diff options
author | Justin Lecher <jlec@gentoo.org> | 2011-05-04 19:06:17 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2011-05-04 19:06:17 +0000 |
commit | eba27bfe645fb213f5250fbd43fa28c417ce5d35 (patch) | |
tree | c7ebe2cc0209de995393609dfd6f6b5388b99128 /sci-biology/ncbi-tools++ | |
parent | Stable on amd64 wrt bug #342239 (diff) | |
download | gentoo-2-eba27bfe645fb213f5250fbd43fa28c417ce5d35.tar.gz gentoo-2-eba27bfe645fb213f5250fbd43fa28c417ce5d35.tar.bz2 gentoo-2-eba27bfe645fb213f5250fbd43fa28c417ce5d35.zip |
Fix for asneeded, #297193; removed old, #312921
(Portage version: 2.2.0_alpha30/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology/ncbi-tools++')
6 files changed, 1453 insertions, 112 deletions
diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index a8b48b6f9fbe..d48c7a88c482 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -1,6 +1,15 @@ # ChangeLog for sci-biology/ncbi-tools++ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.18 2011/05/02 09:43:44 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.19 2011/05/04 19:06:17 jlec Exp $ + +*ncbi-tools++-2010.06.15-r1 (04 May 2011) + + 04 May 2011; Justin Lecher <jlec@gentoo.org> + -ncbi-tools++-2009.05.15-r6.ebuild, ncbi-tools++-2010.06.15.ebuild, + +ncbi-tools++-2010.06.15-r1.ebuild, + +files/ncbi-tools++-2010.06.15-asneeded.patch, + +files/ncbi-tools++-2010.06.15-asneeded-ng.patch: + Fix for asneeded, #297193; removed old, #312921 02 May 2011; Justin Lecher <jlec@gentoo.org> ncbi-tools++-2010.06.15.ebuild, +files/ncbi-tools++-2010.06.15-gcc46.patch: diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-asneeded-ng.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-asneeded-ng.patch new file mode 100644 index 000000000000..15b64bc3f8de --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-asneeded-ng.patch @@ -0,0 +1,719 @@ + src/algo/align/nw/Makefile.xalgoalignnw.lib | 2 ++ + src/algo/blast/api/Makefile.xblast.lib | 2 +- + src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +- + src/algo/winmask/Makefile.xalgowinmask.lib | 1 + + src/build-system/configure | 4 ++-- + src/build-system/configure.ac | 4 ++-- + src/cgi/Makefile.cgi.lib | 2 ++ + src/cgi/Makefile.fcgi.lib | 2 ++ + src/connect/Makefile.connssl.lib | 2 ++ + src/connect/Makefile.xconnect.lib | 2 ++ + src/connect/Makefile.xthrserv.lib | 3 ++- + src/connect/Makefile.xxconnect.lib | 1 + + .../services/Makefile.ncbi_xcache_netcache.lib | 3 ++- + 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 | 3 +++ + src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +- + src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++ + src/dbapi/Makefile.dbapi.lib | 3 +++ + src/dbapi/driver/Makefile.dbapi_driver.lib | 1 + + .../driver/samples/Makefile.dbapi_sample_base.lib | 2 ++ + .../python/Makefile.python_ncbi_dbapi.lib | 2 +- + src/dbapi/simple/Makefile.sdbapi.lib | 2 ++ + src/html/Makefile.html.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/general/Makefile.general.lib | 2 ++ + src/objects/medline/Makefile.medline.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/submit/Makefile.submit.lib | 3 +++ + src/objects/valid/Makefile.valid.lib | 2 ++ + src/objmgr/util/Makefile.util.lib | 2 ++ + .../align_format/Makefile.align_format.lib | 2 ++ + src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 1 + + src/objtools/cleanup/Makefile.cleanup.lib | 2 ++ + .../blastdb/Makefile.ncbi_xloader_blastdb.lib | 1 + + .../data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- + src/objtools/readers/Makefile.xobjread.lib | 3 +-- + src/objtools/readers/Makefile.xobjreadex.lib | 2 ++ + 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 | 2 ++ + 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 +- + 58 files changed, 105 insertions(+), 16 deletions(-) + +diff --git a/src/algo/align/nw/Makefile.xalgoalignnw.lib b/src/algo/align/nw/Makefile.xalgoalignnw.lib +index db149c4..25d62b9 100644 +--- a/src/algo/align/nw/Makefile.xalgoalignnw.lib ++++ b/src/algo/align/nw/Makefile.xalgoalignnw.lib +@@ -17,3 +17,5 @@ LIB = xalgoalignnw + + CXXFLAGS = $(FAST_CXXFLAGS) -D ALGOALIGN_NW_SPLIGN_MAKE_PUBLIC_BINARY + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = xser xncbi xutil +diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib +index 68d5ad8..8bf6ab5 100644 +--- a/src/algo/blast/api/Makefile.xblast.lib ++++ b/src/algo/blast/api/Makefile.xblast.lib +@@ -73,7 +73,7 @@ SRC = $(SRC_C:%=.core_%) $(SRC_CXX) + + LIB = xblast + +-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) ++DLL_LIB = xalgowinmask composition_adjustment xalgoblastdbindex xalgodustmask xobjutil $(OBJMGR_LIBS) + + CFLAGS = $(FAST_CFLAGS) + # Strict gcc flags +diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib +index ede2c7b..da2f544 100644 +--- a/src/algo/blast/blastinput/Makefile.blastinput.lib ++++ b/src/algo/blast/blastinput/Makefile.blastinput.lib +@@ -20,7 +20,7 @@ SRC = $(SRC_CXX) + + LIB = blastinput + +-DLL_LIB = xblast $(OBJMGR_LIBS) ++DLL_LIB = xblast $(OBJMGR_LIBS) seqdb + + # should be redundant, given the above :-/ + ASN_DEP = seqset xnetblast +diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib +index 951e656..8297ec7 100644 +--- a/src/algo/winmask/Makefile.xalgowinmask.lib ++++ b/src/algo/winmask/Makefile.xalgowinmask.lib +@@ -19,3 +19,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \ + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = seqmasks_io +diff --git a/src/build-system/configure b/src/build-system/configure +index a088db7..d858c86 100755 +--- a/src/build-system/configure ++++ b/src/build-system/configure +@@ -5054,10 +5054,10 @@ if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then + DEF_FAST_FLAGS="-O2" + ;; + GCC:* ) +- DEF_FAST_FLAGS="-O9 -finline-functions -ffast-math -fstrict-aliasing" ++ DEF_FAST_FLAGS="" + if test "$with_profiling" != "yes"; then + # incompatible with -pg +- DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer" ++ DEF_FAST_FLAGS="$DEF_FAST_FLAGS" + fi + ;; + WorkShop5[89]* | WorkShop510 ) +diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac +index 7810bc3..5ad6d38 100644 +--- a/src/build-system/configure.ac ++++ b/src/build-system/configure.ac +@@ -1276,10 +1276,10 @@ if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then + DEF_FAST_FLAGS="-O2" + ;; + GCC:* ) +- DEF_FAST_FLAGS="-O9 -finline-functions -ffast-math -fstrict-aliasing" ++ DEF_FAST_FLAGS="" + if test "$with_profiling" != "yes"; then + # incompatible with -pg +- DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer" ++ DEF_FAST_FLAGS="$DEF_FAST_FLAGS" + fi + ;; + WorkShop5[[89]]* | WorkShop510 ) +diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib +index a990390..81f4e7e 100644 +--- a/src/cgi/Makefile.cgi.lib ++++ b/src/cgi/Makefile.cgi.lib +@@ -10,4 +10,6 @@ LIB = xcgi + + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + ++DLL_LIB = xncbi xutil ++ + WATCHERS = vakatov +diff --git a/src/cgi/Makefile.fcgi.lib b/src/cgi/Makefile.fcgi.lib +index 2569b41..42b4196 100644 +--- a/src/cgi/Makefile.fcgi.lib ++++ b/src/cgi/Makefile.fcgi.lib +@@ -11,4 +11,6 @@ LIB = xfcgi + + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) -DNCBI_XFCGI_EXPORTS + ++DLL_LIB = xncbi xutil ++ + WATCHERS = vakatov +diff --git a/src/connect/Makefile.connssl.lib b/src/connect/Makefile.connssl.lib +index b400ca2..c252172 100644 +--- a/src/connect/Makefile.connssl.lib ++++ b/src/connect/Makefile.connssl.lib +@@ -4,6 +4,8 @@ SRC = ncbi_gnutls + + LIB = connssl + ++DLL_LIB = connect ++ + CPPFLAGS = $(GNUTLS_INCLUDE) $(ORIG_CPPFLAGS) + LIBS = $(GNUTLS_LIBS) $(ORIG_LIBS) + +diff --git a/src/connect/Makefile.xconnect.lib b/src/connect/Makefile.xconnect.lib +index 473bb0b..2550dda 100644 +--- a/src/connect/Makefile.xconnect.lib ++++ b/src/connect/Makefile.xconnect.lib +@@ -11,6 +11,8 @@ include $(srcdir)/Makefile.xxconnect.lib + SRC = $(SRC_C) $(SRC_CXX) + UNIX_SRC = $(LOCAL_LBSM) + ++DLL_LIB = xncbi xutil ++ + LIB = xconnect + PROJ_TAG = core + +diff --git a/src/connect/Makefile.xthrserv.lib b/src/connect/Makefile.xthrserv.lib +index 23a845b..9d90fd0 100644 +--- a/src/connect/Makefile.xthrserv.lib ++++ b/src/connect/Makefile.xthrserv.lib +@@ -4,6 +4,7 @@ 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 = lavr +diff --git a/src/connect/Makefile.xxconnect.lib b/src/connect/Makefile.xxconnect.lib +index 382f0b9..c31ace3 100644 +--- a/src/connect/Makefile.xxconnect.lib ++++ b/src/connect/Makefile.xxconnect.lib +@@ -13,6 +13,7 @@ SRC = $(SRC_CXX) + LIB = xxconnect + PROJ_TAG = core + ++DLL_LIB = xncbi xutil connect + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr +diff --git a/src/connect/services/Makefile.ncbi_xcache_netcache.lib b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +index 606f4f1..2911eff 100644 +--- a/src/connect/services/Makefile.ncbi_xcache_netcache.lib ++++ b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +@@ -6,7 +6,8 @@ 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 8124a0d..de45848 100644 +--- a/src/connect/services/Makefile.xconnserv.lib ++++ b/src/connect/services/Makefile.xconnserv.lib +@@ -16,6 +16,6 @@ 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 08f7bb9..9389e09 100644 +--- a/src/connect/test/Makefile.conntest.lib ++++ b/src/connect/test/Makefile.conntest.lib +@@ -3,4 +3,6 @@ + SRC = ncbi_conntest + LIB = xconntest + ++DLL_LIB = xncbi xutil connect ++ + WATCHERS = lar +diff --git a/src/corelib/Makefile.test_boost.lib b/src/corelib/Makefile.test_boost.lib +index b19bc5b..036951a 100644 +--- a/src/corelib/Makefile.test_boost.lib ++++ b/src/corelib/Makefile.test_boost.lib +@@ -3,6 +3,8 @@ + SRC = test_boost + LIB = test_boost + ++DLL_LIB = xncbi ++ + CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) + + REQUIRES = Boost.Test.Included +diff --git a/src/corelib/Makefile.test_mt.lib b/src/corelib/Makefile.test_mt.lib +index 90c10d2..d99347b 100644 +--- a/src/corelib/Makefile.test_mt.lib ++++ b/src/corelib/Makefile.test_mt.lib +@@ -3,6 +3,8 @@ + SRC = test_mt + LIB = test_mt + ++DLL_LIB = xncbi ++ + # REQUIRES = MT + + WATCHERS = grichenk +diff --git a/src/corelib/test/Makefile.pbacktest.lib b/src/corelib/test/Makefile.pbacktest.lib +index da0c616..e9aeba7 100644 +--- a/src/corelib/test/Makefile.pbacktest.lib ++++ b/src/corelib/test/Makefile.pbacktest.lib +@@ -3,4 +3,6 @@ + SRC = pbacktest + LIB = xpbacktest + ++DLL_LIB = xncbi ++ + WATCHERS = lavr +diff --git a/src/db/bdb/Makefile.bdb.lib b/src/db/bdb/Makefile.bdb.lib +index 3729707..45874cf 100644 +--- a/src/db/bdb/Makefile.bdb.lib ++++ b/src/db/bdb/Makefile.bdb.lib +@@ -13,4 +13,7 @@ LIB = bdb + + CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE) + ++DLL_LIB = xncbi xutil ++LIBS = $(BERKELEYDB_LIBS) ++ + WATCHERS = kuznets +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..5d72f9c 100644 +--- a/src/db/sqlite/Makefile.sqlitewrapp.lib ++++ b/src/db/sqlite/Makefile.sqlitewrapp.lib +@@ -7,4 +7,7 @@ CPPFLAGS= $(ORIG_CPPFLAGS) $(SQLITE3_INCLUDE) + + REQUIRES = SQLITE3 + ++DLL_LIB = xncbi xutil ++LIBS = $(SQLITE3_LIBS) ++ + WATCHERS = ivanovp +diff --git a/src/dbapi/Makefile.dbapi.lib b/src/dbapi/Makefile.dbapi.lib +index 6e3ad4c..d1b5425 100644 +--- a/src/dbapi/Makefile.dbapi.lib ++++ b/src/dbapi/Makefile.dbapi.lib +@@ -5,7 +5,10 @@ SRC = variant active_obj dbapi driver_mgr err_handler ds_impl conn_impl \ + bytestreambuf blobstream \ + cursor_impl bulkinsert rw_impl + ++#ASN_DEP = dbapi_driver + LIB = dbapi ++DLL_LIB = xncbi xutil ++LIBS = $(PYTHON_LIBS) + + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + +diff --git a/src/dbapi/driver/Makefile.dbapi_driver.lib b/src/dbapi/driver/Makefile.dbapi_driver.lib +index dfeac5a..8128559 100644 +--- a/src/dbapi/driver/Makefile.dbapi_driver.lib ++++ b/src/dbapi/driver/Makefile.dbapi_driver.lib +@@ -15,6 +15,7 @@ LIB_OR_DLL = both + + CPPFLAGS = $(ORIG_CPPFLAGS) + ++DLL_LIB = xncbi xutil + LIBS = $(DL_LIBS) $(ORIG_LIBS) + + # Work around a mysterious bug in Apple's GCC. +diff --git a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +index 941ccd6..ef0226f 100644 +--- a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib ++++ b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +@@ -5,4 +5,6 @@ LIB = dbapi_sample_base + + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + ++DLL_LIB = xncbi xutil dbapi_driver ++ + WATCHERS = ivanovp +diff --git a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +index ebe08c4..86ecda6 100644 +--- a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib ++++ b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +@@ -11,7 +11,7 @@ LIB_OR_DLL = dll + + # Dependencies for shared library + DLL_LIB = dbapi dbapi_driver$(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..ccf87c9 100644 +--- a/src/dbapi/simple/Makefile.sdbapi.lib ++++ b/src/dbapi/simple/Makefile.sdbapi.lib +@@ -3,5 +3,7 @@ + SRC = sdbapi + LIB = sdbapi + ++DLL_LIB = xncbi xutil dbapi_driver ncbi_xdbapi_ftds xconnect xser bdb xconnserv dbapi ++ + WATCHERS = ivanovp + +diff --git a/src/html/Makefile.html.lib b/src/html/Makefile.html.lib +index a57c1e3..dd520a0 100644 +--- a/src/html/Makefile.html.lib ++++ b/src/html/Makefile.html.lib +@@ -7,4 +7,5 @@ SRC = node html htmlhelper page pager selection components \ + jsmenu commentdiag indentstream html_exception writer_htmlenc + LIB = xhtml + ++DLL_LIB = xncbi xutil + WATCHERS = ivanov +diff --git a/src/objects/biblio/Makefile.biblio.lib b/src/objects/biblio/Makefile.biblio.lib +index 275c307..6b5a85b 100644 +--- a/src/objects/biblio/Makefile.biblio.lib ++++ b/src/objects/biblio/Makefile.biblio.lib +@@ -1,2 +1,4 @@ + LIB = biblio + SRC = biblio__ biblio___ label_util ++ ++DLL_LIB = general xser xncbi xutil +diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib +index b9d7d38..0fdb87f 100644 +--- a/src/objects/blast/Makefile.blast.lib ++++ b/src/objects/blast/Makefile.blast.lib +@@ -1,2 +1,4 @@ + LIB = xnetblast + SRC = blast__ blast___ names ++ ++DLL_LIB = xncbi xutil xser seq +diff --git a/src/objects/blast/Makefile.xnetblastcli.lib b/src/objects/blast/Makefile.xnetblastcli.lib +index 96325c4..20ee95c 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 +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/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/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..6260041 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 +diff --git a/src/objects/seq/Makefile.seq.lib b/src/objects/seq/Makefile.seq.lib +index 5ca2820..3671ee1 100644 +--- a/src/objects/seq/Makefile.seq.lib ++++ b/src/objects/seq/Makefile.seq.lib +@@ -10,3 +10,5 @@ LIB = seq + SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \ + seq_id_tree seq_id_handle seq_id_mapper \ + seq_loc_mapper_base seq_align_mapper_base seqlocinfo ++ ++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..1fcd293 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 = xser +diff --git a/src/objects/submit/Makefile.submit.lib b/src/objects/submit/Makefile.submit.lib +index 74798f8..388a187 100644 +--- a/src/objects/submit/Makefile.submit.lib ++++ b/src/objects/submit/Makefile.submit.lib +@@ -1,2 +1,5 @@ + LIB = submit + SRC = submit__ submit___ ++ ++ ++DLL_LIB = xser +diff --git a/src/objects/valid/Makefile.valid.lib b/src/objects/valid/Makefile.valid.lib +index 86a00a0..7090d74 100644 +--- a/src/objects/valid/Makefile.valid.lib ++++ b/src/objects/valid/Makefile.valid.lib +@@ -1,3 +1,5 @@ + # $Id: ncbi-tools++-2010.06.15-asneeded-ng.patch,v 1.1 2011/05/04 19:06:17 jlec Exp $ + LIB = valid + SRC = valid__ valid___ ++ ++DLL_LIB = xregexp +diff --git a/src/objmgr/util/Makefile.util.lib b/src/objmgr/util/Makefile.util.lib +index 90eeee0..5977767 100644 +--- a/src/objmgr/util/Makefile.util.lib ++++ b/src/objmgr/util/Makefile.util.lib +@@ -8,5 +8,7 @@ ASN_DEP = submit + SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util + LIB = xobjutil + ++DLL_LIB = xobjmgr ++ + WATCHERS = ucko vasilche + +diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib +index fe0c16d..c4535ea 100644 +--- a/src/objtools/align_format/Makefile.align_format.lib ++++ b/src/objtools/align_format/Makefile.align_format.lib +@@ -16,3 +16,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) + # CXXFLAGS = $(FAST_CXXFLAGS) + # + # LIB_OR_DLL = dll ++ ++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 11c7fae..b930bc9 100644 +--- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib ++++ b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +@@ -28,3 +28,4 @@ CFLAGS = $(FAST_CFLAGS) + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = blastdb seq xobjmgr +diff --git a/src/objtools/cleanup/Makefile.cleanup.lib b/src/objtools/cleanup/Makefile.cleanup.lib +index d72e4ee..1b46b41 100644 +--- a/src/objtools/cleanup/Makefile.cleanup.lib ++++ b/src/objtools/cleanup/Makefile.cleanup.lib +@@ -8,3 +8,5 @@ SRC = cleanup cleanupp cleanup_feat cleanup_general cleanup_pub \ + cleanup_utils cleanup_biosource cleanup_gbqual cleanup_desc + + LIB = xcleanup ++ ++DLL_LIB = xobjmgr +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 22dc6df..868da0f 100644 +--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib ++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +@@ -5,3 +5,4 @@ SRC = bdbloader cached_sequence local_blastdb_adapter + + ASN_DEP = blastdb seqset + ++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 b938560..07bddd8 100644 +--- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib ++++ b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +@@ -12,4 +12,4 @@ LIB = ncbi_xreader + LIB_OR_DLL = both + + # Dependencies for shared library +-DLL_LIB = ++DLL_LIB = xcompress +diff --git a/src/objtools/readers/Makefile.xobjread.lib b/src/objtools/readers/Makefile.xobjread.lib +index c5c4789..58b304a 100644 +--- a/src/objtools/readers/Makefile.xobjread.lib ++++ b/src/objtools/readers/Makefile.xobjread.lib +@@ -8,5 +8,4 @@ SRC = acc_pattern agp_read agp_util aln_reader bed_reader cigar fasta \ + multireader phrap reader_base readfeat rm_reader wiggle_data \ + wiggle_reader + +-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 8152069..da01b3a 100644 +--- a/src/objtools/readers/Makefile.xobjreadex.lib ++++ b/src/objtools/readers/Makefile.xobjreadex.lib +@@ -5,3 +5,5 @@ ASN_DEP = seq seqset + LIB = xobjreadex + SRC = glimmer_reader idmapper idmapper_builtin idmapper_config \ + idmapper_database ++ ++DLL_LIB = xncbi xutil seq xobjmgr +diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib +index bc8ae31..b16b11e 100644 +--- a/src/objtools/validator/Makefile.validator.lib ++++ b/src/objtools/validator/Makefile.validator.lib +@@ -9,3 +9,5 @@ SRC = validator validatorp valid_biosource valid_pub validerror_align validerror + LIB = xvalidate + + ASN_DEP = general biblio pub seq seqset submit taxon3 valerr valid ++ ++DLL_LIB = general biblio pub seq seqset submit taxon3 valerr valid xobjmgr xalnmgr +diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib +index 2563b5f..d2e23b9 100644 +--- a/src/serial/Makefile.serial.lib ++++ b/src/serial/Makefile.serial.lib +@@ -18,4 +18,6 @@ SRC = \ + + LIB = xser + ++DLL_LIB = xncbi xutil ++ + WATCHERS = gouriano +diff --git a/src/serial/soap/Makefile.soap.lib b/src/serial/soap/Makefile.soap.lib +index e77d4ee..936798a 100644 +--- a/src/serial/soap/Makefile.soap.lib ++++ b/src/serial/soap/Makefile.soap.lib +@@ -7,4 +7,6 @@ SRC = soap_message soap_readhook soap_writehook soap_client \ + soap_11__ soap_11___ + LIB = xsoap + ++DLL_LIB = xncbi xutil xser xconnect ++ + WATCHERS = gouriano +diff --git a/src/serial/soap/Makefile.soap_server.lib b/src/serial/soap/Makefile.soap_server.lib +index c961496..4892f55 100644 +--- a/src/serial/soap/Makefile.soap_server.lib ++++ b/src/serial/soap/Makefile.soap_server.lib +@@ -8,4 +8,6 @@ LIB = xsoap_server + + REQUIRES = cgi + ++DLL_LIB = xncbi xutil xcgi xsoap xser ++ + WATCHERS = gouriano +diff --git a/src/serial/test/Makefile.we_cpp.lib b/src/serial/test/Makefile.we_cpp.lib +index 9877691..1c7250b 100644 +--- a/src/serial/test/Makefile.we_cpp.lib ++++ b/src/serial/test/Makefile.we_cpp.lib +@@ -1,5 +1,7 @@ + LIB = we_cpp + SRC = we_cpp__ we_cpp___ + ++DLL_LIB = xncbi xutil xser ++ + WATCHERS = gouriano + +diff --git a/src/util/Makefile.util.lib b/src/util/Makefile.util.lib +index f103ff1..98d2cd0 100644 +--- a/src/util/Makefile.util.lib ++++ b/src/util/Makefile.util.lib +@@ -11,6 +11,8 @@ SRC = random_gen utf8 checksum bytesrc strbuffer itree smalldns \ + LIB = xutil + PROJ_TAG = core + ++DLL_LIB = xncbi ++ + LIBS = $(ORIG_LIBS) + + WATCHERS = vakatov +diff --git a/src/util/compress/api/Makefile.compress.lib b/src/util/compress/api/Makefile.compress.lib +index f27e8fb..18b0634 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) $(LZO_LIBS) + + WATCHERS = ivanov +diff --git a/src/util/qparse/Makefile.xqueryparse.lib b/src/util/qparse/Makefile.xqueryparse.lib +index a003930..0f59ec0 100644 +--- a/src/util/qparse/Makefile.xqueryparse.lib ++++ b/src/util/qparse/Makefile.xqueryparse.lib +@@ -6,4 +6,6 @@ SRC = query_parse parser query_tree_print query_exec + query_parser_bison.tab.c : query_parser_bison.y + bison -v -p ncbi_q_ -o query_parser_bison.tab.c query_parser_bison.y + ++DLL_LIB = xncbi xutil ++ + WATCHERS = kuznets +diff --git a/src/util/regexp/Makefile.regexp.lib b/src/util/regexp/Makefile.regexp.lib +index 0f8d5e8..04d87d9 100644 +--- a/src/util/regexp/Makefile.regexp.lib ++++ b/src/util/regexp/Makefile.regexp.lib +@@ -7,6 +7,8 @@ SRC = pcre_chartables pcre_compile pcre_config pcre_dfa_exec pcre_exec pcre_full + + LIB = regexp + ++DLL_LIB = xncbi xutil ++ + CPPFLAGS = -I$(includedir)/util/regexp -DHAVE_CONFIG_H $(ORIG_CPPFLAGS) + + WATCHERS = ivanov +diff --git a/src/util/sequtil/Makefile.sequtil.lib b/src/util/sequtil/Makefile.sequtil.lib +index c068a32..5c89253 100644 +--- a/src/util/sequtil/Makefile.sequtil.lib ++++ b/src/util/sequtil/Makefile.sequtil.lib +@@ -3,4 +3,6 @@ + LIB = sequtil + SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared + ++DLL_LIB = xncbi xutil ++ + WATCHERS = shomrat +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++-2010.06.15-asneeded.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-asneeded.patch new file mode 100644 index 000000000000..28ff4c6c6edb --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-asneeded.patch @@ -0,0 +1,652 @@ + src/algo/align/nw/Makefile.xalgoalignnw.lib | 2 ++ + src/algo/blast/api/Makefile.xblast.lib | 2 +- + src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +- + src/algo/winmask/Makefile.xalgowinmask.lib | 1 + + src/build-system/configure | 4 ++-- + src/build-system/configure.ac | 4 ++-- + src/cgi/Makefile.cgi.lib | 2 ++ + src/cgi/Makefile.fcgi.lib | 2 ++ + src/connect/Makefile.connssl.lib | 2 ++ + src/connect/Makefile.xconnect.lib | 2 ++ + src/connect/Makefile.xthrserv.lib | 3 ++- + src/connect/Makefile.xxconnect.lib | 1 + + .../services/Makefile.ncbi_xcache_netcache.lib | 3 ++- + 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 | 3 +++ + src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +- + src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++ + src/dbapi/Makefile.dbapi.lib | 3 +++ + src/dbapi/driver/Makefile.dbapi_driver.lib | 1 + + .../driver/samples/Makefile.dbapi_sample_base.lib | 2 ++ + .../python/Makefile.python_ncbi_dbapi.lib | 2 +- + src/dbapi/simple/Makefile.sdbapi.lib | 2 ++ + src/html/Makefile.html.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/general/Makefile.general.lib | 2 ++ + src/objects/medline/Makefile.medline.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 ++ + .../align_format/Makefile.align_format.lib | 2 ++ + src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 1 + + .../blastdb/Makefile.ncbi_xloader_blastdb.lib | 1 + + .../data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- + src/objtools/readers/Makefile.xobjread.lib | 3 +-- + src/objtools/readers/Makefile.xobjreadex.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 | 2 ++ + 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 +- + 52 files changed, 92 insertions(+), 16 deletions(-) + +diff --git a/src/algo/align/nw/Makefile.xalgoalignnw.lib b/src/algo/align/nw/Makefile.xalgoalignnw.lib +index db149c4..25d62b9 100644 +--- a/src/algo/align/nw/Makefile.xalgoalignnw.lib ++++ b/src/algo/align/nw/Makefile.xalgoalignnw.lib +@@ -17,3 +17,5 @@ LIB = xalgoalignnw + + CXXFLAGS = $(FAST_CXXFLAGS) -D ALGOALIGN_NW_SPLIGN_MAKE_PUBLIC_BINARY + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = xser xncbi xutil +diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib +index 68d5ad8..8bf6ab5 100644 +--- a/src/algo/blast/api/Makefile.xblast.lib ++++ b/src/algo/blast/api/Makefile.xblast.lib +@@ -73,7 +73,7 @@ SRC = $(SRC_C:%=.core_%) $(SRC_CXX) + + LIB = xblast + +-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) ++DLL_LIB = xalgowinmask composition_adjustment xalgoblastdbindex xalgodustmask xobjutil $(OBJMGR_LIBS) + + CFLAGS = $(FAST_CFLAGS) + # Strict gcc flags +diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib +index ede2c7b..da2f544 100644 +--- a/src/algo/blast/blastinput/Makefile.blastinput.lib ++++ b/src/algo/blast/blastinput/Makefile.blastinput.lib +@@ -20,7 +20,7 @@ SRC = $(SRC_CXX) + + LIB = blastinput + +-DLL_LIB = xblast $(OBJMGR_LIBS) ++DLL_LIB = xblast $(OBJMGR_LIBS) seqdb + + # should be redundant, given the above :-/ + ASN_DEP = seqset xnetblast +diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib +index 951e656..8297ec7 100644 +--- a/src/algo/winmask/Makefile.xalgowinmask.lib ++++ b/src/algo/winmask/Makefile.xalgowinmask.lib +@@ -19,3 +19,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \ + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = seqmasks_io +diff --git a/src/build-system/configure b/src/build-system/configure +index a088db7..d858c86 100755 +--- a/src/build-system/configure ++++ b/src/build-system/configure +@@ -5054,10 +5054,10 @@ if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then + DEF_FAST_FLAGS="-O2" + ;; + GCC:* ) +- DEF_FAST_FLAGS="-O9 -finline-functions -ffast-math -fstrict-aliasing" ++ DEF_FAST_FLAGS="" + if test "$with_profiling" != "yes"; then + # incompatible with -pg +- DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer" ++ DEF_FAST_FLAGS="$DEF_FAST_FLAGS" + fi + ;; + WorkShop5[89]* | WorkShop510 ) +diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac +index 7810bc3..5ad6d38 100644 +--- a/src/build-system/configure.ac ++++ b/src/build-system/configure.ac +@@ -1276,10 +1276,10 @@ if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then + DEF_FAST_FLAGS="-O2" + ;; + GCC:* ) +- DEF_FAST_FLAGS="-O9 -finline-functions -ffast-math -fstrict-aliasing" ++ DEF_FAST_FLAGS="" + if test "$with_profiling" != "yes"; then + # incompatible with -pg +- DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer" ++ DEF_FAST_FLAGS="$DEF_FAST_FLAGS" + fi + ;; + WorkShop5[[89]]* | WorkShop510 ) +diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib +index a990390..81f4e7e 100644 +--- a/src/cgi/Makefile.cgi.lib ++++ b/src/cgi/Makefile.cgi.lib +@@ -10,4 +10,6 @@ LIB = xcgi + + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + ++DLL_LIB = xncbi xutil ++ + WATCHERS = vakatov +diff --git a/src/cgi/Makefile.fcgi.lib b/src/cgi/Makefile.fcgi.lib +index 2569b41..42b4196 100644 +--- a/src/cgi/Makefile.fcgi.lib ++++ b/src/cgi/Makefile.fcgi.lib +@@ -11,4 +11,6 @@ LIB = xfcgi + + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) -DNCBI_XFCGI_EXPORTS + ++DLL_LIB = xncbi xutil ++ + WATCHERS = vakatov +diff --git a/src/connect/Makefile.connssl.lib b/src/connect/Makefile.connssl.lib +index b400ca2..c252172 100644 +--- a/src/connect/Makefile.connssl.lib ++++ b/src/connect/Makefile.connssl.lib +@@ -4,6 +4,8 @@ SRC = ncbi_gnutls + + LIB = connssl + ++DLL_LIB = connect ++ + CPPFLAGS = $(GNUTLS_INCLUDE) $(ORIG_CPPFLAGS) + LIBS = $(GNUTLS_LIBS) $(ORIG_LIBS) + +diff --git a/src/connect/Makefile.xconnect.lib b/src/connect/Makefile.xconnect.lib +index 473bb0b..2550dda 100644 +--- a/src/connect/Makefile.xconnect.lib ++++ b/src/connect/Makefile.xconnect.lib +@@ -11,6 +11,8 @@ include $(srcdir)/Makefile.xxconnect.lib + SRC = $(SRC_C) $(SRC_CXX) + UNIX_SRC = $(LOCAL_LBSM) + ++DLL_LIB = xncbi xutil ++ + LIB = xconnect + PROJ_TAG = core + +diff --git a/src/connect/Makefile.xthrserv.lib b/src/connect/Makefile.xthrserv.lib +index 23a845b..9d90fd0 100644 +--- a/src/connect/Makefile.xthrserv.lib ++++ b/src/connect/Makefile.xthrserv.lib +@@ -4,6 +4,7 @@ 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 = lavr +diff --git a/src/connect/Makefile.xxconnect.lib b/src/connect/Makefile.xxconnect.lib +index 382f0b9..c31ace3 100644 +--- a/src/connect/Makefile.xxconnect.lib ++++ b/src/connect/Makefile.xxconnect.lib +@@ -13,6 +13,7 @@ SRC = $(SRC_CXX) + LIB = xxconnect + PROJ_TAG = core + ++DLL_LIB = xncbi xutil connect + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr +diff --git a/src/connect/services/Makefile.ncbi_xcache_netcache.lib b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +index 606f4f1..2911eff 100644 +--- a/src/connect/services/Makefile.ncbi_xcache_netcache.lib ++++ b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +@@ -6,7 +6,8 @@ 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 8124a0d..de45848 100644 +--- a/src/connect/services/Makefile.xconnserv.lib ++++ b/src/connect/services/Makefile.xconnserv.lib +@@ -16,6 +16,6 @@ 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 08f7bb9..9389e09 100644 +--- a/src/connect/test/Makefile.conntest.lib ++++ b/src/connect/test/Makefile.conntest.lib +@@ -3,4 +3,6 @@ + SRC = ncbi_conntest + LIB = xconntest + ++DLL_LIB = xncbi xutil connect ++ + WATCHERS = lar +diff --git a/src/corelib/Makefile.test_boost.lib b/src/corelib/Makefile.test_boost.lib +index b19bc5b..036951a 100644 +--- a/src/corelib/Makefile.test_boost.lib ++++ b/src/corelib/Makefile.test_boost.lib +@@ -3,6 +3,8 @@ + SRC = test_boost + LIB = test_boost + ++DLL_LIB = xncbi ++ + CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) + + REQUIRES = Boost.Test.Included +diff --git a/src/corelib/Makefile.test_mt.lib b/src/corelib/Makefile.test_mt.lib +index 90c10d2..d99347b 100644 +--- a/src/corelib/Makefile.test_mt.lib ++++ b/src/corelib/Makefile.test_mt.lib +@@ -3,6 +3,8 @@ + SRC = test_mt + LIB = test_mt + ++DLL_LIB = xncbi ++ + # REQUIRES = MT + + WATCHERS = grichenk +diff --git a/src/corelib/test/Makefile.pbacktest.lib b/src/corelib/test/Makefile.pbacktest.lib +index da0c616..e9aeba7 100644 +--- a/src/corelib/test/Makefile.pbacktest.lib ++++ b/src/corelib/test/Makefile.pbacktest.lib +@@ -3,4 +3,6 @@ + SRC = pbacktest + LIB = xpbacktest + ++DLL_LIB = xncbi ++ + WATCHERS = lavr +diff --git a/src/db/bdb/Makefile.bdb.lib b/src/db/bdb/Makefile.bdb.lib +index 3729707..45874cf 100644 +--- a/src/db/bdb/Makefile.bdb.lib ++++ b/src/db/bdb/Makefile.bdb.lib +@@ -13,4 +13,7 @@ LIB = bdb + + CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE) + ++DLL_LIB = xncbi xutil ++LIBS = $(BERKELEYDB_LIBS) ++ + WATCHERS = kuznets +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..5d72f9c 100644 +--- a/src/db/sqlite/Makefile.sqlitewrapp.lib ++++ b/src/db/sqlite/Makefile.sqlitewrapp.lib +@@ -7,4 +7,7 @@ CPPFLAGS= $(ORIG_CPPFLAGS) $(SQLITE3_INCLUDE) + + REQUIRES = SQLITE3 + ++DLL_LIB = xncbi xutil ++LIBS = $(SQLITE3_LIBS) ++ + WATCHERS = ivanovp +diff --git a/src/dbapi/Makefile.dbapi.lib b/src/dbapi/Makefile.dbapi.lib +index 6e3ad4c..d1b5425 100644 +--- a/src/dbapi/Makefile.dbapi.lib ++++ b/src/dbapi/Makefile.dbapi.lib +@@ -5,7 +5,10 @@ SRC = variant active_obj dbapi driver_mgr err_handler ds_impl conn_impl \ + bytestreambuf blobstream \ + cursor_impl bulkinsert rw_impl + ++#ASN_DEP = dbapi_driver + LIB = dbapi ++DLL_LIB = xncbi xutil ++LIBS = $(PYTHON_LIBS) + + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + +diff --git a/src/dbapi/driver/Makefile.dbapi_driver.lib b/src/dbapi/driver/Makefile.dbapi_driver.lib +index dfeac5a..8128559 100644 +--- a/src/dbapi/driver/Makefile.dbapi_driver.lib ++++ b/src/dbapi/driver/Makefile.dbapi_driver.lib +@@ -15,6 +15,7 @@ LIB_OR_DLL = both + + CPPFLAGS = $(ORIG_CPPFLAGS) + ++DLL_LIB = xncbi xutil + LIBS = $(DL_LIBS) $(ORIG_LIBS) + + # Work around a mysterious bug in Apple's GCC. +diff --git a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +index 941ccd6..ef0226f 100644 +--- a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib ++++ b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +@@ -5,4 +5,6 @@ LIB = dbapi_sample_base + + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + ++DLL_LIB = xncbi xutil dbapi_driver ++ + WATCHERS = ivanovp +diff --git a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +index ebe08c4..86ecda6 100644 +--- a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib ++++ b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +@@ -11,7 +11,7 @@ LIB_OR_DLL = dll + + # Dependencies for shared library + DLL_LIB = dbapi dbapi_driver$(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..72d3a5c 100644 +--- a/src/dbapi/simple/Makefile.sdbapi.lib ++++ b/src/dbapi/simple/Makefile.sdbapi.lib +@@ -3,5 +3,7 @@ + SRC = sdbapi + LIB = sdbapi + ++DLL_LIB = xncbi xutil dbapi_driver ncbi_xdbapi_ftds xconnect xser bdb xconnserv ++ + WATCHERS = ivanovp + +diff --git a/src/html/Makefile.html.lib b/src/html/Makefile.html.lib +index a57c1e3..dd520a0 100644 +--- a/src/html/Makefile.html.lib ++++ b/src/html/Makefile.html.lib +@@ -7,4 +7,5 @@ SRC = node html htmlhelper page pager selection components \ + jsmenu commentdiag indentstream html_exception writer_htmlenc + LIB = xhtml + ++DLL_LIB = xncbi xutil + WATCHERS = ivanov +diff --git a/src/objects/biblio/Makefile.biblio.lib b/src/objects/biblio/Makefile.biblio.lib +index 275c307..6b5a85b 100644 +--- a/src/objects/biblio/Makefile.biblio.lib ++++ b/src/objects/biblio/Makefile.biblio.lib +@@ -1,2 +1,4 @@ + LIB = biblio + SRC = biblio__ biblio___ label_util ++ ++DLL_LIB = general xser xncbi xutil +diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib +index b9d7d38..e736a95 100644 +--- a/src/objects/blast/Makefile.blast.lib ++++ b/src/objects/blast/Makefile.blast.lib +@@ -1,2 +1,4 @@ + LIB = xnetblast + SRC = blast__ blast___ names ++ ++DLL_LIB = xncbi xutil +diff --git a/src/objects/blast/Makefile.xnetblastcli.lib b/src/objects/blast/Makefile.xnetblastcli.lib +index 96325c4..20ee95c 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 +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/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/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..6260041 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 +diff --git a/src/objects/seq/Makefile.seq.lib b/src/objects/seq/Makefile.seq.lib +index 5ca2820..3671ee1 100644 +--- a/src/objects/seq/Makefile.seq.lib ++++ b/src/objects/seq/Makefile.seq.lib +@@ -10,3 +10,5 @@ LIB = seq + SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \ + seq_id_tree seq_id_handle seq_id_mapper \ + seq_loc_mapper_base seq_align_mapper_base seqlocinfo ++ ++DLL_LIB = general seqcode pub sequtil biblio xser xncbi xutil +diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib +index fe0c16d..c4535ea 100644 +--- a/src/objtools/align_format/Makefile.align_format.lib ++++ b/src/objtools/align_format/Makefile.align_format.lib +@@ -16,3 +16,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) + # CXXFLAGS = $(FAST_CXXFLAGS) + # + # LIB_OR_DLL = dll ++ ++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 11c7fae..855e0fb 100644 +--- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib ++++ b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +@@ -28,3 +28,4 @@ CFLAGS = $(FAST_CFLAGS) + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++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 22dc6df..868da0f 100644 +--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib ++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +@@ -5,3 +5,4 @@ SRC = bdbloader cached_sequence local_blastdb_adapter + + ASN_DEP = blastdb seqset + ++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 b938560..07bddd8 100644 +--- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib ++++ b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +@@ -12,4 +12,4 @@ LIB = ncbi_xreader + LIB_OR_DLL = both + + # Dependencies for shared library +-DLL_LIB = ++DLL_LIB = xcompress +diff --git a/src/objtools/readers/Makefile.xobjread.lib b/src/objtools/readers/Makefile.xobjread.lib +index c5c4789..58b304a 100644 +--- a/src/objtools/readers/Makefile.xobjread.lib ++++ b/src/objtools/readers/Makefile.xobjread.lib +@@ -8,5 +8,4 @@ SRC = acc_pattern agp_read agp_util aln_reader bed_reader cigar fasta \ + multireader phrap reader_base readfeat rm_reader wiggle_data \ + wiggle_reader + +-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 8152069..62c1e64 100644 +--- a/src/objtools/readers/Makefile.xobjreadex.lib ++++ b/src/objtools/readers/Makefile.xobjreadex.lib +@@ -5,3 +5,5 @@ ASN_DEP = seq seqset + LIB = xobjreadex + SRC = glimmer_reader idmapper idmapper_builtin idmapper_config \ + idmapper_database ++ ++DLL_LIB = xncbi xutil seq +diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib +index 2563b5f..d2e23b9 100644 +--- a/src/serial/Makefile.serial.lib ++++ b/src/serial/Makefile.serial.lib +@@ -18,4 +18,6 @@ SRC = \ + + LIB = xser + ++DLL_LIB = xncbi xutil ++ + WATCHERS = gouriano +diff --git a/src/serial/soap/Makefile.soap.lib b/src/serial/soap/Makefile.soap.lib +index e77d4ee..936798a 100644 +--- a/src/serial/soap/Makefile.soap.lib ++++ b/src/serial/soap/Makefile.soap.lib +@@ -7,4 +7,6 @@ SRC = soap_message soap_readhook soap_writehook soap_client \ + soap_11__ soap_11___ + LIB = xsoap + ++DLL_LIB = xncbi xutil xser xconnect ++ + WATCHERS = gouriano +diff --git a/src/serial/soap/Makefile.soap_server.lib b/src/serial/soap/Makefile.soap_server.lib +index c961496..4892f55 100644 +--- a/src/serial/soap/Makefile.soap_server.lib ++++ b/src/serial/soap/Makefile.soap_server.lib +@@ -8,4 +8,6 @@ LIB = xsoap_server + + REQUIRES = cgi + ++DLL_LIB = xncbi xutil xcgi xsoap xser ++ + WATCHERS = gouriano +diff --git a/src/serial/test/Makefile.we_cpp.lib b/src/serial/test/Makefile.we_cpp.lib +index 9877691..1c7250b 100644 +--- a/src/serial/test/Makefile.we_cpp.lib ++++ b/src/serial/test/Makefile.we_cpp.lib +@@ -1,5 +1,7 @@ + LIB = we_cpp + SRC = we_cpp__ we_cpp___ + ++DLL_LIB = xncbi xutil xser ++ + WATCHERS = gouriano + +diff --git a/src/util/Makefile.util.lib b/src/util/Makefile.util.lib +index f103ff1..98d2cd0 100644 +--- a/src/util/Makefile.util.lib ++++ b/src/util/Makefile.util.lib +@@ -11,6 +11,8 @@ SRC = random_gen utf8 checksum bytesrc strbuffer itree smalldns \ + LIB = xutil + PROJ_TAG = core + ++DLL_LIB = xncbi ++ + LIBS = $(ORIG_LIBS) + + WATCHERS = vakatov +diff --git a/src/util/compress/api/Makefile.compress.lib b/src/util/compress/api/Makefile.compress.lib +index f27e8fb..18b0634 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) $(LZO_LIBS) + + WATCHERS = ivanov +diff --git a/src/util/qparse/Makefile.xqueryparse.lib b/src/util/qparse/Makefile.xqueryparse.lib +index a003930..0f59ec0 100644 +--- a/src/util/qparse/Makefile.xqueryparse.lib ++++ b/src/util/qparse/Makefile.xqueryparse.lib +@@ -6,4 +6,6 @@ SRC = query_parse parser query_tree_print query_exec + query_parser_bison.tab.c : query_parser_bison.y + bison -v -p ncbi_q_ -o query_parser_bison.tab.c query_parser_bison.y + ++DLL_LIB = xncbi xutil ++ + WATCHERS = kuznets +diff --git a/src/util/regexp/Makefile.regexp.lib b/src/util/regexp/Makefile.regexp.lib +index 0f8d5e8..04d87d9 100644 +--- a/src/util/regexp/Makefile.regexp.lib ++++ b/src/util/regexp/Makefile.regexp.lib +@@ -7,6 +7,8 @@ SRC = pcre_chartables pcre_compile pcre_config pcre_dfa_exec pcre_exec pcre_full + + LIB = regexp + ++DLL_LIB = xncbi xutil ++ + CPPFLAGS = -I$(includedir)/util/regexp -DHAVE_CONFIG_H $(ORIG_CPPFLAGS) + + WATCHERS = ivanov +diff --git a/src/util/sequtil/Makefile.sequtil.lib b/src/util/sequtil/Makefile.sequtil.lib +index c068a32..5c89253 100644 +--- a/src/util/sequtil/Makefile.sequtil.lib ++++ b/src/util/sequtil/Makefile.sequtil.lib +@@ -3,4 +3,6 @@ + LIB = sequtil + SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared + ++DLL_LIB = xncbi xutil ++ + WATCHERS = shomrat +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++/ncbi-tools++-2009.05.15-r6.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r6.ebuild deleted file mode 100644 index 2c7245bfa155..000000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r6.ebuild +++ /dev/null @@ -1,109 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r6.ebuild,v 1.2 2011/03/21 18:36:29 ssuominen Exp $ - -EAPI="3" - -inherit eutils flag-o-matic multilib toolchain-funcs - -MY_TAG="May_15_2009" -MY_Y="${MY_TAG/*_/}" -MY_P="ncbi_cxx--${MY_TAG}" - -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" -SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/${MY_Y}/${MY_TAG}/${MY_P}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -#IUSE="X unicode opengl gnutls test" -IUSE="sqlite" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -# wxGTK: must run eselect wxwindows after installing wxgtk or build will fail. Check and abort here. -# dev-libs/xalan-c - problems detecting, api mismatch? - -# apparently gbench-only dependencies -# dev-libs/libxml2 -# dev-libs/libxslt -# dev-libs/xerces-c -# dev-libs/lzo:2 -# dev-libs/boost -# app-text/sablotron -# media-libs/libpng -# media-libs/tiff -# media-libs/jpeg -# x11-libs/libXpm -# unicode? ( dev-libs/icu ) -# opengl? ( media-libs/glut -# media-libs/mesa ) -# gnutls? ( net-libs/gnutls ) -# X? ( x11-libs/fltk:1 -# x11-libs/wxGTK ) - -DEPEND="sqlite? ( dev-db/sqlite:3 )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - epatch "${FILESDIR}"/${P}-gcc44.patch \ - "${FILESDIR}"/${P}-asneeded.patch - sed -i -e 's/-print-file-name=libstdc++.a//' \ - -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ - src/build-system/configure || die -} - -src_configure() { - # required with gcc-4.4 and code turned on by --with-mt - append-cxxflags -fpermissive - - tc-export CXX CC - - # econf fails - # --with-bin-release and --without-ftds are workarounds for build system bugs - # --without-boost: see bug 312921 - # NB: build system supports ICC - "${S}"/configure --without-debug \ - --with-bin-release \ - --without-static \ - --with-dll \ - --without-ftds \ - --without-boost \ - --prefix="${ED}"/usr \ - --libdir="${ED}"/usr/$(get_libdir)/${PN} \ - --with-z="${EPREFIX}/usr" \ - --with-bz2="${EPREFIX}/usr" \ - --with-pcre="${EPREFIX}/usr" \ - --with-openssl="${EPREFIX}/usr" \ - --with-mt \ - || die - -# apparently gbench-only configs -# --with-boost="/usr" \ -# --with-sablot="/usr" \ -# --with-icu="/usr" \ -# --with-fltk="/usr" \ -# --with-mesa="/usr" \ -# --with-glut="/usr" \ -# --with-wxwidgets="/usr" \ -# problems detecting this -# --with-xalan="/usr" \ -} - -src_compile() { - emake all_r -C GCC*-Release*/build || die -} - -src_install() { - emake install || die - # File collisions with sci-biology/ncbi-tools - rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp} - - 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.' -} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild new file mode 100644 index 000000000000..3968e582aea9 --- /dev/null +++ b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild,v 1.1 2011/05/04 19:06:17 jlec Exp $ + +EAPI="3" + +inherit eutils flag-o-matic multilib toolchain-funcs + +MY_TAG="Jun_15_2010" +MY_Y="${MY_TAG/*_/}" +MY_P="ncbi_cxx--${MY_TAG}" + +DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" +SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/${MY_Y}/${MY_TAG}/${MY_P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +IUSE="sqlite mysql" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +DEPEND=" + sqlite? ( dev-db/sqlite:3 ) + mysql? ( virtual/mysql )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MY_P}" + +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 \ + "${FILESDIR}"/${P}-gcc46.patch \ + "${FILESDIR}"/${P}-asneeded.patch +} + +src_configure() { + tc-export CXX CC +# conf check for sqlite and mysql + "${S}"/configure --without-debug \ + --with-bin-release \ + --with-bincopy \ + --without-static \ + --with-dll \ + --with-mt \ + --prefix="${ED}"/usr \ + --libdir="${ED}"/usr/$(get_libdir)/${PN} \ + || die +} + +src_compile() { + emake all_r -C GCC*-Release*/build || die +} + +src_install() { + emake install || die + # File collisions with sci-biology/ncbi-tools + rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp} + + 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.' +} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15.ebuild index fd76f8b88266..a5b6690cd46b 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15.ebuild,v 1.2 2011/05/02 09:43:44 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15.ebuild,v 1.3 2011/05/04 19:06:17 jlec Exp $ EAPI="3" @@ -19,7 +19,8 @@ SLOT="0" IUSE="sqlite mysql" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -DEPEND="sqlite? ( dev-db/sqlite:3 ) +DEPEND=" + sqlite? ( dev-db/sqlite:3 ) mysql? ( virtual/mysql )" RDEPEND="${DEPEND}" |