commit: 1dda583691843fed4b3b2363558c7944ad91e429 Author: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> AuthorDate: Thu May 2 18:44:18 2019 +0000 Commit: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> CommitDate: Thu May 2 18:44:18 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1dda5836
sci-biology/arb: remove last rited package Signed-off-by: Mikle Kolyada <zlogene <AT> gentoo.org> sci-biology/arb/Manifest | 1 - 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 ------------- sci-biology/arb/metadata.xml | 8 -- 6 files changed, 281 deletions(-) diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest deleted file mode 100644 index 4f19d30ed17..00000000000 --- a/sci-biology/arb/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST arb-6.0.6.tgz 13286019 BLAKE2B fd9591321111363013084030aef7130ccac580aeb9b16e93e72613dc0b3922873aa3f3b1e76d28c1ed14846c0b0d2d497257366fc5deebf4c40c79f0b7eee859 SHA512 053d4d964d8a299f86d4cab9113f0d2181780bf51e0ccec0459a4d568d09bb4e9723fa8493d8e4fa5c72e6d1f022241721cadf7ceb75ee27142d48f2f9f269b4 diff --git a/sci-biology/arb/arb-6.0.6.ebuild b/sci-biology/arb/arb-6.0.6.ebuild deleted file mode 100644 index e2f81e08471..00000000000 --- a/sci-biology/arb/arb-6.0.6.ebuild +++ /dev/null @@ -1,100 +0,0 @@ -# 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 deleted file mode 100644 index 926c8e0e289..00000000000 --- a/sci-biology/arb/files/arb-6.0.6-arb_install.patch +++ /dev/null @@ -1,99 +0,0 @@ ---- 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 deleted file mode 100644 index 755cb685862..00000000000 --- a/sci-biology/arb/files/arb-6.0.6-glapi.patch +++ /dev/null @@ -1,15 +0,0 @@ -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 deleted file mode 100644 index 4c8f22d7940..00000000000 --- a/sci-biology/arb/files/arb-6.0.6-tc-flags.patch +++ /dev/null @@ -1,58 +0,0 @@ ---- 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 diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml deleted file mode 100644 index 959160fe46b..00000000000 --- a/sci-biology/arb/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>