reinit the tree, so we can have metadata

9 files changed, 350 insertions, 0 deletions

diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
new file mode 100644
index 000000000000..b5c586194c5f
--- /dev/null
+++ b/sci-biology/arb/Manifest
@@ -0,0 +1,17 @@
+AUX 5.1-bfr-overflow.patch 715 SHA256 bedb03c70bd0e4e180f8d6e966bfaf34af32125a1595aae8a994617e6a2f2833 SHA512 840dc83a2f6a6c7da05437a72bbc9372a229a18f6de08758141c6ed142a034f4b2954e9a650185fcdcdd5e672cabad32d9b2496098a2369094f502f87143710c WHIRLPOOL 8c7a986da48f147962456ecef668e516b1c14bd60ce7084b59d4dec2ca24d5e785f1e5ecb59ce6a824676736566cfedf8aa19746492aaa1062b584d3c799fb8a
+AUX 5.1-libs.patch 503 SHA256 dfa5f131eafbf163b9a3862360694a7b1f9d6231357247c7f18f696c4c4dd983 SHA512 9130fd43a7a6c43ac5dce56eeb85cabe881ddd12a2786ae0ec73432584d498afb1b7f28514c9d078e6c19f6654f2ef88192e96cac2f4be5a04474f534a2bdcdd WHIRLPOOL e82d5ae89ed7ffab4d26d6ca4049db1ebb9744c2dc41626c219d5263b8e09a27dd8cebb880821e8d4707bdbcf70a02ede760745fbd34567dca72883d937f2dbe
+AUX 5.2-libpng15.patch 1545 SHA256 e0fca903aef6c23173a6484717bdbc08e520a47f6f80c589747bddb557169e50 SHA512 8215bead0ff0d579b43b6c75f82306aacf5248833b13536ec0bbd703433343f2920c2fb68e015ea39b105630c1c06bc45cc9e165f230deddd52e76a2d7f82bdc WHIRLPOOL ad3edfb1db9f6c811fef635e8d1fa03961a8906b253e06a705ee7e712fbb5dfb16b0e1a08af07eb30b6040b61050f53b73c872af09edef3d60c7e2f558ec44a3
+AUX arb-5.2-gcc-47.patch 330 SHA256 994883702df6406e9d44ff4e3b362046428db25735910e211fc15c6e7ccc7b08 SHA512 36b2afbc6c177c44728da92fd596881b5035d5d7b8880fabbdaa360c9f59057816952112bb98ae0fa5b04352ea99b85318f262a6d91001bc177dd1e6069611c0 WHIRLPOOL c7b0ef45be2a567cd2d5c2032fd9195350f71651c8d9dd7269f94d32586b514b0cf4d2857cf4a2b63ff33cee3620cf87403d484214e95c780d28a450ce9d4928
+DIST arb-5.1-glibc2.10.patch.bz2 24659 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f SHA512 a490066efc5001e22bfeab8ce3e05690f5024217261b7b71c5a31116d18611a93f5b15aa7d57fca40e2b5e17e64b695873ccb810bd649b2b109c9b710d3ddfe1 WHIRLPOOL 9dd4f116a9050de9ca2f222017acf11ab5574891a64d2ca3043745a8912fc786973b31dce8a4274d47752893a13edf471cf3b9592aa657d8b0efaf77d700ff14
+DIST arb-5.1-linker.patch.bz2 4406 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43 SHA512 44518d500be457d16e7f6cd5f0863d2dc48cc8a1c8abcbaea79eefec5cd063258aea78d03e9601cd0bdea3c7e57949373d7a909eeed98bf48a6d98576f298e58 WHIRLPOOL 3abfd7fa5e8bc5d767395cb61f3a626adf605436d016c1597efd4255cb6bc0a27241a1f6e2149f925f910fbe4fa23c667fc2cfe6367b6d3a73ae1d7928c09714
+DIST arb-5.1.tgz 9727285 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf SHA512 236f7c40217146cf5b43d15c7252901a09f2081c1da6db1b90d7720d313e21a2808b31879d700bf894b3c576952c43be751fd0027af8a58d953403028589dd8c WHIRLPOOL 10c9d4755353471457390049f74ae5735d3fd1fe13d8ae6ca44829aee40f7990cb1e6c23d60febe9b05f598b1ab1e227c472802218cd3fe9c902465cb6e8e627
+DIST arb-5.2-linker.patch.bz2 4441 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677a3f2216021eed04ba76ac886c6 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903 WHIRLPOOL 95435cfc7f5a530442ad294cb8cd79a666f54cc3c99195e9c05a923e41b0211e5bad7b67cd4d8c5ee37ef30de22fba4472dc8990d95aaf3c8d3edb2d3d26c984
+DIST arb-5.2.tgz 9729004 SHA256 cd68cfae317aae378da69c4c4ec8036a2babec064896d0b9d845fac2133f6edd SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56 WHIRLPOOL ec5422b4b689a77b479231c04d7b5a2f4f0ef23cd06b024920432134132d7c2c5b24c407b2561074a41606e7945ce88970789f5db82e43cc9ef9313ea48c0583
+DIST arb-5.3-linker.patch.xz 3604 SHA256 09580d0c1ff54c4956382cef850aecb9008e62e083f3246604cac72f06d05e95 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7 WHIRLPOOL f77d767c5b5c911ba3ddc9ef5b3e482cb1975b5d56f50b76166bd4a0b55e251e73eeee46709147207b2f3553d482bab99398d8bd03aef8f0b79928a8a66d0bfe
+DIST arb-5.3.tgz 9543106 SHA256 c40a3f33f39996e3e331fb41acd452e5a20b7e638b856b0b66ea8e07c977abf8 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282 WHIRLPOOL 9b4723043b4f8b9a68973f49cb7dc8c3cf3558ff646d20f7d4f20f6e4797b6c9a986fdb1dc47178f2c80251db59f61dffd1b01bbdd880f864fc749ef59e62958
+EBUILD arb-5.1-r1.ebuild 2058 SHA256 333f27f6b3261695f448327ae263c9eb66fd438c33e3e669de09abc28b91d124 SHA512 686ba259e12bc336f08a0c9cfbccf52aacec57dd69abb5bdebff636579cfc564ce59efbb105500cf0ad58fcbc7ffb4876d85bff082fed48dd67849b89a7719ed WHIRLPOOL adb05065919be0b30eba206b04b030f39fe7b5d1a8a27b2d70a39d4223187178bec2d34c1db0c76a58efaad5fe1a2ff3936aaaaf4b41604ce0764f5a6a498b5d
+EBUILD arb-5.2.ebuild 2064 SHA256 23a79fd8941c27fefe8484466305b5d5a721edf13edcbe00059792d742be2356 SHA512 a05aabf3eaa0aca33c28d4e7bf89a119797d56b9d1a66c385e03a71bc8125db50236ce73d1f5e3288f0194e4fe7c75637281f13c9f51ca59061bd42e29a97836 WHIRLPOOL 877f403d2ebd8d266f455c260bdfd36c0e9999405751814b62d6bdbd9ae4b84b9ae143c8691b6c4d59625069d04f991c45fea546f7b01e2301f890545e04d31c
+EBUILD arb-5.3.ebuild 2028 SHA256 e3d4b5263af87f1377e764543018e15cfe68da8292c72dfd6cc809cf6eb95572 SHA512 d614a2b107b0bb9b0e0e1d9fdf647215165a7844cd73fe34870f24f3cbe1a50399e3e790ce202019eb90a42d0d122b20dce2a45bbdb2c134d9520666b79844a2 WHIRLPOOL af225d222868e36400859b485ea155c443db2b7a075652704aac29281bfe613693ccab1a4a464cdc4e5b9d783e60f4bc92811cc3563e3bd4f673ffabd0887489
+MISC ChangeLog 2829 SHA256 521f731051d90d9c5c6527999b6e946a9ee46678145c9d54ae4a5b32b502f35f SHA512 b464847b77a6a2a7e24dfba0332b8ef38abb030b19b10df977869bb7198a04c6ee2e6d768515f17376b3a7db159681c36b35085bf4bcfb60d87657fe536a5098 WHIRLPOOL 180a966394f15fe9bc1c442ce05fb3c4a4e03c206604a6dac388375593b06b58698fe5b78f47416844103f9dfcf10c9b4f2f0cc0d8bf57fac7ed445736b6d682
+MISC ChangeLog-2015 1976 SHA256 6fc35aa3de6891c63a3606d78ecd30e81f735d898039e324ddd6bbde6835845b SHA512 5ac257c7afa34f964a02a2236e8e0314bf7848fd6829df73a022d550446b49b5de529c19c190f89691cab272caf0105c7ee2d9d70755427c1a3043c7d849b733 WHIRLPOOL 5c0982b3243f24cf774b78ab2ed1534b4232a45b0b87d4a4a79e2db32591c95151fb7d2a262f9a006305fd32a26d30c273206656fad23292264930ef45276bd8
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
new file mode 100644
index 000000000000..f52beded359c
--- /dev/null
+++ b/sci-biology/arb/arb-5.1-r1.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=2
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	mirror://gentoo/${P}-glibc2.10.patch.bz2
+	https://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
+
+LICENSE="arb"
+SLOT="0"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/motif:0
+	opengl? (
+		media-libs/glew
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+RDEPEND="${DEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${P}-glibc2.10.patch\
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/${PV}-libs.patch \
+		"${FILESDIR}"/${PV}-bfr-overflow.patch
+	sed -i \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-e 's/--export-dynamic/-Wl,--export-dynamic/g' \
+		"${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links || die
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}" || die
+}
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
new file mode 100644
index 000000000000..a7388bf9b816
--- /dev/null
+++ b/sci-biology/arb/arb-5.2.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/motif:0
+	opengl? (
+		media-libs/glew
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+	sys-process/time"
+RDEPEND="${CDEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/5.1-libs.patch \
+		"${FILESDIR}"/5.1-bfr-overflow.patch \
+		"${FILESDIR}"/${PV}-libpng15.patch \
+		"${FILESDIR}"/${P}-gcc-47.patch
+	sed \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-e 's:-O4::g' \
+		-e 's:-pipe::g' \
+		-i "${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild
new file mode 100644
index 000000000000..135bec2695ce
--- /dev/null
+++ b/sci-biology/arb/arb-5.3.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/motif:0
+	opengl? (
+		media-libs/glew
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+	sys-process/time"
+RDEPEND="${CDEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/5.1-libs.patch \
+		"${FILESDIR}"/5.1-bfr-overflow.patch \
+		"${FILESDIR}"/5.2-libpng15.patch \
+		"${FILESDIR}"/${PN}-5.2-gcc-47.patch
+	sed \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-i "${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch
new file mode 100644
index 000000000000..21d21f5ac17f
--- /dev/null
+++ b/sci-biology/arb/files/5.1-bfr-overflow.patch
@@ -0,0 +1,16 @@
+ ARB_GDE/GDE_HGLfile.cxx |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx
+index e353a89..f69635a 100644
+--- a/ARB_GDE/GDE_HGLfile.cxx
++++ b/ARB_GDE/GDE_HGLfile.cxx
+@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type)
+             if(this_elem->id[0] == '\0')
+                 strncpy(this_elem->id,uniqueID(),79);
+             if(this_elem->short_name[0] == '\0')
+-                strncpy(this_elem->short_name,this_elem->id,79);
++                strncpy(this_elem->short_name,this_elem->id,31);
+             if(this_elem->seqlen == 0)
+                 this_elem->protect=
+                     PROT_BASE_CHANGES+
diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch
new file mode 100644
index 000000000000..bf0bacad3286
--- /dev/null
+++ b/sci-biology/arb/files/5.1-libs.patch
@@ -0,0 +1,16 @@
+diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl
+index b653a66..b346c96 100644
+--- a/SOURCE_TOOLS/provide_libs.pl
++++ b/SOURCE_TOOLS/provide_libs.pl
+@@ -118,11 +118,6 @@ sub provide_libs($$$) {
+   foreach my $lib (keys %needed_by) {
+     update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir);
+   }
+-  if ($opengl==1) {
+-    foreach my $lib (keys %needed_by_opengl) {
+-      update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir);
+-    }
+-  }
+ }
+ 
+ sub main() {
diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch
new file mode 100644
index 000000000000..3d750e76efe3
--- /dev/null
+++ b/sci-biology/arb/files/5.2-libpng15.patch
@@ -0,0 +1,45 @@
+Fix building with libpng-1.5
+
+https://bugs.gentoo.org/show_bug.cgi?id=378353
+
+Patch written by Samuli Suominen <ssuominen@gentoo.org>
+--- a/GL/glpng/glpng.c
++++ b/GL/glpng/glpng.c
+@@ -285,7 +285,7 @@
+     endinfo = png_create_info_struct(png);
+ 
+     // DH: added following lines
+-    if (setjmp(png->jmpbuf))
++    if (setjmp(png_jmpbuf(png)))
+     {
+         png_destroy_read_struct(&png, &info, &endinfo);
+         return 0;
+@@ -390,7 +390,7 @@
+     endinfo = png_create_info_struct(png);
+ 
+     // DH: added following lines
+-    if (setjmp(png->jmpbuf))
++    if (setjmp(png_jmpbuf(png)))
+     {
+         png_destroy_read_struct(&png, &info, &endinfo);
+         return 0;
+@@ -569,7 +569,7 @@
+ #define ALPHA *q
+ 
+                 switch (trans) {
+-                    case PNG_CALLBACK:
++                    case PNG_CALLBACKT:
+                         FORSTART
+                             ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b);
+                         FOREND
+--- a/GL/glpng/glpng.h
++++ b/GL/glpng/glpng.h
+@@ -57,7 +57,7 @@
+ #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS
+ 
+     /* Transparency parameters */
+-#define PNG_CALLBACK  -3 /* Call the callback function to generate alpha   */
++#define PNG_CALLBACKT  -3 /* Call the callback function to generate alpha   */
+ #define PNG_ALPHA     -2 /* Use alpha channel in PNG file, if there is one */
+ #define PNG_SOLID     -1 /* No transparency                                */
+ #define PNG_STENCIL    0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise       */
diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch
new file mode 100644
index 000000000000..186e78e450b3
--- /dev/null
+++ b/sci-biology/arb/files/arb-5.2-gcc-47.patch
@@ -0,0 +1,15 @@
+ AWTI/AWTI_import.cxx |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx
+index 8e730ac..e3f9ff4 100644
+--- a/AWTI/AWTI_import.cxx
++++ b/AWTI/AWTI_import.cxx
+@@ -12,6 +12,7 @@
+ #include <GEN.hxx>
+ 
+ #include <climits>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/arb/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>