commit: 69763b2b7798dac7b061b881c2b76e6ec7fa005b Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Mar 23 17:17:40 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Mar 23 17:17:40 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=69763b2b
sci-biology/ncbi-tools++: more patches Package-Manager: Portage-2.3.3, Repoman-2.3.1 ...i-tools++-18.0.0-fix-app-compartp-linking.patch | 31 ++++++++++++++++++++++ ...tools++-18.0.0-fix-sample-app-cgi-linking.patch | 11 ++++++++ .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 ++ 3 files changed, 44 insertions(+) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch new file mode 100644 index 000000000..0b4b76e4f --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch @@ -0,0 +1,31 @@ +--- ncbi_cxx--18_0_0/src/app/compart/Makefile.compart.app.ori 2017-03-23 14:49:24.915182566 +0100 ++++ ncbi_cxx--18_0_0/src/app/compart/Makefile.compart.app 2017-03-23 14:50:32.926896138 +0100 +@@ -5,11 +5,11 @@ + APP = compart + SRC = compart + +-LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xqueryparse \ +- $(BLAST_LIBS:%=%$(STATIC)) \ ++LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xalgoseq taxon1 xqueryparse \ ++ $(BLAST_LIBS:%=%$(STATIC)) xregexp $(REGEXP_LIB) \ + $(OBJMGR_LIBS:%=%$(STATIC)) + +-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(REGEXP_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) +--- ncbi_cxx--18_0_0/src/app/compart/Makefile.compartp.app.ori 2017-03-23 18:05:44.135172346 +0100 ++++ ncbi_cxx--18_0_0/src/app/compart/Makefile.compartp.app 2017-03-23 18:09:00.990132154 +0100 +@@ -5,9 +5,9 @@ + APP = compartp + SRC = compartp + +-LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) ++LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse xregexp $(REGEXP_LIB) $(OBJMGR_LIBS) + +-LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(REGEXP_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch new file mode 100644 index 000000000..c45d4ad96 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch @@ -0,0 +1,11 @@ +--- ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori 2017-03-22 23:52:58.984696074 +0100 ++++ ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app 2017-03-22 23:53:54.746258126 +0100 +@@ -11,7 +11,7 @@ + # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. + + ### BEGIN COPIED SETTINGS +-LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi ++LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi + + LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild index 761058824..7a70e8f5e 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild @@ -116,6 +116,8 @@ src_prepare() { "${FILESDIR}"/${P}-fix-annotwriter-linking.patch "${FILESDIR}"/${P}-fix-undefined-xobjread.patch "${FILESDIR}"/${P}-fix-apps-blast-linking.patch + "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch + "${FILESDIR}"/${P}-fix-app-compartp-linking.patch ) #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch epatch ${PATCHES[@]}