root
10 years ago
parent
fbdb80ed7e
commit
1222e5eafd
@ -1,5 +1,9 @@
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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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<herd>fonts</herd>
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<herd>fonts</herd>
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<use>
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<flag name='tahoma'>Also install the Tahoma font. Due to the lack of a free
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bold variant, this may render badly. See bug 184790.</flag>
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</use>
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</pkgmetadata>
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@ -1 +1 @@
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DIST hp2xx-3.4.4.tar.gz 610330 SHA256 47b72fb386a189b52f07e31e424c038954c4e0ce405803841bed742bab488817
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DIST hp2xx-3.4.4.tar.gz 610330 SHA256 47b72fb386a189b52f07e31e424c038954c4e0ce405803841bed742bab488817 SHA512 ccfe4a23ca482471506e59d6d459ce3ed56d9d775613e3238bd82d11cf4ea0595bf57ff95b3bd22a674865ec7f07dc63c1bcf0deb2a430b7ae241734c7e57ccd WHIRLPOOL ee3415eadaef3065239859de414d78f6619feef9e70c80a53fc835b52a2acb476645d7040880d2ab480cd92b53f002f58da7a6774bc436a5bfe587acc6b38f00
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@ -0,0 +1,14 @@
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https://bugs.gentoo.org/attachment.cgi?id=399898
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Only first hunk preserved.
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diff -ruN hp2xx-3.4.4-r0/doc/hp2xxinf.tex hp2xx-3.4.4-r3/doc/hp2xxinf.tex
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--- hp2xx-3.4.4-r0/doc/hp2xxinf.tex 2003-06-21 17:41:16.000000000 +0200
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+++ hp2xx-3.4.4-r3/doc/hp2xxinf.tex 2015-03-27 20:36:32.000000000 +0100
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@@ -92,7 +92,7 @@
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@page
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@tex
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{\parskip=0pt
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-\hfill mk\@daveg.com\par
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+\hfill mk@@daveg.com\par
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\hfill {\it Using HP2XX}, \manvers\par
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\hfill \TeX{}info \texinfoversion\par
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}
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@ -0,0 +1,70 @@
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# Copyright 1999-2015 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: /var/cvsroot/gentoo-x86/media-gfx/hp2xx/hp2xx-3.4.4-r1.ebuild,v 1.1 2015/03/29 13:37:30 idella4 Exp $
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EAPI=4
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inherit eutils base
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DESCRIPTION="Versatile tool to convert Hewlett-Packard's HP-GL plotter language into other graphics formats"
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HOMEPAGE="http://www.gnu.org/software/hp2xx/"
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SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
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LICENSE="GPL-2"
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SLOT="0"
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KEYWORDS="~x86 ~amd64"
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IUSE="X jpeg png tiff"
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RDEPEND="
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png? ( media-libs/libpng sys-libs/zlib )
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tiff? ( media-libs/tiff )
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jpeg? ( virtual/jpeg )
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X? ( x11-libs/libX11 )"
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DEPEND="${RDEPEND}
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sys-apps/texinfo"
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PATCHES=( "${FILESDIR}"/${P}-r1.patch
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"${FILESDIR}"/${P}-docbuild.patch )
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src_prepare() {
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base_src_prepare
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cp -v makes/generic.mak sources/Makefile || die
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}
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src_compile() {
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cd "${S}/sources" || die
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export PREVIEWER="no_prev"
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export EX_SRC=
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export EX_OBJ=
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export EX_DEFS=-DUNIX
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export ALL_LIBS=-lm
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use X && \
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PREVIEWER="to_x11" \
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EX_DEFS="-DHAS_UNIX_X11" \
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ALL_LIBS="${ALL_LIBS} -lX11"
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use jpeg && \
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EX_SRC="${EX_SRC} to_jpg.c" \
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EX_OBJ="${EX_OBJ} to_jpg.o" \
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EX_DEFS="${EX_DEFS} -DJPG" \
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ALL_LIBS="${ALL_LIBS} -ljpeg"
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use png && \
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EX_SRC="${EX_SRC} png.c to_png.c" \
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EX_OBJ="${EX_OBJ} png.o to_png.o" \
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EX_DEFS="${EX_DEFS} -DPNG" \
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ALL_LIBS="${ALL_LIBS} -lpng"
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use tiff && \
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EX_SRC="${EX_SRC} to_tif.c" \
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EX_OBJ="${EX_OBJ} to_tif.o" \
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EX_DEFS="${EX_DEFS} -DTIF" \
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ALL_LIBS="${ALL_LIBS} -ltiff"
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emake all
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}
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src_install() {
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dodir /usr/bin /usr/share/info /usr/share/man/man1
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make prefix="${D}/usr" \
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mandir="${D}/usr/share/man" \
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infodir="${D}/usr/share/info" \
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install || die
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}
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@ -1 +1 @@
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Sun, 29 Mar 2015 13:37:00 +0000
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Sun, 29 Mar 2015 16:06:53 +0000
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@ -1 +1 @@
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Sun, 29 Mar 2015 13:37:00 +0000
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Sun, 29 Mar 2015 16:06:53 +0000
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@ -1,14 +1,14 @@
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DEFINED_PHASES=configure install postinst prepare
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DEPEND=alsa? ( media-libs/alsa-lib ) cddb? ( media-libs/libcddb ) drmkms? ( x11-libs/libdrm[libkms] ) gif? ( media-libs/giflib ) gstreamer? ( media-libs/gstreamer:1.0 media-libs/gst-plugins-base:1.0 ) imlib2? ( media-libs/imlib2 ) jpeg? ( virtual/jpeg ) jpeg2k? ( media-libs/jasper[jpeg] ) mad? ( media-libs/libmad ) mng? ( media-libs/libmng ) mpeg3? ( media-libs/libmpeg3 ) opengl? ( media-libs/mesa[gbm,egl?,gles2?] x11-libs/libdrm ) png? ( media-libs/libpng:0 ) sdl? ( media-libs/libsdl ) svg? ( x11-libs/libsvg-cairo ) swfdec? ( media-libs/swfdec ) tiff? ( media-libs/tiff:0 ) timidity? ( media-libs/libtimidity media-sound/timidity++ ) tremor? ( media-libs/tremor ) truetype? ( >=media-libs/freetype-2.0.1 ) vdpau? ( x11-proto/xproto x11-libs/libX11 x11-libs/libXext x11-libs/libvdpau ) vorbis? ( media-libs/libvorbis ) webp? ( media-libs/libwebp ) X? ( x11-libs/libXext x11-libs/libX11 ) xine? ( media-libs/xine-lib[vdpau?] ) zlib? ( sys-libs/zlib ) X? ( x11-proto/xextproto x11-proto/xproto ) !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.13:1.13 >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4
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DEPEND=alsa? ( media-libs/alsa-lib ) cddb? ( media-libs/libcddb ) drmkms? ( x11-libs/libdrm[libkms] ) gif? ( media-libs/giflib ) gstreamer? ( media-libs/gstreamer:1.0 media-libs/gst-plugins-base:1.0 ) imlib2? ( media-libs/imlib2 ) jpeg? ( virtual/jpeg ) jpeg2k? ( media-libs/jasper[jpeg] ) mad? ( media-libs/libmad ) mng? ( media-libs/libmng ) mpeg3? ( media-libs/libmpeg3 ) opengl? ( media-libs/mesa[gbm,egl?,gles2?] x11-libs/libdrm ) png? ( media-libs/libpng:0 ) sdl? ( media-libs/libsdl ) swfdec? ( media-libs/swfdec ) tiff? ( media-libs/tiff:0 ) timidity? ( media-libs/libtimidity media-sound/timidity++ ) tremor? ( media-libs/tremor ) truetype? ( >=media-libs/freetype-2.0.1 ) vdpau? ( x11-proto/xproto x11-libs/libX11 x11-libs/libXext x11-libs/libvdpau ) vorbis? ( media-libs/libvorbis ) webp? ( media-libs/libwebp ) X? ( x11-libs/libXext x11-libs/libX11 ) xine? ( media-libs/xine-lib[vdpau?] ) zlib? ( sys-libs/zlib ) X? ( x11-proto/xextproto x11-proto/xproto ) !<sys-devel/gettext-0.18.1.1-r3 || ( >=sys-devel/automake-1.13:1.13 >=sys-devel/automake-1.15:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4
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DESCRIPTION=Thin library on top of the Linux framebuffer devices
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EAPI=5
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HOMEPAGE=http://www.directfb.org/
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IUSE=alsa bmp cddb debug divine drmkms +dynload doc egl fbcon fusiondale fusionsound gif gles2 gstreamer imlib2 input_hub jpeg jpeg2k mad cpu_flags_x86_mmx mng mpeg2 mpeg3 multicore opengl oss png pnm sawman sdl cpu_flags_x86_sse static-libs svg swfdec tiff timidity tremor truetype v4l vdpau vorbis webp X xine zlib video_cards_intel video_cards_mach64 video_cards_mga video_cards_neomagic video_cards_nsc video_cards_nvidia video_cards_r128 video_cards_radeon video_cards_s3 video_cards_sis video_cards_tdfx video_cards_via video_cards_vmware input_devices_dynapro input_devices_elo2300 input_devices_evdev input_devices_joystick input_devices_keyboard input_devices_lirc input_devices_mouse input_devices_mutouch input_devices_tslib
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IUSE=alsa bmp cddb debug divine drmkms +dynload doc egl fbcon fusiondale fusionsound gif gles2 gstreamer imlib2 input_hub jpeg jpeg2k mad cpu_flags_x86_mmx mng mpeg2 mpeg3 multicore opengl oss png pnm sawman sdl cpu_flags_x86_sse static-libs swfdec tiff timidity tremor truetype v4l vdpau vorbis webp X xine zlib video_cards_intel video_cards_mach64 video_cards_mga video_cards_neomagic video_cards_nsc video_cards_nvidia video_cards_r128 video_cards_radeon video_cards_s3 video_cards_sis video_cards_tdfx video_cards_via video_cards_vmware input_devices_dynapro input_devices_elo2300 input_devices_evdev input_devices_joystick input_devices_keyboard input_devices_lirc input_devices_mouse input_devices_mutouch input_devices_tslib
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KEYWORDS=~alpha ~amd64 ~arm ~hppa ~ia64 -mips ~ppc ~ppc64 ~sh -sparc ~x86
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LICENSE=LGPL-2.1
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RDEPEND=alsa? ( media-libs/alsa-lib ) cddb? ( media-libs/libcddb ) drmkms? ( x11-libs/libdrm[libkms] ) gif? ( media-libs/giflib ) gstreamer? ( media-libs/gstreamer:1.0 media-libs/gst-plugins-base:1.0 ) imlib2? ( media-libs/imlib2 ) jpeg? ( virtual/jpeg ) jpeg2k? ( media-libs/jasper[jpeg] ) mad? ( media-libs/libmad ) mng? ( media-libs/libmng ) mpeg3? ( media-libs/libmpeg3 ) opengl? ( media-libs/mesa[gbm,egl?,gles2?] x11-libs/libdrm ) png? ( media-libs/libpng:0 ) sdl? ( media-libs/libsdl ) svg? ( x11-libs/libsvg-cairo ) swfdec? ( media-libs/swfdec ) tiff? ( media-libs/tiff:0 ) timidity? ( media-libs/libtimidity media-sound/timidity++ ) tremor? ( media-libs/tremor ) truetype? ( >=media-libs/freetype-2.0.1 ) vdpau? ( x11-proto/xproto x11-libs/libX11 x11-libs/libXext x11-libs/libvdpau ) vorbis? ( media-libs/libvorbis ) webp? ( media-libs/libwebp ) X? ( x11-libs/libXext x11-libs/libX11 ) xine? ( media-libs/xine-lib[vdpau?] ) zlib? ( sys-libs/zlib )
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RDEPEND=alsa? ( media-libs/alsa-lib ) cddb? ( media-libs/libcddb ) drmkms? ( x11-libs/libdrm[libkms] ) gif? ( media-libs/giflib ) gstreamer? ( media-libs/gstreamer:1.0 media-libs/gst-plugins-base:1.0 ) imlib2? ( media-libs/imlib2 ) jpeg? ( virtual/jpeg ) jpeg2k? ( media-libs/jasper[jpeg] ) mad? ( media-libs/libmad ) mng? ( media-libs/libmng ) mpeg3? ( media-libs/libmpeg3 ) opengl? ( media-libs/mesa[gbm,egl?,gles2?] x11-libs/libdrm ) png? ( media-libs/libpng:0 ) sdl? ( media-libs/libsdl ) swfdec? ( media-libs/swfdec ) tiff? ( media-libs/tiff:0 ) timidity? ( media-libs/libtimidity media-sound/timidity++ ) tremor? ( media-libs/tremor ) truetype? ( >=media-libs/freetype-2.0.1 ) vdpau? ( x11-proto/xproto x11-libs/libX11 x11-libs/libXext x11-libs/libvdpau ) vorbis? ( media-libs/libvorbis ) webp? ( media-libs/libwebp ) X? ( x11-libs/libXext x11-libs/libX11 ) xine? ( media-libs/xine-lib[vdpau?] ) zlib? ( sys-libs/zlib )
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REQUIRED_USE=gles2? ( opengl )
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SLOT=0
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SRC_URI=http://directfb.org/downloads/Core/DirectFB-1.7/DirectFB-1.7.6.tar.gz http://directfb.org/downloads/Old/DirectFB-1.7.6.tar.gz
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_eclasses_=autotools 999c8f6cf5d91495cb0779588f20716c eutils 9fb270e417e0e83d64ca52586c4a79de libtool 52d0e17251d04645ffaa61bfdd858944 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
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_md5_=02febf0ef94d2d769f85f6125e3c0bab
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_md5_=1cf513e5f06029a09989ebbff91c8a5a
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@ -1,14 +1,14 @@
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DEFINED_PHASES=compile configure install postinst postrm prepare test unpack
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DEPEND=>=dev-qt/linguist-tools-5.4.1:5 >=dev-qt/qtcore-5.4.1:5[debug=] test? ( !prefix? ( x11-base/xorg-server[xvfb] ) x11-apps/xhost ) dev-lang/perl virtual/pkgconfig test? ( >=dev-qt/qttest-5.4.1:5[debug=] )
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DEPEND=>=dev-qt/linguist-tools-5.4.1:5 >=dev-qt/qtcore-5.4.1:5 test? ( !prefix? ( x11-base/xorg-server[xvfb] ) x11-apps/xhost ) dev-lang/perl virtual/pkgconfig test? ( >=dev-qt/qttest-5.4.1:5[debug=] )
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DESCRIPTION=Translation files for the Qt5 framework
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EAPI=5
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HOMEPAGE=https://www.qt.io/ https://qt-project.org/
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IUSE=test debug test
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KEYWORDS=~amd64 ~arm ~hppa ~x86
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LICENSE=|| ( LGPL-2.1 LGPL-3 )
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RDEPEND=>=dev-qt/linguist-tools-5.4.1:5 >=dev-qt/qtcore-5.4.1:5[debug=] dev-qt/qtchooser
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RDEPEND=dev-qt/qtchooser
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RESTRICT=test
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SLOT=5
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SRC_URI=http://download.qt.io/official_releases/qt/5.4/5.4.1/submodules/qttranslations-opensource-src-5.4.1.tar.xz
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_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multilib 3bf24e6abb9b76d9f6c20600f0b716bf qt5-build 4203236286fd6aee7ce37d52ef232052 toolchain-funcs b99aa37f734b5d426efd83b2f271cece virtualx 73cfc129b4b9ba23aed1abb10c825d86
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_md5_=ed8dffaf0979ac5d7544f50b0bf9ca1e
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_md5_=7608775a0eccc5c8d3dcb3749e1adb2d
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@ -1,11 +0,0 @@
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DEFINED_PHASES=install postinst postrm setup unpack
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DEPEND=app-arch/cabextract X? ( x11-apps/mkfontdir media-fonts/encodings )
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DESCRIPTION=Microsoft's TrueType core fonts
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HOMEPAGE=http://corefonts.sourceforge.net/
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IUSE=X X
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KEYWORDS=~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~x64-freebsd ~x86-freebsd ~x86-interix ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris ~x86-winnt
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LICENSE=MSttfEULA
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SLOT=0
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SRC_URI=mirror://sourceforge/corefonts/andale32.exe mirror://sourceforge/corefonts/arial32.exe mirror://sourceforge/corefonts/arialb32.exe mirror://sourceforge/corefonts/comic32.exe mirror://sourceforge/corefonts/courie32.exe mirror://sourceforge/corefonts/georgi32.exe mirror://sourceforge/corefonts/impact32.exe mirror://sourceforge/corefonts/times32.exe mirror://sourceforge/corefonts/trebuc32.exe mirror://sourceforge/corefonts/verdan32.exe mirror://sourceforge/corefonts/webdin32.exe
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_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de font b3239d2dc442d1717b9725e2be7cb5d6 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
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_md5_=849cdab8dfa335ab159a7852b38c1a34
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@ -0,0 +1,12 @@
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DEFINED_PHASES=install postinst postrm setup unpack
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DEPEND=app-arch/cabextract X? ( x11-apps/mkfontdir media-fonts/encodings )
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DESCRIPTION=Microsoft's TrueType core fonts
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||||
EAPI=5
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||||
HOMEPAGE=http://corefonts.sourceforge.net/
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IUSE=X tahoma X
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KEYWORDS=~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~x86-interix ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris ~x86-winnt
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||||
LICENSE=MSttfEULA
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SLOT=0
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||||
SRC_URI=mirror://gentoo/EUupdate.EXE mirror://sourceforge/corefonts/andale32.exe mirror://sourceforge/corefonts/arialb32.exe mirror://sourceforge/corefonts/comic32.exe mirror://sourceforge/corefonts/courie32.exe mirror://sourceforge/corefonts/georgi32.exe mirror://sourceforge/corefonts/impact32.exe mirror://sourceforge/corefonts/webdin32.exe mirror://sourceforge/corefonts/wd97vwr32.exe
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||||
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de font b3239d2dc442d1717b9725e2be7cb5d6 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
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||||
_md5_=68c480b473f8a05dfdac2876c0e8d178
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||||
@ -0,0 +1,13 @@
|
||||
DEFINED_PHASES=compile configure install prepare unpack
|
||||
DEPEND=png? ( media-libs/libpng sys-libs/zlib ) tiff? ( media-libs/tiff ) jpeg? ( virtual/jpeg ) X? ( x11-libs/libX11 ) sys-apps/texinfo
|
||||
DESCRIPTION=Versatile tool to convert Hewlett-Packard's HP-GL plotter language into other graphics formats
|
||||
EAPI=4
|
||||
HOMEPAGE=http://www.gnu.org/software/hp2xx/
|
||||
IUSE=X jpeg png tiff
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||||
KEYWORDS=~x86 ~amd64
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||||
LICENSE=GPL-2
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||||
RDEPEND=png? ( media-libs/libpng sys-libs/zlib ) tiff? ( media-libs/tiff ) jpeg? ( virtual/jpeg ) X? ( x11-libs/libX11 )
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||||
SLOT=0
|
||||
SRC_URI=mirror://gnu/hp2xx/hp2xx-3.4.4.tar.gz
|
||||
_eclasses_=base 87f7447ccfc06fd0729ff4684e11e0d6 eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
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||||
_md5_=ea0b036e5e28b246c675e9106e1b58df
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||||
@ -1,14 +0,0 @@
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||||
DEFINED_PHASES=compile config configure install postinst prepare setup test
|
||||
DEPEND=dev-qt/qtcore:4[ssl?] sys-libs/zlib monolithic? ( dev-qt/qtscript:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( dev-qt/qtsql:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( dev-qt/qtsql:4[postgres] ) syslog? ( virtual/logger ) dev-qt/qtgui:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( dev-qt/qtdbus:4 dev-libs/libdbusmenu-qt ) kde? ( kde-base/kdelibs:4 || ( kde-apps/oxygen-icons kde-base/oxygen-icons:4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] dev-qt/qtphonon:4 ) ) webkit? ( dev-qt/qtwebkit:4 ) ) !monolithic? ( server? ( dev-qt/qtscript:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( dev-qt/qtsql:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( dev-qt/qtsql:4[postgres] ) syslog? ( virtual/logger ) ) X? ( dev-qt/qtgui:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( dev-qt/qtdbus:4 dev-libs/libdbusmenu-qt ) kde? ( kde-base/kdelibs:4 || ( kde-apps/oxygen-icons kde-base/oxygen-icons:4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] dev-qt/qtphonon:4 ) ) webkit? ( dev-qt/qtwebkit:4 ) ) ) kde? ( dev-util/automoc ) sys-devel/make >=dev-util/cmake-2.8.12 userland_GNU? ( >=sys-apps/findutils-4.4.0 ) virtual/pkgconfig
|
||||
DESCRIPTION=Qt/KDE IRC client supporting a remote daemon for 24/7 connectivity
|
||||
EAPI=5
|
||||
HOMEPAGE=http://quassel-irc.org/
|
||||
IUSE=ayatana crypt dbus debug kde monolithic phonon postgres +server +ssl syslog webkit X
|
||||
KEYWORDS=~amd64 ~arm ~ppc ~x86 ~amd64-linux ~sparc-solaris
|
||||
LICENSE=GPL-3
|
||||
RDEPEND=dev-qt/qtcore:4[ssl?] sys-libs/zlib monolithic? ( dev-qt/qtscript:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( dev-qt/qtsql:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( dev-qt/qtsql:4[postgres] ) syslog? ( virtual/logger ) dev-qt/qtgui:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( dev-qt/qtdbus:4 dev-libs/libdbusmenu-qt ) kde? ( kde-base/kdelibs:4 || ( kde-apps/oxygen-icons kde-base/oxygen-icons:4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] dev-qt/qtphonon:4 ) ) webkit? ( dev-qt/qtwebkit:4 ) ) !monolithic? ( server? ( dev-qt/qtscript:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( dev-qt/qtsql:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( dev-qt/qtsql:4[postgres] ) syslog? ( virtual/logger ) ) X? ( dev-qt/qtgui:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( dev-qt/qtdbus:4 dev-libs/libdbusmenu-qt ) kde? ( kde-base/kdelibs:4 || ( kde-apps/oxygen-icons kde-base/oxygen-icons:4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] dev-qt/qtphonon:4 ) ) webkit? ( dev-qt/qtwebkit:4 ) ) )
|
||||
REQUIRED_USE=|| ( X server monolithic ) crypt? ( || ( server monolithic ) ) postgres? ( || ( server monolithic ) ) syslog? ( || ( server monolithic ) ) kde? ( || ( X monolithic ) ) phonon? ( || ( X monolithic ) ) dbus? ( || ( X monolithic ) ) ayatana? ( || ( X monolithic ) ) webkit? ( || ( X monolithic ) )
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||||
SLOT=0
|
||||
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||||
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||||
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||||
DEPEND=>=dev-qt/qtcore-4.6.0:4[ssl?] monolithic? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) !monolithic? ( server? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) ) X? ( >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) ) kde? ( dev-util/automoc ) sys-devel/make >=dev-util/cmake-2.8.12 userland_GNU? ( >=sys-apps/findutils-4.4.0 )
|
||||
DESCRIPTION=Qt4/KDE4 IRC client supporting a remote daemon for 24/7 connectivity
|
||||
EAPI=4
|
||||
HOMEPAGE=http://quassel-irc.org/
|
||||
IUSE=ayatana crypt dbus debug kde monolithic phonon postgres +server +ssl syslog webkit X
|
||||
KEYWORDS=amd64 ~arm ppc x86 ~amd64-linux ~sparc-solaris
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||||
LICENSE=GPL-3
|
||||
RDEPEND=>=dev-qt/qtcore-4.6.0:4[ssl?] monolithic? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) !monolithic? ( server? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) ) X? ( >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) )
|
||||
REQUIRED_USE=|| ( X server monolithic ) crypt? ( || ( server monolithic ) ) postgres? ( || ( server monolithic ) ) syslog? ( || ( server monolithic ) ) kde? ( || ( X monolithic ) ) phonon? ( || ( X monolithic ) ) dbus? ( || ( X monolithic ) ) ayatana? ( || ( X monolithic ) ) webkit? ( || ( X monolithic ) )
|
||||
SLOT=0
|
||||
SRC_URI=http://quassel-irc.org/pub/quassel-0.9.2.tar.bz2
|
||||
_eclasses_=cmake-utils 0430c386d85cec959d72640afd63ea91 eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multilib 3bf24e6abb9b76d9f6c20600f0b716bf pax-utils dfe060cb70d89757fde5c1ff8405e950 toolchain-funcs b99aa37f734b5d426efd83b2f271cece user f54e098dd38ba1c0847a13e685b87747 versionator cd0bcdb170807e4a1984115e9d53a26f
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DEFINED_PHASES=compile config configure install postinst prepare setup test
|
||||
DEPEND=>=dev-qt/qtcore-4.6.0:4[ssl?] monolithic? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) !monolithic? ( server? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) ) X? ( >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) ) kde? ( dev-util/automoc ) sys-devel/make >=dev-util/cmake-2.8.12 userland_GNU? ( >=sys-apps/findutils-4.4.0 )
|
||||
DESCRIPTION=Qt4/KDE4 IRC client supporting a remote daemon for 24/7 connectivity
|
||||
EAPI=5
|
||||
HOMEPAGE=http://quassel-irc.org/
|
||||
IUSE=ayatana crypt dbus debug kde monolithic phonon postgres +server +ssl syslog webkit X
|
||||
KEYWORDS=amd64 ~arm ~ppc x86 ~amd64-linux ~sparc-solaris
|
||||
LICENSE=GPL-3
|
||||
RDEPEND=>=dev-qt/qtcore-4.6.0:4[ssl?] monolithic? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) !monolithic? ( server? ( >=dev-qt/qtscript-4.6.0:4 crypt? ( app-crypt/qca:2[openssl,qt4(+)] ) !postgres? ( >=dev-qt/qtsql-4.6.0:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] ) postgres? ( >=dev-qt/qtsql-4.6.0:4[postgres] ) syslog? ( virtual/logger ) ) X? ( >=dev-qt/qtgui-4.6.0:4 ayatana? ( dev-libs/libindicate-qt ) dbus? ( >=dev-qt/qtdbus-4.6.0:4 dev-libs/libdbusmenu-qt ) kde? ( >=kde-base/kdelibs-4.4 || ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-4.4 ) ayatana? ( kde-misc/plasma-widget-message-indicator ) ) phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-4.6.0:4 ) ) webkit? ( >=dev-qt/qtwebkit-4.6.0:4 ) ) )
|
||||
REQUIRED_USE=|| ( X server monolithic ) crypt? ( || ( server monolithic ) ) postgres? ( || ( server monolithic ) ) syslog? ( || ( server monolithic ) ) kde? ( || ( X monolithic ) ) phonon? ( || ( X monolithic ) ) dbus? ( || ( X monolithic ) ) ayatana? ( || ( X monolithic ) ) webkit? ( || ( X monolithic ) )
|
||||
SLOT=0
|
||||
SRC_URI=http://quassel-irc.org/pub/quassel-0.9.3.tar.bz2
|
||||
_eclasses_=cmake-utils 0430c386d85cec959d72640afd63ea91 eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multilib 3bf24e6abb9b76d9f6c20600f0b716bf pax-utils dfe060cb70d89757fde5c1ff8405e950 toolchain-funcs b99aa37f734b5d426efd83b2f271cece user f54e098dd38ba1c0847a13e685b87747 versionator cd0bcdb170807e4a1984115e9d53a26f
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
HOMEPAGE=http://mafft.cbrc.jp/alignment/software/index.html
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
DEPEND=!sci-libs/libmuscle
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
|
||||
@ -1,10 +1,10 @@
|
||||
DEFINED_PHASES=compile install prepare
|
||||
DESCRIPTION=Probabilistic Alignment Kit
|
||||
EAPI=4
|
||||
HOMEPAGE=http://code.google.com/p/prank-msa/ http://www.ebi.ac.uk/goldman-srv/prank/prank/
|
||||
HOMEPAGE=http://wasabiapp.org/software/prank/
|
||||
KEYWORDS=~amd64 ~x86
|
||||
LICENSE=GPL-3
|
||||
SLOT=0
|
||||
SRC_URI=http://prank-msa.googlecode.com/files/prank.src.111130.tgz
|
||||
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
|
||||
_md5_=baca7e062e10c19de586718ace0af969
|
||||
_md5_=b76183fb62f9632a20d990a02541d603
|
||||
|
||||
@ -0,0 +1,10 @@
|
||||
DEFINED_PHASES=compile install prepare
|
||||
DESCRIPTION=Probabilistic Alignment Kit
|
||||
EAPI=4
|
||||
HOMEPAGE=http://wasabiapp.org/software/prank/
|
||||
KEYWORDS=~amd64 ~x86
|
||||
LICENSE=GPL-3
|
||||
SLOT=0
|
||||
SRC_URI=http://wasabiapp.org/download/prank/prank.source.140603.tgz
|
||||
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
|
||||
_md5_=32de59f9fa1435a5881cbd89610f2887
|
||||
@ -1,10 +0,0 @@
|
||||
DEFINED_PHASES=compile install postinst unpack
|
||||
DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
|
||||
HOMEPAGE=http://probcons.stanford.edu/
|
||||
KEYWORDS=x86
|
||||
LICENSE=public-domain
|
||||
RDEPEND=!sci-geosciences/gmt sci-visualization/gnuplot
|
||||
SLOT=0
|
||||
SRC_URI=http://probcons.stanford.edu/probcons_v1_10.tar.gz
|
||||
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
|
||||
_md5_=72bd590dd72cc304340f6c0ac28f8553
|
||||
@ -1,10 +0,0 @@
|
||||
DEFINED_PHASES=compile install postinst unpack
|
||||
DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
|
||||
HOMEPAGE=http://probcons.stanford.edu/
|
||||
KEYWORDS=~amd64 ~x86
|
||||
LICENSE=public-domain
|
||||
RDEPEND=!sci-geosciences/gmt sci-visualization/gnuplot
|
||||
SLOT=0
|
||||
SRC_URI=http://probcons.stanford.edu/probcons_v1_12.tar.gz
|
||||
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
|
||||
_md5_=4c551f0fb61ffa56bc2bd4f86192516a
|
||||
@ -1,13 +1,13 @@
|
||||
DEFINED_PHASES=compile install prepare test
|
||||
DEPEND=~sci-biology/hmmer-2.3.2 app-shells/tcsh dev-lang/perl virtual/latex-base
|
||||
DESCRIPTION=Intelligent algorithms for DNA searches
|
||||
EAPI=3
|
||||
EAPI=5
|
||||
HOMEPAGE=http://www.ebi.ac.uk/Wise2/
|
||||
IUSE=doc
|
||||
IUSE=doc static-libs
|
||||
KEYWORDS=~alpha ~amd64 ~ia64 ~sparc ~x86
|
||||
LICENSE=BSD
|
||||
RDEPEND=~sci-biology/hmmer-2.3.2
|
||||
SLOT=0
|
||||
SRC_URI=ftp://ftp.ebi.ac.uk/pub/software/wise2/wise2.4.0alpha.tar.gz
|
||||
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece versionator cd0bcdb170807e4a1984115e9d53a26f
|
||||
_md5_=7a5c957a4ae3fe60e4b6f19c8b5f119d
|
||||
_md5_=3bd4bd5029e307d3c37a4192e2b8d6a4
|
||||
|
||||
@ -1 +1 @@
|
||||
Sun, 29 Mar 2015 13:37:03 +0000
|
||||
Sun, 29 Mar 2015 16:06:56 +0000
|
||||
|
||||
@ -1 +1 @@
|
||||
Sun Mar 29 13:37:00 UTC 2015
|
||||
Sun Mar 29 16:06:53 UTC 2015
|
||||
|
||||
@ -1 +1 @@
|
||||
Sun, 29 Mar 2015 14:00:01 +0000
|
||||
Sun, 29 Mar 2015 16:30:01 +0000
|
||||
|
||||
@ -1 +1 @@
|
||||
1427636101 Sun 29 Mar 2015 01:35:01 PM UTC
|
||||
1427645101 Sun 29 Mar 2015 04:05:01 PM UTC
|
||||
|
||||
@ -1,33 +0,0 @@
|
||||
From 9e798c47eac3f01295016b6f27a48e787a072c25 Mon Sep 17 00:00:00 2001
|
||||
From: Manuel Nickschas <sputnick@quassel-irc.org>
|
||||
Date: Thu, 28 Nov 2013 01:45:43 +0100
|
||||
Subject: [PATCH] Make sys includes POSIX-compliant
|
||||
|
||||
We're using <sys/resources.h> in quassel.cpp for the backtrace generation
|
||||
stuff. Documentation for that header indicates that <sys/time.h> shall also
|
||||
be included (even though it doesn't seem to be needed for our usage).
|
||||
Additionally, compiling started to fail in recent FreeBSD versions, because
|
||||
we lacked the <sys/types.h> include, which seems to be mandated by POSIX
|
||||
(but not on Linux, although it won't hurt to have it).
|
||||
|
||||
tl;dr: This should make Quassel compile on recent versions of FreeBSD again.
|
||||
---
|
||||
src/common/quassel.cpp | 2 ++
|
||||
1 file changed, 2 insertions(+)
|
||||
|
||||
diff --git a/src/common/quassel.cpp b/src/common/quassel.cpp
|
||||
index e081775..058b4b9 100644
|
||||
--- a/src/common/quassel.cpp
|
||||
+++ b/src/common/quassel.cpp
|
||||
@@ -23,6 +23,8 @@
|
||||
#include <iostream>
|
||||
#include <signal.h>
|
||||
#if !defined Q_OS_WIN32 && !defined Q_OS_MAC
|
||||
+# include <sys/types.h>
|
||||
+# include <sys/time.h>
|
||||
# include <sys/resource.h>
|
||||
#endif
|
||||
|
||||
--
|
||||
1.8.4
|
||||
|
||||
@ -1,173 +0,0 @@
|
||||
# Copyright 1999-2015 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/net-irc/quassel/quassel-0.10.1.ebuild,v 1.4 2015/02/22 18:41:23 mgorny Exp $
|
||||
|
||||
EAPI=5
|
||||
|
||||
inherit cmake-utils eutils pax-utils systemd user versionator
|
||||
|
||||
EGIT_REPO_URI="git://git.quassel-irc.org/quassel"
|
||||
[[ "${PV}" == "9999" ]] && inherit git-r3
|
||||
|
||||
DESCRIPTION="Qt/KDE IRC client supporting a remote daemon for 24/7 connectivity"
|
||||
HOMEPAGE="http://quassel-irc.org/"
|
||||
[[ "${PV}" == "9999" ]] || SRC_URI="http://quassel-irc.org/pub/${P/_/-}.tar.bz2"
|
||||
|
||||
LICENSE="GPL-3"
|
||||
KEYWORDS="~amd64 ~arm ~ppc ~x86 ~amd64-linux ~sparc-solaris"
|
||||
SLOT="0"
|
||||
IUSE="ayatana crypt dbus debug kde monolithic phonon postgres +server +ssl syslog webkit X"
|
||||
|
||||
SERVER_RDEPEND="
|
||||
dev-qt/qtscript:4
|
||||
crypt? ( app-crypt/qca:2[openssl,qt4(+)] )
|
||||
!postgres? ( dev-qt/qtsql:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] )
|
||||
postgres? ( dev-qt/qtsql:4[postgres] )
|
||||
syslog? ( virtual/logger )
|
||||
"
|
||||
|
||||
GUI_RDEPEND="
|
||||
dev-qt/qtgui:4
|
||||
ayatana? ( dev-libs/libindicate-qt )
|
||||
dbus? (
|
||||
dev-qt/qtdbus:4
|
||||
dev-libs/libdbusmenu-qt
|
||||
)
|
||||
kde? (
|
||||
kde-base/kdelibs:4
|
||||
|| ( kde-apps/oxygen-icons kde-base/oxygen-icons:4 )
|
||||
ayatana? ( kde-misc/plasma-widget-message-indicator )
|
||||
)
|
||||
phonon? ( || ( media-libs/phonon[qt4] dev-qt/qtphonon:4 ) )
|
||||
webkit? ( dev-qt/qtwebkit:4 )
|
||||
"
|
||||
|
||||
RDEPEND="
|
||||
dev-qt/qtcore:4[ssl?]
|
||||
sys-libs/zlib
|
||||
monolithic? (
|
||||
${SERVER_RDEPEND}
|
||||
${GUI_RDEPEND}
|
||||
)
|
||||
!monolithic? (
|
||||
server? ( ${SERVER_RDEPEND} )
|
||||
X? ( ${GUI_RDEPEND} )
|
||||
)
|
||||
"
|
||||
DEPEND="${RDEPEND}
|
||||
kde? ( dev-util/automoc )"
|
||||
|
||||
DOCS="AUTHORS ChangeLog README"
|
||||
|
||||
S="${WORKDIR}/${P/_/-}"
|
||||
|
||||
REQUIRED_USE="
|
||||
|| ( X server monolithic )
|
||||
crypt? ( || ( server monolithic ) )
|
||||
postgres? ( || ( server monolithic ) )
|
||||
syslog? ( || ( server monolithic ) )
|
||||
kde? ( || ( X monolithic ) )
|
||||
phonon? ( || ( X monolithic ) )
|
||||
dbus? ( || ( X monolithic ) )
|
||||
ayatana? ( || ( X monolithic ) )
|
||||
webkit? ( || ( X monolithic ) )
|
||||
"
|
||||
|
||||
pkg_setup() {
|
||||
if use server; then
|
||||
QUASSEL_DIR=/var/lib/${PN}
|
||||
QUASSEL_USER=${PN}
|
||||
# create quassel:quassel user
|
||||
enewgroup "${QUASSEL_USER}"
|
||||
enewuser "${QUASSEL_USER}" -1 -1 "${QUASSEL_DIR}" "${QUASSEL_USER}"
|
||||
fi
|
||||
}
|
||||
|
||||
src_configure() {
|
||||
local mycmakeargs=(
|
||||
$(cmake-utils_use_with ayatana LIBINDICATE)
|
||||
$(cmake-utils_use_want X QTCLIENT)
|
||||
$(cmake-utils_use_want server CORE)
|
||||
$(cmake-utils_use_want monolithic MONO)
|
||||
$(cmake-utils_use_with webkit)
|
||||
$(cmake-utils_use_with phonon)
|
||||
$(cmake-utils_use_with kde)
|
||||
$(cmake-utils_use_with dbus)
|
||||
$(cmake-utils_use_with ssl OPENSSL)
|
||||
$(cmake-utils_use_with syslog)
|
||||
$(cmake-utils_use_with !kde OXYGEN)
|
||||
$(cmake-utils_use_with crypt)
|
||||
"-DEMBED_DATA=OFF"
|
||||
)
|
||||
|
||||
cmake-utils_src_configure
|
||||
}
|
||||
|
||||
src_install() {
|
||||
cmake-utils_src_install
|
||||
|
||||
if use server ; then
|
||||
# needs PAX marking wrt bug#346255
|
||||
pax-mark m "${ED}/usr/bin/quasselcore"
|
||||
|
||||
# prepare folders in /var/
|
||||
keepdir "${QUASSEL_DIR}"
|
||||
fowners "${QUASSEL_USER}":"${QUASSEL_USER}" "${QUASSEL_DIR}"
|
||||
|
||||
# init scripts & systemd unit
|
||||
newinitd "${FILESDIR}"/quasselcore.init quasselcore
|
||||
newconfd "${FILESDIR}"/quasselcore.conf quasselcore
|
||||
systemd_dounit "${FILESDIR}"/quasselcore.service
|
||||
|
||||
# logrotate
|
||||
insinto /etc/logrotate.d
|
||||
newins "${FILESDIR}/quassel.logrotate" quassel
|
||||
fi
|
||||
}
|
||||
|
||||
pkg_postinst() {
|
||||
if use monolithic && use ssl ; then
|
||||
elog "Information on how to enable SSL support for client/core connections"
|
||||
elog "is available at http://bugs.quassel-irc.org/wiki/quassel-irc."
|
||||
fi
|
||||
|
||||
if use server; then
|
||||
einfo "If you want to generate SSL certificate remember to run:"
|
||||
einfo " emerge --config =${CATEGORY}/${PF}"
|
||||
fi
|
||||
|
||||
if use server || use monolithic ; then
|
||||
einfo "Quassel can use net-misc/oidentd package if installed on your system."
|
||||
einfo "Consider installing it if you want to run quassel within identd daemon."
|
||||
fi
|
||||
|
||||
# temporary info mesage
|
||||
if use server && [[ $(get_version_component_range 2 ${REPLACING_VERSIONS}) -lt 7 ]]; then
|
||||
echo
|
||||
ewarn "Please note that all configuration moved from"
|
||||
ewarn "/home/\${QUASSEL_USER}/.config/quassel-irc.org/"
|
||||
ewarn "to: ${QUASSEL_DIR}."
|
||||
echo
|
||||
ewarn "For migration, stop the core, move quasselcore files (pretty much"
|
||||
ewarn "everything apart from quasselclient.conf and settings.qss) into"
|
||||
ewarn "new location and then start server again."
|
||||
fi
|
||||
}
|
||||
|
||||
pkg_config() {
|
||||
if use server && use ssl; then
|
||||
# generate the pem file only when it does not already exist
|
||||
if [ ! -f "${QUASSEL_DIR}/quasselCert.pem" ]; then
|
||||
einfo "Generating QUASSEL SSL certificate to: \"${QUASSEL_DIR}/quasselCert.pem\""
|
||||
openssl req -x509 -nodes -days 365 -newkey rsa:2048 \
|
||||
-keyout "${QUASSEL_DIR}/quasselCert.pem" \
|
||||
-out "${QUASSEL_DIR}/quasselCert.pem"
|
||||
# permissions for the key
|
||||
chown ${QUASSEL_USER}:${QUASSEL_USER} "${QUASSEL_DIR}/quasselCert.pem"
|
||||
chmod 400 "${QUASSEL_DIR}/quasselCert.pem"
|
||||
else
|
||||
einfo "Certificate \"${QUASSEL_DIR}/quasselCert.pem\" already exists."
|
||||
einfo "Remove it if you want to create new one."
|
||||
fi
|
||||
fi
|
||||
}
|
||||
@ -1,180 +0,0 @@
|
||||
# Copyright 1999-2015 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/net-irc/quassel/quassel-0.9.2.ebuild,v 1.11 2015/02/22 18:41:23 mgorny Exp $
|
||||
|
||||
EAPI=4
|
||||
|
||||
inherit cmake-utils eutils pax-utils user versionator
|
||||
|
||||
EGIT_REPO_URI="git://git.quassel-irc.org/quassel.git"
|
||||
EGIT_BRANCH="master"
|
||||
[[ "${PV}" == "9999" ]] && inherit git-2
|
||||
|
||||
QT_MINIMAL="4.6.0"
|
||||
KDE_MINIMAL="4.4"
|
||||
|
||||
DESCRIPTION="Qt4/KDE4 IRC client supporting a remote daemon for 24/7 connectivity"
|
||||
HOMEPAGE="http://quassel-irc.org/"
|
||||
[[ "${PV}" == "9999" ]] || SRC_URI="http://quassel-irc.org/pub/${P/_/-}.tar.bz2"
|
||||
|
||||
LICENSE="GPL-3"
|
||||
KEYWORDS="amd64 ~arm ppc x86 ~amd64-linux ~sparc-solaris"
|
||||
SLOT="0"
|
||||
IUSE="ayatana crypt dbus debug kde monolithic phonon postgres +server +ssl syslog webkit X"
|
||||
|
||||
SERVER_RDEPEND="
|
||||
>=dev-qt/qtscript-${QT_MINIMAL}:4
|
||||
crypt? ( app-crypt/qca:2[openssl,qt4(+)] )
|
||||
!postgres? ( >=dev-qt/qtsql-${QT_MINIMAL}:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] )
|
||||
postgres? ( >=dev-qt/qtsql-${QT_MINIMAL}:4[postgres] )
|
||||
syslog? ( virtual/logger )
|
||||
"
|
||||
|
||||
GUI_RDEPEND="
|
||||
>=dev-qt/qtgui-${QT_MINIMAL}:4
|
||||
ayatana? ( dev-libs/libindicate-qt )
|
||||
dbus? (
|
||||
>=dev-qt/qtdbus-${QT_MINIMAL}:4
|
||||
dev-libs/libdbusmenu-qt
|
||||
)
|
||||
kde? (
|
||||
>=kde-base/kdelibs-${KDE_MINIMAL}
|
||||
|| ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-${KDE_MINIMAL} )
|
||||
ayatana? ( kde-misc/plasma-widget-message-indicator )
|
||||
)
|
||||
phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-${QT_MINIMAL}:4 ) )
|
||||
webkit? ( >=dev-qt/qtwebkit-${QT_MINIMAL}:4 )
|
||||
"
|
||||
|
||||
RDEPEND="
|
||||
>=dev-qt/qtcore-${QT_MINIMAL}:4[ssl?]
|
||||
monolithic? (
|
||||
${SERVER_RDEPEND}
|
||||
${GUI_RDEPEND}
|
||||
)
|
||||
!monolithic? (
|
||||
server? ( ${SERVER_RDEPEND} )
|
||||
X? ( ${GUI_RDEPEND} )
|
||||
)
|
||||
"
|
||||
DEPEND="${RDEPEND}
|
||||
kde? ( dev-util/automoc )"
|
||||
|
||||
DOCS="AUTHORS ChangeLog README"
|
||||
|
||||
S="${WORKDIR}/${P/_/-}"
|
||||
|
||||
REQUIRED_USE="
|
||||
|| ( X server monolithic )
|
||||
crypt? ( || ( server monolithic ) )
|
||||
postgres? ( || ( server monolithic ) )
|
||||
syslog? ( || ( server monolithic ) )
|
||||
kde? ( || ( X monolithic ) )
|
||||
phonon? ( || ( X monolithic ) )
|
||||
dbus? ( || ( X monolithic ) )
|
||||
ayatana? ( || ( X monolithic ) )
|
||||
webkit? ( || ( X monolithic ) )
|
||||
"
|
||||
|
||||
pkg_setup() {
|
||||
if use server; then
|
||||
QUASSEL_DIR=/var/lib/${PN}
|
||||
QUASSEL_USER=${PN}
|
||||
# create quassel:quassel user
|
||||
enewgroup "${QUASSEL_USER}"
|
||||
enewuser "${QUASSEL_USER}" -1 -1 "${QUASSEL_DIR}" "${QUASSEL_USER}"
|
||||
fi
|
||||
}
|
||||
|
||||
src_prepare() {
|
||||
# fix for #492756
|
||||
epatch "${FILESDIR}/missing-bsd-includes.patch" || die
|
||||
}
|
||||
|
||||
src_configure() {
|
||||
local mycmakeargs=(
|
||||
$(cmake-utils_use_with ayatana LIBINDICATE)
|
||||
$(cmake-utils_use_want X QTCLIENT)
|
||||
$(cmake-utils_use_want server CORE)
|
||||
$(cmake-utils_use_want monolithic MONO)
|
||||
$(cmake-utils_use_with webkit)
|
||||
$(cmake-utils_use_with phonon)
|
||||
$(cmake-utils_use_with kde)
|
||||
$(cmake-utils_use_with dbus)
|
||||
$(cmake-utils_use_with ssl OPENSSL)
|
||||
$(cmake-utils_use_with syslog)
|
||||
$(cmake-utils_use_with !kde OXYGEN)
|
||||
$(cmake-utils_use_with crypt)
|
||||
"-DEMBED_DATA=OFF"
|
||||
)
|
||||
|
||||
cmake-utils_src_configure
|
||||
}
|
||||
|
||||
src_install() {
|
||||
cmake-utils_src_install
|
||||
|
||||
if use server ; then
|
||||
# needs PAX marking wrt bug#346255
|
||||
pax-mark m "${ED}/usr/bin/quasselcore"
|
||||
|
||||
# prepare folders in /var/
|
||||
keepdir "${QUASSEL_DIR}"
|
||||
fowners "${QUASSEL_USER}":"${QUASSEL_USER}" "${QUASSEL_DIR}"
|
||||
|
||||
# init scripts
|
||||
newinitd "${FILESDIR}"/quasselcore.init quasselcore
|
||||
newconfd "${FILESDIR}"/quasselcore.conf quasselcore
|
||||
|
||||
# logrotate
|
||||
insinto /etc/logrotate.d
|
||||
newins "${FILESDIR}/quassel.logrotate" quassel
|
||||
fi
|
||||
}
|
||||
|
||||
pkg_postinst() {
|
||||
if use monolithic && use ssl ; then
|
||||
elog "Information on how to enable SSL support for client/core connections"
|
||||
elog "is available at http://bugs.quassel-irc.org/wiki/quassel-irc."
|
||||
fi
|
||||
|
||||
if use server; then
|
||||
einfo "If you want to generate SSL certificate remember to run:"
|
||||
einfo " emerge --config =${CATEGORY}/${PF}"
|
||||
fi
|
||||
|
||||
if use server || use monolithic ; then
|
||||
einfo "Quassel can use net-misc/oidentd package if installed on your system."
|
||||
einfo "Consider installing it if you want to run quassel within identd daemon."
|
||||
fi
|
||||
|
||||
# temporary info mesage
|
||||
if use server && [[ $(get_version_component_range 2 ${REPLACING_VERSIONS}) -lt 7 ]]; then
|
||||
echo
|
||||
ewarn "Please note that all configuration moved from"
|
||||
ewarn "/home/\${QUASSEL_USER}/.config/quassel-irc.org/"
|
||||
ewarn "to: ${QUASSEL_DIR}."
|
||||
echo
|
||||
ewarn "For migration, stop the core, move quasselcore files (pretty much"
|
||||
ewarn "everything apart from quasselclient.conf and settings.qss) into"
|
||||
ewarn "new location and then start server again."
|
||||
fi
|
||||
}
|
||||
|
||||
pkg_config() {
|
||||
if use server && use ssl; then
|
||||
# generate the pem file only when it does not already exist
|
||||
if [ ! -f "${QUASSEL_DIR}/quasselCert.pem" ]; then
|
||||
einfo "Generating QUASSEL SSL certificate to: \"${QUASSEL_DIR}/quasselCert.pem\""
|
||||
openssl req -x509 -nodes -days 365 -newkey rsa:2048 \
|
||||
-keyout "${QUASSEL_DIR}/quasselCert.pem" \
|
||||
-out "${QUASSEL_DIR}/quasselCert.pem"
|
||||
# permissions for the key
|
||||
chown ${QUASSEL_USER}:${QUASSEL_USER} "${QUASSEL_DIR}/quasselCert.pem"
|
||||
chmod 400 "${QUASSEL_DIR}/quasselCert.pem"
|
||||
else
|
||||
einfo "Certificate \"${QUASSEL_DIR}/quasselCert.pem\" already exists."
|
||||
einfo "Remove it if you want to create new one."
|
||||
fi
|
||||
fi
|
||||
}
|
||||
@ -1,175 +0,0 @@
|
||||
# Copyright 1999-2015 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/net-irc/quassel/quassel-0.9.3.ebuild,v 1.8 2015/02/22 18:41:23 mgorny Exp $
|
||||
|
||||
EAPI=5
|
||||
|
||||
inherit cmake-utils eutils pax-utils user versionator
|
||||
|
||||
EGIT_REPO_URI="git://git.quassel-irc.org/quassel.git"
|
||||
EGIT_BRANCH="master"
|
||||
[[ "${PV}" == "9999" ]] && inherit git-2
|
||||
|
||||
QT_MINIMAL="4.6.0"
|
||||
KDE_MINIMAL="4.4"
|
||||
|
||||
DESCRIPTION="Qt4/KDE4 IRC client supporting a remote daemon for 24/7 connectivity"
|
||||
HOMEPAGE="http://quassel-irc.org/"
|
||||
[[ "${PV}" == "9999" ]] || SRC_URI="http://quassel-irc.org/pub/${P/_/-}.tar.bz2"
|
||||
|
||||
LICENSE="GPL-3"
|
||||
KEYWORDS="amd64 ~arm ~ppc x86 ~amd64-linux ~sparc-solaris"
|
||||
SLOT="0"
|
||||
IUSE="ayatana crypt dbus debug kde monolithic phonon postgres +server +ssl syslog webkit X"
|
||||
|
||||
SERVER_RDEPEND="
|
||||
>=dev-qt/qtscript-${QT_MINIMAL}:4
|
||||
crypt? ( app-crypt/qca:2[openssl,qt4(+)] )
|
||||
!postgres? ( >=dev-qt/qtsql-${QT_MINIMAL}:4[sqlite] dev-db/sqlite:3[threadsafe(+),-secure-delete] )
|
||||
postgres? ( >=dev-qt/qtsql-${QT_MINIMAL}:4[postgres] )
|
||||
syslog? ( virtual/logger )
|
||||
"
|
||||
|
||||
GUI_RDEPEND="
|
||||
>=dev-qt/qtgui-${QT_MINIMAL}:4
|
||||
ayatana? ( dev-libs/libindicate-qt )
|
||||
dbus? (
|
||||
>=dev-qt/qtdbus-${QT_MINIMAL}:4
|
||||
dev-libs/libdbusmenu-qt
|
||||
)
|
||||
kde? (
|
||||
>=kde-base/kdelibs-${KDE_MINIMAL}
|
||||
|| ( kde-apps/oxygen-icons >=kde-base/oxygen-icons-${KDE_MINIMAL} )
|
||||
ayatana? ( kde-misc/plasma-widget-message-indicator )
|
||||
)
|
||||
phonon? ( || ( media-libs/phonon[qt4] >=dev-qt/qtphonon-${QT_MINIMAL}:4 ) )
|
||||
webkit? ( >=dev-qt/qtwebkit-${QT_MINIMAL}:4 )
|
||||
"
|
||||
|
||||
RDEPEND="
|
||||
>=dev-qt/qtcore-${QT_MINIMAL}:4[ssl?]
|
||||
monolithic? (
|
||||
${SERVER_RDEPEND}
|
||||
${GUI_RDEPEND}
|
||||
)
|
||||
!monolithic? (
|
||||
server? ( ${SERVER_RDEPEND} )
|
||||
X? ( ${GUI_RDEPEND} )
|
||||
)
|
||||
"
|
||||
DEPEND="${RDEPEND}
|
||||
kde? ( dev-util/automoc )"
|
||||
|
||||
DOCS="AUTHORS ChangeLog README"
|
||||
|
||||
S="${WORKDIR}/${P/_/-}"
|
||||
|
||||
REQUIRED_USE="
|
||||
|| ( X server monolithic )
|
||||
crypt? ( || ( server monolithic ) )
|
||||
postgres? ( || ( server monolithic ) )
|
||||
syslog? ( || ( server monolithic ) )
|
||||
kde? ( || ( X monolithic ) )
|
||||
phonon? ( || ( X monolithic ) )
|
||||
dbus? ( || ( X monolithic ) )
|
||||
ayatana? ( || ( X monolithic ) )
|
||||
webkit? ( || ( X monolithic ) )
|
||||
"
|
||||
|
||||
pkg_setup() {
|
||||
if use server; then
|
||||
QUASSEL_DIR=/var/lib/${PN}
|
||||
QUASSEL_USER=${PN}
|
||||
# create quassel:quassel user
|
||||
enewgroup "${QUASSEL_USER}"
|
||||
enewuser "${QUASSEL_USER}" -1 -1 "${QUASSEL_DIR}" "${QUASSEL_USER}"
|
||||
fi
|
||||
}
|
||||
|
||||
src_configure() {
|
||||
local mycmakeargs=(
|
||||
$(cmake-utils_use_with ayatana LIBINDICATE)
|
||||
$(cmake-utils_use_want X QTCLIENT)
|
||||
$(cmake-utils_use_want server CORE)
|
||||
$(cmake-utils_use_want monolithic MONO)
|
||||
$(cmake-utils_use_with webkit)
|
||||
$(cmake-utils_use_with phonon)
|
||||
$(cmake-utils_use_with kde)
|
||||
$(cmake-utils_use_with dbus)
|
||||
$(cmake-utils_use_with ssl OPENSSL)
|
||||
$(cmake-utils_use_with syslog)
|
||||
$(cmake-utils_use_with !kde OXYGEN)
|
||||
$(cmake-utils_use_with crypt)
|
||||
"-DEMBED_DATA=OFF"
|
||||
)
|
||||
|
||||
cmake-utils_src_configure
|
||||
}
|
||||
|
||||
src_install() {
|
||||
cmake-utils_src_install
|
||||
|
||||
if use server ; then
|
||||
# needs PAX marking wrt bug#346255
|
||||
pax-mark m "${ED}/usr/bin/quasselcore"
|
||||
|
||||
# prepare folders in /var/
|
||||
keepdir "${QUASSEL_DIR}"
|
||||
fowners "${QUASSEL_USER}":"${QUASSEL_USER}" "${QUASSEL_DIR}"
|
||||
|
||||
# init scripts
|
||||
newinitd "${FILESDIR}"/quasselcore.init quasselcore
|
||||
newconfd "${FILESDIR}"/quasselcore.conf quasselcore
|
||||
|
||||
# logrotate
|
||||
insinto /etc/logrotate.d
|
||||
newins "${FILESDIR}/quassel.logrotate" quassel
|
||||
fi
|
||||
}
|
||||
|
||||
pkg_postinst() {
|
||||
if use monolithic && use ssl ; then
|
||||
elog "Information on how to enable SSL support for client/core connections"
|
||||
elog "is available at http://bugs.quassel-irc.org/wiki/quassel-irc."
|
||||
fi
|
||||
|
||||
if use server; then
|
||||
einfo "If you want to generate SSL certificate remember to run:"
|
||||
einfo " emerge --config =${CATEGORY}/${PF}"
|
||||
fi
|
||||
|
||||
if use server || use monolithic ; then
|
||||
einfo "Quassel can use net-misc/oidentd package if installed on your system."
|
||||
einfo "Consider installing it if you want to run quassel within identd daemon."
|
||||
fi
|
||||
|
||||
# temporary info mesage
|
||||
if use server && [[ $(get_version_component_range 2 ${REPLACING_VERSIONS}) -lt 7 ]]; then
|
||||
echo
|
||||
ewarn "Please note that all configuration moved from"
|
||||
ewarn "/home/\${QUASSEL_USER}/.config/quassel-irc.org/"
|
||||
ewarn "to: ${QUASSEL_DIR}."
|
||||
echo
|
||||
ewarn "For migration, stop the core, move quasselcore files (pretty much"
|
||||
ewarn "everything apart from quasselclient.conf and settings.qss) into"
|
||||
ewarn "new location and then start server again."
|
||||
fi
|
||||
}
|
||||
|
||||
pkg_config() {
|
||||
if use server && use ssl; then
|
||||
# generate the pem file only when it does not already exist
|
||||
if [ ! -f "${QUASSEL_DIR}/quasselCert.pem" ]; then
|
||||
einfo "Generating QUASSEL SSL certificate to: \"${QUASSEL_DIR}/quasselCert.pem\""
|
||||
openssl req -x509 -nodes -days 365 -newkey rsa:2048 \
|
||||
-keyout "${QUASSEL_DIR}/quasselCert.pem" \
|
||||
-out "${QUASSEL_DIR}/quasselCert.pem"
|
||||
# permissions for the key
|
||||
chown ${QUASSEL_USER}:${QUASSEL_USER} "${QUASSEL_DIR}/quasselCert.pem"
|
||||
chmod 400 "${QUASSEL_DIR}/quasselCert.pem"
|
||||
else
|
||||
einfo "Certificate \"${QUASSEL_DIR}/quasselCert.pem\" already exists."
|
||||
einfo "Remove it if you want to create new one."
|
||||
fi
|
||||
fi
|
||||
}
|
||||
@ -0,0 +1 @@
|
||||
DIST dialign-2.2.1-src.tar.gz 209015 SHA256 046361bb4ca6e4ab2ac5e634cfcd673f964a887006c09c1b8bd3310fac86f519 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 WHIRLPOOL a6c5cd25e8e1f3d3738ae0a7f9eaac2509a17400cc3492b9b0b5991c08df08b586c003bbaa3f92d22ae8dd13a66488e6acbbce0aca798cfd20938cb391a02f84
|
||||
@ -0,0 +1,35 @@
|
||||
# Copyright 1999-2015 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign2/dialign2-2.2.1.ebuild,v 1.1 2015/03/29 14:22:43 jlec Exp $
|
||||
|
||||
EAPI=5
|
||||
|
||||
inherit toolchain-funcs
|
||||
|
||||
DESCRIPTION="Multiple sequence alignment"
|
||||
HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign"
|
||||
SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz"
|
||||
|
||||
SLOT="0"
|
||||
LICENSE="LGPL-2.1"
|
||||
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
|
||||
IUSE=""
|
||||
|
||||
S="${WORKDIR}"/dialign_package
|
||||
|
||||
src_compile() {
|
||||
emake -C src \
|
||||
CC="$(tc-getCC)" \
|
||||
CFLAGS="${CFLAGS} -I. -DCONS -c"
|
||||
}
|
||||
|
||||
src_install() {
|
||||
dobin src/${PN}-2
|
||||
insinto /usr/share/${PN}
|
||||
doins dialign2_dir/*
|
||||
|
||||
cat >> "${T}"/80${PN} <<- EOF
|
||||
DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}"
|
||||
EOF
|
||||
doenvd "${T}"/80${PN}
|
||||
}
|
||||
@ -0,0 +1,8 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
|
||||
<pkgmetadata>
|
||||
<maintainer>
|
||||
<email>jlec@gentoo.org</email>
|
||||
<name>Justin Lecher</name>
|
||||
</maintainer>
|
||||
</pkgmetadata>
|
||||
@ -1,4 +1,6 @@
|
||||
DIST FastTree-2.1.7.c 383551 SHA256 da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0 SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e WHIRLPOOL c4b267d8c3d92f0e76110eed31fcbdb4c142a967c3df31ca30ef816716231e1a9867094d183173af28fc3e7cb9acba81a55d455fcb8833539b2cad0667683775
|
||||
DIST FastTree-2.1.8.c 385231 SHA256 b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 WHIRLPOOL 31331c85584c2030f56955e79250c6d6c06147007c6dd10f324c207fdebd4a1b89c87dcce52e5bab6e8d89cc69656d95a51bd808f52b8d61f6d29af40a5d4976
|
||||
DIST FastTreeUPGMA-2.1.7.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496
|
||||
DIST FastTreeUPGMA-2.1.8.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496
|
||||
DIST MOTreeComparison-2.1.7.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
|
||||
DIST fasttree-2.0.1.tar.bz2 149279 SHA256 968a42f126c67f471a21c6ffe621cbedb3ed406838a3d80e799487aedc137fb4 SHA512 b6c7fb9f2eb3ac859164ce459da0a258827550020973e126b984c8f4f87a7f708f46731b6c6bb148cc3fe5cf5ddc19c7c1211b78c19880644fcfb05b65b42367 WHIRLPOOL 1aa3b811afb34b4331f411005fb7e2f9972fcefc022fa3bf68d0156f13be89ec969979c8431d0cd209f6994f8241698b10ef0599c5684e3f943edb61ae59b1bc
|
||||
DIST MOTreeComparison-2.1.8.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
|
||||
|
||||
@ -1,32 +0,0 @@
|
||||
# Copyright 1999-2010 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.0.1.ebuild,v 1.2 2010/06/20 18:20:40 xarthisius Exp $
|
||||
|
||||
EAPI="2"
|
||||
|
||||
inherit eutils toolchain-funcs
|
||||
|
||||
DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
|
||||
HOMEPAGE="http://www.microbesonline.org/fasttree/"
|
||||
#SRC_URI="http://www.microbesonline.org/fasttree/FastTree.c"
|
||||
SRC_URI="mirror://gentoo/${P}.tar.bz2"
|
||||
|
||||
LICENSE="GPL-2"
|
||||
SLOT="0"
|
||||
IUSE=""
|
||||
KEYWORDS="~amd64 ~x86"
|
||||
|
||||
pkg_setup() {
|
||||
tc-export CC
|
||||
}
|
||||
|
||||
src_prepare() {
|
||||
epatch "${FILESDIR}"/${P}-asneeded.patch
|
||||
}
|
||||
|
||||
src_install() {
|
||||
dobin FastTree FastTreeUPGMA || die
|
||||
insinto /usr/share/${PN}
|
||||
doins *.pl *.pm || die
|
||||
dodoc README* || die
|
||||
}
|
||||
@ -0,0 +1,48 @@
|
||||
# Copyright 1999-2015 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.8.ebuild,v 1.1 2015/03/29 14:30:36 jlec Exp $
|
||||
|
||||
EAPI=5
|
||||
|
||||
inherit cmake-utils
|
||||
|
||||
DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
|
||||
HOMEPAGE="http://www.microbesonline.org/fasttree/"
|
||||
SRC_URI="
|
||||
http://www.microbesonline.org/fasttree/FastTree-${PV}.c
|
||||
http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c
|
||||
http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz
|
||||
"
|
||||
|
||||
LICENSE="GPL-2"
|
||||
SLOT="0"
|
||||
KEYWORDS="~amd64 ~x86"
|
||||
IUSE="double-precision openmp cpu_flags_x86_sse3"
|
||||
|
||||
REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
|
||||
|
||||
DOCS=( README )
|
||||
|
||||
PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
|
||||
|
||||
src_unpack() {
|
||||
mkdir "${S}" || die
|
||||
cd "${S}" || die
|
||||
unpack ${A}
|
||||
cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die
|
||||
}
|
||||
|
||||
src_prepare() {
|
||||
cp "${FILESDIR}"/CMakeLists.txt . || die
|
||||
cmake-utils_src_prepare
|
||||
}
|
||||
|
||||
src_configure() {
|
||||
local mycmakeargs=(
|
||||
-DVERSION="${PV}"
|
||||
$(cmake-utils_use_has cpu_flags_x86_sse3 sse3)
|
||||
$(cmake-utils_use_use openmp)
|
||||
$(cmake-utils_use_use double-precision double)
|
||||
)
|
||||
cmake-utils_src_configure
|
||||
}
|
||||
@ -1,15 +0,0 @@
|
||||
Respect FLAGS and fix as-needed issues
|
||||
|
||||
https://bugs.gentoo.org/show_bug.cgi?id=295199
|
||||
|
||||
--- Makefile
|
||||
+++ Makefile
|
||||
@@ -1,6 +1,5 @@
|
||||
-CFLAGS := ${CFLAGS} -Wall -O3 -finline-functions -funroll-loops
|
||||
LIBS := -lm
|
||||
|
||||
all:
|
||||
- ${CC} ${CFLAGS} ${LIBS} -o FastTree FastTree.c
|
||||
- ${CC} ${CFLAGS} ${LIBS} -o FastTreeUPGMA FastTreeUPGMA.c
|
||||
+ ${CC} ${CFLAGS} ${LDFLAGS} -o FastTree FastTree.c ${LIBS}
|
||||
+ ${CC} ${CFLAGS} ${LDFLAGS} -o FastTreeUPGMA FastTreeUPGMA.c ${LIBS}
|
||||
@ -0,0 +1,25 @@
|
||||
FastTreeUPGMA-2.1.7.c | 4 ++--
|
||||
1 file changed, 2 insertions(+), 2 deletions(-)
|
||||
|
||||
diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c
|
||||
index af76cb1..4065f42 100644
|
||||
--- a/FastTreeUPGMA-2.1.7.c
|
||||
+++ b/FastTreeUPGMA-2.1.7.c
|
||||
@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
|
||||
break;
|
||||
}
|
||||
if(iArg < argc-1) {
|
||||
- fprintf(stderr, usage);
|
||||
+ fprintf(stderr, "%s", usage);
|
||||
exit(1);
|
||||
}
|
||||
|
||||
@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
|
||||
assert(first >= 0);
|
||||
/* Print the name, or the subtree of duplicate names */
|
||||
if (nameNext[first] == -1) {
|
||||
- fprintf(fp, names[uniqueFirst[node]]);
|
||||
+ fprintf(fp, "%s", names[uniqueFirst[node]]);
|
||||
} else {
|
||||
fprintf(fp,"(%s:0.0",names[first]);
|
||||
int iName = nameNext[first];
|
||||
@ -0,0 +1,25 @@
|
||||
FastTreeUPGMA-2.1.8.c | 4 ++--
|
||||
1 file changed, 2 insertions(+), 2 deletions(-)
|
||||
|
||||
diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c
|
||||
index af76cb1..4065f42 100644
|
||||
--- a/FastTreeUPGMA-2.1.8.c
|
||||
+++ b/FastTreeUPGMA-2.1.8.c
|
||||
@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
|
||||
break;
|
||||
}
|
||||
if(iArg < argc-1) {
|
||||
- fprintf(stderr, usage);
|
||||
+ fprintf(stderr, "%s", usage);
|
||||
exit(1);
|
||||
}
|
||||
|
||||
@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
|
||||
assert(first >= 0);
|
||||
/* Print the name, or the subtree of duplicate names */
|
||||
if (nameNext[first] == -1) {
|
||||
- fprintf(fp, names[uniqueFirst[node]]);
|
||||
+ fprintf(fp, "%s", names[uniqueFirst[node]]);
|
||||
} else {
|
||||
fprintf(fp,"(%s:0.0",names[first]);
|
||||
int iName = nameNext[first];
|
||||
@ -1 +1,2 @@
|
||||
DIST mafft-7.050-without-extensions-src.tgz 380375 SHA256 29ddb276bfca24f5815acc41f1e640a705bb12c9d29b7c74902ebca68cece7bc SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e WHIRLPOOL d46d7d4dfe453bfb54b9e418308772fb063bffce1d6d45d92262bee45504301daff9a6e57ecde41912a6c11852bb64510fb5ba6df04c7e79dc671e7a31444d49
|
||||
DIST mafft-7.215-without-extensions-src.tgz 393239 SHA256 22099e42274ef0078302d7cb87180880ee5fd64ef15fdcafd8c95d0018191408 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada WHIRLPOOL de43ba4107e3c1149d5ce47085bacc996393a7ef73535777439b7024eea1dce5f28c1b3c7e518f644345b7b5ea5e70fccbcaba18f16ecb9a6f5f5c31a6b5dca4
|
||||
|
||||
@ -1,191 +0,0 @@
|
||||
diff -Naur mafft-6.240/src/mafft-homologs.tmpl mafft-6.240.new/src/mafft-homologs.tmpl
|
||||
--- mafft-6.240/src/mafft-homologs.tmpl 2006-10-01 20:31:38.000000000 -0400
|
||||
+++ mafft-6.240.new/src/mafft-homologs.tmpl 2008-09-05 17:14:17.000000000 -0400
|
||||
@@ -31,11 +31,22 @@
|
||||
# -w entire sequences are subjected to BLAST search
|
||||
# (default: well-aligned region only)
|
||||
|
||||
-
|
||||
require 'getopts'
|
||||
+require 'tempfile'
|
||||
+
|
||||
+# create temporary files
|
||||
+temp_vf = Tempfile.new("_vf").path
|
||||
+temp_if = Tempfile.new("_if").path
|
||||
+temp_pf = Tempfile.new("_pf").path
|
||||
+temp_af = Tempfile.new("_af").path
|
||||
+temp_qf = Tempfile.new("_qf").path
|
||||
+temp_bf = Tempfile.new("_bf").path
|
||||
+temp_rid = Tempfile.new("_rid").path
|
||||
+temp_res = Tempfile.new("_res").path
|
||||
|
||||
-system( mafftpath + " --help > /tmp/_vf#{$$} 2>&1" )
|
||||
-pfp = File.open( "/tmp/_vf#{$$}", 'r' )
|
||||
+
|
||||
+system( mafftpath + " --help > #{temp_vf} 2>&1" )
|
||||
+pfp = File.open( "#{temp_vf}", 'r' )
|
||||
while pfp.gets
|
||||
break if $_ =~ /MAFFT v/
|
||||
end
|
||||
@@ -114,35 +125,38 @@
|
||||
mafftopt += " " + $OPT_o + " "
|
||||
end
|
||||
|
||||
-system "cat " + ARGV.to_s + " > /tmp/_if#{$$}"
|
||||
+system "cat " + ARGV.to_s + " > #{temp_if}"
|
||||
ar = mafftopt.split(" ")
|
||||
nar = ar.length
|
||||
for i in 0..(nar-1)
|
||||
if ar[i] == "--seed" then
|
||||
- system "cat #{ar[i+1]} >> /tmp/_if#{$$}"
|
||||
+ system "cat #{ar[i+1]} >> #{temp_if}"
|
||||
end
|
||||
end
|
||||
|
||||
nseq = 0
|
||||
-ifp = File.open( "/tmp/_if#{$$}", 'r' )
|
||||
+ifp = File.open( "#{temp_if}", 'r' )
|
||||
while ifp.gets
|
||||
nseq += 1 if $_ =~ /^>/
|
||||
end
|
||||
ifp.close
|
||||
|
||||
-STDERR.puts "Performing preliminary alignment .. "
|
||||
-if nseq == 1 then
|
||||
- system( "cp /tmp/_if#{$$}" + " /tmp/_pf#{$$}" )
|
||||
+if nseq >= 100 then
|
||||
+ STDERR.puts "The number of input sequences must be <100."
|
||||
+ exit
|
||||
+elsif nseq == 1 then
|
||||
+ system( "cp #{temp_if}" + " #{temp_pf}" )
|
||||
else
|
||||
+ STDERR.puts "Performing preliminary alignment .. "
|
||||
if entiresearch == 1 then
|
||||
-# system( mafftpath + " --maxiterate 1000 --localpair /tmp/_if#{$$} > /tmp/_pf#{$$}" )
|
||||
- system( mafftpath + " --maxiterate 0 --retree 2 /tmp/_if#{$$} > /tmp/_pf#{$$}" )
|
||||
+# system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" )
|
||||
+ system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" )
|
||||
else
|
||||
- system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} /tmp/_if#{$$} > /tmp/_pf#{$$}" )
|
||||
+ system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" )
|
||||
end
|
||||
end
|
||||
|
||||
-pfp = File.open( "/tmp/_pf#{$$}", 'r' )
|
||||
+pfp = File.open( "#{temp_pf}", 'r' )
|
||||
inname = []
|
||||
inseq = []
|
||||
slen = []
|
||||
@@ -155,7 +169,7 @@
|
||||
end
|
||||
pfp.close
|
||||
|
||||
-pfp = File.open( "/tmp/_if#{$$}", 'r' )
|
||||
+pfp = File.open( "#{temp_if}", 'r' )
|
||||
orname = []
|
||||
orseq = []
|
||||
nin = 0
|
||||
@@ -188,7 +202,7 @@
|
||||
#p act
|
||||
|
||||
|
||||
-afp = File.open( "/tmp/_af#{$$}", 'w' )
|
||||
+afp = File.open( "#{temp_af}", 'w' )
|
||||
|
||||
STDERR.puts "Searching .. \n"
|
||||
ids = []
|
||||
@@ -209,10 +223,10 @@
|
||||
end
|
||||
|
||||
if local == 0 then
|
||||
- command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > /tmp/_rid#{$$}"
|
||||
+ command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}"
|
||||
system command
|
||||
|
||||
- ridp = File.open( "/tmp/_rid#{$$}", 'r' )
|
||||
+ ridp = File.open( "#{temp_rid}", 'r' )
|
||||
while ridp.gets
|
||||
break if $_ =~ / RID = (.*)/
|
||||
end
|
||||
@@ -224,9 +238,9 @@
|
||||
while 1
|
||||
STDERR.printf "."
|
||||
sleep 10
|
||||
- command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > /tmp/_res#{$$}"
|
||||
+ command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}"
|
||||
system command
|
||||
- resp = File.open( "/tmp/_res#{$$}", 'r' )
|
||||
+ resp = File.open( "#{temp_res}", 'r' )
|
||||
# resp.gets
|
||||
# if $_ =~ /WAITING/ then
|
||||
# resp.close
|
||||
@@ -247,17 +261,17 @@
|
||||
else
|
||||
# puts "Not supported"
|
||||
# exit
|
||||
- qfp = File.open( "/tmp/_q#{$$}", 'w' )
|
||||
+ qfp = File.open( "#{temp_qf}", 'w' )
|
||||
qfp.puts "> "
|
||||
qfp.puts inseq[i]
|
||||
qfp.close
|
||||
- command = blastpath + " -p blastp -e #{eval} -b 1000 -m 7 -i /tmp/_q#{$$} -d #{localdb} > /tmp/_res#{$$}"
|
||||
+ command = blastpath + " -p blastp -e #{eval} -b 1000 -m 7 -i #{temp_qf} -d #{localdb} > #{temp_res}"
|
||||
system command
|
||||
- resp = File.open( "/tmp/_res#{$$}", 'r' )
|
||||
+ resp = File.open( "#{temp_res}", 'r' )
|
||||
end
|
||||
STDERR.puts " Done.\n\n"
|
||||
|
||||
- resp = File.open( "/tmp/_res#{$$}", 'r' )
|
||||
+ resp = File.open( "#{temp_res}", 'r' )
|
||||
while 1
|
||||
while resp.gets
|
||||
break if $_ =~ /<Hit_id>(.*)<\/Hit_id>/ || $_ =~ /(<Iteration_stat>)/
|
||||
@@ -310,17 +324,15 @@
|
||||
afp.close
|
||||
|
||||
STDERR.puts "Performing alignment .. "
|
||||
-system( mafftpath + mafftopt + " /tmp/_af#{$$} > /tmp/_bf#{$$}" )
|
||||
+system( mafftpath + mafftopt + " #{temp_af} > #{temp_bf}" )
|
||||
STDERR.puts "done."
|
||||
|
||||
-bfp = File.open( "/tmp/_bf#{$$}", 'r' )
|
||||
+bfp = File.open( "#{temp_bf}", 'r' )
|
||||
outseq = []
|
||||
outnam = []
|
||||
readfasta( bfp, outnam, outseq )
|
||||
bfp.close
|
||||
|
||||
-
|
||||
-
|
||||
outseq2 = []
|
||||
outnam2 = []
|
||||
|
||||
@@ -356,5 +368,3 @@
|
||||
puts ">" + outnam2[i]
|
||||
puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
|
||||
end
|
||||
-
|
||||
-system( "rm -rf /tmp/_if#{$$} /tmp/_vf#{$$} /tmp/_af#{$$} /tmp/_bf#{$$} /tmp/_pf#{$$} /tmp/_q#{$$} /tmp/_res#{$$} /tmp/_rid#{$$}" )
|
||||
diff -Naur mafft-6.240/src/mafft.tmpl mafft-6.240.new/src/mafft.tmpl
|
||||
--- mafft-6.240/src/mafft.tmpl 2007-04-03 19:16:51.000000000 -0400
|
||||
+++ mafft-6.240.new/src/mafft.tmpl 2008-09-05 17:18:04.000000000 -0400
|
||||
@@ -240,11 +240,14 @@
|
||||
shift
|
||||
done;
|
||||
|
||||
-# TMPFILE=/tmp/`basename $0`.`whoami`.$$.`date +%y%m%d%H%M%S`
|
||||
- TMPFILE=/tmp/$progname.$$
|
||||
+ # create temporary directory; terminate script in case of failure
|
||||
+ if ! TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`; then
|
||||
+ echo "Failed to create temporary directory"
|
||||
+ exit 1
|
||||
+ fi
|
||||
+
|
||||
umask 077
|
||||
- mkdir $TMPFILE || er=1
|
||||
- trap "rm -r $TMPFILE " 0
|
||||
+ trap "rm -rf $TMPFILE " 0
|
||||
if [ $# -eq 1 ]; then
|
||||
if [ -r "$1" -o "$1" = - ]; then
|
||||
cat "$1" | tr "\r" "\n" > $TMPFILE/infile
|
||||
@ -0,0 +1,65 @@
|
||||
# Copyright 1999-2015 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.215.ebuild,v 1.1 2015/03/29 14:48:58 jlec Exp $
|
||||
|
||||
EAPI=5
|
||||
|
||||
inherit eutils flag-o-matic multilib toolchain-funcs
|
||||
|
||||
EXTENSIONS="-without-extensions"
|
||||
|
||||
DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
|
||||
HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
|
||||
SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
|
||||
|
||||
LICENSE="BSD"
|
||||
SLOT="0"
|
||||
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
|
||||
IUSE="threads"
|
||||
|
||||
S="${WORKDIR}"/${P}${EXTENSIONS}
|
||||
|
||||
src_prepare() {
|
||||
# epatch "${FILESDIR}"/${PN}-7.037-respect.patch
|
||||
use threads && append-cppflags -Denablemultithread
|
||||
# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
|
||||
sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
|
||||
sed \
|
||||
-e 's:$(LDFLAGS)::g' \
|
||||
-e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \
|
||||
-e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \
|
||||
-e '/INSTALL/s: -s : :g' \
|
||||
-i core/Makefile || die
|
||||
}
|
||||
|
||||
src_compile() {
|
||||
cd core || die
|
||||
emake \
|
||||
$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
|
||||
PREFIX="${EPREFIX}"/usr \
|
||||
CC="$(tc-getCC)" \
|
||||
CFLAGS="${CFLAGS} -Wno-unused-result"
|
||||
}
|
||||
|
||||
src_test() {
|
||||
export MAFFT_BINARIES="${S}"/core
|
||||
cd test || die
|
||||
bash ../core/mafft sample > test.fftns2 || die
|
||||
bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die
|
||||
bash ../core/mafft --globalpair sample > test.gins1 || die
|
||||
bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die
|
||||
bash ../core/mafft --localpair sample > test.lins1 || die
|
||||
bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die
|
||||
|
||||
diff test.fftns2 sample.fftns2 || die
|
||||
diff test.fftnsi sample.fftnsi || die
|
||||
diff test.gins1 sample.gins1 || die
|
||||
diff test.ginsi sample.ginsi || die
|
||||
diff test.lins1 sample.lins1 || die
|
||||
}
|
||||
|
||||
src_install() {
|
||||
dodoc readme
|
||||
cd core || die
|
||||
emake PREFIX="${ED}usr" install
|
||||
}
|
||||
@ -1,3 +1,2 @@
|
||||
DIST muscle3.6_src.tar.gz 185267 RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 SHA1 e8a4998ee10a8f067fd1ba63966e32e69da62d36 SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431
|
||||
DIST muscle3.7_src.tar.gz 189907 RMD160 6eb64afd2032914781f453b925589c35e432b96c SHA1 6a3cbef3a8a00cf230f17bf90592f7108607d103 SHA256 a028f545612f9d260e35909959e98ae7aec552b1eac8806c3ae59cf1b00f7235
|
||||
DIST muscle3.8.31_src.tar.gz 515267 RMD160 18c9cf465f330a77d6a06ff9323c311a6f6be662 SHA1 2fe55db73ff4e7ac6d4ca692f8f213d1c5071dac SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad
|
||||
DIST muscle3.7_src.tar.gz 189907 SHA256 a028f545612f9d260e35909959e98ae7aec552b1eac8806c3ae59cf1b00f7235
|
||||
DIST muscle3.8.31_src.tar.gz 515267 SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce WHIRLPOOL daea88aaeaaacf5a2da68484010091ae46c69713659f92f45e5e2096af9e7d8c645d14e5b6c4c8e73e4df35a086dee823fcab6d442cd3881b773fb0113ce897d
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
|
||||
<pkgmetadata>
|
||||
<herd>sci-biology</herd>
|
||||
<herd>sci-biology</herd>
|
||||
</pkgmetadata>
|
||||
|
||||
@ -1,41 +0,0 @@
|
||||
# Copyright 1999-2010 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.6.ebuild,v 1.6 2010/06/24 19:03:18 jlec Exp $
|
||||
|
||||
inherit toolchain-funcs
|
||||
|
||||
MY_P="${PN}${PV}_src"
|
||||
DESCRIPTION="Multiple sequence comparison by log-expectation"
|
||||
HOMEPAGE="http://www.drive5.com/muscle/"
|
||||
SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
|
||||
LICENSE="public-domain"
|
||||
|
||||
SLOT="0"
|
||||
KEYWORDS="amd64 ppc x86"
|
||||
IUSE=""
|
||||
|
||||
RDEPEND="!sci-libs/libmuscle"
|
||||
DEPEND="${RDEPEND}"
|
||||
|
||||
S="${WORKDIR}/${MY_P}"
|
||||
|
||||
src_unpack() {
|
||||
unpack ${A}
|
||||
sed -i \
|
||||
"s:-static::g" \
|
||||
"${S}/Makefile"
|
||||
sed -i \
|
||||
"/strip/d" \
|
||||
"${S}/Makefile"
|
||||
}
|
||||
|
||||
src_compile() {
|
||||
emake \
|
||||
GPP="$(tc-getCXX)" \
|
||||
CFLAGS="${CXXFLAGS}" \
|
||||
|| die "make failed"
|
||||
}
|
||||
|
||||
src_install() {
|
||||
DESTTREE="/usr" dobin muscle
|
||||
}
|
||||
@ -1,41 +0,0 @@
|
||||
# Copyright 1999-2010 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.7.ebuild,v 1.3 2010/06/24 20:47:35 angelos Exp $
|
||||
|
||||
inherit toolchain-funcs
|
||||
|
||||
MY_P="${PN}${PV}_src"
|
||||
DESCRIPTION="Multiple sequence comparison by log-expectation"
|
||||
HOMEPAGE="http://www.drive5.com/muscle/"
|
||||
SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
|
||||
|
||||
LICENSE="public-domain"
|
||||
SLOT="0"
|
||||
KEYWORDS="amd64 ~ppc ~x86"
|
||||
IUSE=""
|
||||
|
||||
RDEPEND="!sci-libs/libmuscle"
|
||||
DEPEND="${RDEPEND}"
|
||||
|
||||
S="${WORKDIR}"
|
||||
|
||||
src_unpack() {
|
||||
unpack ${A}
|
||||
sed -i \
|
||||
"s:-static::g" \
|
||||
"${S}/Makefile"
|
||||
sed -i \
|
||||
"/strip/d" \
|
||||
"${S}/Makefile"
|
||||
}
|
||||
|
||||
src_compile() {
|
||||
emake \
|
||||
GPP="$(tc-getCXX)" \
|
||||
CFLAGS="${CXXFLAGS}" \
|
||||
|| die "make failed"
|
||||
}
|
||||
|
||||
src_install() {
|
||||
DESTTREE="/usr" dobin muscle
|
||||
}
|
||||
@ -1,2 +1,3 @@
|
||||
DIST phylip-3.67.tar.gz 1467526 SHA256 089f31c0519b1af162628c02d4ff78570b42cd261f39b87c6406733f2f759b5d
|
||||
DIST phylip-3.69.tar.gz 1511935 SHA256 27947ce8dab4416e4823db38b3d1b0bf17bc545b6907cf09dcf6177df94c1a8f SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d WHIRLPOOL 25c45ac2a96278eaef9a62aecc367aa32a894df0cd5aff9b626abd013ecbe52f9d4bdaf7805ba5c5d8699f9a74d3d26cfe6e1c1b22960c03061171625d16415f
|
||||
DIST phylip-3.696.tar.gz 3955721 SHA256 cd0a452ca51922142ad06d585e2ef98565536a227cbd2bd47a2243af72c84a06 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be WHIRLPOOL 7d4d4bd703ecd84b7570c937484c15f52643221ca178fb494f81b18991149fc2f8d1c8c5b99b57e20ada0bef7e93dcb15c55410f8f1012b1656419fab19b3cab
|
||||
|
||||
@ -1,2 +1,3 @@
|
||||
DIST prank.source.140603.tgz 150346 SHA256 9a48064132c01b6dba1eec90279172bf6c13d96b3f1b8dd18297b1a53d17dec6 SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7 WHIRLPOOL 5884563e6035b7e5a06b064035980e9fcee1cafcf559d86c8b9c8fc23628c7e9d1ba3e153a06f7322bb536120adcc6c8d169381f95d0a491b57836ada35a0de6
|
||||
DIST prank.src.100701.tgz 115444 SHA256 2ba63fc8f998a86e6fc688170b03f831eeb8d8deda95cbf0986e8a3a3b09ec79
|
||||
DIST prank.src.111130.tgz 133330 SHA256 61473a6b7b199f2d05e35a31adf813a2813decc9aa1429de118b62a51d7aac14
|
||||
DIST prank.src.111130.tgz 133330 SHA256 61473a6b7b199f2d05e35a31adf813a2813decc9aa1429de118b62a51d7aac14 SHA512 94f382bd71d6a58fe9b87b436bdec97ed297ebf88f3074d8e2971a24dcdc4509e737161aa057be0ac15783c1cfe7ca6d0a09ad80d0247b92426134097d4b400c WHIRLPOOL 37b96f3dc0e53f7d0b70ddfc5664dc65eff4dbec322788d391c32f5d74103663b547825dcc58fe5da3b5b44086c36fcf00a3a2253e696d6212baa3958d13fc5b
|
||||
|
||||
@ -0,0 +1,37 @@
|
||||
# Copyright 1999-2015 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/prank-140603.ebuild,v 1.1 2015/03/29 13:52:32 jlec Exp $
|
||||
|
||||
EAPI=4
|
||||
|
||||
inherit eutils multilib toolchain-funcs
|
||||
|
||||
DESCRIPTION="Probabilistic Alignment Kit"
|
||||
HOMEPAGE="http://wasabiapp.org/software/prank/"
|
||||
SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
|
||||
|
||||
LICENSE="GPL-3"
|
||||
SLOT="0"
|
||||
IUSE=""
|
||||
KEYWORDS="~amd64 ~x86"
|
||||
|
||||
S="${WORKDIR}/${PN}-msa/src"
|
||||
|
||||
src_prepare() {
|
||||
sed \
|
||||
-e "s/\$(LINK)/& \$(LDFLAGS)/" \
|
||||
-e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
|
||||
-i Makefile || die
|
||||
}
|
||||
|
||||
src_compile() {
|
||||
emake \
|
||||
LINK="$(tc-getCXX)" \
|
||||
CXX="$(tc-getCXX)" \
|
||||
CFLAGS="${CFLAGS}" \
|
||||
CXXFLAGS="${CXXFLAGS}"
|
||||
}
|
||||
|
||||
src_install() {
|
||||
dobin ${PN}
|
||||
}
|
||||
@ -1,2 +1 @@
|
||||
DIST probcons_v1_10.tar.gz 43004 RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 SHA1 773d82f6883202ec41e5dee39713b5db649ef5b0 SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518
|
||||
DIST probcons_v1_12.tar.gz 43200 RMD160 4d7d9a89c2c95f22056719c8349216ca1ba635c9 SHA1 ee6ce81777c9ce366f575ab4096ff07f39af9829 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383
|
||||
DIST probcons_v1_12.tar.gz 43200 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383
|
||||
|
||||
@ -1,21 +0,0 @@
|
||||
diff -urN probcons.orig/Makefile probcons/Makefile
|
||||
--- probcons.orig/Makefile 2006-02-21 12:14:37.000000000 -0800
|
||||
+++ probcons/Makefile 2006-02-21 12:15:15.000000000 -0800
|
||||
@@ -15,6 +15,8 @@
|
||||
# c) RELEASE mode
|
||||
################################################################################
|
||||
|
||||
+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
|
||||
+
|
||||
OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
|
||||
|
||||
# debug mode
|
||||
@@ -25,7 +27,7 @@
|
||||
|
||||
# release mode
|
||||
#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
|
||||
-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
|
||||
+CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
|
||||
|
||||
################################################################################
|
||||
# 3) Dependencies
|
||||
@ -1,5 +1,5 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
|
||||
<pkgmetadata>
|
||||
<herd>sci-biology</herd>
|
||||
<herd>sci-biology</herd>
|
||||
</pkgmetadata>
|
||||
|
||||
@ -1,46 +0,0 @@
|
||||
# Copyright 1999-2010 Gentoo Foundation
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/probcons-1.10.ebuild,v 1.3 2010/06/17 09:46:52 jlec Exp $
|
||||
|
||||
inherit eutils toolchain-funcs
|
||||
|
||||
MY_P="${PN}_v${PV/./_}"
|
||||
DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
|
||||
HOMEPAGE="http://probcons.stanford.edu/"
|
||||
SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
|
||||
LICENSE="public-domain"
|
||||
SLOT="0"
|
||||
KEYWORDS="x86"
|
||||
IUSE=""
|
||||
# Gnuplot is explicitly runtime-only, it's run using system()
|
||||
RDEPEND="
|
||||
!sci-geosciences/gmt
|
||||
sci-visualization/gnuplot"
|
||||
DEPEND=""
|
||||
S="${WORKDIR}/${PN}"
|
||||
|
||||
src_unpack() {
|
||||
unpack ${A}
|
||||
epatch ${FILESDIR}/${PV}-fix-cxxflags.patch
|
||||
}
|
||||
|
||||
src_compile() {
|
||||
emake \
|
||||
CXX="$(tc-getCXX)" \
|
||||
OPT_CXXFLAGS="${CXXFLAGS}" \
|
||||
|| die "make failed"
|
||||
}
|
||||
|
||||
src_install() {
|
||||
DESTTREE="/usr" dobin probcons project makegnuplot
|
||||
# Overlap with imagemagick
|
||||
DESTTREE="/usr" newbin compare compare-probcons
|
||||
dodoc README
|
||||
}
|
||||
|
||||
pkg_postinst() {
|
||||
ewarn "The 'compare' binary is installed as 'compare-probcons'"
|
||||
ewarn "to avoid overlap with other packages."
|
||||
einfo "You may also want to download the user manual"
|
||||
einfo "from http://probcons.stanford.edu/manual.pdf"
|
||||
}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in new issue