From 20d8e9cfb95a9f054d654ab6405e848807186aa0 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 19 Nov 2017 10:19:50 +0000 Subject: gentoo resync : 19.11.2017 --- sci-biology/arb/Manifest | 5 ++ sci-biology/arb/arb-6.0.6.ebuild | 100 ++++++++++++++++++++++ sci-biology/arb/files/arb-6.0.6-arb_install.patch | 99 +++++++++++++++++++++ sci-biology/arb/files/arb-6.0.6-glapi.patch | 15 ++++ sci-biology/arb/files/arb-6.0.6-tc-flags.patch | 58 +++++++++++++ 5 files changed, 277 insertions(+) create mode 100644 sci-biology/arb/arb-6.0.6.ebuild create mode 100644 sci-biology/arb/files/arb-6.0.6-arb_install.patch create mode 100644 sci-biology/arb/files/arb-6.0.6-glapi.patch create mode 100644 sci-biology/arb/files/arb-6.0.6-tc-flags.patch (limited to 'sci-biology') 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 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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 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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 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 ++#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 -- cgit v1.2.3