diff options
3 files changed, 1049 insertions, 119 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch new file mode 100644 index 000000000..7763361e7 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch @@ -0,0 +1,767 @@ + src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +- + src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++ + src/algo/sequence/Makefile.xalgoseq.lib | 2 ++ + src/algo/winmask/Makefile.xalgowinmask.lib | 1 + + src/cgi/Makefile.cgi.lib | 2 ++ + src/cgi/Makefile.fcgi.lib | 2 ++ + src/connect/Makefile.connssl.lib | 2 ++ + src/connect/Makefile.xconnect.lib | 4 ++++ + src/connect/Makefile.xthrserv.lib | 2 +- + src/connect/Makefile.xxconnect.lib | 2 ++ + src/connect/services/Makefile.ncbi_xcache_netcache.lib | 2 +- + src/connect/services/Makefile.xconnserv.lib | 2 +- + src/connect/test/Makefile.conntest.lib | 2 ++ + src/corelib/Makefile.test_boost.lib | 2 ++ + src/corelib/Makefile.test_mt.lib | 2 ++ + src/corelib/test/Makefile.pbacktest.lib | 2 ++ + src/db/bdb/Makefile.bdb.lib | 4 ++++ + src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +- + src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++ + src/dbapi/Makefile.dbapi.lib | 5 +++++ + src/dbapi/driver/Makefile.dbapi_driver.lib | 2 ++ + src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib | 2 ++ + src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib | 2 +- + src/dbapi/simple/Makefile.sdbapi.lib | 1 + + src/html/Makefile.html.lib | 2 ++ + src/objects/access/Makefile.access.lib | 1 + + src/objects/biblio/Makefile.biblio.lib | 2 ++ + src/objects/blast/Makefile.blast.lib | 2 ++ + src/objects/blast/Makefile.xnetblastcli.lib | 2 ++ + src/objects/cdd/Makefile.cdd.lib | 2 ++ + src/objects/cn3d/Makefile.cn3d.lib | 2 ++ + src/objects/general/Makefile.general.lib | 2 ++ + src/objects/id2/Makefile.id2.lib | 2 ++ + src/objects/medlars/Makefile.medlars.lib | 2 ++ + src/objects/medline/Makefile.medline.lib | 2 ++ + src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++ + src/objects/omssa/Makefile.omssa.lib | 2 ++ + src/objects/pub/Makefile.pub.lib | 2 ++ + src/objects/scoremat/Makefile.scoremat.lib | 2 ++ + src/objects/seq/Makefile.seq.lib | 2 ++ + src/objects/seqcode/Makefile.seqcode.lib | 2 ++ + src/objects/seqedit/Makefile.seqedit.lib | 1 + + src/objects/seqset/Makefile.seqset.lib | 1 + + src/objects/seqsplit/Makefile.seqsplit.lib | 2 ++ + src/objects/submit/Makefile.submit.lib | 1 + + src/objects/taxon1/Makefile.taxon1.lib | 2 ++ + src/objects/valerr/Makefile.valerr.lib | 2 ++ + src/objects/valid/Makefile.valid.lib | 2 ++ + src/objects/variation/Makefile.variation.lib | 1 + + src/objmgr/util/Makefile.util.lib | 1 + + src/objtools/align_format/Makefile.align_format.lib | 2 ++ + src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++ + src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++ + src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- + src/objtools/readers/Makefile.xobjread.lib | 3 +-- + src/objtools/readers/Makefile.xobjreadex.lib | 2 +- + src/objtools/simple/Makefile.xobjsimple.lib | 1 + + src/objtools/validator/Makefile.validator.lib | 2 ++ + src/serial/Makefile.serial.lib | 2 ++ + src/serial/soap/Makefile.soap.lib | 2 ++ + src/serial/soap/Makefile.soap_server.lib | 2 ++ + src/serial/test/Makefile.we_cpp.lib | 1 + + src/util/Makefile.util.lib | 2 ++ + src/util/compress/api/Makefile.compress.lib | 2 +- + src/util/qparse/Makefile.xqueryparse.lib | 2 ++ + src/util/regexp/Makefile.regexp.lib | 2 ++ + src/util/sequtil/Makefile.sequtil.lib | 2 ++ + src/util/xregexp/Makefile.xregexp.lib | 2 +- + 68 files changed, 124 insertions(+), 12 deletions(-) + +diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib +index bfb315c..25873a2 100644 +--- a/src/algo/blast/blastinput/Makefile.blastinput.lib ++++ b/src/algo/blast/blastinput/Makefile.blastinput.lib +@@ -24,7 +24,7 @@ SRC = $(SRC_CXX) + + LIB = blastinput + +-DLL_LIB = xblast $(OBJMGR_LIBS) ++DLL_LIB = xblast seqdb $(OBJMGR_LIBS) + + # should be redundant, given the above :-/ + ASN_DEP = seqset xnetblast +diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib +index 872b92e..82cc8b6 100644 +--- a/src/algo/ms/omssa/Makefile.xomssa.lib ++++ b/src/algo/ms/omssa/Makefile.xomssa.lib +@@ -19,3 +19,5 @@ LIB = xomssa + CFLAGS = $(FAST_CFLAGS) + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = xutil +diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib +index 51f4cd7..0c20790 100644 +--- a/src/algo/sequence/Makefile.xalgoseq.lib ++++ b/src/algo/sequence/Makefile.xalgoseq.lib +@@ -13,3 +13,5 @@ LDFLAGS = $(FAST_LDFLAGS) + CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) + + WATCHERS = dicuccio ++ ++DLL_LIB = taxon1 xalnmgr +diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib +index afaf676..7344871 100644 +--- a/src/algo/winmask/Makefile.xalgowinmask.lib ++++ b/src/algo/winmask/Makefile.xalgowinmask.lib +@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \ + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = seqmasks_io +diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib +index a990390..edf40aa 100644 +--- a/src/cgi/Makefile.cgi.lib ++++ b/src/cgi/Makefile.cgi.lib +@@ -11,3 +11,5 @@ LIB = xcgi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/cgi/Makefile.fcgi.lib b/src/cgi/Makefile.fcgi.lib +index 2569b41..6b85780 100644 +--- a/src/cgi/Makefile.fcgi.lib ++++ b/src/cgi/Makefile.fcgi.lib +@@ -12,3 +12,5 @@ LIB = xfcgi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) -DNCBI_XFCGI_EXPORTS + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/connect/Makefile.connssl.lib b/src/connect/Makefile.connssl.lib +index b400ca2..8756320 100644 +--- a/src/connect/Makefile.connssl.lib ++++ b/src/connect/Makefile.connssl.lib +@@ -8,3 +8,5 @@ CPPFLAGS = $(GNUTLS_INCLUDE) $(ORIG_CPPFLAGS) + LIBS = $(GNUTLS_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr ++ ++DLL_LIB = connect +diff --git a/src/connect/Makefile.xconnect.lib b/src/connect/Makefile.xconnect.lib +index 473bb0b..88dae10 100644 +--- a/src/connect/Makefile.xconnect.lib ++++ b/src/connect/Makefile.xconnect.lib +@@ -11,9 +11,13 @@ include $(srcdir)/Makefile.xxconnect.lib + SRC = $(SRC_C) $(SRC_CXX) + UNIX_SRC = $(LOCAL_LBSM) + ++DLL_LIB = xncbi ++ + LIB = xconnect + PROJ_TAG = core + + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr ++ ++DLL_LIB = xncbi xutil +diff --git a/src/connect/Makefile.xthrserv.lib b/src/connect/Makefile.xthrserv.lib +index 1e5b857..0833a78 100644 +--- a/src/connect/Makefile.xthrserv.lib ++++ b/src/connect/Makefile.xthrserv.lib +@@ -4,6 +4,6 @@ SRC = threaded_server server server_monitor connection_pool + LIB = xthrserv + PROJ_TAG = core + LIBS = $(NETWORK_LIBS) +-DLL_LIB = xutil xconnect ++DLL_LIB = xncbi xutil xconnect + + WATCHERS = ivanovp +diff --git a/src/connect/Makefile.xxconnect.lib b/src/connect/Makefile.xxconnect.lib +index d7ba751..8e27819 100644 +--- a/src/connect/Makefile.xxconnect.lib ++++ b/src/connect/Makefile.xxconnect.lib +@@ -16,3 +16,5 @@ PROJ_TAG = core + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr ++ ++DLL_LIB = xncbi xutil connect +diff --git a/src/connect/services/Makefile.ncbi_xcache_netcache.lib b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +index 606f4f1..e6cfdac 100644 +--- a/src/connect/services/Makefile.ncbi_xcache_netcache.lib ++++ b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +@@ -6,7 +6,7 @@ SRC = neticache_client + LIB = ncbi_xcache_netcache + + LIB_OR_DLL = both +-DLL_LIB = xconnserv xconnect xutil ++DLL_LIB = xconnserv xconnect xutil xncbi + + CPPFLAGS = $(ORIG_CPPFLAGS) + LIBS = $(ORIG_LIBS) +diff --git a/src/connect/services/Makefile.xconnserv.lib b/src/connect/services/Makefile.xconnserv.lib +index 4b8f21f..04fcbf8 100644 +--- a/src/connect/services/Makefile.xconnserv.lib ++++ b/src/connect/services/Makefile.xconnserv.lib +@@ -15,6 +15,6 @@ LIB = xconnserv + PROJ_TAG = core + LIBS = $(NETWORK_LIBS) + +-DLL_LIB = xthrserv xconnect xutil ++DLL_LIB = xthrserv xconnect xutil xncbi + + WATCHERS = kazimird +diff --git a/src/connect/test/Makefile.conntest.lib b/src/connect/test/Makefile.conntest.lib +index 58a2fa5..3d9876c 100644 +--- a/src/connect/test/Makefile.conntest.lib ++++ b/src/connect/test/Makefile.conntest.lib +@@ -4,3 +4,5 @@ SRC = ncbi_conntest + LIB = xconntest + + WATCHERS = lavr ++ ++DLL_LIB = xncbi xutil connect +diff --git a/src/corelib/Makefile.test_boost.lib b/src/corelib/Makefile.test_boost.lib +index e8fa174..f90441d 100644 +--- a/src/corelib/Makefile.test_boost.lib ++++ b/src/corelib/Makefile.test_boost.lib +@@ -9,3 +9,5 @@ REQUIRES = Boost.Test.Included + + WATCHERS = ivanovp + PROJ_TAG = test ++ ++DLL_LIB = xncbi +diff --git a/src/corelib/Makefile.test_mt.lib b/src/corelib/Makefile.test_mt.lib +index 6153eab..f64c3a2 100644 +--- a/src/corelib/Makefile.test_mt.lib ++++ b/src/corelib/Makefile.test_mt.lib +@@ -8,3 +8,5 @@ LIB = test_mt + USE_PCH = no + WATCHERS = grichenk + PROJ_TAG = test ++ ++DLL_LIB = xncbi +diff --git a/src/corelib/test/Makefile.pbacktest.lib b/src/corelib/test/Makefile.pbacktest.lib +index da0c616..c4c62ab 100644 +--- a/src/corelib/test/Makefile.pbacktest.lib ++++ b/src/corelib/test/Makefile.pbacktest.lib +@@ -4,3 +4,5 @@ SRC = pbacktest + LIB = xpbacktest + + WATCHERS = lavr ++ ++DLL_LIB = xncbi +diff --git a/src/db/bdb/Makefile.bdb.lib b/src/db/bdb/Makefile.bdb.lib +index 3729707..cd2827c 100644 +--- a/src/db/bdb/Makefile.bdb.lib ++++ b/src/db/bdb/Makefile.bdb.lib +@@ -14,3 +14,7 @@ LIB = bdb + CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE) + + WATCHERS = kuznets ++ ++DLL_LIB = xncbi xutil ++LIBS = $(BERKELEYDB_LIBS) ++ +diff --git a/src/db/bdb/Makefile.ncbi_xcache_bdb.lib b/src/db/bdb/Makefile.ncbi_xcache_bdb.lib +index 7e97a26..8f54efc 100644 +--- a/src/db/bdb/Makefile.ncbi_xcache_bdb.lib ++++ b/src/db/bdb/Makefile.ncbi_xcache_bdb.lib +@@ -8,7 +8,7 @@ SRC = bdb_blobcache + LIB = ncbi_xcache_bdb + + LIB_OR_DLL = both +-DLL_LIB = bdb xutil ++DLL_LIB = bdb xutil xncbi + + CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE) + LIBS = $(BERKELEYDB_LIBS) $(ORIG_LIBS) +diff --git a/src/db/sqlite/Makefile.sqlitewrapp.lib b/src/db/sqlite/Makefile.sqlitewrapp.lib +index cecfd16..c01668b 100644 +--- a/src/db/sqlite/Makefile.sqlitewrapp.lib ++++ b/src/db/sqlite/Makefile.sqlitewrapp.lib +@@ -8,3 +8,6 @@ CPPFLAGS= $(ORIG_CPPFLAGS) $(SQLITE3_INCLUDE) + REQUIRES = SQLITE3 + + WATCHERS = ivanovp ++ ++DLL_LIB = xncbi xutil ++LIBS = $(SQLITE3_LIBS) +diff --git a/src/dbapi/Makefile.dbapi.lib b/src/dbapi/Makefile.dbapi.lib +index 6e3ad4c..4475a78 100644 +--- a/src/dbapi/Makefile.dbapi.lib ++++ b/src/dbapi/Makefile.dbapi.lib +@@ -10,3 +10,8 @@ LIB = dbapi + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + + WATCHERS = ivanovp ++ ++#ASN_DEP = driver ++ ++DLL_LIB = xncbi xutil # dbapi_driver$(DLL) ++LIBS = $(PYTHON_LIBS) +diff --git a/src/dbapi/driver/Makefile.dbapi_driver.lib b/src/dbapi/driver/Makefile.dbapi_driver.lib +index dfeac5a..bc113ed 100644 +--- a/src/dbapi/driver/Makefile.dbapi_driver.lib ++++ b/src/dbapi/driver/Makefile.dbapi_driver.lib +@@ -22,3 +22,5 @@ CXXFLAGS_darwin = -fno-inline + CXXFLAGS = $(ORIG_CXXFLAGS) $(CXXFLAGS_$(OSTYPE)) + + WATCHERS = ivanovp ++ ++DLL_LIB = xncbi xutil +diff --git a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +index 941ccd6..f1f872c 100644 +--- a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib ++++ b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +@@ -6,3 +6,5 @@ LIB = dbapi_sample_base + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + + WATCHERS = ivanovp ++ ++DLL_LIB = xncbi xutil dbapi_driver +diff --git a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +index ebe08c4..86ecda6 100644 +--- a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib ++++ b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +@@ -11,7 +11,7 @@ LIB_OR_DLL = dll + + # Dependencies for shared library + DLL_LIB = dbapi dbapi_driver$(DLL) $(XCONNEXT) xconnect xutil xncbi +-LIBS = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS) ++LIBS = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS) $(PYTHON_LIBS) + # Drop other flags to build with full dependencies under ICC. + DLL_LDFLAGS = $(DLL_UNDEF_FLAGS) + +diff --git a/src/dbapi/simple/Makefile.sdbapi.lib b/src/dbapi/simple/Makefile.sdbapi.lib +index 603fd1e..0d06323 100644 +--- a/src/dbapi/simple/Makefile.sdbapi.lib ++++ b/src/dbapi/simple/Makefile.sdbapi.lib +@@ -5,3 +5,4 @@ LIB = sdbapi + + WATCHERS = ivanovp + ++DLL_LIB = xncbi xutil dbapi_driver ncbi_xdbapi_ftds xconnect xser bdb xconnserv +diff --git a/src/html/Makefile.html.lib b/src/html/Makefile.html.lib +index a57c1e3..0005299 100644 +--- a/src/html/Makefile.html.lib ++++ b/src/html/Makefile.html.lib +@@ -8,3 +8,5 @@ SRC = node html htmlhelper page pager selection components \ + LIB = xhtml + + WATCHERS = ivanov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib +index 11421d9..cf3a300 100644 +--- a/src/objects/access/Makefile.access.lib ++++ b/src/objects/access/Makefile.access.lib +@@ -1,2 +1,3 @@ + LIB = access + SRC = access__ access___ ++DLL_LIB = xncbi +diff --git a/src/objects/biblio/Makefile.biblio.lib b/src/objects/biblio/Makefile.biblio.lib +index 2c7d491..cb54ba6 100644 +--- a/src/objects/biblio/Makefile.biblio.lib ++++ b/src/objects/biblio/Makefile.biblio.lib +@@ -1,2 +1,4 @@ + LIB = biblio + SRC = biblio__ biblio___ citation_base ++ ++DLL_LIB = general xser xncbi xutil +diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib +index 0dd0fa3..5ffe052 100644 +--- a/src/objects/blast/Makefile.blast.lib ++++ b/src/objects/blast/Makefile.blast.lib +@@ -2,3 +2,5 @@ LIB = xnetblast + SRC = blast__ blast___ names + + WATCHERS = camacho ++ ++DLL_LIB = xncbi xutil xser +diff --git a/src/objects/blast/Makefile.xnetblastcli.lib b/src/objects/blast/Makefile.xnetblastcli.lib +index 96325c4..5a72805 100644 +--- a/src/objects/blast/Makefile.xnetblastcli.lib ++++ b/src/objects/blast/Makefile.xnetblastcli.lib +@@ -2,3 +2,5 @@ ASN_DEP = xnetblast + + LIB = xnetblastcli + SRC = blastclient blastclient_ ++ ++DLL_LIB = xncbi xutil seqset connect xconnect xnetblast +diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib +index 978cae9..e3176b2 100644 +--- a/src/objects/cdd/Makefile.cdd.lib ++++ b/src/objects/cdd/Makefile.cdd.lib +@@ -1,2 +1,4 @@ + LIB = cdd + SRC = cdd__ cdd___ ++ ++DLL_LIB = mmdb +diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib +index 1af5d1d..b34a966 100644 +--- a/src/objects/cn3d/Makefile.cn3d.lib ++++ b/src/objects/cn3d/Makefile.cn3d.lib +@@ -1,3 +1,5 @@ + ASN_DEP = mmdb + LIB = cn3d + SRC = cn3d__ cn3d___ ++ ++DLL_LIB = mmdb +diff --git a/src/objects/general/Makefile.general.lib b/src/objects/general/Makefile.general.lib +index 951304f..3be083d 100644 +--- a/src/objects/general/Makefile.general.lib ++++ b/src/objects/general/Makefile.general.lib +@@ -1,2 +1,4 @@ + LIB = general + SRC = general__ general___ uoconv ++ ++DLL_LIB = xser xncbi xutil +diff --git a/src/objects/id2/Makefile.id2.lib b/src/objects/id2/Makefile.id2.lib +index 09d8b36..b25700d 100644 +--- a/src/objects/id2/Makefile.id2.lib ++++ b/src/objects/id2/Makefile.id2.lib +@@ -2,3 +2,5 @@ LIB = id2 + SRC = id2__ id2___ + + WATCHERS = vasilche ++ ++DLL_LIB = xser +diff --git a/src/objects/medlars/Makefile.medlars.lib b/src/objects/medlars/Makefile.medlars.lib +index 3a6d0cd..5230940 100644 +--- a/src/objects/medlars/Makefile.medlars.lib ++++ b/src/objects/medlars/Makefile.medlars.lib +@@ -1,2 +1,4 @@ + LIB = medlars + SRC = medlars__ medlars___ ++ ++DLL_LIB = xser +diff --git a/src/objects/medline/Makefile.medline.lib b/src/objects/medline/Makefile.medline.lib +index ea28066..eb42aa4 100644 +--- a/src/objects/medline/Makefile.medline.lib ++++ b/src/objects/medline/Makefile.medline.lib +@@ -1,2 +1,4 @@ + LIB = medline + SRC = medline__ medline___ ++ ++DLL_LIB = general biblio +diff --git a/src/objects/ncbimime/Makefile.ncbimime.lib b/src/objects/ncbimime/Makefile.ncbimime.lib +index 93cafdf..e5aa4eb 100644 +--- a/src/objects/ncbimime/Makefile.ncbimime.lib ++++ b/src/objects/ncbimime/Makefile.ncbimime.lib +@@ -1,2 +1,4 @@ + LIB = ncbimime + SRC = ncbimime__ ncbimime___ ++ ++DLL_LIB = mmdb +diff --git a/src/objects/omssa/Makefile.omssa.lib b/src/objects/omssa/Makefile.omssa.lib +index b79617f..e1d4a9e 100644 +--- a/src/objects/omssa/Makefile.omssa.lib ++++ b/src/objects/omssa/Makefile.omssa.lib +@@ -2,3 +2,5 @@ APP_DEP = seq + + LIB = omssa + SRC = omssa__ omssa___ ++ ++DLL_LIB = seq +diff --git a/src/objects/pub/Makefile.pub.lib b/src/objects/pub/Makefile.pub.lib +index 78c12e1..9baa08d 100644 +--- a/src/objects/pub/Makefile.pub.lib ++++ b/src/objects/pub/Makefile.pub.lib +@@ -1,2 +1,4 @@ + LIB = pub + SRC = pub__ pub___ ++ ++DLL_LIB = medline biblio +diff --git a/src/objects/scoremat/Makefile.scoremat.lib b/src/objects/scoremat/Makefile.scoremat.lib +index 62e01f5..93bb071 100644 +--- a/src/objects/scoremat/Makefile.scoremat.lib ++++ b/src/objects/scoremat/Makefile.scoremat.lib +@@ -1,2 +1,4 @@ + LIB = scoremat + SRC = scoremat__ scoremat___ ++ ++DLL_LIB = seqset seq +diff --git a/src/objects/seq/Makefile.seq.lib b/src/objects/seq/Makefile.seq.lib +index 1b5edc5..30ef316 100644 +--- a/src/objects/seq/Makefile.seq.lib ++++ b/src/objects/seq/Makefile.seq.lib +@@ -13,3 +13,5 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \ + seq_loc_from_string seq_loc_reverse_complementer + + WATCHERS = vasilche grichenk ++ ++DLL_LIB = general seqcode pub sequtil biblio xser xncbi xutil +diff --git a/src/objects/seqcode/Makefile.seqcode.lib b/src/objects/seqcode/Makefile.seqcode.lib +index dc9d60e..dabd95b 100644 +--- a/src/objects/seqcode/Makefile.seqcode.lib ++++ b/src/objects/seqcode/Makefile.seqcode.lib +@@ -1,2 +1,4 @@ + LIB = seqcode + SRC = seqcode__ seqcode___ ++ ++DLL_LIB = xncbi xser +diff --git a/src/objects/seqedit/Makefile.seqedit.lib b/src/objects/seqedit/Makefile.seqedit.lib +index 283a9b7..80724b1 100644 +--- a/src/objects/seqedit/Makefile.seqedit.lib ++++ b/src/objects/seqedit/Makefile.seqedit.lib +@@ -1,3 +1,4 @@ + LIB = seqedit + SRC = seqedit__ seqedit___ + ++DLL_LIB = xser seq +diff --git a/src/objects/seqset/Makefile.seqset.lib b/src/objects/seqset/Makefile.seqset.lib +index 87f16d0..febce67 100644 +--- a/src/objects/seqset/Makefile.seqset.lib ++++ b/src/objects/seqset/Makefile.seqset.lib +@@ -1,2 +1,3 @@ + LIB = seqset + SRC = seqset__ seqset___ gb_release_file ++DLL_LIB = xser seq +diff --git a/src/objects/seqsplit/Makefile.seqsplit.lib b/src/objects/seqsplit/Makefile.seqsplit.lib +index 87ae869..a693f50 100644 +--- a/src/objects/seqsplit/Makefile.seqsplit.lib ++++ b/src/objects/seqsplit/Makefile.seqsplit.lib +@@ -2,3 +2,5 @@ LIB = seqsplit + SRC = seqsplit__ seqsplit___ + + WATCHERS = vasilche ++ ++DLL_LIB = xser +diff --git a/src/objects/submit/Makefile.submit.lib b/src/objects/submit/Makefile.submit.lib +index 74798f8..34dd5a8 100644 +--- a/src/objects/submit/Makefile.submit.lib ++++ b/src/objects/submit/Makefile.submit.lib +@@ -1,2 +1,3 @@ + LIB = submit + SRC = submit__ submit___ ++DLL_LIB = xser xncbi # lds +diff --git a/src/objects/taxon1/Makefile.taxon1.lib b/src/objects/taxon1/Makefile.taxon1.lib +index 61658ab..d735117 100644 +--- a/src/objects/taxon1/Makefile.taxon1.lib ++++ b/src/objects/taxon1/Makefile.taxon1.lib +@@ -3,3 +3,5 @@ LIB = taxon1 + SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont + + WATCHERS = domrach ++ ++DLL_LIB = xser +diff --git a/src/objects/valerr/Makefile.valerr.lib b/src/objects/valerr/Makefile.valerr.lib +index b202355..9699bb2 100644 +--- a/src/objects/valerr/Makefile.valerr.lib ++++ b/src/objects/valerr/Makefile.valerr.lib +@@ -2,3 +2,5 @@ LIB = valerr + SRC = valerr__ valerr___ + + ASN_DEP = seqset ++ ++DLL_LIB = xser +diff --git a/src/objects/valid/Makefile.valid.lib b/src/objects/valid/Makefile.valid.lib +index 86a00a0..ee7402f 100644 +--- a/src/objects/valid/Makefile.valid.lib ++++ b/src/objects/valid/Makefile.valid.lib +@@ -1,3 +1,5 @@ + # $Id: Makefile.valid.lib 156738 2009-04-07 16:35:10Z ucko $ + LIB = valid + SRC = valid__ valid___ ++ ++DLL_LIB = xser +diff --git a/src/objects/variation/Makefile.variation.lib b/src/objects/variation/Makefile.variation.lib +index f21f84a..b08e210 100644 +--- a/src/objects/variation/Makefile.variation.lib ++++ b/src/objects/variation/Makefile.variation.lib +@@ -1,2 +1,3 @@ + LIB = variation + SRC = variation__ variation___ ++DLL_LIB = xser +diff --git a/src/objmgr/util/Makefile.util.lib b/src/objmgr/util/Makefile.util.lib +index 90eeee0..138e836 100644 +--- a/src/objmgr/util/Makefile.util.lib ++++ b/src/objmgr/util/Makefile.util.lib +@@ -10,3 +10,4 @@ LIB = xobjutil + + WATCHERS = ucko vasilche + ++DLL_LIB = xser xobjmgr +diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib +index 4b3e59e..94fc319 100644 +--- a/src/objtools/align_format/Makefile.align_format.lib ++++ b/src/objtools/align_format/Makefile.align_format.lib +@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) + # LIB_OR_DLL = dll + + WATCHERS = zaretska jianye madden camacho ++ ++DLL_LIB = seqdb blastdb +diff --git a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +index 25898aa..92d4d59 100644 +--- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib ++++ b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +@@ -29,3 +29,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + + WATCHERS = maning camacho ++ ++DLL_LIB = blastdb +diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +index 80af69f..704ed7a 100644 +--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib ++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +@@ -6,3 +6,6 @@ SRC = bdbloader cached_sequence local_blastdb_adapter + ASN_DEP = blastdb seqset + + WATCHERS = camacho ++ ++DLL_LIB = seqdb ++ +diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +index f2b2b49..a8ee667 100644 +--- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib ++++ b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +@@ -12,6 +12,6 @@ LIB = ncbi_xreader + LIB_OR_DLL = both + + # Dependencies for shared library +-DLL_LIB = ++DLL_LIB = xcompress + + WATCHERS = vasilche +diff --git a/src/objtools/readers/Makefile.xobjread.lib b/src/objtools/readers/Makefile.xobjread.lib +index 0fbffd4..4ca9fed 100644 +--- a/src/objtools/readers/Makefile.xobjread.lib ++++ b/src/objtools/readers/Makefile.xobjread.lib +@@ -19,5 +19,4 @@ SRC = read_util format_guess_ex \ + best_feat_finder source_mod_parser fasta_exception + + +-DLL_LIB = creaders +- ++DLL_LIB = creaders xncbi seq biblio seqset +diff --git a/src/objtools/readers/Makefile.xobjreadex.lib b/src/objtools/readers/Makefile.xobjreadex.lib +index 85eefe2..f238782 100644 +--- a/src/objtools/readers/Makefile.xobjreadex.lib ++++ b/src/objtools/readers/Makefile.xobjreadex.lib +@@ -8,4 +8,4 @@ LIB = xobjreadex + SRC = glimmer_reader idmapper idmapper_builtin idmapper_config \ + idmapper_database source_mod_parser_wrapper + +-DLL_LIB = xobjread ++DLL_LIB = xobjread xncbi xutil seq xobjmgr +diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib +index dab25d6..a29b960 100644 +--- a/src/objtools/simple/Makefile.xobjsimple.lib ++++ b/src/objtools/simple/Makefile.xobjsimple.lib +@@ -10,3 +10,4 @@ ASN_DEP = seqset + LIB = xobjsimple + SRC = simple_om + ++DLL_LIB = xobjmgr +diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib +index 80a74d8..69c4ef6 100644 +--- a/src/objtools/validator/Makefile.validator.lib ++++ b/src/objtools/validator/Makefile.validator.lib +@@ -19,3 +19,5 @@ NOOPT_CXX = $(CXX_WRAPPER) $(CXX) $(CXXFLAGS_ALL:-xO%=) + + lat_lon_country_map.o: $(srcdir)/lat_lon_country_map.cpp + $(NOOPT_CXX) $(srcdir)/lat_lon_country_map.cpp -o $@ $(CXX_FILTER) ++ ++DLL_LIB = xncbi xobjutil xalnmgr +diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib +index 2563b5f..efad054 100644 +--- a/src/serial/Makefile.serial.lib ++++ b/src/serial/Makefile.serial.lib +@@ -19,3 +19,5 @@ SRC = \ + LIB = xser + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi xutil +diff --git a/src/serial/soap/Makefile.soap.lib b/src/serial/soap/Makefile.soap.lib +index e77d4ee..3b28bc4 100644 +--- a/src/serial/soap/Makefile.soap.lib ++++ b/src/serial/soap/Makefile.soap.lib +@@ -8,3 +8,5 @@ SRC = soap_message soap_readhook soap_writehook soap_client \ + LIB = xsoap + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi xutil xser xconnect +diff --git a/src/serial/soap/Makefile.soap_server.lib b/src/serial/soap/Makefile.soap_server.lib +index c961496..0ccb2f0 100644 +--- a/src/serial/soap/Makefile.soap_server.lib ++++ b/src/serial/soap/Makefile.soap_server.lib +@@ -9,3 +9,5 @@ LIB = xsoap_server + REQUIRES = cgi + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi xutil xcgi xsoap xser +diff --git a/src/serial/test/Makefile.we_cpp.lib b/src/serial/test/Makefile.we_cpp.lib +index 9877691..599ef5d 100644 +--- a/src/serial/test/Makefile.we_cpp.lib ++++ b/src/serial/test/Makefile.we_cpp.lib +@@ -3,3 +3,4 @@ SRC = we_cpp__ we_cpp___ + + WATCHERS = gouriano + ++DLL_LIB = xncbi xutil xser +diff --git a/src/util/Makefile.util.lib b/src/util/Makefile.util.lib +index f103ff1..829a71c 100644 +--- a/src/util/Makefile.util.lib ++++ b/src/util/Makefile.util.lib +@@ -14,3 +14,5 @@ PROJ_TAG = core + LIBS = $(ORIG_LIBS) + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi +diff --git a/src/util/compress/api/Makefile.compress.lib b/src/util/compress/api/Makefile.compress.lib +index ae22234..2ce803a 100644 +--- a/src/util/compress/api/Makefile.compress.lib ++++ b/src/util/compress/api/Makefile.compress.lib +@@ -6,7 +6,7 @@ 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) $(LZO_LIBS) + + WATCHERS = ivanov +diff --git a/src/util/qparse/Makefile.xqueryparse.lib b/src/util/qparse/Makefile.xqueryparse.lib +index a003930..0505da7 100644 +--- a/src/util/qparse/Makefile.xqueryparse.lib ++++ b/src/util/qparse/Makefile.xqueryparse.lib +@@ -7,3 +7,5 @@ query_parser_bison.tab.c : query_parser_bison.y + bison -v -p ncbi_q_ -o query_parser_bison.tab.c query_parser_bison.y + + WATCHERS = kuznets ++ ++DLL_LIB = xncbi xutil +diff --git a/src/util/regexp/Makefile.regexp.lib b/src/util/regexp/Makefile.regexp.lib +index 0f8d5e8..83a82af 100644 +--- a/src/util/regexp/Makefile.regexp.lib ++++ b/src/util/regexp/Makefile.regexp.lib +@@ -10,3 +10,5 @@ LIB = regexp + CPPFLAGS = -I$(includedir)/util/regexp -DHAVE_CONFIG_H $(ORIG_CPPFLAGS) + + WATCHERS = ivanov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/util/sequtil/Makefile.sequtil.lib b/src/util/sequtil/Makefile.sequtil.lib +index c068a32..453c911 100644 +--- a/src/util/sequtil/Makefile.sequtil.lib ++++ b/src/util/sequtil/Makefile.sequtil.lib +@@ -4,3 +4,5 @@ LIB = sequtil + SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared + + WATCHERS = shomrat ++ ++DLL_LIB = xncbi xutil +diff --git a/src/util/xregexp/Makefile.xregexp.lib b/src/util/xregexp/Makefile.xregexp.lib +index 965fac4..3accea3 100644 +--- a/src/util/xregexp/Makefile.xregexp.lib ++++ b/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) xutil xncbi + LIBS = $(PCRE_LIBS) + + WATCHERS = ivanov diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch new file mode 100644 index 000000000..820960354 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch @@ -0,0 +1,213 @@ + src/build-system/configure | 34 +++++++++++++++++++++++----------- + src/build-system/configure.ac | 33 ++++++++++++++++++++++----------- + 2 files changed, 45 insertions(+), 22 deletions(-) + +diff --git a/src/build-system/configure b/src/build-system/configure +index 82fc9ef..d31a4f2 100755 +--- a/src/build-system/configure ++++ b/src/build-system/configure +@@ -924,7 +924,7 @@ Optional Packages: + --without-distcc do not automatically use distcc if available + --without-ncbi-c do not use NCBI C Toolkit + --without-sss do not use NCBI SSS libraries +- --without-utils do not use NCBI SSS UTIL library ++ --without-sssutils do not use NCBI SSS UTIL library + --without-sssdb do not use NCBI SSS DB library + --with-included-sss use the in-tree copy of SSS + --with-z=DIR use zlib installation in DIR +@@ -2835,12 +2835,12 @@ check ncbi-public strip pch caution ccache distcc \ + ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ + geo included-geo \ + z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ +-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ ++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ + bdb python jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ + gif jpeg tiff png xpm magic curl 3psw \ + local-lbsm ncbi-crypt connext \ +-serial objects dbapi app ctools gui algo internal gbench" ++serial objects dbapi app ctools gui algo internal gbench x" + + x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` + +@@ -2864,6 +2864,7 @@ for x_arg in "$@" ; do + case "$x_arg" in + --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ + | --cache-file= | --build= | --host= | --target= | --with-runpath= \ ++ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ + | --with-relative-runpath= | --x-includes= | --x-libraries= ) + { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5 + echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} +@@ -2876,6 +2877,7 @@ echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} + | --with-universal=* | --with-tcheck=* \ + | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ + | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ ++ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ + | [A-Z]*=* \ + | --with-z=* | --with-bz2=* | --with-lzo=* \ + | --with-pcre=* \ +@@ -3023,7 +3025,8 @@ echo "$as_me: error: --without-extra-action is not allowed" >&2;} + fi + + case "$with_projects" in +- "") if test -r projects; then ++ ""|yes) ++ if test -r projects; then + { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5 + echo "$as_me: using default projects file \"projects\"." >&6;} + with_projects=projects +@@ -3049,6 +3052,16 @@ echo "$as_me: WARNING: default projects file \"projects\" is a dangling link." > + ;; + esac + ++if test -n "$with_projects"; then ++ case "$with_projects" in ++ /* ) abs_projects=$with_projects ;; ++ yes) abs_projects=$srcdir/projects ;; ++ * ) abs_projects=$srcdir/$with_projects ;; ++ esac ++ test -r "$abs_projects" || \ ++ as_fn_error $? "unable to read requested projects file \"$abs_projects\"." "$LINENO" 5 ++fi ++ + + #### Always define this + +@@ -32712,7 +32725,7 @@ else + sep=", " + fi + if test -n "$reason" -a "$with_internal" = "yes"; then +- if test -z "$with_projects" -o "$with_projects" = "no"; then ++ if test -z "$with_projects"; then + { { echo "$as_me:$LINENO: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&5 + echo "$as_me: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&2;} + { (exit 1); exit 1; }; } +@@ -34949,11 +34962,9 @@ if test "$with_flat_makefile" != "no"; then + else + cfm_flags='-remoteptb' + fi +- case "$with_projects" in +- yes ) cfm_flags="$cfm_flags -p projects" ;; +- no | '' ) ;; +- * ) cfm_flags="$cfm_flags -p $with_projects" ;; +- esac ++ if test -n "$with_projects"; then ++ cfm_flags="$cfm_flags -p $with_projects" ++ fi + if test "$with_configure_dialog" = yes; then + cfm_flags="$cfm_flags -cfg" + fi +@@ -34997,7 +35008,8 @@ lib) + esac + + if test -n "$with_projects"; then +- build_proj="To build selected projects: cd $builddir && make all_p" ++ build_proj="To build selected projects (as listed in \"$with_projects\"): ++ cd $builddir && make all_p" + fi + + cat << EOCONF +diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac +index 7b733af..3b55bf5 100644 +--- a/src/build-system/configure.ac ++++ b/src/build-system/configure.ac +@@ -222,7 +222,7 @@ AC_ARG_WITH(ncbi-c, + AC_ARG_WITH(sss, + [ --without-sss do not use NCBI SSS libraries]) + AC_ARG_WITH(sssutils, +- [ --without-utils do not use NCBI SSS UTIL library]) ++ [ --without-sssutils do not use NCBI SSS UTIL library]) + AC_ARG_WITH(sssdb, + [ --without-sssdb do not use NCBI SSS DB library]) + AC_ARG_WITH(included-sss, +@@ -462,12 +462,12 @@ check ncbi-public strip pch caution ccache distcc \ + ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ + geo included-geo \ + z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ +-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ ++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ + bdb python jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ + gif jpeg tiff png xpm magic curl 3psw \ + local-lbsm ncbi-crypt connext \ +-serial objects dbapi app ctools gui algo internal gbench" ++serial objects dbapi app ctools gui algo internal gbench x" + + changequote(, )dnl + x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` +@@ -493,6 +493,7 @@ for x_arg in "$@" ; do + case "$x_arg" in + --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ + | --cache-file= | --build= | --host= | --target= | --with-runpath= \ ++ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ + | --with-relative-runpath= | --x-includes= | --x-libraries= ) + AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) + ;; +@@ -503,6 +504,7 @@ for x_arg in "$@" ; do + | --with-universal=* | --with-tcheck=* \ + | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ + | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ ++ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ + | [[A-Z]*=*] \ + | --with-z=* | --with-bz2=* | --with-lzo=* \ + | --with-pcre=* \ +@@ -581,7 +583,8 @@ if test "$with_extra_action" = "no" ; then + fi + + case "$with_projects" in +- "") if test -r projects; then ++ ""|yes) ++ if test -r projects; then + AC_MSG_NOTICE([using default projects file "projects".]) + with_projects=projects + AC_SUBST(PROJECTS, "\$(top_srcdir)/projects") +@@ -599,6 +602,15 @@ case "$with_projects" in + * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; + esac + ++if test -n "$with_projects"; then ++ case "$with_projects" in ++ /* ) abs_projects=$with_projects ;; ++ yes) abs_projects=$srcdir/projects ;; ++ * ) abs_projects=$srcdir/$with_projects ;; ++ esac ++ test -r "$abs_projects" || \ ++ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) ++fi + + #### Always define this + AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) +@@ -6198,7 +6210,7 @@ else + sep=", " + fi + if test -n "$reason" -a "$with_internal" = "yes"; then +- if test -z "$with_projects" -o "$with_projects" = "no"; then ++ if test -z "$with_projects"; then + AC_MSG_ERROR([--with-internal: Cannot build INTERNAL projects: missing $reason]) + else + AC_MSG_WARN([--with-internal: Cannot build all INTERNAL projects: missing $reason]) +@@ -6807,11 +6819,9 @@ if test "$with_flat_makefile" != "no"; then + else + cfm_flags='-remoteptb' + fi +- case "$with_projects" in +- yes ) cfm_flags="$cfm_flags -p projects" ;; +- no | '' ) ;; +- * ) cfm_flags="$cfm_flags -p $with_projects" ;; +- esac ++ if test -n "$with_projects"; then ++ cfm_flags="$cfm_flags -p $with_projects" ++ fi + if test "$with_configure_dialog" = yes; then + cfm_flags="$cfm_flags -cfg" + fi +@@ -6854,7 +6864,8 @@ lib) + esac + + if test -n "$with_projects"; then +- build_proj="To build selected projects: cd $builddir && make all_p" ++ build_proj="To build selected projects (as listed in \"$with_projects\"): ++ cd $builddir && make all_p" + fi + + cat << EOCONF diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild index 9806b413d..439e91722 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit eutils flag-o-matic multilib toolchain-funcs +inherit autotools eutils flag-o-matic multilib toolchain-funcs MY_TAG="Jun_15_2010" MY_Y="${MY_TAG/*_/}" @@ -68,70 +68,6 @@ DEPEND=" dev-libs/libpcre" # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# configure options, may want to expose some -# --without-debug build non-debug versions of libs and apps -# --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-dll build all libraries as DLLs -# --with-static build all libraries statically even if --with-dll -# --with-static-exe build all executables as statically as possible -# --with-plugin-auto-load always enable the plugin manager by default -# --with-bin-release build executables suitable for public release -# --with-mt compile in a MultiThread-safe manner -# --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-runpath= hard-code the runtime path to DLLs -# --with-lfs enable large file support to the extent possible -# --with-extra-action= script to call after the configuration is complete -# --with-autodep automatic generation of dependencies (GNU make) -# --with-build-root=DIR specify a non-default build directory name -# --with-fake-root=DIR appear to have been built under DIR -# --without-suffix no Release/Debug, MT or DLL sfx in the build dir name -# --with-hostspec add full host specs to the build dir name -# --without-version don't always include the cplr ver in the bd name -# --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-bincopy populate lib and bin with copies, not hard links -# --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 run test suite after the build -# --with-check-tools=... use the specified tools for testing -# --with-ncbi-public ensure compatibility for all in-house platforms -# --with-strip strip binaries at build time -# --with-pch use precompiled headers if possible -# --with-caution cancel configuration unconditionally when in doubt -# --without-caution proceed without asking when in doubt -# --without-ccache do not automatically use ccache if available -# --without-distcc do not automatically use distcc if available -# --without-ncbi-c do not use NCBI C Toolkit -# --without-sss do not use NCBI SSS libraries -# --without-utils do not use NCBI SSS UTIL library -# --without-sssdb do not use NCBI SSS DB library -# --with-included-sss use the in-tree copy of SSS - -# --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-ctools do not build NCBI C Toolkit based projects -# --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 - RDEPEND="${DEPEND}" S="${WORKDIR}/${MY_P}" @@ -162,7 +98,17 @@ src_prepare() { # "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch # use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" + + local PATCHES=( + "${FILESDIR}"/${P}-conf-opts.patch + "${FILESDIR}"/${P}-as-needed.patch + ) + epatch ${PATCHES[@]} + tc-export CXX CC +# cd src/build-system || die +# eaclocal -I. +# eautoconf } src_configure() { @@ -175,54 +121,54 @@ src_configure() { #--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-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-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-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 + #--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-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) + #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) #--without-ftds-renamed do not rename Sybase DBLIB symbols in built-in FTDS #--without-sp do not use SP libraries #--without-orbacus do not use ORBacus CORBA libraries - # --with-orbacus=DIR use ORBacus installation in DIR + #--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 + #--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 + #--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-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-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 + #--with-gbench ensure that Genome Workbench can be built + #--without-gbench do not build Genome Workbench myconf+=( --with-dll --with-lfs @@ -234,17 +180,18 @@ src_configure() { --without-strip --without-ccache --without-distcc - --with-ncbi-c +# --with-ncbi-c --without-ctools - --with-sss - --with-utils - --with-sssdb - --with-included-sss +# --with-sss +# --with-sssutils +# --with-sssdb +# --with-included-sss --with-z="${EPREFIX}"/usr --with-bz2="${EPREFIX}"/usr --with-muparser="${EPREFIX}"/usr --without-sybase -# --with-3psw=std:netopt + --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) @@ -265,7 +212,7 @@ src_configure() { $(use_with mesa mesa "${EPREFIX}"/usr) $(use_with opengl glut "${EPREFIX}"/usr) $(use_with opengl glew "${EPREFIX}"/usr) - $(use_with opengl glew-m) + $(use_with opengl glew-mx) $(use_with wxwidgets wxwidgets "${EPREFIX}"/usr) $(use_with wxwidgets wxwidgets-ucs) $(use_with freetype freetype "${EPREFIX}"/usr) @@ -277,18 +224,19 @@ src_configure() { $(use_with sqlite sqlite3 "${EPREFIX}"/usr) $(use_with icu icu "${EPREFIX}"/usr) $(use_with expat expat "${EPREFIX}"/usr) - $(use_with xml libxml2 "${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) +# $(use_with gif gif "${EPREFIX}"/usr) $(use_with jpeg jpeg "${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) +# $(use_with X x "${EPREFIX}"/usr) + $(use_with X x) ) # http://www.ncbi.nlm.nih.gov/books/NBK7167/ @@ -298,16 +246,16 @@ src_configure() { # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure # otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9 - "${S}"/configure \ - --prefix="${EPREFIX}"/usr \ - --build=x86_64-pc-linux-gnu \ - --host=x86_64-pc-linux-gnu \ - --infodir=/usr/share/info \ - --datadir=/usr/share \ - --sysconfdir=/etc \ - --localstatedir=/var/lib \ - --libdir=/usr/lib64 \ - ${myconf[@]} || die + einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}"/usr --libdir=/usr/lib64 ${myconf[@]}" + +# bash \ +# ./src/build-system/configure \ +# cd src/build-system || die + econf \ + --srcdir="${S}" \ + --prefix="${EPREFIX}"/usr \ + --libdir=/usr/lib64 \ + ${myconf[@]} || die #--without-debug \ # --with-bin-release \ # --with-bincopy \ @@ -326,7 +274,9 @@ src_compile() { # all_r would ignore the --with-projects contents and build more # emake all_r -C GCC*-Release*/build || die # all_p with compile only selected/required components - emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" +# cd "${S}"_build &&\ + emake all_p -C "${S}"_build/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?" } src_install() { |