[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/

[Martin Mokrejs]

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[@]}