* [gentoo-commits] repo/gentoo:master commit in: sci-biology/arb/, sci-biology/arb/files/
@ 2017-11-18 18:10 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-11-18 18:10 UTC (permalink / raw
To: gentoo-commits
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
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/arb/, sci-biology/arb/files/
@ 2018-01-01 12:43 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2018-01-01 12:43 UTC (permalink / raw
To: gentoo-commits
commit: fa85d5355b3c7d3f6d25127e1b6f4ea7450a5a88
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 1 12:42:51 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Jan 1 12:42:51 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fa85d535
sci-biology/arb: Remove old
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/arb/Manifest | 7 ---
sci-biology/arb/arb-5.1-r1.ebuild | 77 ---------------------------
sci-biology/arb/arb-5.2.ebuild | 79 ----------------------------
sci-biology/arb/arb-5.3.ebuild | 77 ---------------------------
sci-biology/arb/files/5.1-bfr-overflow.patch | 16 ------
sci-biology/arb/files/5.1-libs.patch | 16 ------
sci-biology/arb/files/5.2-libpng15.patch | 45 ----------------
sci-biology/arb/files/arb-5.2-gcc-47.patch | 15 ------
8 files changed, 332 deletions(-)
diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
index 60bfb783165..4f19d30ed17 100644
--- a/sci-biology/arb/Manifest
+++ b/sci-biology/arb/Manifest
@@ -1,8 +1 @@
-DIST arb-5.1-glibc2.10.patch.bz2 24659 BLAKE2B 856b4735c98f13b21af537486f27ae89cca724590f7f4d7975dc7df05d3e3388a29198f6b9bb14b2ef885f5442d6687d6fbcdb44c076656b8e2ff521c633f940 SHA512 a490066efc5001e22bfeab8ce3e05690f5024217261b7b71c5a31116d18611a93f5b15aa7d57fca40e2b5e17e64b695873ccb810bd649b2b109c9b710d3ddfe1
-DIST arb-5.1-linker.patch.bz2 4406 BLAKE2B 3214f875c7d58e9a60032397f34a38ec13fc1672cecca475223fe8b79c684d4839e3e7dcf7c1df8290f00912b6268493bf89d77b744c923b3a9769bb466bef15 SHA512 44518d500be457d16e7f6cd5f0863d2dc48cc8a1c8abcbaea79eefec5cd063258aea78d03e9601cd0bdea3c7e57949373d7a909eeed98bf48a6d98576f298e58
-DIST arb-5.1.tgz 9727285 BLAKE2B 97660214b1dc513a946256cfdcbbefff282bb125e81e05a92005bd62b4ec00a478fb6639c6f5b0b3893e1c49d8eb9f13d04ec36271daec41c41b9093fefea09a SHA512 236f7c40217146cf5b43d15c7252901a09f2081c1da6db1b90d7720d313e21a2808b31879d700bf894b3c576952c43be751fd0027af8a58d953403028589dd8c
-DIST arb-5.2-linker.patch.bz2 4441 BLAKE2B c2554cf4e24ab9257dfac06482f05a42e89ad06ecf1b069d80df16d512ce675a29f7c3dbe0bca6b0f3add910617cc5853462aa5593cb9ccb2fb2656cdd5183c1 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903
-DIST arb-5.2.tgz 9729004 BLAKE2B 2ae85529c9c7afdbc0debc0317e0ab3772f881b606f849b6cb60872e2e123b612399dc4dcfa07c5e886703478140515fa31e9b69b37383a12d8526ecb771f77b SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56
-DIST arb-5.3-linker.patch.xz 3604 BLAKE2B 0327a94ee4daaca9cc4aa41601ae52b8616d26fd0ede19b36cb2ea72135bc9609d21db74b9588cc79e08242d3e32bb3398d78663c90dc4e3c248877953249789 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7
-DIST arb-5.3.tgz 9543106 BLAKE2B e67859accad1f5aeae3fe3a85530543beb1141e1fe340760e55b2bcef84f1f5cd18fe82ff75beafbf49b1945def0436d862487a630192345568931a335454210 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282
DIST arb-6.0.6.tgz 13286019 BLAKE2B fd9591321111363013084030aef7130ccac580aeb9b16e93e72613dc0b3922873aa3f3b1e76d28c1ed14846c0b0d2d497257366fc5deebf4c40c79f0b7eee859 SHA512 053d4d964d8a299f86d4cab9113f0d2181780bf51e0ccec0459a4d568d09bb4e9723fa8493d8e4fa5c72e6d1f022241721cadf7ceb75ee27142d48f2f9f269b4
diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
deleted file mode 100644
index f52beded359..00000000000
--- a/sci-biology/arb/arb-5.1-r1.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=2
-
-inherit eutils 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/arb_${PV}/arbsrc.tgz -> ${P}.tgz
- mirror://gentoo/${P}-glibc2.10.patch.bz2
- https://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
-
-LICENSE="arb"
-SLOT="0"
-IUSE="+opengl"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- app-text/sablotron
- media-libs/libpng
- media-libs/tiff
- www-client/lynx
- x11-libs/libXaw
- x11-libs/libXpm
- x11-libs/motif:0
- opengl? (
- media-libs/glew
- media-libs/freeglut
- || (
- media-libs/mesa[motif]
- ( media-libs/mesa x11-libs/libGLw ) ) )"
-RDEPEND="${DEPEND}
- sci-visualization/gnuplot"
-# Recommended: libmotif3 gv xfig xterm treetool java
-
-src_unpack() {
- unpack ${A}
- mv arbsrc* ${P}
-}
-
-src_prepare() {
- epatch \
- "${WORKDIR}"/${P}-glibc2.10.patch\
- "${WORKDIR}"/${P}-linker.patch \
- "${FILESDIR}"/${PV}-libs.patch \
- "${FILESDIR}"/${PV}-bfr-overflow.patch
- sed -i \
- -e 's/all: checks/all:/' \
- -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
- -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
- -e 's/--export-dynamic/-Wl,--export-dynamic/g' \
- "${S}/Makefile" || die
- cp config.makefile.template config.makefile
- sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
- use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
- use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
- emake ARBHOME="${S}" links || die
-}
-
-src_compile() {
- emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die
- use amd64 && mv arb.tgz arb.64.gentoo.tgz
- use x86 && mv arb.tgz arb.32.gentoo.tgz
- ln -s arb.*.tgz arb.tgz || die
-}
-
-src_install() {
- ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
- cat <<- EOF > "${S}/99${PN}"
- ARBHOME=/opt/arb
- PATH=/opt/arb/bin
- LD_LIBRARY_PATH=/opt/arb/lib
- EOF
- doenvd "${S}/99${PN}" || die
-}
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
deleted file mode 100644
index a7388bf9b81..00000000000
--- a/sci-biology/arb/arb-5.2.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
-HOMEPAGE="http://www.arb-home.de/"
-SRC_URI="
- http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
- https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2"
-
-SLOT="0"
-LICENSE="arb"
-IUSE="+opengl"
-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="${CDEPEND}
- sys-process/time"
-RDEPEND="${CDEPEND}
- sci-visualization/gnuplot"
-# Recommended: libmotif3 gv xfig xterm treetool java
-
-src_unpack() {
- unpack ${A}
- mv arbsrc* ${P}
-}
-
-src_prepare() {
- epatch \
- "${WORKDIR}"/${P}-linker.patch \
- "${FILESDIR}"/5.1-libs.patch \
- "${FILESDIR}"/5.1-bfr-overflow.patch \
- "${FILESDIR}"/${PV}-libpng15.patch \
- "${FILESDIR}"/${P}-gcc-47.patch
- sed \
- -e 's/all: checks/all:/' \
- -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
- -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
- -e 's:-O4::g' \
- -e 's:-pipe::g' \
- -i "${S}/Makefile" || die
- cp config.makefile.template config.makefile
- sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
- use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
- use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
- emake ARBHOME="${S}" links
-}
-
-src_compile() {
- emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
- use amd64 && mv arb.tgz arb.64.gentoo.tgz
- use x86 && mv arb.tgz arb.32.gentoo.tgz
- ln -s arb.*.tgz arb.tgz || die
-}
-
-src_install() {
- ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
- cat <<- EOF > "${S}/99${PN}"
- ARBHOME=/opt/arb
- PATH=/opt/arb/bin
- LD_LIBRARY_PATH=/opt/arb/lib
- EOF
- doenvd "${S}/99${PN}"
-}
diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild
deleted file mode 100644
index 135bec2695c..00000000000
--- a/sci-biology/arb/arb-5.3.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
-HOMEPAGE="http://www.arb-home.de/"
-SRC_URI="
- http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
- https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"
-
-SLOT="0"
-LICENSE="arb"
-IUSE="+opengl"
-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="${CDEPEND}
- sys-process/time"
-RDEPEND="${CDEPEND}
- sci-visualization/gnuplot"
-# Recommended: libmotif3 gv xfig xterm treetool java
-
-src_unpack() {
- unpack ${A}
- mv arbsrc* ${P}
-}
-
-src_prepare() {
- epatch \
- "${WORKDIR}"/${P}-linker.patch \
- "${FILESDIR}"/5.1-libs.patch \
- "${FILESDIR}"/5.1-bfr-overflow.patch \
- "${FILESDIR}"/5.2-libpng15.patch \
- "${FILESDIR}"/${PN}-5.2-gcc-47.patch
- sed \
- -e 's/all: checks/all:/' \
- -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
- -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
- -i "${S}/Makefile" || die
- cp config.makefile.template config.makefile
- sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
- use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
- use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
- emake ARBHOME="${S}" links
-}
-
-src_compile() {
- emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
- use amd64 && mv arb.tgz arb.64.gentoo.tgz
- use x86 && mv arb.tgz arb.32.gentoo.tgz
- ln -s arb.*.tgz arb.tgz || die
-}
-
-src_install() {
- ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
- cat <<- EOF > "${S}/99${PN}"
- ARBHOME=/opt/arb
- PATH=/opt/arb/bin
- LD_LIBRARY_PATH=/opt/arb/lib
- EOF
- doenvd "${S}/99${PN}"
-}
diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch
deleted file mode 100644
index 21d21f5ac17..00000000000
--- a/sci-biology/arb/files/5.1-bfr-overflow.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- ARB_GDE/GDE_HGLfile.cxx | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx
-index e353a89..f69635a 100644
---- a/ARB_GDE/GDE_HGLfile.cxx
-+++ b/ARB_GDE/GDE_HGLfile.cxx
-@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type)
- if(this_elem->id[0] == '\0')
- strncpy(this_elem->id,uniqueID(),79);
- if(this_elem->short_name[0] == '\0')
-- strncpy(this_elem->short_name,this_elem->id,79);
-+ strncpy(this_elem->short_name,this_elem->id,31);
- if(this_elem->seqlen == 0)
- this_elem->protect=
- PROT_BASE_CHANGES+
diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch
deleted file mode 100644
index bf0bacad328..00000000000
--- a/sci-biology/arb/files/5.1-libs.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl
-index b653a66..b346c96 100644
---- a/SOURCE_TOOLS/provide_libs.pl
-+++ b/SOURCE_TOOLS/provide_libs.pl
-@@ -118,11 +118,6 @@ sub provide_libs($$$) {
- foreach my $lib (keys %needed_by) {
- update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir);
- }
-- if ($opengl==1) {
-- foreach my $lib (keys %needed_by_opengl) {
-- update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir);
-- }
-- }
- }
-
- sub main() {
diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch
deleted file mode 100644
index 3d750e76efe..00000000000
--- a/sci-biology/arb/files/5.2-libpng15.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Fix building with libpng-1.5
-
-https://bugs.gentoo.org/show_bug.cgi?id=378353
-
-Patch written by Samuli Suominen <ssuominen@gentoo.org>
---- a/GL/glpng/glpng.c
-+++ b/GL/glpng/glpng.c
-@@ -285,7 +285,7 @@
- endinfo = png_create_info_struct(png);
-
- // DH: added following lines
-- if (setjmp(png->jmpbuf))
-+ if (setjmp(png_jmpbuf(png)))
- {
- png_destroy_read_struct(&png, &info, &endinfo);
- return 0;
-@@ -390,7 +390,7 @@
- endinfo = png_create_info_struct(png);
-
- // DH: added following lines
-- if (setjmp(png->jmpbuf))
-+ if (setjmp(png_jmpbuf(png)))
- {
- png_destroy_read_struct(&png, &info, &endinfo);
- return 0;
-@@ -569,7 +569,7 @@
- #define ALPHA *q
-
- switch (trans) {
-- case PNG_CALLBACK:
-+ case PNG_CALLBACKT:
- FORSTART
- ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b);
- FOREND
---- a/GL/glpng/glpng.h
-+++ b/GL/glpng/glpng.h
-@@ -57,7 +57,7 @@
- #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS
-
- /* Transparency parameters */
--#define PNG_CALLBACK -3 /* Call the callback function to generate alpha */
-+#define PNG_CALLBACKT -3 /* Call the callback function to generate alpha */
- #define PNG_ALPHA -2 /* Use alpha channel in PNG file, if there is one */
- #define PNG_SOLID -1 /* No transparency */
- #define PNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */
diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch
deleted file mode 100644
index 186e78e450b..00000000000
--- a/sci-biology/arb/files/arb-5.2-gcc-47.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- AWTI/AWTI_import.cxx | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx
-index 8e730ac..e3f9ff4 100644
---- a/AWTI/AWTI_import.cxx
-+++ b/AWTI/AWTI_import.cxx
-@@ -12,6 +12,7 @@
- #include <GEN.hxx>
-
- #include <climits>
-+#include <unistd.h>
-
- using namespace std;
-
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