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commit: 1dda583691843fed4b3b2363558c7944ad91e429 |
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Author: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> |
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AuthorDate: Thu May 2 18:44:18 2019 +0000 |
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Commit: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> |
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CommitDate: Thu May 2 18:44:18 2019 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1dda5836 |
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|
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sci-biology/arb: remove last rited package |
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|
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Signed-off-by: Mikle Kolyada <zlogene <AT> gentoo.org> |
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|
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sci-biology/arb/Manifest | 1 - |
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sci-biology/arb/arb-6.0.6.ebuild | 100 ---------------------- |
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sci-biology/arb/files/arb-6.0.6-arb_install.patch | 99 --------------------- |
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sci-biology/arb/files/arb-6.0.6-glapi.patch | 15 ---- |
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sci-biology/arb/files/arb-6.0.6-tc-flags.patch | 58 ------------- |
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sci-biology/arb/metadata.xml | 8 -- |
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6 files changed, 281 deletions(-) |
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|
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diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest |
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deleted file mode 100644 |
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index 4f19d30ed17..00000000000 |
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--- a/sci-biology/arb/Manifest |
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+++ /dev/null |
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@@ -1 +0,0 @@ |
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-DIST arb-6.0.6.tgz 13286019 BLAKE2B fd9591321111363013084030aef7130ccac580aeb9b16e93e72613dc0b3922873aa3f3b1e76d28c1ed14846c0b0d2d497257366fc5deebf4c40c79f0b7eee859 SHA512 053d4d964d8a299f86d4cab9113f0d2181780bf51e0ccec0459a4d568d09bb4e9723fa8493d8e4fa5c72e6d1f022241721cadf7ceb75ee27142d48f2f9f269b4 |
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|
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diff --git a/sci-biology/arb/arb-6.0.6.ebuild b/sci-biology/arb/arb-6.0.6.ebuild |
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deleted file mode 100644 |
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index e2f81e08471..00000000000 |
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--- a/sci-biology/arb/arb-6.0.6.ebuild |
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+++ /dev/null |
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@@ -1,100 +0,0 @@ |
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-# Copyright 1999-2017 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-inherit toolchain-funcs |
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- |
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-DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis" |
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-HOMEPAGE="http://www.arb-home.de/" |
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-SRC_URI="http://download.arb-home.de/release/${P}/${P}-source.tgz -> ${P}.tgz" |
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- |
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-SLOT="0" |
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-LICENSE="arb" |
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-IUSE="debug +opengl test" |
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-KEYWORDS="~amd64 ~x86" |
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- |
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-CDEPEND="app-text/sablotron |
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- media-libs/libpng:= |
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- media-libs/tiff:= |
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- www-client/lynx |
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- x11-libs/libXaw |
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- x11-libs/libXpm |
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- x11-libs/motif:0 |
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- opengl? ( |
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- media-libs/glew:= |
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- media-libs/freeglut |
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- || ( |
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- media-libs/mesa[motif] |
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- ( media-libs/mesa x11-libs/libGLw ) ) )" |
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-DEPEND="${CDEPEND} |
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- sys-process/time |
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- x11-misc/makedepend" |
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-RDEPEND="${CDEPEND} |
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- sci-visualization/gnuplot" |
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- |
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-# Almost half of tests are broken with debug |
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-RESTRICT="debug? ( test )" |
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- |
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-PATCHES=( |
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- "${FILESDIR}"/${PN}-6.0.6-glapi.patch |
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- "${FILESDIR}"/${PN}-6.0.6-tc-flags.patch |
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- "${FILESDIR}"/${PN}-6.0.6-arb_install.patch |
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-) |
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- |
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-src_unpack() { |
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- default |
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- mv arbsrc* ${P} || die |
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-} |
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- |
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-src_prepare() { |
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- default |
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- |
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- cp config.makefile.template config.makefile |
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- mkdir "${S}"/patches.arb || die # Test script expects ${ARBHOME}/patches.arb to exist |
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- |
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- if use amd64; then |
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- sed -i -e 's@ARB_64 := 0@ARB_64 := 1@' config.makefile || die |
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- fi |
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- if use opengl; then |
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- sed -i -e 's@OPENGL := 0@OPENGL := 1@' config.makefile || die |
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- fi |
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- if use test; then |
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- sed -i -e 's@UNIT_TESTS := 0@UNIT_TESTS := 1@' config.makefile || die |
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- fi |
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- if use debug; then |
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- sed -i -e 's@DEBUG := 0@DEBUG := 1@' \ |
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- -e 's@DEBUG_GRAPHICS := 0@DEBUG_GRAPHICS := 1@' config.makefile || die |
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- fi |
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-} |
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- |
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-src_compile() { |
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- emake ARBHOME="${S}" PATH="${S}/bin:${PATH}" LD_LIBRARY_PATH="${S}/lib:${LD_LIBRARY_PATH}" \ |
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- CC="$(tc-getCC)" CXX="$(tc-getCXX)" build |
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-} |
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- |
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-src_test() { |
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- emake ARBHOME="${S}" PATH="${S}/bin:${PATH}" LD_LIBRARY_PATH="${S}/lib:${LD_LIBRARY_PATH}" \ |
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- CC="$(tc-getCC)" CXX="$(tc-getCXX)" run_tests |
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-} |
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- |
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-src_install() { |
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- emake ARBHOME="${S}" PATH="${S}/bin:${PATH}" LD_LIBRARY_PATH="${S}/lib:${LD_LIBRARY_PATH}" \ |
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- CC="$(tc-getCC)" CXX="$(tc-getCXX)" prepare_libdir |
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- "${S}"/util/arb_compress || die |
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- if use amd64; then |
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- mv arb.tgz arb.64.gentoo.tgz || die |
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- fi |
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- if use x86; then |
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- mv arb.tgz arb.32.gentoo.tgz || die |
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- fi |
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- ln -s arb.*.tgz arb.tgz || die |
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- ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die |
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- |
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- cat <<- EOF > "${S}/99${PN}" || die |
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- ARBHOME=/opt/arb |
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- PATH=/opt/arb/bin |
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- LD_LIBRARY_PATH=/opt/arb/lib |
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- EOF |
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- doenvd "${S}/99${PN}" |
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-} |
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|
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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 |
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deleted file mode 100644 |
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index 926c8e0e289..00000000000 |
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--- a/sci-biology/arb/files/arb-6.0.6-arb_install.patch |
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+++ /dev/null |
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@@ -1,99 +0,0 @@ |
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---- a/arb_install.sh |
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-+++ b/arb_install.sh |
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-@@ -13,7 +13,6 @@ |
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- cont() { |
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- echo "Warning: $@" 1>&2 |
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- echo 'Do you want to continue [y]' |
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-- read var |
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- case "$var" in |
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- n) err "Script aborted by user" ;; |
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- *) echo 'Continuing...' ;; |
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-@@ -79,7 +78,6 @@ |
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- fi |
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- |
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- echo "Enter full installation path: [${ARBHOME:-/usr/arb}]" |
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--read ARBHOMEI |
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- echo |
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- echo |
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- |
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-@@ -127,7 +125,6 @@ |
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- echo ' You can delete the old directory before installing ARB' |
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- echo ' or only update/change options of the old version.' |
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- echo 'Delete old directory (y/n)[n]?' |
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-- read delete_dir |
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- echo |
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- case "$delete_dir" in |
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- y) |
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-@@ -163,7 +160,6 @@ |
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- separator |
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- echo "Old ARB package found (type n to change only some options)." |
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- echo " Do you want to update the old package: (y/n)[y]" |
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-- read var; |
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- case "$var" in |
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- n) |
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- echo "Old version unchanged";; |
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-@@ -197,7 +193,6 @@ |
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- echo ' 2. "Path" to link pt_server data directory to' |
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- echo " (if you choose this option you won't loose your PT-Servers when doing future software updates)" |
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- echo 'Enter path:' |
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--read pt_dir |
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- echo |
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- case "$pt_dir" in |
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- "") |
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-@@ -222,7 +217,6 @@ |
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- if test -d ${ARBHOME}/lib/pts; then |
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- echo ">>> data in default location found" |
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- echo 'Do you want to remove old ptserver data (recommended)? [y]' |
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-- read ANSWER |
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- case "$ANSWER" in |
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- n) echo 'data not deleted' ;; |
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- *) rm -r lib/pts |
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-@@ -247,7 +241,6 @@ |
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- echo ' n: if PT_SERVER files shall only be changable by administrator' |
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- echo ' or simply press return to keep the settings of an old installation.' |
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- echo 'Should everybody be allowed to build/update PT_SERVER files (y/n/dont_change)[dont_change]?' |
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--read var |
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- echo |
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- case "$var" in |
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- y) |
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-@@ -273,7 +266,6 @@ |
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- echo ' n: if there are some mean untrusty users' |
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- echo ' or simply press return to keep the old settings' |
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- echo 'Do you trust your users (y/n/dont_change)[dont_change]?' |
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--read var |
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- echo |
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- case "$var" in |
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- y) |
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-@@ -310,7 +302,6 @@ |
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- echo 'Choose (s/n)[s]?' |
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- |
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- fi |
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--read var |
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- echo |
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- |
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- |
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-@@ -322,7 +313,6 @@ |
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- n) |
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- separator |
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- echo "Enter the name of your host for the pt_server" |
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-- read host |
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- echo "Checking connection to $host" |
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- if ssh $host ls >/dev/zero; then |
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- echo ">>> ssh $host ok" |
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-@@ -341,7 +331,7 @@ |
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- echo ">>> Installation Complete" |
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- |
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- separator |
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--SHELL_ANS=0 |
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-+SHELL_ANS=1 |
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- |
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- while [ "$SHELL_ANS" = "0" ]; do |
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- |
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-@@ -359,7 +349,6 @@ |
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- |
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- echo "Enter (1,2 or 3) to achieve further installation instructions:" |
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- |
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-- read var |
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- |
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- echo ''; |
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- echo '**********************************************************************************************'; |
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|
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diff --git a/sci-biology/arb/files/arb-6.0.6-glapi.patch b/sci-biology/arb/files/arb-6.0.6-glapi.patch |
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deleted file mode 100644 |
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index 755cb685862..00000000000 |
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--- a/sci-biology/arb/files/arb-6.0.6-glapi.patch |
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+++ /dev/null |
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@@ -1,15 +0,0 @@ |
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-When built with USE=opengl, the macro GLAPI either doesn't get defined |
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-or gets undefed in some header. Header <GL/GLwMDrawA.h> seems to expect |
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-it to be defined as 'extern', as defining it as '__attribute__((visibility("default")))' |
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-leads to multiple definition errors. |
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- |
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---- a/RNA3D/RNA3D_GlobalHeader.hxx |
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-+++ b/RNA3D/RNA3D_GlobalHeader.hxx |
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-@@ -44,6 +44,7 @@ |
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- // Undefining it here does the job: |
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- #undef __GLX_glx_h__ |
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- #include <GL/glx.h> |
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-+#define GLAPI extern |
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- #endif // OPEN_GL_WAY_TO_INCLUDE == 3 |
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- // ------------------------------ |
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- |
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|
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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 |
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deleted file mode 100644 |
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index 4c8f22d7940..00000000000 |
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--- a/sci-biology/arb/files/arb-6.0.6-tc-flags.patch |
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+++ /dev/null |
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@@ -1,58 +0,0 @@ |
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---- a/Makefile |
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-+++ b/Makefile |
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-@@ -61,8 +61,8 @@ |
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- # compiler settings: |
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- ifneq ($(CC),use__A_CC__instead_of__CC) |
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- |
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--A_CC:=$(CC)# compile C |
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--A_CXX:=$(CXX)# compile C++ |
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-+A_CC:=${CC}# compile C |
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-+A_CXX:=${CXX}# compile C++ |
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- |
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- # uncomment to ensure no submakefile uses CC and CXX directly |
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- override CC:=use__A_CC__instead_of__CC |
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-@@ -119,12 +119,7 @@ |
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- endif |
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- endif |
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- |
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--ifeq ($(USE_CLANG),1) |
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--# accept all clang versions: |
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- ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION) |
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--else |
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--ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS) |
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--endif |
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- |
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- COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___)))) |
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- |
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-@@ -184,20 +179,13 @@ |
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- |
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- shared_cflags :=# flags for shared lib compilation |
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- lflags :=# linker flags |
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--clflags :=# linker flags (when passed through gcc) |
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-+clflags := ${LDFLAGS} # linker flags (when passed through gcc) |
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- extended_warnings :=# warning flags for C and C++-compiler |
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- extended_cpp_warnings :=# warning flags for C++-compiler only |
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- |
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- |
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- ifeq ($(DEBUG),0) |
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- dflags := -DNDEBUG# defines |
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-- ifeq ($(USE_CLANG),1) |
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-- cflags := -O3# compiler flags (C and C++) |
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-- else |
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-- cflags := -O3# compiler flags (C and C++) |
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-- lflags += -O2# linker flags |
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-- clflags += -Wl,-O2# passthrough linker flags |
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-- endif |
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- endif |
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- |
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- ifeq ($(DEBIAN),1) |
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-@@ -526,6 +514,9 @@ |
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- cxxflags += $(CPPFLAGS) |
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- endif |
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- |
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-+cflags := ${CFLAGS} $(cflags) |
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-+cxxflags += ${CXXFLAGS} |
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-+ |
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- ifeq ('$(USE_GCC_47_OR_HIGHER)','yes') |
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- cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11 |
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- else |
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|
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diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml |
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deleted file mode 100644 |
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index 959160fe46b..00000000000 |
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--- a/sci-biology/arb/metadata.xml |
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+++ /dev/null |
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@@ -1,8 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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-</pkgmetadata> |