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Sync with portage [Sun Mar 29 19:35:13 MSK 2015].

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root 2015-03-29 19:35:14 +03:00
parent fbdb80ed7e
commit 1222e5eafd
108 changed files with 722 additions and 1274 deletions
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4
app-admin/lib_users/lib_users-0.9.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/app-admin/lib_users/lib_users-0.9.ebuild,v 1.4 2015/03/02 09:29:29 ago Exp $
# $Header: /var/cvsroot/gentoo-x86/app-admin/lib_users/lib_users-0.9.ebuild,v 1.5 2015/03/29 14:09:45 zlogene Exp $
EAPI=5
@ -14,7 +14,7 @@ SRC_URI="http://schwarzvogel.de/pkgs/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="alpha amd64 hppa ppc ~x86 ~amd64-linux ~x86-linux"
KEYWORDS="alpha amd64 hppa ppc x86 ~amd64-linux ~x86-linux"
IUSE="test"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"

7
dev-libs/DirectFB/DirectFB-1.7.6.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-libs/DirectFB/DirectFB-1.7.6.ebuild,v 1.4 2015/02/16 07:58:33 vapier Exp $
# $Header: /var/cvsroot/gentoo-x86/dev-libs/DirectFB/DirectFB-1.7.6.ebuild,v 1.5 2015/03/29 14:01:19 pacho Exp $
EAPI=5
inherit autotools eutils toolchain-funcs
@ -32,7 +32,7 @@ SRC_URI="http://directfb.org/downloads/Core/${PN}-${PV:0:3}/${P}.tar.gz
LICENSE="LGPL-2.1"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 -mips ~ppc ~ppc64 ~sh -sparc ~x86"
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 ${IUV} ${IUD}"
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 ${IUV} ${IUD}"
REQUIRED_USE="gles2? ( opengl )"
# ffmpeg useflag broken
@ -53,7 +53,6 @@ RDEPEND="
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? (
@ -152,7 +151,7 @@ src_configure() {
$(use_enable tiff) \
$(use_enable imlib2) \
$(use_enable pnm) \
$(use_enable svg) \
--disable-svg \
$(use_enable mpeg2) \
$(use_enable mpeg3 libmpeg3) \
--disable-flash \

6
dev-qt/qt-creator/qt-creator-2.8.1.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qt-creator/qt-creator-2.8.1.ebuild,v 1.6 2015/01/18 04:56:40 pesa Exp $
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qt-creator/qt-creator-2.8.1.ebuild,v 1.7 2015/03/29 13:57:41 pesa Exp $
EAPI=5
@ -14,8 +14,8 @@ LICENSE="LGPL-2.1"
if [[ ${PV} == *9999* ]]; then
inherit git-2
EGIT_REPO_URI="git://gitorious.org/${PN}/${PN}.git
https://git.gitorious.org/${PN}/${PN}.git"
EGIT_REPO_URI="git://code.qt.io/${PN}/${PN}.git
https://code.qt.io/git/${PN}/${PN}.git"
else
MY_PV=${PV/_/-}
MY_P=${PN}-${MY_PV}-src

6
dev-qt/qt-creator/qt-creator-3.2.2.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qt-creator/qt-creator-3.2.2.ebuild,v 1.5 2015/02/18 18:31:41 pesa Exp $
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qt-creator/qt-creator-3.2.2.ebuild,v 1.6 2015/03/29 13:57:41 pesa Exp $
EAPI=5
@ -15,8 +15,8 @@ LICENSE="|| ( LGPL-2.1 LGPL-3 )"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
EGIT_REPO_URI=(
"git://gitorious.org/${PN}/${PN}.git"
"https://git.gitorious.org/${PN}/${PN}.git"
"git://code.qt.io/${PN}/${PN}.git"
"https://code.qt.io/git/${PN}/${PN}.git"
)
else
MY_PV=${PV/_/-}

6
dev-qt/qt-creator/qt-creator-3.3.2.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qt-creator/qt-creator-3.3.2.ebuild,v 1.2 2015/03/18 20:43:28 pesa Exp $
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qt-creator/qt-creator-3.3.2.ebuild,v 1.3 2015/03/29 13:57:41 pesa Exp $
EAPI=5
@ -15,8 +15,8 @@ LICENSE="|| ( LGPL-2.1 LGPL-3 )"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
EGIT_REPO_URI=(
"git://gitorious.org/${PN}/${PN}.git"
"https://git.gitorious.org/${PN}/${PN}.git"
"git://code.qt.io/${PN}/${PN}.git"
"https://code.qt.io/git/${PN}/${PN}.git"
)
else
MY_PV=${PV/_/-}

6
dev-qt/qttranslations/qttranslations-5.4.1.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qttranslations/qttranslations-5.4.1.ebuild,v 1.2 2015/03/08 14:03:31 pesa Exp $
# $Header: /var/cvsroot/gentoo-x86/dev-qt/qttranslations/qttranslations-5.4.1.ebuild,v 1.3 2015/03/29 14:31:05 pesa Exp $
EAPI=5
@ -18,6 +18,6 @@ IUSE=""
DEPEND="
>=dev-qt/linguist-tools-${PV}:5
>=dev-qt/qtcore-${PV}:5[debug=]
>=dev-qt/qtcore-${PV}:5
"
RDEPEND="${DEPEND}"
RDEPEND=""

1
media-fonts/corefonts/Manifest
View file

@ -9,4 +9,5 @@ DIST impact32.exe 173288 SHA256 6061ef3b7401d9642f5dfdb5f2b376aa14663f6275e60a51
DIST times32.exe 661728 SHA256 db56595ec6ef5d3de5c24994f001f03b2a13e37cee27bc25c58f6f43e8f807ab SHA512 6035b971290cd0795389c2e8a0f02d2f079468e197a1db791189519e12aaf3fcdaf6e8842a7eeca386ad7f48f85a0b07cc5480b98ee06b0529688fd5550d3ee2 WHIRLPOOL 62306ceb9e50a99099e1334c64a71ece8b5a0227d443f5a9527272b1c51a24e058130999a1b2ab7b1d80e30b910f4ecfe90aebfe6a7eef1852f35f37415000a2
DIST trebuc32.exe 357200 SHA256 5a690d9bb8510be1b8b4fe49f1f2319651fe51bbe54775ddddd8ef0bd07fdac9 SHA512 4ba8afac0a419e30286f5b209b9fabf41aa480ceabb1bf3141deb775793510db826ba915b67fdfe3423d227c3e640bf7d682b26c0ce90f3c0e2cdf8d4831537e WHIRLPOOL 645030fdf78d9c327218231ef2d9e2b5a6cde6ddd4a7ae0361963dd2f67e6a3454543c061d93167451fb0e82a1fe94204e6542c5fa01ed06ae421a61733ac7e0
DIST verdan32.exe 351992 SHA256 c1cb61255e363166794e47664e2f21af8e3a26cb6346eb8d2ae2fa85dd5aad96 SHA512 96749fd17e4efeccdd467cb8f42ce30fc3a9e86eceef8b9c0934a4693d12944b54864006c5852c0d641a5c7b250553e5c6c21d716e446d02ef392299c7833d58 WHIRLPOOL 3872c60c371220c186a99834f5c9af593f0d7a3d84dffdf18864a623a42b7510cf9e46171ea9bb548d0d1803e7eb0107abcbfd4792be4ea20e92bf54b7f11919
DIST wd97vwr32.exe 3953640 SHA256 f61126a6d17b2d126a7f31b142504dce4934f7989c55f1c13c6477b3fe80b3d2 SHA512 e5db496471970e358af5fdb6d02853fd45bfca1aa89d49ba8644622c28610f09a4b85c2387407b9d33a4055965e0b5e184704c161741ac69250327449da12122 WHIRLPOOL b46516a4f4bdba1eac696ae604ad06691eb2fa3a4d3e9de8ca336dcd1e3a745a8d24bd448fb07854586712dd0fd8029db6147c93f5268f2ef4c4e8397edc3469
DIST webdin32.exe 185072 SHA256 64595b5abc1080fba8610c5c34fab5863408e806aafe84653ca8575bed17d75a SHA512 2784ce1cee66f0f00f77d84d7aaa52a44d017245e0269558729003205c10a5e5368f9909beee733e77e202730b3cee2b2357fdbdb597a0023c6412e050b3a3ad WHIRLPOOL 1fc9a10d40bf4a81384897dcdcd08d8dfbb5e8ddf5f93f721a80a2462a49dae65d16c88f9ef0b477d13eafb5a9af110400350e8852213ed5e867681983e10d9e

8
media-fonts/corefonts/corefonts-1-r6.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2014 Gentoo Foundation
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/media-fonts/corefonts/corefonts-1-r6.ebuild,v 1.3 2014/01/18 12:17:10 vapier Exp $
# $Header: /var/cvsroot/gentoo-x86/media-fonts/corefonts/corefonts-1-r6.ebuild,v 1.4 2015/03/29 14:22:51 yngwin Exp $
inherit font
@ -39,7 +39,5 @@ src_install() {
font_src_install
# The license explicitly states that the license must be distributed with the
# fonts. The only way to do that for the binpkg is to include it.
# We just have to copy it from the portdir because it's not actually inside
# upstream's own files...
dodoc "${PORTDIR}"/licenses/"${LICENSE}"
dodoc licen.txt
}

28
media-fonts/corefonts/corefonts-1-r5.ebuild → media-fonts/corefonts/corefonts-1-r7.ebuild
View file

@ -1,30 +1,28 @@
# Copyright 1999-2014 Gentoo Foundation
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/media-fonts/corefonts/corefonts-1-r5.ebuild,v 1.2 2014/01/18 12:17:10 vapier Exp $
# $Header: /var/cvsroot/gentoo-x86/media-fonts/corefonts/corefonts-1-r7.ebuild,v 1.1 2015/03/29 14:22:51 yngwin Exp $
EAPI=5
inherit font
DESCRIPTION="Microsoft's TrueType core fonts"
HOMEPAGE="http://corefonts.sourceforge.net/"
SRC_URI="mirror://sourceforge/corefonts/andale32.exe
mirror://sourceforge/corefonts/arial32.exe
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/times32.exe
mirror://sourceforge/corefonts/trebuc32.exe
mirror://sourceforge/corefonts/verdan32.exe
mirror://sourceforge/corefonts/webdin32.exe"
mirror://sourceforge/corefonts/webdin32.exe
mirror://sourceforge/corefonts/wd97vwr32.exe"
LICENSE="MSttfEULA"
SLOT="0"
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"
IUSE="X"
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"
IUSE="X tahoma"
DEPEND="app-arch/cabextract"
RDEPEND=""
S=${WORKDIR}
FONT_S=${WORKDIR}
@ -36,13 +34,15 @@ src_unpack() {
cabextract --lowercase "${DISTDIR}"/${exe} > /dev/null \
|| die "failed to unpack ${exe}"
done
if use tahoma; then
cabextract -F 'tahoma.ttf' "${WORKDIR}/viewer1.cab" > /dev/null \
|| die "failed to unpack tahoma.ttf"
fi
}
src_install() {
font_src_install
# The license explicitly states that the license must be distributed with the
# fonts. The only way to do that for the binpkg is to include it.
# We just have to copy it from the portdir because it's not actually inside
# upstream's own files...
dodoc "${PORTDIR}"/licenses/"${LICENSE}"
dodoc license.txt
}

6
media-fonts/corefonts/metadata.xml
View file

@ -1,5 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>fonts</herd>
<herd>fonts</herd>
<use>
<flag name='tahoma'>Also install the Tahoma font. Due to the lack of a free
bold variant, this may render badly. See bug 184790.</flag>
</use>
</pkgmetadata>

2
media-gfx/hp2xx/Manifest
View file

@ -1 +1 @@
DIST hp2xx-3.4.4.tar.gz 610330 SHA256 47b72fb386a189b52f07e31e424c038954c4e0ce405803841bed742bab488817
DIST hp2xx-3.4.4.tar.gz 610330 SHA256 47b72fb386a189b52f07e31e424c038954c4e0ce405803841bed742bab488817 SHA512 ccfe4a23ca482471506e59d6d459ce3ed56d9d775613e3238bd82d11cf4ea0595bf57ff95b3bd22a674865ec7f07dc63c1bcf0deb2a430b7ae241734c7e57ccd WHIRLPOOL ee3415eadaef3065239859de414d78f6619feef9e70c80a53fc835b52a2acb476645d7040880d2ab480cd92b53f002f58da7a6774bc436a5bfe587acc6b38f00

14
media-gfx/hp2xx/files/hp2xx-3.4.4-docbuild.patch Normal file
View file

@ -0,0 +1,14 @@
https://bugs.gentoo.org/attachment.cgi?id=399898
Only first hunk preserved.
diff -ruN hp2xx-3.4.4-r0/doc/hp2xxinf.tex hp2xx-3.4.4-r3/doc/hp2xxinf.tex
--- hp2xx-3.4.4-r0/doc/hp2xxinf.tex 2003-06-21 17:41:16.000000000 +0200
+++ hp2xx-3.4.4-r3/doc/hp2xxinf.tex 2015-03-27 20:36:32.000000000 +0100
@@ -92,7 +92,7 @@
@page
@tex
{\parskip=0pt
-\hfill mk\@daveg.com\par
+\hfill mk@@daveg.com\par
\hfill {\it Using HP2XX}, \manvers\par
\hfill \TeX{}info \texinfoversion\par
}

70
media-gfx/hp2xx/hp2xx-3.4.4-r1.ebuild Normal file
View file

@ -0,0 +1,70 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $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 $
EAPI=4
inherit eutils base
DESCRIPTION="Versatile tool to convert Hewlett-Packard's HP-GL plotter language into other graphics formats"
HOMEPAGE="http://www.gnu.org/software/hp2xx/"
SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE="X jpeg png tiff"
RDEPEND="
png? ( media-libs/libpng sys-libs/zlib )
tiff? ( media-libs/tiff )
jpeg? ( virtual/jpeg )
X? ( x11-libs/libX11 )"
DEPEND="${RDEPEND}
sys-apps/texinfo"
PATCHES=( "${FILESDIR}"/${P}-r1.patch
"${FILESDIR}"/${P}-docbuild.patch )
src_prepare() {
base_src_prepare
cp -v makes/generic.mak sources/Makefile || die
}
src_compile() {
cd "${S}/sources" || die
export PREVIEWER="no_prev"
export EX_SRC=
export EX_OBJ=
export EX_DEFS=-DUNIX
export ALL_LIBS=-lm
use X && \
PREVIEWER="to_x11" \
EX_DEFS="-DHAS_UNIX_X11" \
ALL_LIBS="${ALL_LIBS} -lX11"
use jpeg && \
EX_SRC="${EX_SRC} to_jpg.c" \
EX_OBJ="${EX_OBJ} to_jpg.o" \
EX_DEFS="${EX_DEFS} -DJPG" \
ALL_LIBS="${ALL_LIBS} -ljpeg"
use png && \
EX_SRC="${EX_SRC} png.c to_png.c" \
EX_OBJ="${EX_OBJ} png.o to_png.o" \
EX_DEFS="${EX_DEFS} -DPNG" \
ALL_LIBS="${ALL_LIBS} -lpng"
use tiff && \
EX_SRC="${EX_SRC} to_tif.c" \
EX_OBJ="${EX_OBJ} to_tif.o" \
EX_DEFS="${EX_DEFS} -DTIF" \
ALL_LIBS="${ALL_LIBS} -ltiff"
emake all
}
src_install() {
dodir /usr/bin /usr/share/info /usr/share/man/man1
make prefix="${D}/usr" \
mandir="${D}/usr/share/man" \
infodir="${D}/usr/share/info" \
install || die
}

4
media-libs/libextractor/libextractor-1.3.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/media-libs/libextractor/libextractor-1.3.ebuild,v 1.6 2015/03/28 21:41:24 ago Exp $
# $Header: /var/cvsroot/gentoo-x86/media-libs/libextractor/libextractor-1.3.ebuild,v 1.7 2015/03/29 14:30:55 zlogene Exp $
EAPI=5
inherit eutils flag-o-matic multilib toolchain-funcs
@ -11,7 +11,7 @@ SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="amd64 ~arm ppc ~ppc64 ~x86"
KEYWORDS="amd64 ~arm ppc ~ppc64 x86"
IUSE="+archive +bzip2 ffmpeg flac gif gsf gtk jpeg mp4 +magic midi mpeg tidy tiff vorbis +zlib" # test
RESTRICT="test"

2
metadata/dtd/timestamp.chk
View file

@ -1 +1 @@
Sun, 29 Mar 2015 13:37:00 +0000
Sun, 29 Mar 2015 16:06:53 +0000

2
metadata/glsa/timestamp.chk
View file

@ -1 +1 @@
Sun, 29 Mar 2015 13:37:00 +0000
Sun, 29 Mar 2015 16:06:53 +0000

4
metadata/md5-cache/app-admin/lib_users-0.9
View file

@ -4,11 +4,11 @@ DESCRIPTION=Checks /proc for libraries being mapped but marked as deleted
EAPI=5
HOMEPAGE=http://schwarzvogel.de/software-misc.shtml
IUSE=test python_targets_python2_7 python_targets_python3_3 python_targets_python3_4
KEYWORDS=alpha amd64 hppa ppc ~x86 ~amd64-linux ~x86-linux
KEYWORDS=alpha amd64 hppa ppc x86 ~amd64-linux ~x86-linux
LICENSE=GPL-2
RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) python_targets_python3_3? ( >=dev-lang/python-3.3.2-r2:3.3 ) python_targets_python3_4? ( dev-lang/python:3.4 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,python_targets_python3_3(-)?,python_targets_python3_4(-)?,-python_single_target_python2_7(-),-python_single_target_python3_3(-),-python_single_target_python3_4(-)]
REQUIRED_USE=|| ( python_targets_python2_7 python_targets_python3_3 python_targets_python3_4 )
SLOT=0
SRC_URI=http://schwarzvogel.de/pkgs/lib_users-0.9.tar.gz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multibuild 6d4858dc00f8bc51caf3f957f8430eb0 multilib 3bf24e6abb9b76d9f6c20600f0b716bf python-r1 6d3a3cb5705b9fff1aeb7cfa4e3336fe python-utils-r1 096f8247eae93026af13ab88cf4305cd toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=b8e1ca8cf60590ae0c2b6edf08faed3a
_md5_=6684bff2399bac7c0bf585461c6b1eb3

8
metadata/md5-cache/dev-libs/DirectFB-1.7.6
View file

@ -1,14 +1,14 @@
DEFINED_PHASES=configure install postinst prepare
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
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
DESCRIPTION=Thin library on top of the Linux framebuffer devices
EAPI=5
HOMEPAGE=http://www.directfb.org/
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
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
KEYWORDS=~alpha ~amd64 ~arm ~hppa ~ia64 -mips ~ppc ~ppc64 ~sh -sparc ~x86
LICENSE=LGPL-2.1
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 )
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 )
REQUIRED_USE=gles2? ( opengl )
SLOT=0
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
_eclasses_=autotools 999c8f6cf5d91495cb0779588f20716c eutils 9fb270e417e0e83d64ca52586c4a79de libtool 52d0e17251d04645ffaa61bfdd858944 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=02febf0ef94d2d769f85f6125e3c0bab
_md5_=1cf513e5f06029a09989ebbff91c8a5a

2
metadata/md5-cache/dev-qt/qt-creator-2.8.1
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@ -11,4 +11,4 @@ RDEPEND==dev-libs/botan-1.10*[threads] >=dev-qt/designer-4.8.5:4 >=dev-qt/qtcore
SLOT=0
SRC_URI=http://download.qt.io/official_releases/qtcreator/2.8/2.8.1/qt-creator-2.8.1-src.tar.gz
_eclasses_=base 87f7447ccfc06fd0729ff4684e11e0d6 eutils 9fb270e417e0e83d64ca52586c4a79de l10n 33bde4fb0cfd3a21a277b66bfd837e19 multilib 3bf24e6abb9b76d9f6c20600f0b716bf qmake-utils ea709b525d28e3087eddedb2f884dbbe qt4-r2 7199e3db5b5908325487d379c6f67cf0 toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=1e698e8f2b13b4b338ef75bfbc6c5a93
_md5_=657081fbbd50e1a9e862ce7d3f54ae8f

2
metadata/md5-cache/dev-qt/qt-creator-3.2.2
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@ -11,4 +11,4 @@ RDEPEND==dev-libs/botan-1.10*[threads] >=dev-qt/designer-4.8.5:4 >=dev-qt/qtcore
SLOT=0
SRC_URI=http://download.qt.io/official_releases/qtcreator/3.2/3.2.2/qt-creator-opensource-src-3.2.2.tar.gz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de l10n 33bde4fb0cfd3a21a277b66bfd837e19 multilib 3bf24e6abb9b76d9f6c20600f0b716bf qmake-utils ea709b525d28e3087eddedb2f884dbbe toolchain-funcs b99aa37f734b5d426efd83b2f271cece virtualx 73cfc129b4b9ba23aed1abb10c825d86
_md5_=e1a37e3b8a1224d0343b2fef9936761f
_md5_=5a62300e548b5c44a6701dfaf7b6510d

2
metadata/md5-cache/dev-qt/qt-creator-3.3.2
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@ -11,4 +11,4 @@ RDEPEND==dev-libs/botan-1.10*[threads] >=dev-qt/designer-5.3.2:5 >=dev-qt/qtconc
SLOT=0
SRC_URI=http://download.qt.io/official_releases/qtcreator/3.3/3.3.2/qt-creator-opensource-src-3.3.2.tar.gz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de l10n 33bde4fb0cfd3a21a277b66bfd837e19 multilib 3bf24e6abb9b76d9f6c20600f0b716bf qmake-utils ea709b525d28e3087eddedb2f884dbbe toolchain-funcs b99aa37f734b5d426efd83b2f271cece virtualx 73cfc129b4b9ba23aed1abb10c825d86
_md5_=244d6ee1c63562ae048f8a9a12dfc001
_md5_=3e55f8e0a9c0756157de8de4e4b5b07e

6
metadata/md5-cache/dev-qt/qttranslations-5.4.1
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@ -1,14 +1,14 @@
DEFINED_PHASES=compile configure install postinst postrm prepare test unpack
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=] )
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=] )
DESCRIPTION=Translation files for the Qt5 framework
EAPI=5
HOMEPAGE=https://www.qt.io/ https://qt-project.org/
IUSE=test debug test
KEYWORDS=~amd64 ~arm ~hppa ~x86
LICENSE=|| ( LGPL-2.1 LGPL-3 )
RDEPEND=>=dev-qt/linguist-tools-5.4.1:5 >=dev-qt/qtcore-5.4.1:5[debug=] dev-qt/qtchooser
RDEPEND=dev-qt/qtchooser
RESTRICT=test
SLOT=5
SRC_URI=http://download.qt.io/official_releases/qt/5.4/5.4.1/submodules/qttranslations-opensource-src-5.4.1.tar.xz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multilib 3bf24e6abb9b76d9f6c20600f0b716bf qt5-build 4203236286fd6aee7ce37d52ef232052 toolchain-funcs b99aa37f734b5d426efd83b2f271cece virtualx 73cfc129b4b9ba23aed1abb10c825d86
_md5_=ed8dffaf0979ac5d7544f50b0bf9ca1e
_md5_=7608775a0eccc5c8d3dcb3749e1adb2d

11
metadata/md5-cache/media-fonts/corefonts-1-r5
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@ -1,11 +0,0 @@
DEFINED_PHASES=install postinst postrm setup unpack
DEPEND=app-arch/cabextract X? ( x11-apps/mkfontdir media-fonts/encodings )
DESCRIPTION=Microsoft's TrueType core fonts
HOMEPAGE=http://corefonts.sourceforge.net/
IUSE=X X
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
LICENSE=MSttfEULA
SLOT=0
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
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de font b3239d2dc442d1717b9725e2be7cb5d6 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=849cdab8dfa335ab159a7852b38c1a34

2
metadata/md5-cache/media-fonts/corefonts-1-r6
View file

@ -8,4 +8,4 @@ LICENSE=MSttfEULA
SLOT=0
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
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de font b3239d2dc442d1717b9725e2be7cb5d6 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=b1bdc98f8f3de9c0703bab1a727d390e
_md5_=ac2eb84d08bd340b559e5f9007abd006

12
metadata/md5-cache/media-fonts/corefonts-1-r7 Normal file
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@ -0,0 +1,12 @@
DEFINED_PHASES=install postinst postrm setup unpack
DEPEND=app-arch/cabextract X? ( x11-apps/mkfontdir media-fonts/encodings )
DESCRIPTION=Microsoft's TrueType core fonts
EAPI=5
HOMEPAGE=http://corefonts.sourceforge.net/
IUSE=X tahoma X
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
LICENSE=MSttfEULA
SLOT=0
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
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de font b3239d2dc442d1717b9725e2be7cb5d6 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=68c480b473f8a05dfdac2876c0e8d178

13
metadata/md5-cache/media-gfx/hp2xx-3.4.4-r1 Normal file
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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
KEYWORDS=~x86 ~amd64
LICENSE=GPL-2
RDEPEND=png? ( media-libs/libpng sys-libs/zlib ) tiff? ( media-libs/tiff ) jpeg? ( virtual/jpeg ) X? ( x11-libs/libX11 )
SLOT=0
SRC_URI=mirror://gnu/hp2xx/hp2xx-3.4.4.tar.gz
_eclasses_=base 87f7447ccfc06fd0729ff4684e11e0d6 eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=ea0b036e5e28b246c675e9106e1b58df

4
metadata/md5-cache/media-libs/libextractor-1.3
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@ -4,11 +4,11 @@ DESCRIPTION=A library used to extract metadata from files of arbitrary type
EAPI=5
HOMEPAGE=http://www.gnu.org/software/libextractor/
IUSE=+archive +bzip2 ffmpeg flac gif gsf gtk jpeg mp4 +magic midi mpeg tidy tiff vorbis +zlib
KEYWORDS=amd64 ~arm ppc ~ppc64 ~x86
KEYWORDS=amd64 ~arm ppc ~ppc64 x86
LICENSE=GPL-3
RDEPEND=app-text/iso-codes >=dev-libs/glib-2 media-gfx/exiv2 sys-devel/libtool virtual/libiconv virtual/libintl archive? ( app-arch/libarchive ) bzip2? ( app-arch/bzip2 ) ffmpeg? ( virtual/ffmpeg ) flac? ( media-libs/flac media-libs/libogg ) gif? ( media-libs/giflib ) gsf? ( gnome-extra/libgsf ) gtk? ( x11-libs/gtk+:3 ) jpeg? ( virtual/jpeg ) mp4? ( media-libs/libmp4v2:0 ) magic? ( sys-apps/file ) midi? ( media-libs/libsmf ) mpeg? ( media-libs/libmpeg2 ) tidy? ( app-text/htmltidy ) tiff? ( media-libs/tiff:0 ) vorbis? ( media-libs/libogg media-libs/libvorbis ) zlib? ( sys-libs/zlib ) !<app-crypt/pkcrack-1.2.2-r1 !sci-biology/glimmer !sci-chemistry/pdb-extract
RESTRICT=test
SLOT=0
SRC_URI=mirror://gnu/libextractor/libextractor-1.3.tar.gz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=e0f21adfcf8c9bac52702db8969707a2
_md5_=b16bf2e09b54fa2cb589236c4c4e8db6

4
metadata/md5-cache/net-im/gajim-0.16
View file

@ -4,7 +4,7 @@ DESCRIPTION=Jabber client written in PyGTK
EAPI=5
HOMEPAGE=http://www.gajim.org/
IUSE=avahi crypt dbus gnome gnome-keyring kde idle jingle libnotify networkmanager nls spell +srv test X xhtml python_targets_python2_7
KEYWORDS=amd64 arm ~ppc ~ppc64 ~x86 ~x86-fbsd
KEYWORDS=amd64 arm ~ppc ~ppc64 x86 ~x86-fbsd
LICENSE=GPL-3
RDEPEND=python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7[sqlite,xml] ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/pygtk:2[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] x11-libs/gtk+:2 dev-python/pyasn1[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] >=dev-python/pyopenssl-0.14[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] >=dev-python/python-nbxmpp-0.5.1[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] crypt? ( app-crypt/gnupg dev-python/pycrypto[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) dbus? ( dev-python/dbus-python[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-libs/dbus-glib libnotify? ( dev-python/notify-python[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) avahi? ( net-dns/avahi[dbus,gtk,python,python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) ) gnome? ( dev-python/libgnome-python[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] dev-python/egg-python[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) gnome-keyring? ( dev-python/gnome-keyring-python[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) idle? ( x11-libs/libXScrnSaver ) jingle? ( net-libs/farstream:0.1[python,python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) kde? ( kde-base/kwalletmanager ) networkmanager? ( dev-python/dbus-python[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] net-misc/networkmanager ) spell? ( app-text/gtkspell:2 ) srv? ( || ( dev-python/libasyncns-python[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] net-dns/bind-tools ) ) xhtml? ( dev-python/docutils[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] )
REQUIRED_USE=|| ( python_targets_python2_7 ) libnotify? ( dbus ) avahi? ( dbus ) gnome? ( gnome-keyring )
@ -12,4 +12,4 @@ RESTRICT=test
SLOT=0
SRC_URI=http://www.gajim.org/downloads/0.16/gajim-0.16.tar.bz2
_eclasses_=autotools 999c8f6cf5d91495cb0779588f20716c autotools-utils 3727db64c7b960903d5033280f108080 eutils 9fb270e417e0e83d64ca52586c4a79de libtool 52d0e17251d04645ffaa61bfdd858944 multibuild 6d4858dc00f8bc51caf3f957f8430eb0 multilib 3bf24e6abb9b76d9f6c20600f0b716bf python-r1 6d3a3cb5705b9fff1aeb7cfa4e3336fe python-utils-r1 096f8247eae93026af13ab88cf4305cd toolchain-funcs b99aa37f734b5d426efd83b2f271cece versionator cd0bcdb170807e4a1984115e9d53a26f
_md5_=e57bd2f09c9286737c9a00408fafbc88
_md5_=fcc28e25f5c6bda555fdb006b76eb1bf

4
metadata/md5-cache/net-irc/quassel-0.10.0-r1
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@ -4,11 +4,11 @@ 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
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 ) )
SLOT=0
SRC_URI=http://quassel-irc.org/pub/quassel-0.10.0.tar.bz2
_eclasses_=cmake-utils 0430c386d85cec959d72640afd63ea91 eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multilib 3bf24e6abb9b76d9f6c20600f0b716bf pax-utils dfe060cb70d89757fde5c1ff8405e950 systemd 090342761f573a8280dd5aa6b0345f3b toolchain-funcs b99aa37f734b5d426efd83b2f271cece user f54e098dd38ba1c0847a13e685b87747 versionator cd0bcdb170807e4a1984115e9d53a26f
_md5_=053e9733654e4e0b3bea8b66bba42e4e
_md5_=cf5efd406839ab7caf2763db88c963b9

14
metadata/md5-cache/net-irc/quassel-0.10.1
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@ -1,14 +0,0 @@
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 ) )
SLOT=0
SRC_URI=http://quassel-irc.org/pub/quassel-0.10.1.tar.bz2
_eclasses_=cmake-utils 0430c386d85cec959d72640afd63ea91 eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multilib 3bf24e6abb9b76d9f6c20600f0b716bf pax-utils dfe060cb70d89757fde5c1ff8405e950 systemd 090342761f573a8280dd5aa6b0345f3b toolchain-funcs b99aa37f734b5d426efd83b2f271cece user f54e098dd38ba1c0847a13e685b87747 versionator cd0bcdb170807e4a1984115e9d53a26f
_md5_=cb0984023d3fc232e51733ee9d874485

14
metadata/md5-cache/net-irc/quassel-0.9.2
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@ -1,14 +0,0 @@
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=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
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
_md5_=09edbe2e54676325a964a9297d2fb8e8

14
metadata/md5-cache/net-irc/quassel-0.9.3
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@ -1,14 +0,0 @@
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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10
metadata/md5-cache/sci-biology/dialign2-2.2.1 Normal file
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@ -0,0 +1,10 @@
DEFINED_PHASES=compile install
DESCRIPTION=Multiple sequence alignment
EAPI=5
HOMEPAGE=http://bibiserv.techfak.uni-bielefeld.de/dialign
KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
LICENSE=LGPL-2.1
SLOT=0
SRC_URI=http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz
_eclasses_=multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
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10
metadata/md5-cache/sci-biology/fasttree-2.0.1
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@ -1,10 +0,0 @@
DEFINED_PHASES=install prepare setup
DESCRIPTION=Fast inference of approximately-maximum-likelihood phylogenetic trees
EAPI=2
HOMEPAGE=http://www.microbesonline.org/fasttree/
KEYWORDS=~amd64 ~x86
LICENSE=GPL-2
SLOT=0
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_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
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2
metadata/md5-cache/sci-biology/fasttree-2.1.7
View file

@ -10,4 +10,4 @@ REQUIRED_USE=?? ( double-precision cpu_flags_x86_sse3 )
SLOT=0
SRC_URI=http://www.microbesonline.org/fasttree/FastTree-2.1.7.c http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-2.1.7.c http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-2.1.7.tar.gz
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13
metadata/md5-cache/sci-biology/fasttree-2.1.8 Normal file
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@ -0,0 +1,13 @@
DEFINED_PHASES=compile configure install prepare test unpack
DEPEND=sys-devel/make >=dev-util/cmake-2.8.12 userland_GNU? ( >=sys-apps/findutils-4.4.0 )
DESCRIPTION=Fast inference of approximately-maximum-likelihood phylogenetic trees
EAPI=5
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IUSE=double-precision openmp cpu_flags_x86_sse3
KEYWORDS=~amd64 ~x86
LICENSE=GPL-2
REQUIRED_USE=?? ( double-precision cpu_flags_x86_sse3 )
SLOT=0
SRC_URI=http://www.microbesonline.org/fasttree/FastTree-2.1.8.c http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-2.1.8.c http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-2.1.8.tar.gz
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11
metadata/md5-cache/sci-biology/mafft-7.215 Normal file
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@ -0,0 +1,11 @@
DEFINED_PHASES=compile install prepare test
DESCRIPTION=Multiple sequence alignments using a variety of algorithms
EAPI=5
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LICENSE=BSD
SLOT=0
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11
metadata/md5-cache/sci-biology/muscle-3.6
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@ -1,11 +0,0 @@
DEFINED_PHASES=compile install unpack
DEPEND=!sci-libs/libmuscle
DESCRIPTION=Multiple sequence comparison by log-expectation
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11
metadata/md5-cache/sci-biology/muscle-3.7
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@ -1,11 +0,0 @@
DEFINED_PHASES=compile install unpack
DEPEND=!sci-libs/libmuscle
DESCRIPTION=Multiple sequence comparison by log-expectation
HOMEPAGE=http://www.drive5.com/muscle/
KEYWORDS=amd64 ~ppc ~x86
LICENSE=public-domain
RDEPEND=!sci-libs/libmuscle
SLOT=0
SRC_URI=http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz
_eclasses_=multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=0b4305318e9262278964760a975c934f

4
metadata/md5-cache/sci-biology/muscle-3.8.31
View file

@ -1,6 +1,6 @@
DEFINED_PHASES=install prepare
DESCRIPTION=Multiple sequence comparison by log-expectation
EAPI=3
EAPI=5
HOMEPAGE=http://www.drive5.com/muscle/
KEYWORDS=~amd64 ~ppc ~x86
LICENSE=public-domain
@ -8,4 +8,4 @@ RDEPEND=!sci-libs/libmuscle
SLOT=0
SRC_URI=http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=f91a0aa56285471f305ac474e34944da
_md5_=8ac7b0309b7dba9768262233b6bcbac0

2
metadata/md5-cache/sci-biology/paml-4.4c-r1
View file

@ -7,4 +7,4 @@ LICENSE=free-noncomm
SLOT=0
SRC_URI=http://abacus.gene.ucl.ac.uk/software/paml4.4c.tar.gz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece versionator cd0bcdb170807e4a1984115e9d53a26f
_md5_=3c450eb5b217d97a60d8c7f83ab7ebcd
_md5_=4c15fe44dde77324e853300afba7bcf0

4
metadata/md5-cache/sci-biology/phylip-3.67
View file

@ -1,6 +1,6 @@
DEFINED_PHASES=compile install
DEPEND=x11-libs/libXaw x11-proto/xproto
DESCRIPTION=PHYLIP - The PHYLogeny Inference Package
DESCRIPTION=The PHYLogeny Inference Package
HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html
KEYWORDS=amd64 ppc x86
LICENSE=freedist
@ -8,4 +8,4 @@ RDEPEND=x11-libs/libXaw
SLOT=0
SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.67.tar.gz
_eclasses_=multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=821dbf7fbb3a4aee6ecd744169af6269
_md5_=1459b8f08b530bc9966999f312c2fee7

4
metadata/md5-cache/sci-biology/phylip-3.69
View file

@ -1,6 +1,6 @@
DEFINED_PHASES=compile install
DEPEND=x11-libs/libXaw x11-proto/xproto
DESCRIPTION=PHYLIP - The PHYLogeny Inference Package
DESCRIPTION=The PHYLogeny Inference Package
HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html
KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos
LICENSE=freedist
@ -8,4 +8,4 @@ RDEPEND=x11-libs/libXaw
SLOT=0
SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz
_eclasses_=multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=7a2bbd2b7835e08d780c0e2c11f6176b
_md5_=97152766d9bb778785ac88b130ee4674

4
metadata/md5-cache/sci-biology/phylip-3.69-r1
View file

@ -1,6 +1,6 @@
DEFINED_PHASES=compile install prepare
DEPEND=x11-libs/libXaw x11-proto/xproto
DESCRIPTION=PHYLIP - The PHYLogeny Inference Package
DESCRIPTION=The PHYLogeny Inference Package
EAPI=5
HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html
KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos
@ -9,4 +9,4 @@ RDEPEND=x11-libs/libXaw
SLOT=0
SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz
_eclasses_=multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=85e758db75ad54ebedac68b7e3ad588f
_md5_=e09a6e0e6cfdf96b2fabfa1bd1929129

12
metadata/md5-cache/sci-biology/phylip-3.696 Normal file
View file

@ -0,0 +1,12 @@
DEFINED_PHASES=compile install prepare
DEPEND=x11-libs/libXaw x11-proto/xproto
DESCRIPTION=The PHYLogeny Inference Package
EAPI=5
HOMEPAGE=http://evolution.genetics.washington.edu/phylip.html
KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos
LICENSE=BSD-2
RDEPEND=x11-libs/libXaw
SLOT=0
SRC_URI=http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz
_eclasses_=multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=dfffcfd1879bb53d6714b3d2f0bae4da

4
metadata/md5-cache/sci-biology/prank-100701
View file

@ -1,10 +1,10 @@
DEFINED_PHASES=compile install prepare
DESCRIPTION=Probabilistic Alignment Kit
EAPI=4
HOMEPAGE=http://www.ebi.ac.uk/goldman-srv/prank/prank/
HOMEPAGE=http://wasabiapp.org/software/prank/
KEYWORDS=~amd64 ~x86
LICENSE=GPL-2
SLOT=0
SRC_URI=http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100701.tgz
_eclasses_=multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=d737493c1c34c5e1a5d8cee831a75322
_md5_=e6dccb6b469728927186cd5a61a49fb2

4
metadata/md5-cache/sci-biology/prank-111130
View file

@ -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

10
metadata/md5-cache/sci-biology/prank-140603 Normal file
View file

@ -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

10
metadata/md5-cache/sci-biology/probcons-1.10
View file

@ -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

10
metadata/md5-cache/sci-biology/probcons-1.12
View file

@ -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

4
metadata/md5-cache/sci-biology/probcons-1.12-r1
View file

@ -1,6 +1,6 @@
DEFINED_PHASES=compile install postinst prepare
DESCRIPTION=Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
EAPI=3
EAPI=5
HOMEPAGE=http://probcons.stanford.edu/
KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux
LICENSE=public-domain
@ -8,4 +8,4 @@ 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_=ff99fbc88d1f3d5d4af928b5bd79aa0b
_md5_=ae6434816edc7c0381cbef5eb69ce3c4

6
metadata/md5-cache/sci-biology/wise-2.4.0_alpha
View file

@ -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

4
metadata/md5-cache/sci-mathematics/maxima-5.34.1
View file

@ -4,11 +4,11 @@ DESCRIPTION=Free computer algebra environment based on Macsyma
EAPI=5
HOMEPAGE=http://maxima.sourceforge.net/
IUSE=latex emacs tk nls unicode xemacs X sbcl cmucl gcl ecls clozurecl clisp linguas_es linguas_pt linguas_pt_BR
KEYWORDS=amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos
KEYWORDS=amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos
LICENSE=GPL-2
PDEPEND=emacs? ( app-emacs/imaxima )
RDEPEND=X? ( x11-misc/xdg-utils sci-visualization/gnuplot[gd] tk? ( dev-lang/tk ) ) latex? ( virtual/latex-base ) emacs? ( virtual/emacs latex? ( app-emacs/auctex ) ) xemacs? ( app-editors/xemacs latex? ( app-emacs/auctex ) ) clisp? ( dev-lisp/clisp:= ) clozurecl? ( dev-lisp/clozurecl:= app-misc/rlwrap ) ecls? ( dev-lisp/ecls:= app-misc/rlwrap ) gcl? ( dev-lisp/gcl:= ) cmucl? ( dev-lisp/cmucl:= app-misc/rlwrap ) sbcl? ( dev-lisp/sbcl:= app-misc/rlwrap ) !clisp? ( !clozurecl? ( !ecls? ( !gcl? ( !cmucl? ( dev-lisp/sbcl:= app-misc/rlwrap ) ) ) ) )
SLOT=0
SRC_URI=mirror://sourceforge/maxima/maxima-5.34.1.tar.gz
_eclasses_=autotools 999c8f6cf5d91495cb0779588f20716c elisp-common 1aa23b3de5dae55456fa2071428eb5bf eutils 9fb270e417e0e83d64ca52586c4a79de libtool 52d0e17251d04645ffaa61bfdd858944 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=cbf0b7891a5b001c1c01f75edd9fa60d
_md5_=fd7aacb39fa0cbe17cd12d217307224d

4
metadata/md5-cache/sys-auth/polkit-qt-0.112.0-r1
View file

@ -4,7 +4,7 @@ DESCRIPTION=PolicyKit Qt4 API wrapper library
EAPI=5
HOMEPAGE=http://www.kde.org/
IUSE=debug examples +qt4 qt5
KEYWORDS=amd64 ~arm ppc ~ppc64 ~x86 ~x86-fbsd
KEYWORDS=amd64 ~arm ppc ~ppc64 x86 ~x86-fbsd
LICENSE=LGPL-2
RDEPEND=dev-libs/glib:2 >=sys-auth/polkit-0.103 qt4? ( dev-qt/qtcore:4[glib] dev-qt/qtdbus:4 dev-qt/qtgui:4[glib] ) qt5? ( dev-qt/qtcore:5 dev-qt/qtdbus:5 dev-qt/qtgui:5 dev-qt/qtwidgets:5 examples? ( dev-qt/qtxml:5 ) )
REQUIRED_USE=|| ( qt4 qt5 )
@ -12,4 +12,4 @@ RESTRICT=test
SLOT=0
SRC_URI=mirror://kde/stable/apps/KDE4.x/admin/polkit-qt-1-0.112.0.tar.bz2
_eclasses_=cmake-utils 0430c386d85cec959d72640afd63ea91 eutils 9fb270e417e0e83d64ca52586c4a79de flag-o-matic c263990f1b677b0f0be0a3299f179762 multibuild 6d4858dc00f8bc51caf3f957f8430eb0 multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=eddb49848ec5f3ecc8d11c19bf63cf46
_md5_=0b284ad2eefb9a349bf7dc5d7c0a7edd

4
metadata/md5-cache/sys-block/di-4.35
View file

@ -2,10 +2,10 @@ DEFINED_PHASES=compile configure install prepare
DESCRIPTION=Disk Information Utility
EAPI=4
HOMEPAGE=http://www.gentoo.com/di/
KEYWORDS=amd64 ppc ppc64 ~x86 ~x86-fbsd
KEYWORDS=amd64 ppc ppc64 x86 ~x86-fbsd
LICENSE=ZLIB
RESTRICT=test
SLOT=0
SRC_URI=http://www.gentoo.com/di/di-4.35.tar.gz
_eclasses_=eutils 9fb270e417e0e83d64ca52586c4a79de multilib 3bf24e6abb9b76d9f6c20600f0b716bf toolchain-funcs b99aa37f734b5d426efd83b2f271cece
_md5_=4dd551e31d6665887e1054c3ed6f2f5e
_md5_=621f6e12ecf33514e976e4ae3f346001

2
metadata/news/timestamp.chk
View file

@ -1 +1 @@
Sun, 29 Mar 2015 13:37:03 +0000
Sun, 29 Mar 2015 16:06:56 +0000

2
metadata/timestamp
View file

@ -1 +1 @@
Sun Mar 29 13:37:00 UTC 2015
Sun Mar 29 16:06:53 UTC 2015

2
metadata/timestamp.chk
View file

@ -1 +1 @@
Sun, 29 Mar 2015 14:00:01 +0000
Sun, 29 Mar 2015 16:30:01 +0000

2
metadata/timestamp.x
View file

@ -1 +1 @@
1427636101 Sun 29 Mar 2015 01:35:01 PM UTC
1427645101 Sun 29 Mar 2015 04:05:01 PM UTC

4
net-im/gajim/gajim-0.16.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/net-im/gajim/gajim-0.16.ebuild,v 1.6 2015/03/27 16:26:42 ago Exp $
# $Header: /var/cvsroot/gentoo-x86/net-im/gajim/gajim-0.16.ebuild,v 1.7 2015/03/29 13:39:04 zlogene Exp $
EAPI=5
@ -22,7 +22,7 @@ SRC_URI="
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="amd64 arm ~ppc ~ppc64 ~x86 ~x86-fbsd"
KEYWORDS="amd64 arm ~ppc ~ppc64 x86 ~x86-fbsd"
IUSE="avahi crypt dbus gnome gnome-keyring kde idle jingle libnotify networkmanager nls spell +srv test X xhtml"
REQUIRED_USE="

3
net-irc/quassel/Manifest
View file

@ -1,7 +1,4 @@
DIST quassel-0.10.0.tar.bz2 2873233 SHA256 68228ce23aa3a992add3d00cb1e8b4863d8ca64bea99c881edf6d16ff9ec7c23 SHA512 e194d4f9bbcecedfebd72c48d5f1e2a4185ff9d69134629b79e532af8f3fa9841e3cb99a6aae30e9bd79440c08487eeb23d6d6914690b90d1ae0952bb6168693 WHIRLPOOL bedd3de56e7625219a2970842ff0b073abbdc3488c8efece112c92f277386d5a3b63bde100a6e3daf2d5c0011e515e9fef81b888feec58d2a6571b4f898e8578
DIST quassel-0.10.1.tar.bz2 2872973 SHA256 0d17b7d2284d9ef29ba4dad515ec84ce41a560237b3c8e7505d0ef028e95df80 SHA512 2d94b2ebf54101393356f378fd6a4fd68b24155a3ed52b7a36e47149d89d43b884a98d712c6212f4ea1bed151a9a713de63449c793f7d3e5e09e8bb595ff14f3 WHIRLPOOL 05db2c91ff4aeeccf12a68ac655efc24f4d698e4da60d36bb8580955d9b9fcc98f7e400e058cd2f42e2ad6596a214255a30250e9da8cf89881576aac83e03a6d
DIST quassel-0.11.0.tar.bz2 2875387 SHA256 99a191b8bc2a410f7020b890ec57e0be49313f539da9f4843675bb108b0f4504 SHA512 51450559df2c0fee9a54b76a9342edb9a3b834f1f58edc556e0c1bf1f9366c846d95e7953e1b48c6ecf67ea4255b3574ed3ce537962eec222c5c03ab02852c1d WHIRLPOOL c2ffb7e052a5d412aec5d1b8bacc8cdb8144c20d62d699ca1d8972fd5e8fe6ce89da49251a02c22008061b344d9408b3f018b3b39623703b4d980c289cd5613a
DIST quassel-0.12-rc1.tar.bz2 3640851 SHA256 be2a982a2725dbebb5c4f908787b5173febcd2a7511f0a54ab6cf1a742a1464a SHA512 345325c69e26781864120bfb057e79e36b2bba391ee7a0cd700af432a83946939a308c7e90e50b959036fa9b583570147adfb6c804dad3819f6faf3d8a585166 WHIRLPOOL 571794d396fd047d6447b4c79f7031485785ded9592eb4ce5f0a86a7bda80e9d2464a4f94c07b5e591dcdc9386dfb0cadffa780d15eaf5a2258eaeb23110073b
DIST quassel-0.12_rc1-fix-ftbfs.patch 597 SHA256 f26e219f07f01508d73fe216bc1d040855aa35645828c070e121c0409b131fcc SHA512 d0239a12dc5b0348ffdca232565f610ed92aa2e1a055096262126ec3caafbd3b4599b94dd30b52473a663f579fccbe40ebbe3ded62de88c3c929b2b0c4253a6b WHIRLPOOL 044ef09bdf9f067b17153c61d0125effe9a4a1a002c67d1864ba749e9a43025192dfe0ca136cbb5b722b519015497b7215aec07974e15e529d5d2e011571db43
DIST quassel-0.9.2.tar.bz2 2782855 SHA256 f04d01602509c1d950602502e5f51aba47d99c73a9c70e77c563bb7749fc53c0 SHA512 81e343b9b7df7473c9d899df9ad8c4baa779545ac4fe15c3b7d47f3e9473d24aa78c8cfc1833b79ec5b4b3173e8d83e22394a50b7184f348b3f1155bb3724f3d WHIRLPOOL 0b5b45c1bb400f5e2728d5e74f35bc5ef010c029c242940b83c4e6ec3a0c0d16d0c9d9848278d075a548e4e15736f142cc99d4741b8e4901d6589b7f7e05996f
DIST quassel-0.9.3.tar.bz2 2783132 SHA256 ec29df5c55a02f91d15fa23618b42fc82b0bb912594420cc6340a40567ea3d4d SHA512 f200c23fe0e0459dfc116dcd194184a8be28e65d8116859925c1887c6cff290316a704ca3666c0a5b65ed93e2a6a65aed890babb466fe3996bf9c0e08f988e98 WHIRLPOOL fd9b3bd2241845de69e907d2fc3d895054289c271584b07c99b3032effda44183cd2ba3f0d4b1590e93a72a3735ecca6a1d53c1ccd0a3fc32fc6dc5ec5b2281a

33
net-irc/quassel/files/missing-bsd-includes.patch
View file

@ -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

4
net-irc/quassel/quassel-0.10.0-r1.ebuild
View file

@ -1,6 +1,6 @@
# 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-0.10.0-r1.ebuild,v 1.8 2015/03/02 09:29:54 ago Exp $
# $Header: /var/cvsroot/gentoo-x86/net-irc/quassel/quassel-0.10.0-r1.ebuild,v 1.9 2015/03/29 14:26:05 zlogene Exp $
EAPI=5
@ -14,7 +14,7 @@ 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"
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"

173
net-irc/quassel/quassel-0.10.1.ebuild
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@ -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
}

180
net-irc/quassel/quassel-0.9.2.ebuild
View file

@ -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
}

175
net-irc/quassel/quassel-0.9.3.ebuild
View file

@ -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
}

74
profiles/package.mask
View file

@ -1,5 +1,5 @@
####################################################################
# $Header: /var/cvsroot/gentoo-x86/profiles/package.mask,v 1.16445 2015/03/29 05:06:16 mgorny Exp $
# $Header: /var/cvsroot/gentoo-x86/profiles/package.mask,v 1.16446 2015/03/29 13:47:14 dilfridge Exp $
#
# When you add an entry to the top of this file, add your name, the date, and
# an explanation of why something is getting masked. Please be extremely
@ -30,6 +30,78 @@
#--- END OF EXAMPLES ---
# Andreas K. Huettel <dilfridge@gentoo.org> (29 Mar 2015)
# Mask Perl 5.18 for removal. Please upgrade to Perl 5.20
=dev-lang/perl-5.18.2-r2
=virtual/perl-Archive-Tar-1.900.0-r2
=virtual/perl-Attribute-Handlers-0.940.0-r1
=virtual/perl-AutoLoader-5.730.0-r2
=virtual/perl-B-Debug-1.180.0-r2
=virtual/perl-CGI-3.630.0-r2
=virtual/perl-CPAN-Meta-Requirements-2.122.0-r2
=virtual/perl-CPAN-Meta-YAML-0.8.0-r2
=virtual/perl-CPAN-Meta-2.120.921-r2
=virtual/perl-CPAN-2.0.0-r1
=virtual/perl-Carp-1.290.0-r1
=virtual/perl-Compress-Raw-Bzip2-2.60.0-r2
=virtual/perl-Compress-Raw-Zlib-2.60.0-r2
=virtual/perl-DB_File-1.827.0-r2
=virtual/perl-Devel-PPPort-3.200.0-r4
=virtual/perl-Digest-MD5-2.520.0-r2
=virtual/perl-Encode-2.490.0-r2
=virtual/perl-Exporter-5.680.0-r2
=virtual/perl-ExtUtils-CBuilder-0.280.210-r1
=virtual/perl-ExtUtils-Command-1.170.0-r6
=virtual/perl-ExtUtils-Install-1.590.0-r1
=virtual/perl-ExtUtils-MakeMaker-6.660.0-r1
=virtual/perl-ExtUtils-ParseXS-3.180.0-r2
=virtual/perl-File-Spec-3.400.0-r2
=virtual/perl-File-Temp-0.230.0-r1
=virtual/perl-Filter-Simple-0.890.0-r1
=virtual/perl-Getopt-Long-2.390.0-r1
=virtual/perl-I18N-LangTags-0.390.0
=virtual/perl-IO-Compress-2.60.0-r1
=virtual/perl-IO-1.280.0-r1
=virtual/perl-IPC-Cmd-0.800.0-r1
=virtual/perl-JSON-PP-2.272.20-r1
=virtual/perl-Locale-Maketext-1.230.0-r1
=virtual/perl-MIME-Base64-3.130.0-r4
=virtual/perl-Math-BigInt-FastCalc-0.300.0-r4
=virtual/perl-Math-BigInt-1.999.100
=virtual/perl-Math-BigRat-0.260.400
=virtual/perl-Module-Build-0.400.300-r1
=virtual/perl-Module-CoreList-3.30.0
=virtual/perl-Module-Load-Conditional-0.540.0-r1
=virtual/perl-Module-Load-0.240.0-r1
=virtual/perl-Module-Metadata-1.0.11-r1
=virtual/perl-Net-Ping-2.41-r1
=virtual/perl-Package-Constants-0.20.0-r5
=virtual/perl-Params-Check-0.360.0-r1
=virtual/perl-Parse-CPAN-Meta-1.440.400-r1
=virtual/perl-Perl-OSType-1.3.0-r1
=virtual/perl-Pod-Escapes-1.40.0-r5
=virtual/perl-Pod-Parser-1.600.0
=virtual/perl-Safe-2.350.0-r2
=virtual/perl-Scalar-List-Utils-1.270.0-r2
=virtual/perl-Socket-2.9.0-r2
=virtual/perl-Storable-2.410.0-r1
=virtual/perl-Sys-Syslog-0.320.0-r2
=virtual/perl-Term-ReadLine-1.120.0
=virtual/perl-Test-Harness-3.260.0-r2
=virtual/perl-Test-Simple-0.980.0-r6
=virtual/perl-Text-ParseWords-3.280.0-r2
=virtual/perl-Thread-Queue-3.20.0-r1
=virtual/perl-Time-HiRes-1.972.500-r3
=virtual/perl-Time-Piece-1.20-r2
=virtual/perl-XSLoader-0.160.0-r2
=virtual/perl-bignum-0.330.0
=virtual/perl-if-0.60.200-r2
=virtual/perl-libnet-1.220.0-r3
=virtual/perl-parent-0.225.0-r5
=virtual/perl-threads-shared-1.430.0-r1
=virtual/perl-threads-1.860.0-r4
=virtual/perl-version-0.990.200-r1
# Ben de Groot <yngwin@gentoo.org> (29 Mar 2015)
# Merged with qtcurve-qt4 into x11-themes/qtcurve (with gtk useflag)
# Removal in 30 days. See also bug #544406.

1
profiles/use.local.desc
View file

@ -3435,6 +3435,7 @@ mate-extra/mate-power-manager:man - Build power manager's man page.
mate-extra/mate-power-manager:unique - Enable single instance support using dev-libs/libunique.
mate-extra/mate-screensaver:consolekit - Enable support for sys-auth/consolkekit
mate-extra/mate-utils:applet - Enable the mate dictionary applet
media-fonts/corefonts:tahoma - Also install the Tahoma font. Due to the lack of a free bold variant, this may render badly. See bug 184790.
media-fonts/culmus:ancient - Install ancient semitic scripts
media-fonts/culmus:fancy - Install fancy fonts
media-fonts/culmus:fontforge - Use media-gfx/fontforge to build fonts from source

1
sci-biology/dialign2/Manifest Normal file
View file

@ -0,0 +1 @@
DIST dialign-2.2.1-src.tar.gz 209015 SHA256 046361bb4ca6e4ab2ac5e634cfcd673f964a887006c09c1b8bd3310fac86f519 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 WHIRLPOOL a6c5cd25e8e1f3d3738ae0a7f9eaac2509a17400cc3492b9b0b5991c08df08b586c003bbaa3f92d22ae8dd13a66488e6acbbce0aca798cfd20938cb391a02f84

35
sci-biology/dialign2/dialign2-2.2.1.ebuild Normal file
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@ -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}
}

8
sci-biology/dialign2/metadata.xml Normal file
View file

@ -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>

4
sci-biology/fasttree/Manifest
View file

@ -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

32
sci-biology/fasttree/fasttree-2.0.1.ebuild
View file

@ -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
}

4
sci-biology/fasttree/fasttree-2.1.7.ebuild
View file

@ -1,6 +1,6 @@
# 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-2.1.7.ebuild,v 1.2 2015/01/29 21:21:10 mgorny Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.7.ebuild,v 1.3 2015/03/29 14:30:36 jlec Exp $
EAPI=5
@ -23,6 +23,8 @@ REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
DOCS=( README )
PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
src_unpack() {
mkdir "${S}" || die
cd "${S}" || die

48
sci-biology/fasttree/fasttree-2.1.8.ebuild Normal file
View file

@ -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
}

15
sci-biology/fasttree/files/fasttree-2.0.1-asneeded.patch
View file

@ -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}

25
sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch Normal file
View file

@ -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];

25
sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch Normal file
View file

@ -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
sci-biology/mafft/Manifest
View file

@ -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

191
sci-biology/mafft/files/mafft-6.240-mktemp.patch
View file

@ -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

65
sci-biology/mafft/mafft-7.215.ebuild Normal file
View file

@ -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
}

5
sci-biology/muscle/Manifest
View file

@ -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

2
sci-biology/muscle/metadata.xml
View file

@ -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>

41
sci-biology/muscle/muscle-3.6.ebuild
View file

@ -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
}

41
sci-biology/muscle/muscle-3.7.ebuild
View file

@ -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
}

10
sci-biology/muscle/muscle-3.8.31.ebuild
View file

@ -1,8 +1,8 @@
# Copyright 1999-2010 Gentoo Foundation
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.8.31.ebuild,v 1.1 2010/06/24 19:03:18 jlec Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.8.31.ebuild,v 1.2 2015/03/29 14:51:05 jlec Exp $
EAPI="3"
EAPI=5
inherit eutils toolchain-funcs
@ -28,6 +28,6 @@ src_prepare() {
}
src_install() {
dobin "${PN}" || die
dodoc *.txt || die
dobin "${PN}"
dodoc *.txt
}

17
sci-biology/paml/paml-4.4c-r1.ebuild
View file

@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.4c-r1.ebuild,v 1.1 2015/03/03 15:26:16 jlec Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.4c-r1.ebuild,v 1.2 2015/03/29 14:59:48 jlec Exp $
EAPI=5
@ -25,19 +25,24 @@ src_prepare() {
}
src_compile() {
emake -C src CC="$(tc-getCC)" \
CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
emake -C src \
CC="$(tc-getCC)" \
CFLAGS="${CFLAGS} -Wno-unused-result" \
LDFLAGS="${LDFLAGS}"
}
src_install() {
pushd "${S}"/src
dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
popd
dodoc README.txt doc/*
insinto /usr/share/${PN}/control
doins *.ctl
insinto /usr/share/${PN}/dat
doins stewart* *.dat dat/*
insinto /usr/share/${PN}
doins -r examples/
cd src || die
dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
}

1
sci-biology/phylip/Manifest
View file

@ -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

6
sci-biology/phylip/phylip-3.67.ebuild
View file

@ -1,10 +1,10 @@
# Copyright 1999-2008 Gentoo Foundation
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.67.ebuild,v 1.6 2008/06/29 08:24:01 tove Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.67.ebuild,v 1.7 2015/03/29 14:05:50 jlec Exp $
inherit toolchain-funcs
DESCRIPTION="PHYLIP - The PHYLogeny Inference Package"
DESCRIPTION=" The PHYLogeny Inference Package"
LICENSE="freedist"
HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"

10
sci-biology/phylip/phylip-3.69-r1.ebuild
View file

@ -1,12 +1,12 @@
# Copyright 1999-2013 Gentoo Foundation
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.69-r1.ebuild,v 1.1 2013/02/17 11:28:00 jlec Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.69-r1.ebuild,v 1.2 2015/03/29 14:05:50 jlec Exp $
EAPI=5
inherit toolchain-funcs
DESCRIPTION="PHYLIP - The PHYLogeny Inference Package"
DESCRIPTION=" The PHYLogeny Inference Package"
HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
@ -28,7 +28,7 @@ src_prepare() {
-e "s/DC = cc/DC = $(tc-getCC)/" \
-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-i Makefile || die "Patching Makefile failed."
mkdir ../fonts
mkdir ../fonts || die
}
src_compile() {
@ -36,7 +36,7 @@ src_compile() {
}
src_install() {
cd "${WORKDIR}/${P}"
cd "${WORKDIR}/${P}" || die
mv exe/font* fonts || die "Font move failed."
mv exe/factor exe/factor-${PN} || die "Renaming factor failed."

6
sci-biology/phylip/phylip-3.69.ebuild
View file

@ -1,10 +1,10 @@
# Copyright 1999-2010 Gentoo Foundation
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.69.ebuild,v 1.3 2010/01/01 21:38:17 fauli Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.69.ebuild,v 1.4 2015/03/29 14:05:50 jlec Exp $
inherit toolchain-funcs
DESCRIPTION="PHYLIP - The PHYLogeny Inference Package"
DESCRIPTION=" The PHYLogeny Inference Package"
LICENSE="freedist"
HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"

54
sci-biology/phylip/phylip-3.696.ebuild Normal file
View file

@ -0,0 +1,54 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.696.ebuild,v 1.1 2015/03/29 14:05:50 jlec Exp $
EAPI=5
inherit toolchain-funcs
DESCRIPTION=" The PHYLogeny Inference Package"
HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
SLOT="0"
LICENSE="BSD-2"
IUSE=""
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
RDEPEND="x11-libs/libXaw"
DEPEND="${RDEPEND}
x11-proto/xproto"
S="${WORKDIR}/${P}/src"
src_prepare() {
mv Makefile.unx Makefile || die
sed \
-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-i Makefile || die "Patching Makefile failed."
mkdir ../fonts || die
}
src_compile() {
emake -j1 \
CC="$(tc-getCC)" \
DC="$(tc-getCC)" \
CFLAGS="${CFLAGS} -Wno-unused-result" \
all put
}
src_install() {
cd "${WORKDIR}/${P}" || die
mv exe/font* fonts || die "Font move failed."
mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
dobin exe/*
dodoc "${FILESDIR}"/README.Gentoo
dohtml -r phylip.html doc
insinto /usr/share/${PN}/
doins -r fonts
}

3
sci-biology/prank/Manifest
View file

@ -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

6
sci-biology/prank/prank-100701.ebuild
View file

@ -1,13 +1,13 @@
# Copyright 1999-2012 Gentoo Foundation
# 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-100701.ebuild,v 1.3 2012/06/20 21:12:38 jlec Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/prank-100701.ebuild,v 1.4 2015/03/29 13:52:32 jlec Exp $
EAPI=4
inherit toolchain-funcs
DESCRIPTION="Probabilistic Alignment Kit"
HOMEPAGE="http://www.ebi.ac.uk/goldman-srv/prank/prank/"
HOMEPAGE="http://wasabiapp.org/software/prank/"
SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.${PV}.tgz"
LICENSE="GPL-2"

6
sci-biology/prank/prank-111130.ebuild
View file

@ -1,13 +1,13 @@
# Copyright 1999-2012 Gentoo Foundation
# 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-111130.ebuild,v 1.2 2012/06/20 21:12:38 jlec Exp $
# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/prank-111130.ebuild,v 1.3 2015/03/29 13:52:32 jlec Exp $
EAPI=4
inherit eutils multilib toolchain-funcs
DESCRIPTION="Probabilistic Alignment Kit"
HOMEPAGE="http://code.google.com/p/prank-msa/ http://www.ebi.ac.uk/goldman-srv/prank/prank/"
HOMEPAGE="http://wasabiapp.org/software/prank/"
SRC_URI="http://prank-msa.googlecode.com/files/prank.src.${PV}.tgz"
LICENSE="GPL-3"

37
sci-biology/prank/prank-140603.ebuild Normal file
View file

@ -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}
}

3
sci-biology/probcons/Manifest
View file

@ -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

21
sci-biology/probcons/files/1.10-fix-cxxflags.patch
View file

@ -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

2
sci-biology/probcons/metadata.xml
View file

@ -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>

46
sci-biology/probcons/probcons-1.10.ebuild
View file

@ -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"
}

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