gentoo resync : 19.11.2017

5 files changed, 277 insertions, 0 deletions

diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
index b5c586194c5f..01a07452c4d3 100644
--- a/sci-biology/arb/Manifest
+++ b/sci-biology/arb/Manifest
@@ -2,6 +2,9 @@ AUX 5.1-bfr-overflow.patch 715 SHA256 bedb03c70bd0e4e180f8d6e966bfaf34af32125a15
 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
+AUX arb-6.0.6-arb_install.patch 2752 SHA256 939d1859f656f3ef6c15bdf4787a38ab15e9059f502cfaded593b429b67b8cfe SHA512 468d7e1ee599334e593ce95374a29a1815ba8559afb6d773f533a07b0b520115e1aafcbb228ec82f331cd2d580816d68bf2f9351774ed8f52942b13e23eb5746 WHIRLPOOL 1335819b869cba0821001830a3531f1bbcedad51e53629bb49a9a932247ad8ef0d8b955e0ce3c465a56a2e60530710513c6031bddec01bdae963ea94c7cd5298
+AUX arb-6.0.6-glapi.patch 537 SHA256 7a0618c981cbdb6ac771d44772955ad0c58f0b6f32660807322c190f847b16db SHA512 249847d0b563460447c7c53167ec50ba541270614943a471aab5c8dccc1c9e253af79746834fd722d33f9a96607e9a382f7ae80fb96656f52d9a143fd4760be5 WHIRLPOOL 99c17da6f16843e2bba55b1b5711f98bd86681dc314024bdf84cdfe6117d05976f4be60681f3f815b56768c455fb10655305a2a43f537cbca9962c7ed6f503b5
+AUX arb-6.0.6-tc-flags.patch 1540 SHA256 dcaf98761d17ed65ba7e7644d2bed769601e1965c4180d8a4a6d4fbeccd55443 SHA512 e5bcd297196f473c6cece3e5a28380011f20e5d0389b6de508c4ae0f82f0d6bb4502b755a89b1f9ddf582ab3a9722793c6f7727168b442c08dd99f95799d3418 WHIRLPOOL 0cce159018047fbfe168ce79a1d235407f3629700489f8b4d14128d1b42fae12a7219ce481ee2ecedd7d1ffc4e484437b2fe2c7f4669789bdb7e22ca6850fc8f
 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
@@ -9,9 +12,11 @@ DIST arb-5.2-linker.patch.bz2 4441 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677
 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
+DIST arb-6.0.6.tgz 13286019 SHA256 8b1fc3fd11bbb05aca4731ac8803c004a4f2b6b87c11b543660d07ea349a6c21 SHA512 053d4d964d8a299f86d4cab9113f0d2181780bf51e0ccec0459a4d568d09bb4e9723fa8493d8e4fa5c72e6d1f022241721cadf7ceb75ee27142d48f2f9f269b4 WHIRLPOOL 199ad8a5eac7d5e3d84520ba9a0de4bb0202906e3b71746eef929978d5a28c092c7aa204d4035301ceb42f5385c6077cc3c53aba5e8d9c3e3665cf83020387c4
 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
+EBUILD arb-6.0.6.ebuild 2482 SHA256 456a1f84510a28f0d713210bee78fef688ff133b69cab7310517e75bbec9765b SHA512 afb90afeb3d01aceeddafd52b0e173c240a166e325298ac3eecd3fe130ef8248237a13a6d42c81d66f3103343333a80a19d84e2c077ba6c6ddaf1efb271fa14d WHIRLPOOL d9aee00dda9023efb2f606b35685887a21876480ec736dbc4a73d7439936c3e6db32a289e7fa4b1166c4db3a2fce715f9656d47622fdd6be24243047a1e6c8bf
 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-6.0.6.ebuild b/sci-biology/arb/arb-6.0.6.ebuild
new file mode 100644
index 000000000000..e2f81e08471e
--- /dev/null
+++ b/sci-biology/arb/arb-6.0.6.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit 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/${P}/${P}-source.tgz -> ${P}.tgz"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="debug +opengl test"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+	media-libs/libpng:=
+	media-libs/tiff:=
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/motif:0
+	opengl? (
+		media-libs/glew:=
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+	sys-process/time
+	x11-misc/makedepend"
+RDEPEND="${CDEPEND}
+	sci-visualization/gnuplot"
+
+# Almost half of tests are broken with debug
+RESTRICT="debug? ( test )"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-6.0.6-glapi.patch
+	"${FILESDIR}"/${PN}-6.0.6-tc-flags.patch
+	"${FILESDIR}"/${PN}-6.0.6-arb_install.patch
+)
+
+src_unpack() {
+	default
+	mv arbsrc* ${P} || die
+}
+
+src_prepare() {
+	default
+
+	cp config.makefile.template config.makefile
+	mkdir "${S}"/patches.arb || die  # Test script expects ${ARBHOME}/patches.arb to exist
+
+	if use amd64; then
+		sed -i -e 's@ARB_64 := 0@ARB_64 := 1@' config.makefile || die
+	fi
+	if use opengl; then
+		sed -i -e 's@OPENGL := 0@OPENGL := 1@' config.makefile || die
+	fi
+	if use test; then
+		sed -i -e 's@UNIT_TESTS := 0@UNIT_TESTS := 1@' config.makefile || die
+	fi
+	if use debug; then
+		sed -i -e 's@DEBUG := 0@DEBUG := 1@' \
+		-e 's@DEBUG_GRAPHICS := 0@DEBUG_GRAPHICS := 1@' config.makefile || die
+	fi
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${S}/bin:${PATH}" LD_LIBRARY_PATH="${S}/lib:${LD_LIBRARY_PATH}" \
+		CC="$(tc-getCC)" CXX="$(tc-getCXX)" build
+}
+
+src_test() {
+	emake ARBHOME="${S}" PATH="${S}/bin:${PATH}" LD_LIBRARY_PATH="${S}/lib:${LD_LIBRARY_PATH}" \
+		CC="$(tc-getCC)" CXX="$(tc-getCXX)" run_tests
+}
+
+src_install() {
+	emake ARBHOME="${S}" PATH="${S}/bin:${PATH}" LD_LIBRARY_PATH="${S}/lib:${LD_LIBRARY_PATH}" \
+		CC="$(tc-getCC)" CXX="$(tc-getCXX)" prepare_libdir
+	"${S}"/util/arb_compress  || die
+	if use amd64; then
+		mv arb.tgz arb.64.gentoo.tgz || die
+	fi
+	if use x86; then
+		mv arb.tgz arb.32.gentoo.tgz || die
+	fi
+	ln -s arb.*.tgz arb.tgz || die
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+
+	cat <<- EOF > "${S}/99${PN}" || die
+		ARBHOME=/opt/arb
+		PATH=/opt/arb/bin
+		LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/files/arb-6.0.6-arb_install.patch b/sci-biology/arb/files/arb-6.0.6-arb_install.patch
new file mode 100644
index 000000000000..926c8e0e2894
--- /dev/null
+++ b/sci-biology/arb/files/arb-6.0.6-arb_install.patch
@@ -0,0 +1,99 @@
+--- a/arb_install.sh
++++ b/arb_install.sh
+@@ -13,7 +13,6 @@
+ cont() {
+     echo "Warning: $@" 1>&2
+     echo 'Do you want to continue [y]'
+-    read var
+     case "$var" in
+         n) err "Script aborted by user" ;;
+         *) echo 'Continuing...' ;;
+@@ -79,7 +78,6 @@
+ fi
+ 
+ echo "Enter full installation path: [${ARBHOME:-/usr/arb}]"
+-read ARBHOMEI
+ echo
+ echo
+ 
+@@ -127,7 +125,6 @@
+         echo '  You can delete the old directory before installing ARB'
+         echo '  or only update/change options of the old version.'
+         echo 'Delete old directory (y/n)[n]?'
+-        read delete_dir
+         echo
+         case "$delete_dir" in
+             y)
+@@ -163,7 +160,6 @@
+     separator
+     echo "Old ARB package found (type n to change only some options)."
+     echo "  Do you want to update the old package: (y/n)[y]"
+-    read var;
+     case "$var" in
+         n)
+         echo "Old version unchanged";;
+@@ -197,7 +193,6 @@
+ echo '          2. "Path" to link pt_server data directory to'
+ echo "              (if you choose this option you won't loose your PT-Servers when doing future software updates)"
+ echo 'Enter path:'
+-read pt_dir
+ echo
+ case "$pt_dir" in
+     "")
+@@ -222,7 +217,6 @@
+         if test -d ${ARBHOME}/lib/pts; then
+             echo ">>> data in default location found"
+             echo 'Do you want to remove old ptserver data (recommended)? [y]'
+-            read ANSWER
+             case "$ANSWER" in
+                 n) echo 'data not deleted' ;;
+                 *) rm -r lib/pts
+@@ -247,7 +241,6 @@
+ echo '          n: if PT_SERVER files shall only be changable by administrator'
+ echo '  or simply press return to keep the settings of an old installation.'
+ echo 'Should everybody be allowed to build/update PT_SERVER files (y/n/dont_change)[dont_change]?'
+-read var
+ echo
+ case "$var" in
+     y)
+@@ -273,7 +266,6 @@
+ echo '          n: if there are some mean untrusty users'
+ echo '  or simply press return to keep the old settings'
+ echo 'Do you trust your users (y/n/dont_change)[dont_change]?'
+-read var
+ echo
+ case "$var" in
+     y)
+@@ -310,7 +302,6 @@
+     echo 'Choose (s/n)[s]?'
+ 
+ fi
+-read var
+ echo
+ 
+ 
+@@ -322,7 +313,6 @@
+     n)
+     separator
+     echo "Enter the name of your host for the pt_server"
+-    read host
+     echo "Checking connection to $host"
+     if ssh $host ls >/dev/zero; then
+         echo ">>> ssh $host ok"
+@@ -341,7 +331,7 @@
+ echo ">>> Installation Complete"
+ 
+ separator
+-SHELL_ANS=0
++SHELL_ANS=1
+ 
+ while [ "$SHELL_ANS" = "0" ]; do
+ 
+@@ -359,7 +349,6 @@
+ 
+     echo "Enter (1,2 or 3) to achieve further installation instructions:"
+ 
+-    read var
+ 
+     echo '';
+     echo '**********************************************************************************************';
diff --git a/sci-biology/arb/files/arb-6.0.6-glapi.patch b/sci-biology/arb/files/arb-6.0.6-glapi.patch
new file mode 100644
index 000000000000..755cb6858624
--- /dev/null
+++ b/sci-biology/arb/files/arb-6.0.6-glapi.patch
@@ -0,0 +1,15 @@
+When built with USE=opengl, the macro GLAPI either doesn't get defined
+or gets undefed in some header.  Header <GL/GLwMDrawA.h> seems to expect
+it to be defined as 'extern', as defining it as '__attribute__((visibility("default")))'
+leads to multiple definition errors.
+
+--- a/RNA3D/RNA3D_GlobalHeader.hxx
++++ b/RNA3D/RNA3D_GlobalHeader.hxx
+@@ -44,6 +44,7 @@
+ // Undefining it here does the job:
+ #undef __GLX_glx_h__
+ #include <GL/glx.h>
++#define GLAPI extern
+ #endif // OPEN_GL_WAY_TO_INCLUDE == 3
+ // ------------------------------
+ 
diff --git a/sci-biology/arb/files/arb-6.0.6-tc-flags.patch b/sci-biology/arb/files/arb-6.0.6-tc-flags.patch
new file mode 100644
index 000000000000..4c8f22d79409
--- /dev/null
+++ b/sci-biology/arb/files/arb-6.0.6-tc-flags.patch
@@ -0,0 +1,58 @@
+--- a/Makefile
++++ b/Makefile
+@@ -61,8 +61,8 @@
+ # compiler settings:
+ ifneq ($(CC),use__A_CC__instead_of__CC)
+ 
+-A_CC:=$(CC)# compile C
+-A_CXX:=$(CXX)# compile C++
++A_CC:=${CC}# compile C
++A_CXX:=${CXX}# compile C++
+ 
+ # uncomment to ensure no submakefile uses CC and CXX directly
+ override CC:=use__A_CC__instead_of__CC
+@@ -119,12 +119,7 @@
+  endif
+ endif
+ 
+-ifeq ($(USE_CLANG),1)
+-# accept all clang versions:
+ ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
+-else
+-ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
+-endif
+ 
+ COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
+ 
+@@ -184,20 +179,13 @@
+ 
+ shared_cflags :=# flags for shared lib compilation
+ lflags :=# linker flags
+-clflags :=# linker flags (when passed through gcc)
++clflags := ${LDFLAGS} # linker flags (when passed through gcc)
+ extended_warnings :=# warning flags for C and C++-compiler
+ extended_cpp_warnings :=# warning flags for C++-compiler only
+ 
+ 
+ ifeq ($(DEBUG),0)
+ 	dflags := -DNDEBUG# defines
+-	ifeq ($(USE_CLANG),1)
+-		cflags := -O3# compiler flags (C and C++)
+-	else
+-		cflags := -O3# compiler flags (C and C++)
+-		lflags += -O2# linker flags
+-		clflags += -Wl,-O2# passthrough linker flags
+-	endif
+ endif
+ 
+ ifeq ($(DEBIAN),1)
+@@ -526,6 +514,9 @@
+ 	cxxflags += $(CPPFLAGS)
+ endif
+ 
++cflags := ${CFLAGS} $(cflags)
++cxxflags += ${CXXFLAGS}
++
+ ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
+ cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
+ else