mirror of
https://github.com/gentoo-mirror/gentoo.git
synced 2026-09-24 04:59:14 -07:00
sci-biology/arb: Remove old
Package-Manager: Portage-2.3.19, Repoman-2.3.6
This commit is contained in:
David Seifert
@@ -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
|
||||
|
||||
@@ -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${PN}" || die
|
||||
}
|
||||
@@ -1,79 +0,0 @@
|
||||
# Copyright 1999-2016 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
|
||||
EAPI=4
|
||||
|
||||
inherit eutils toolchain-funcs
|
||||
|
||||
DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
|
||||
HOMEPAGE="http://www.arb-home.de/"
|
||||
SRC_URI="
|
||||
http://download.arb-home.de/release/arb_${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${PN}"
|
||||
}
|
||||
@@ -1,77 +0,0 @@
|
||||
# Copyright 1999-2016 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
|
||||
EAPI=4
|
||||
|
||||
inherit eutils toolchain-funcs
|
||||
|
||||
DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis"
|
||||
HOMEPAGE="http://www.arb-home.de/"
|
||||
SRC_URI="
|
||||
http://download.arb-home.de/release/arb_${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}"
|
||||
}
|
||||
@@ -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+
|
||||
@@ -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() {
|
||||
@@ -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 */
|
||||
@@ -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;
|
||||
|
||||
Reference in New Issue
Block a user