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

[Martin Mokrejs]

commit:     20b211f3ab9ace0a1ae4bd0a09831ad71ec691da
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 27 01:08:12 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 27 01:08:12 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=20b211f3

sci-biology/ncbi-tools++: compiles via 'make -j1' now

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 ...ols++-18.0.0-fix-app-blast_sample-linking.patch | 28 ++++++++++++++++++++++
 .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild        |  1 +
 2 files changed, 29 insertions(+)

diff --git 
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch
 
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch
new file mode 100644
index 000000000..cc0444d5c
--- /dev/null
+++ 
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch
@@ -0,0 +1,28 @@
+--- ncbi_cxx--18_0_0/src/sample/app/blast/Makefile.blast_sample.app.ori        
2017-03-27 03:01:00.032137965 +0200
++++ ncbi_cxx--18_0_0/src/sample/app/blast/Makefile.blast_sample.app    
2017-03-27 03:01:29.732137720 +0200
+@@ -12,9 +12,9 @@
+ # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
+ 
+ ### BEGIN COPIED SETTINGS
+-LIB_ = xobjsimple $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = xobjsimple $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+ 
+ # These settings are necessary for optimized WorkShop builds, due to
+ # BLAST's own use of them.
+--- ncbi_cxx--18_0_0/src/sample/app/blast/Makefile.vsrun_sample.app.ori        
2017-03-27 03:04:52.632136045 +0200
++++ ncbi_cxx--18_0_0/src/sample/app/blast/Makefile.vsrun_sample.app    
2017-03-27 03:05:26.012135769 +0200
+@@ -12,9 +12,9 @@
+ # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
+ 
+ ### BEGIN COPIED SETTINGS
+-LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) 
$(OBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+ 
+ # These settings are necessary for optimized WorkShop builds, due to
+ # BLAST's own use of them.

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 5d0547875..10e1b7228 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -132,6 +132,7 @@ src_prepare() {
                "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
                "${FILESDIR}"/${P}-fix-app-tls-linking.patch
                "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
+               "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
                )
        #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
        epatch ${PATCHES[@]}