuite-compilation.txt | 3 - .../files/ncbi-blast+-2.2.30__fix_lib_deps.patch | 668 --------------------- sci-biology/ncbi-blast+/metadata.xml | 23 - sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 360 ----------- sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 350 ----------- sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 350 ----------- sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 355 ----------- sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 360 ----------- 8 files changed, 2469 deletions(-) diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt deleted file mode 100644 index aeaf75e45..000000000 --- a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt +++ /dev/null @@ -1,3 +0,0 @@ -.* --.*/test --.*/unit_test diff --git a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch deleted file mode 100644 index 13dffeee7..000000000 --- a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch +++ /dev/null @@ -1,668 +0,0 @@ -Subject: ensure that all libraries link against all direct dependencies - - * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency - loop between libxblast and libxalgoblastdbindex by having the former - provide only the C++ BLAST API, leaving the C core only in libblast. - * src/build-system/library_relations.txt: Change xblast's - relationship to blast from includes to needs, accordingly. - * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect - rather than libconnect for consistency with libblast, which uses the - former to keep the aforementioned cycle-breaking from causing - inconsistency elsewhere. - -Debian-Bug: 633567. -Author: Aaron M. Ucko <u...@debian.org> -Last-Update: 2014-12-02 ---- a/c++/src/algo/blast/core/Makefile.blast.lib -+++ b/c++/src/algo/blast/core/Makefile.blast.lib -@@ -21,6 +21,7 @@ LIB = blast - CFLAGS = $(FAST_CFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = composition_adjustment xconnect tables - - 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 @@ SRC = sequence_istream_fasta \ - CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi -+ - ASN_DEP = seqset - - WATCHERS = morgulis ---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib -+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib -@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - --DLL_LIB = align_format blastxml blastxml2 xhtml xcgi -+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \ -+ 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 -@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s - 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 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb - user_agent - LIB = xcgi - -+DLL_LIB = xutil xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) - - WATCHERS = vakatov ---- 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 - 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 -@@ -3,6 +3,7 @@ ASN_DEP = xnetblast - 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 @@ SRC = format_flags align_format_util sho - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - -+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \ -+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \ -+ xcgi xhtml tables xncbi -+ - ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST - # CFLAGS = $(FAST_CFLAGS) - # CXXFLAGS = $(FAST_CXXFLAGS) ---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib -+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib -@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge - - 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 -@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \ - 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 -@@ -12,7 +12,7 @@ mask_writer_seqloc \ - mask_writer_blastdb_maskinfo - - ASN_DEP = seqset --DLL_LIB = seqdb blastdb -+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 @@ WATCHERS = jcherry - - ASN_DEP = seqset - -+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi -+ - LIB = xobjsimple - SRC = simple_om - ---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -@@ -24,6 +24,8 @@ seqdbobj - - LIB = seqdb - -+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi -+ - CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - 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 -@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_ - - 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 @@ SRC = bdbloader_rmt remote_blastdb_adapt - - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - -+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi -+ - ASN_DEP = blastdb xnetblast - - WATCHERS = camacho ---- a/c++/src/algo/blast/api/Makefile.xblast.lib -+++ b/c++/src/algo/blast/api/Makefile.xblast.lib -@@ -74,14 +74,15 @@ cdd_pssm_input \ - deltablast_options \ - deltablast - --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 -@@ -24,7 +24,9 @@ SRC = $(SRC_CXX) - - LIB = blastinput - --DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil -+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \ -+ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \ -+ scoremat seqset seq xser xutil xncbi - - # should be redundant, given the above :-/ - ASN_DEP = seqset xnetblast ---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib -+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib -@@ -8,6 +8,8 @@ LIB = xalgodustmask - - SRC = symdust - -+DLL_LIB = xobjmgr seq xncbi -+ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - ---- a/c++/src/connect/Makefile.xconnect.lib -+++ b/c++/src/connect/Makefile.xconnect.lib -@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM) - LIB = xconnect - PROJ_TAG = core - -+DLL_LIB = xncbi -+ - LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) - - WATCHERS = lavr ---- a/c++/src/connect/ext/Makefile.xconnext.lib -+++ b/c++/src/connect/ext/Makefile.xconnext.lib -@@ -6,6 +6,8 @@ SRC = $(SRC_C) ncbi_dblb_svcmapper - - LIB = xconnext - -+DLL_LIB = xconnect xncbi -+ - WATCHERS = lavr - - ---- a/c++/src/objects/blast/Makefile.blast.lib -+++ b/c++/src/objects/blast/Makefile.blast.lib -@@ -1,6 +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 -@@ -1,6 +1,8 @@ - LIB = blastxml - SRC = blastxml__ blastxml___ - -+DLL_LIB = xser xncbi -+ - - USES_LIBRARIES = \ - xser ---- a/c++/src/objects/scoremat/Makefile.scoremat.lib -+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib -@@ -1,6 +1,8 @@ - LIB = scoremat - SRC = scoremat__ scoremat___ - -+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 -@@ -1,6 +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 -@@ -1,6 +1,8 @@ - LIB = submit - SRC = submit__ submit___ - -+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 -@@ -8,6 +8,8 @@ ASN_DEP = submit - SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci - LIB = xobjutil - -+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi -+ - 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 @@ SRC = seq_writer blastdb_dataextract bla - - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - -+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi - - ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST - # CFLAGS = $(FAST_CFLAGS) ---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib -+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib -@@ -8,6 +8,8 @@ SRC = blast_services - - LIB = blast_services - -+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi -+ - CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS) - CXXFLAGS = $(FAST_CXXFLAGS) ---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -@@ -12,6 +12,9 @@ LIB_OR_DLL = both - # Dependencies for shared library - DLL_LIB = ncbi_xreader$(DLL) - -+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \ -+ id2 id1 ncbi_xreader 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 -@@ -15,6 +15,9 @@ LIB_OR_DLL = both - DLL_LIB = - DLL_DLIB = $(GENBANK_READER_LDEP) - -+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \ -+ xser xconnect xcompress xutil xncbi -+ - WATCHERS = vasilche - - ---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib -+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib -@@ -12,6 +12,8 @@ LIB_OR_DLL = both - # Dependencies for shared library - DLL_LIB = ncbi_xreader$(DLL) - -+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - - WATCHERS = vasilche ---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib -+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib -@@ -12,6 +12,8 @@ LIB_OR_DLL = both - # Dependencies for shared library - DLL_LIB = xconnect ncbi_xreader$(DLL) - -+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - - 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 - CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) - - # Dependencies for shared library (disabled due to problems on Darwin) --# DLL_LIB = xconnect ncbi_xreader$(DLL) -+DLL_LIB = xconnect ncbi_xreader$(DLL) -+ -+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi -+ - - WATCHERS = vasilche - ---- a/c++/src/util/compress/api/Makefile.compress.lib -+++ b/c++/src/util/compress/api/Makefile.compress.lib -@@ -7,7 +7,7 @@ LIB = xcompress - - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - --DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) -+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi - LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS) - - WATCHERS = ivanov ---- a/c++/src/util/sequtil/Makefile.sequtil.lib -+++ b/c++/src/util/sequtil/Makefile.sequtil.lib -@@ -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 teamcity_messages - LIB = test_boost - -+DLL_LIB = xncbi -+ - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - - REQUIRES = Boost.Test.Included ---- a/c++/src/corelib/Makefile.test_mt.lib -+++ b/c++/src/corelib/Makefile.test_mt.lib -@@ -3,6 +3,8 @@ - SRC = test_mt - LIB = test_mt - -+DLL_LIB = xncbi -+ - # REQUIRES = MT - - USE_PCH = no ---- a/c++/src/objects/biblio/Makefile.biblio.lib -+++ b/c++/src/objects/biblio/Makefile.biblio.lib -@@ -1,6 +1,8 @@ - LIB = biblio - SRC = biblio__ biblio___ citation_base - -+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 427424 2014-02-20 13:38:50Z gouriano $ - -+ -+DLL_LIB = seq xser xncbi - LIB = blastdb - SRC = blastdb__ blastdb___ - ---- a/c++/src/objects/general/Makefile.general.lib -+++ b/c++/src/objects/general/Makefile.general.lib -@@ -1,6 +1,8 @@ - LIB = general - SRC = general__ general___ uoconv - -+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 -@@ -3,6 +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 -@@ -3,6 +3,8 @@ ASN_DEP = seq - 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 -@@ -1,6 +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 -@@ -1,6 +1,8 @@ - LIB = medline - SRC = medline__ medline___ - -+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 -@@ -1,6 +1,8 @@ - LIB = pub - SRC = pub__ pub___ - -+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 -@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport - 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 -@@ -1,6 +1,8 @@ - LIB = seqcode - SRC = seqcode__ seqcode___ - -+DLL_LIB = xser xncbi -+ - - USES_LIBRARIES = \ - xser ---- 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 @@ - 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 -@@ -18,6 +18,8 @@ SRC = \ - - 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 @@ SRC = random_gen utf8 checksum bytesrc s - LIB = xutil - PROJ_TAG = core - -+DLL_LIB = xncbi - LIBS = $(ORIG_LIBS) - - WATCHERS = vakatov kornbluh ---- a/c++/src/util/xregexp/Makefile.xregexp.lib -+++ b/c++/src/util/xregexp/Makefile.xregexp.lib -@@ -6,7 +6,7 @@ LIB = xregexp - - CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) - --DLL_LIB = $(PCRE_LIB) -+DLL_LIB = $(PCRE_LIB) xncbi - LIBS = $(PCRE_LIBS) - - WATCHERS = ivanov ---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib -+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib -@@ -8,6 +8,8 @@ LIB = xalgosegmask - - SRC = segmask - -+DLL_LIB = blast xobjmgr xncbi -+ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - ---- 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 - - CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) - --DLL_LIB = $(SOBJMGR_LIBS) -+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 @@ SRC = writedb writedb_impl writedb_volum - - LIB = writedb - -+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \ -+ xser sequtil xutil xncbi -+ - CFLAGS = $(FAST_CFLAGS) - CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) - CXXFLAGS = $(FAST_CXXFLAGS) ---- a/c++/src/algo/blast/Makefile.blast_macros.mk -+++ b/c++/src/algo/blast/Makefile.blast_macros.mk -@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \ - 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 blast composition_adjustment \ - xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \ - $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr - # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS) ---- 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 - SRC = main mkindex_app - - LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \ -- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS) -+ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - - CXXFLAGS = $(FAST_CXXFLAGS) ---- a/c++/src/build-system/library_relations.txt -+++ b/c++/src/build-system/library_relations.txt -@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS) - xasmcompare needs pub - xasn needs xhtml - xasn needs3party $(NCBI_C_ncbi) --xblast includes blast -+xblast needs blast - xblast needs xalgoblastdbindex - xblast needs xalgodustmask - xblast needs xalgowinmask diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml deleted file mode 100644 index 93556eaa7..000000000 --- a/sci-biology/ncbi-blast+/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild deleted file mode 100644 index 527acfadf..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild +++ /dev/null @@ -1,360 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"; -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"; -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"; - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild deleted file mode 100644 index e90652f38..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild +++ /dev/null @@ -1,350 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"; -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"; -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"; - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -PATCHES=( - "${FILESDIR}"/"${P}"__fix_lib_deps.patch -) - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild deleted file mode 100644 index ddeeac07d..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild +++ /dev/null @@ -1,350 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t"; -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"; -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"; - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild deleted file mode 100644 index 976ea3804..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild +++ /dev/null @@ -1,355 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"; -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"; -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"; - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild deleted file mode 100644 index 527acfadf..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild +++ /dev/null @@ -1,360 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"; -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"; -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"; - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -}
