add ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch; get around a bug in the C++ Toolkit's handling of --without-runpath with certain linker versions by running configure with -Wl,-rpath-link,_build/lib in LDFLAGS (assuming _build is an absolute path; otherwise, prepend /home/mmokrejs/proj/sci/sci-biology/ncbi-tools++/) [from Aaron Ucko].

3 files changed, 28 insertions, 2 deletions

diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
index 33144be75..88fdd5a5e 100644
--- a/sci-biology/ncbi-tools++/Manifest
+++ b/sci-biology/ncbi-tools++/Manifest
@@ -1,2 +1,2 @@
-DIST ncbi_cxx--12_0_0.tar.gz 385648 SHA256 0500192648d84e564de1cba01044039b6c1801d0af67355f1b6b54085fabae24 SHA512 e93683f3d1673699788ed21b235ffb468e43003a67eb46941d49215da4fe4c522e550e320b6633d215f92d3e01bb0775a0cf637a925ac9af2ce4dc4dcf239b43 WHIRLPOOL ded3d15e8065fbec7a62643b30b13eeb97d614fafe47112b0ce856b90b06a67db616ba02e30216a8e84d197f44d1120ec35befbd6ee2f8ef044097f25a778d1c
+DIST ncbi_cxx--12_0_0.tar.gz 37925914 SHA256 432d5c72cc02dad263f1b2f1ab875e04e60b1ded0c5537ed54e8095b50554d20 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed WHIRLPOOL 16f0b6de7e0d898bca7a2a46a64a4aa0795f99673d4715a21cca2dc5aa728143b56f02ad9c108543195a8f86f4267777d2be9428dcf52f5495083a63961ad867
 DIST ncbi_cxx--9_0_0.tar.gz 33815259 SHA256 f561eb6de12dc7a1e3325d6fc1f76ca097099a31116fb407fa52e54174757fc7 SHA512 b8ce298d4e180915c86ea94cd0cba44cabe8ae1173525a7af3038736572427b4cb25191c6b8ad0fcde14c2677a03fbc675ab22dc64d496dd4a21d70b978c2fab WHIRLPOOL 1c5569c5fc73f67850eb6b35eece0e719a97fee5368f43cca9733b6d2a308dc0c66d2814da15e7b64a400ab7df130ab77e9fc6f3412778cc7c003684a1f6b594
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
new file mode 100644
index 000000000..be496254a
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
@@ -0,0 +1,10 @@
+--- src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib	2013-09-13 21:58:59.420013862 +0200
++++ src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib	2013-09-13 21:59:56.060014010 +0200
+@@ -10,6 +10,6 @@
+ LIB_OR_DLL = both
+ 
+ # Dependencies for shared library
+-DLL_LIB = ncbi_xreader$(DLL)
++DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_LDEP)
+ 
+ WATCHERS = vasilche
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 33ee6fb9e..a43dfefba 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -106,6 +106,7 @@ src_prepare() {
 		"${FILESDIR}"/${P}-conf-opts.patch
 		"${FILESDIR}"/${P}-as-needed.patch
 		"${FILESDIR}"/${P}-fix-creaders-linking.patch
+		"${FILESDIR}"/${P}-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
 		)
 	epatch ${PATCHES[@]}
 
@@ -196,6 +197,13 @@ src_configure() {
 	--with-muparser="${EPREFIX}/usr"
 	--without-sybase
 	--with-autodep
+
+# due to \*-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
+# ./configure ... --with-flat-makefile
+# cd .../build
+# make -f Makefile.flat
+#
+	--with-flat-makefile
 #	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
 	$(use_with debug)
 	$(use_with debug max-debug)
@@ -260,6 +268,7 @@ src_configure() {
 		--srcdir="${S}" \
 		--prefix="${EPREFIX}/usr" \
 		--libdir=/usr/lib64 \
+		${myconf} LDFLAGS="-Wl,-rpath-link,${S}_build/lib -Wl,--no-as-needed" \
 		${myconf[@]} || die
 #--without-debug \
 #		--with-bin-release \
@@ -280,7 +289,14 @@ src_compile() {
 	# emake all_r -C GCC*-Release*/build || die
 	# all_p with compile only selected/required components
 #	cd "${S}"_build &&\
-	emake all_p -C "${S}"_build/build
+
+    # disabling this because we need to take the flat Makefile route
+	# emake all_p -C "${S}"_build/build
+
+	# take the flat Makefile route
+	emake -f Makefile.flat -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?"
 }