gentoo resync : 01.01.2018

14 files changed, 0 insertions, 448 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index ab77a5ae6d14..57e346c2db2b 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
index 7690d418e0f6..52b55979193b 100644
--- a/sci-biology/arb/Manifest
+++ b/sci-biology/arb/Manifest
@@ -1,20 +1,6 @@
-AUX 5.1-bfr-overflow.patch 715 BLAKE2B 04586fda551093d2a3f15af52e10c228f5463f46e9c7c6a57eb4a42cde68800902f2e4a0ba6caec1dc2f6dbace915018bb285cf8d40f24e9b3a234f26762245c SHA512 840dc83a2f6a6c7da05437a72bbc9372a229a18f6de08758141c6ed142a034f4b2954e9a650185fcdcdd5e672cabad32d9b2496098a2369094f502f87143710c
-AUX 5.1-libs.patch 503 BLAKE2B a389b2af00275a66ce2a51570b3d6249eec8cc08afb1b32c3319c51698bcbf581671182f13f0aac612ece57299be787257fe8c885b3c323fc133081f0733ed1a SHA512 9130fd43a7a6c43ac5dce56eeb85cabe881ddd12a2786ae0ec73432584d498afb1b7f28514c9d078e6c19f6654f2ef88192e96cac2f4be5a04474f534a2bdcdd
-AUX 5.2-libpng15.patch 1545 BLAKE2B 657d1bdbcf73be2af4391764df043274acb18f1445ebaa425652a5075a2a6a158c0804405524d0291066267f8509861a6d30a22713cf8b28636c41767aa14078 SHA512 8215bead0ff0d579b43b6c75f82306aacf5248833b13536ec0bbd703433343f2920c2fb68e015ea39b105630c1c06bc45cc9e165f230deddd52e76a2d7f82bdc
-AUX arb-5.2-gcc-47.patch 330 BLAKE2B 441bf38b1b2e34ead2a0fe1d1e15399c3c0d31d321fe93abd347e73b22adb8440c54c7aab4bd50caac43ccd6487ef1c834719f072b4fc8656e7735a431c9fefc SHA512 36b2afbc6c177c44728da92fd596881b5035d5d7b8880fabbdaa360c9f59057816952112bb98ae0fa5b04352ea99b85318f262a6d91001bc177dd1e6069611c0
 AUX arb-6.0.6-arb_install.patch 2752 BLAKE2B ca081a0440a29c59c3e46b883c474a2794656d143e975bd53d74fb7a35901f6fd8acf29ba13d75617d6541e2cf8758d7405472884f0d810fcc6fde0d8e3f5082 SHA512 468d7e1ee599334e593ce95374a29a1815ba8559afb6d773f533a07b0b520115e1aafcbb228ec82f331cd2d580816d68bf2f9351774ed8f52942b13e23eb5746
 AUX arb-6.0.6-glapi.patch 537 BLAKE2B 4b0529f61a089816c0ca8535017db9a9d33ffbcd26a881b740709c639c1e893c93f7a49d2e0b628805edd172ef428360283a41be2c255adf9baa4a6128f04d70 SHA512 249847d0b563460447c7c53167ec50ba541270614943a471aab5c8dccc1c9e253af79746834fd722d33f9a96607e9a382f7ae80fb96656f52d9a143fd4760be5
 AUX arb-6.0.6-tc-flags.patch 1540 BLAKE2B a5a93849998c596b47beaae540648203ff4891f450bef27ffe7e602fc0bb9b61f71b99dc0f98121680e93b3ea9c5e1919e600e431d0a641ab52b698ae4375c32 SHA512 e5bcd297196f473c6cece3e5a28380011f20e5d0389b6de508c4ae0f82f0d6bb4502b755a89b1f9ddf582ab3a9722793c6f7727168b442c08dd99f95799d3418
-DIST arb-5.1-glibc2.10.patch.bz2 24659 BLAKE2B 856b4735c98f13b21af537486f27ae89cca724590f7f4d7975dc7df05d3e3388a29198f6b9bb14b2ef885f5442d6687d6fbcdb44c076656b8e2ff521c633f940 SHA512 a490066efc5001e22bfeab8ce3e05690f5024217261b7b71c5a31116d18611a93f5b15aa7d57fca40e2b5e17e64b695873ccb810bd649b2b109c9b710d3ddfe1
-DIST arb-5.1-linker.patch.bz2 4406 BLAKE2B 3214f875c7d58e9a60032397f34a38ec13fc1672cecca475223fe8b79c684d4839e3e7dcf7c1df8290f00912b6268493bf89d77b744c923b3a9769bb466bef15 SHA512 44518d500be457d16e7f6cd5f0863d2dc48cc8a1c8abcbaea79eefec5cd063258aea78d03e9601cd0bdea3c7e57949373d7a909eeed98bf48a6d98576f298e58
-DIST arb-5.1.tgz 9727285 BLAKE2B 97660214b1dc513a946256cfdcbbefff282bb125e81e05a92005bd62b4ec00a478fb6639c6f5b0b3893e1c49d8eb9f13d04ec36271daec41c41b9093fefea09a SHA512 236f7c40217146cf5b43d15c7252901a09f2081c1da6db1b90d7720d313e21a2808b31879d700bf894b3c576952c43be751fd0027af8a58d953403028589dd8c
-DIST arb-5.2-linker.patch.bz2 4441 BLAKE2B c2554cf4e24ab9257dfac06482f05a42e89ad06ecf1b069d80df16d512ce675a29f7c3dbe0bca6b0f3add910617cc5853462aa5593cb9ccb2fb2656cdd5183c1 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903
-DIST arb-5.2.tgz 9729004 BLAKE2B 2ae85529c9c7afdbc0debc0317e0ab3772f881b606f849b6cb60872e2e123b612399dc4dcfa07c5e886703478140515fa31e9b69b37383a12d8526ecb771f77b SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56
-DIST arb-5.3-linker.patch.xz 3604 BLAKE2B 0327a94ee4daaca9cc4aa41601ae52b8616d26fd0ede19b36cb2ea72135bc9609d21db74b9588cc79e08242d3e32bb3398d78663c90dc4e3c248877953249789 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7
-DIST arb-5.3.tgz 9543106 BLAKE2B e67859accad1f5aeae3fe3a85530543beb1141e1fe340760e55b2bcef84f1f5cd18fe82ff75beafbf49b1945def0436d862487a630192345568931a335454210 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282
 DIST arb-6.0.6.tgz 13286019 BLAKE2B fd9591321111363013084030aef7130ccac580aeb9b16e93e72613dc0b3922873aa3f3b1e76d28c1ed14846c0b0d2d497257366fc5deebf4c40c79f0b7eee859 SHA512 053d4d964d8a299f86d4cab9113f0d2181780bf51e0ccec0459a4d568d09bb4e9723fa8493d8e4fa5c72e6d1f022241721cadf7ceb75ee27142d48f2f9f269b4
-EBUILD arb-5.1-r1.ebuild 2058 BLAKE2B 72c6e8816e06ca0880a7196584d5a372cf82036ac15bc1e70f0f44b3f84937a99e090cba6577a799f2760733e2764eb7cdac6b561f22f13c7a941dacd3ef0048 SHA512 686ba259e12bc336f08a0c9cfbccf52aacec57dd69abb5bdebff636579cfc564ce59efbb105500cf0ad58fcbc7ffb4876d85bff082fed48dd67849b89a7719ed
-EBUILD arb-5.2.ebuild 2064 BLAKE2B ca231f973b29c4e952b33c5055aa4e94d27f29fd28e248494a1a603a1bd95ba159b86e36a1cfdd68772a375db0c4bc5f0096123766bff79125d2df3fb66e852f SHA512 a05aabf3eaa0aca33c28d4e7bf89a119797d56b9d1a66c385e03a71bc8125db50236ce73d1f5e3288f0194e4fe7c75637281f13c9f51ca59061bd42e29a97836
-EBUILD arb-5.3.ebuild 2028 BLAKE2B 14281f761050797da0b40a797845d59292c089a2dca6b65455252d76cbcac240872d3c6a3629ced8315792c90ab9bf246b08e5b915aaf163a4c9b77c7e796a1d SHA512 d614a2b107b0bb9b0e0e1d9fdf647215165a7844cd73fe34870f24f3cbe1a50399e3e790ce202019eb90a42d0d122b20dce2a45bbdb2c134d9520666b79844a2
 EBUILD arb-6.0.6.ebuild 2482 BLAKE2B 7ec03e43d84e8c0f9ccc1465a0c5da113224c02b068dddcf2c3712930d1b309789104f8c074511f243ae8fcc76554bd57d4f2ce3eb73ff23eacb523451d11906 SHA512 afb90afeb3d01aceeddafd52b0e173c240a166e325298ac3eecd3fe130ef8248237a13a6d42c81d66f3103343333a80a19d84e2c077ba6c6ddaf1efb271fa14d
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
deleted file mode 100644
index f52beded359c..000000000000
--- a/sci-biology/arb/arb-5.1-r1.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# 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${PN}" || die
-}
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
deleted file mode 100644
index a7388bf9b816..000000000000
--- a/sci-biology/arb/arb-5.2.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
-HOMEPAGE="http://www.arb-home.de/"
-SRC_URI="
-	http://download.arb-home.de/release/arb_${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${PN}"
-}
diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild
deleted file mode 100644
index 135bec2695ce..000000000000
--- a/sci-biology/arb/arb-5.3.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
-HOMEPAGE="http://www.arb-home.de/"
-SRC_URI="
-	http://download.arb-home.de/release/arb_${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
deleted file mode 100644
index 21d21f5ac17f..000000000000
--- a/sci-biology/arb/files/5.1-bfr-overflow.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- 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
deleted file mode 100644
index bf0bacad3286..000000000000
--- a/sci-biology/arb/files/5.1-libs.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-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
deleted file mode 100644
index 3d750e76efe3..000000000000
--- a/sci-biology/arb/files/5.2-libpng15.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-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
deleted file mode 100644
index 186e78e450b3..000000000000
--- a/sci-biology/arb/files/arb-5.2-gcc-47.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- 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/fasta/Manifest b/sci-biology/fasta/Manifest
index e674eb25c94b..90848bfe1f68 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,7 +1,4 @@
-AUX 35.4.10-ldflags.patch 1036 BLAKE2B 5e614e62a99f4ba5808ad33a082c4eb1fb4feb1b7031f69e42a833fdff05c91cf1197a8a838eb347f2c31c59c68536fbae9dad07293d3bd80bdde8f6263a90a5 SHA512 8136536c7f9887920a045dbcd04fa9d01dc0a3b22ed0a1771df715e288d6c889d87b0a6d0f52c947b54185f6a5e92fe902316b502074200a13820cac9dfa6594
 AUX fasta-36.3.5e-ldflags.patch 2781 BLAKE2B e6d4e0984b4dadfc9d38504ab215d769084edc6c79cfe641b6b3fba8264a40add1665027295ec4afa19d26277036bfe1a5103ecdf72ef91a1139542ac8272954 SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7
-DIST fasta-35.4.10.tar.gz 618971 BLAKE2B cbc413c13f7d5151add9886eb0fbe1d55d9b1847f406ff8fe614e729c6c3ab155711b6c38a2085eabd3f27506562a98ca8d9f1409525f27fe091b30f3a1e840d SHA512 f04268f0eea59cd40985c86597ab68bef40ee28e6ca914a7182c0edfe943ec8fb2a860558f422f210a4c03f3c34f36c677bd3971bc240cb87695826c755f5a47
 DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812
-EBUILD fasta-35.4.10.ebuild 1352 BLAKE2B df91cc22840301e1c0182ce7deb116ddeb468074050e9ce84f1e80ac1456de323aedc54d671616fa789eba71da321be86c58fa8007e0a205a0c6d8f83c17eb35 SHA512 eba62f3358ef8553e61be08759202b941df00d7862901899cafe5fe4d76d1dcd8dcb25d0410720393db8263e3b9bfd5d9c627ca09b726c1a66b14a4200fc60fa
 EBUILD fasta-36.3.5e.ebuild 1625 BLAKE2B 20dd1cc003b8ae7a1cabbbcfa06f6968d6486f86751d08d791dca74e4365358f456f88a398b98e65a4bfa85d7220c6e64e91998d57c2b0c4d422c7d3533cb20d SHA512 618aa434a8271332dc1042c731d6f19d99f08eb90cc156af3b855d8df9664d5efa62a40a043c031205a03e768cf8251d246e4e7b14d7ca14deb47678399e5797
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/fasta/fasta-35.4.10.ebuild b/sci-biology/fasta/fasta-35.4.10.ebuild
deleted file mode 100644
index 8cad4d2a8b08..000000000000
--- a/sci-biology/fasta/fasta-35.4.10.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="2"
-
-inherit eutils flag-o-matic toolchain-funcs
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="debug cpu_flags_x86_sse2 test"
-
-DEPEND="test? ( app-shells/tcsh )"
-RDEPEND=""
-
-src_prepare() {
-	CC_ALT=
-	CFLAGS_ALT=
-	ALT=
-
-	use debug && append-flags -DDEBUG
-
-	if [[ $(tc-getCC) == *icc* ]]; then
-		CC_ALT=icc
-		ALT="${ALT}_icc"
-	else
-		CC_ALT=$(tc-getCC)
-		use x86 && ALT="32"
-		use amd64 && ALT="64"
-	fi
-
-	if use cpu_flags_x86_sse2 ; then
-		ALT="${ALT}_sse2"
-		append-flags -msse2
-		[[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
-	fi
-
-	export CC_ALT="${CC_ALT}"
-	export ALT="${ALT}"
-
-	epatch "${FILESDIR}"/${PV}-ldflags.patch
-}
-
-src_compile() {
-	cd src
-	emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all || die
-}
-
-src_install() {
-	dobin bin/* || die
-	doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die
-	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die
-}
diff --git a/sci-biology/fasta/files/35.4.10-ldflags.patch b/sci-biology/fasta/files/35.4.10-ldflags.patch
deleted file mode 100644
index c3b7a9b56904..000000000000
--- a/sci-biology/fasta/files/35.4.10-ldflags.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff --git a/make/Makefile.pcom b/make/Makefile.pcom
-index a808667..405be95 100644
---- a/make/Makefile.pcom
-+++ b/make/Makefile.pcom
-@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
- 
- map_db : map_db.c uascii.h ncbl2_head.h
--	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
- 
- list_db : list_db.c
--	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
- 
- lav2ps : lav2plt.o lavplt_ps.o
--	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
- 
- lav2svg : lav2plt.o lavplt_svg.o
--	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
- 
- res_stats : res_stats.o scale_se.o
--	$(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm
diff --git a/sci-biology/iedera/Manifest b/sci-biology/iedera/Manifest
index dbe92804902a..a9c9e79f4c5a 100644
--- a/sci-biology/iedera/Manifest
+++ b/sci-biology/iedera/Manifest
@@ -1,6 +1,4 @@
 AUX iedera-1.05-fix-buildsystem.patch 385 BLAKE2B ee7ccb9bd08a8be617e0165a4ee6c6f899ef03e297a9839bfa1982960f0e2f132fb8a444d1bdb74c12b55a66068577dd7be127311b71d21b599a4cabe0b3c79e SHA512 7f20d78fce1ab3a9d30290675a6893a73e2935a8842e8ac8a3d4268a0ccd2a3f165ac0201b6bb13978621230f0042460e704f706d6b3e3ee9457d6a4b6417741
-DIST iedera-1.04.tar.gz 123847 BLAKE2B dfb2206fcc5c0703bf6e4f6ea1e44f7fd5a83a00255fa21038fb4a6c0d565fe073c388bbc47abf52034adc1efc76ca9f9b68dd79f8a077392f8b7c7f551ae959 SHA512 7dcbc078d7c7f84c12736573bf5708ef1aaeefcd52af24ed379535069cfb498c17dd166dc84504db7edc19ab628f0af43d0f2744e37b5565234820631784e126
 DIST iedera-1.05.tar.gz 129163 BLAKE2B fe499276da7571be83b847ab98bbe4878470b07fb13ee80ffb55bff1b5674b54fd4bf5e21fa34e10b8296d9c6aad298dbde79910cfa45670ea8afe047de1a979 SHA512 60d35227d5479fea693e8a3c0e629aae9e21f3c7e2be7b2f10aaddcade70cc6525fa18dea1851f73d6c1aadbb5e8776dd4a146b1a81ecfe8c910729a2300066f
-EBUILD iedera-1.04.ebuild 433 BLAKE2B e19da37eb4e19e02c1381023c7da16c2e5bbd140bfbcabc214825e0eaddd48dd8a4d6959ec0f9d3ccb6b1f8dd3cc6d73fcb64725a40c2a010407d1454286ad14 SHA512 c21467718e39ab4599dbe3ee12aa14f3a4ad012084292d0dca191083ce4de26d1e4f61a3902d71377cd76de170a1302a38d54c5354417fb3d78d9afa63163c70
 EBUILD iedera-1.05-r1.ebuild 490 BLAKE2B a343877f79ccc0678765b4548add19e02aa13aa8d434933e7f0218896e838c25ca668d47ab5d9fe3966eaf995f05857b8ab7b4a28bdf568fda0cef917bfd6aa1 SHA512 2d30e9a6a88e085fc1acad0d5b56eb3bf590f26208b56dc195dec84bf7c946cc5d9ae0d36c147b43b812f16c71ddccdb11db28e2c1263ee46be6dd5659ef8754
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/iedera/iedera-1.04.ebuild b/sci-biology/iedera/iedera-1.04.ebuild
deleted file mode 100644
index 6be6fa802c94..000000000000
--- a/sci-biology/iedera/iedera-1.04.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="2"
-
-DESCRIPTION="A subset seed design tool for DNA sequence alignment"
-HOMEPAGE="http://bioinfo.lifl.fr/yass/iedera.php"
-SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND=""
-
-src_install() {
-	einstall || die
-	dodoc AUTHORS README NEWS
-}