commit: c8e2b2611c55a3da8d04b8f36ef9223c44630cd2 Author: Peter Levine <plevine457 <AT> gmail <DOT> com> AuthorDate: Sat Oct 14 08:08:36 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Nov 18 18:09:54 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c8e2b261
sci-biology/arb: Version bump to 6.0.6 Closes: https://bugs.gentoo.org/637118 Package-Manager: Portage-2.3.10, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5942 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 +++++++++++++ 5 files changed, 273 insertions(+) diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest index 2ec5a49babc..0b6b8b4583f 100644 --- a/sci-biology/arb/Manifest +++ b/sci-biology/arb/Manifest @@ -5,3 +5,4 @@ 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 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 00000000000..e2f81e08471 --- /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 00000000000..926c8e0e289 --- /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 00000000000..755cb685862 --- /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 00000000000..4c8f22d7940 --- /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
