From eab5731cdf11d4ae8cdf111461d46fd96c5bdd37 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Sat, 4 May 2019 12:02:00 +0100
Subject: gentoo resync : 04.05.2019
---
sci-biology/Manifest.gz | Bin 25282 -> 25126 bytes
sci-biology/arb/Manifest | 6 --
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 --
7 files changed, 286 deletions(-)
delete mode 100644 sci-biology/arb/Manifest
delete mode 100644 sci-biology/arb/arb-6.0.6.ebuild
delete mode 100644 sci-biology/arb/files/arb-6.0.6-arb_install.patch
delete mode 100644 sci-biology/arb/files/arb-6.0.6-glapi.patch
delete mode 100644 sci-biology/arb/files/arb-6.0.6-tc-flags.patch
delete mode 100644 sci-biology/arb/metadata.xml
(limited to 'sci-biology')
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 89bff10b7570..62558baa4eda 100644
Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ
diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
deleted file mode 100644
index 52b55979193b..000000000000
--- a/sci-biology/arb/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-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-6.0.6.tgz 13286019 BLAKE2B fd9591321111363013084030aef7130ccac580aeb9b16e93e72613dc0b3922873aa3f3b1e76d28c1ed14846c0b0d2d497257366fc5deebf4c40c79f0b7eee859 SHA512 053d4d964d8a299f86d4cab9113f0d2181780bf51e0ccec0459a4d568d09bb4e9723fa8493d8e4fa5c72e6d1f022241721cadf7ceb75ee27142d48f2f9f269b4
-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-6.0.6.ebuild b/sci-biology/arb/arb-6.0.6.ebuild
deleted file mode 100644
index e2f81e08471e..000000000000
--- 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 926c8e0e2894..000000000000
--- 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 755cb6858624..000000000000
--- 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 4c8f22d79409..000000000000
--- 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 959160fe46b1..000000000000
--- 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-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
--
cgit v1.2.3