diff options
21 files changed, 59 insertions, 134 deletions
diff --git a/metadata/md5-cache/media-sound/alsamixergui-0.9.0.1.2-r4 b/metadata/md5-cache/media-sound/alsamixergui-0.9.0.1.2-r4 index eeb18c521de2..140db4469dd9 100644 --- a/metadata/md5-cache/media-sound/alsamixergui-0.9.0.1.2-r4 +++ b/metadata/md5-cache/media-sound/alsamixergui-0.9.0.1.2-r4 @@ -1,12 +1,13 @@ +BDEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 DEFINED_PHASES=configure install prepare -DEPEND=media-libs/alsa-lib media-sound/alsa-utils x11-libs/fltk:1 >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DEPEND=media-libs/alsa-lib:= media-sound/alsa-utils x11-libs/fltk:1 DESCRIPTION=FLTK based amixer Frontend -EAPI=4 +EAPI=7 HOMEPAGE=https://www.gentoo.org/ KEYWORDS=amd64 arm ppc ppc64 sparc x86 LICENSE=GPL-2 -RDEPEND=media-libs/alsa-lib media-sound/alsa-utils x11-libs/fltk:1 +RDEPEND=media-libs/alsa-lib:= media-sound/alsa-utils x11-libs/fltk:1 SLOT=0 SRC_URI=mirror://gentoo/alsamixergui-0.9.0rc1-2.tar.gz -_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic 8a43b9830f1e64a7a5fc0a276afa0275 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=8220d8804510ca73ee5de370b1ea4ebb +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic 8a43b9830f1e64a7a5fc0a276afa0275 libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=c858c7218d7a98d6a215e86983f109d8 diff --git a/metadata/md5-cache/media-sound/flac123-0.0.12 b/metadata/md5-cache/media-sound/flac123-0.0.12 index ffa6c317e58f..2bbd50730c66 100644 --- a/metadata/md5-cache/media-sound/flac123-0.0.12 +++ b/metadata/md5-cache/media-sound/flac123-0.0.12 @@ -1,13 +1,13 @@ BDEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 DEFINED_PHASES=prepare -DEPEND=dev-libs/popt media-libs/flac media-libs/libao media-libs/libogg +DEPEND=dev-libs/popt:= media-libs/flac:= media-libs/libao:= media-libs/libogg DESCRIPTION=console app for playing FLAC audio files EAPI=7 HOMEPAGE=http://flac-tools.sourceforge.net KEYWORDS=~alpha amd64 arm ppc ppc64 sh sparc x86 LICENSE=GPL-2 -RDEPEND=dev-libs/popt media-libs/flac media-libs/libao media-libs/libogg +RDEPEND=dev-libs/popt:= media-libs/flac:= media-libs/libao:= media-libs/libogg SLOT=0 SRC_URI=mirror://sourceforge/flac-tools/flac123-0.0.12-release.tar.gz _eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c -_md5_=6aa5d80e159e84c2dab52e86b161416c +_md5_=d25378d6c6a9cf3ee49de353caf5f5dc diff --git a/metadata/md5-cache/media-sound/gimmix-0.5.7.2-r1 b/metadata/md5-cache/media-sound/gimmix-0.5.7.2-r1 index 60d09a5e191d..ecf817d7d0a2 100644 --- a/metadata/md5-cache/media-sound/gimmix-0.5.7.2-r1 +++ b/metadata/md5-cache/media-sound/gimmix-0.5.7.2-r1 @@ -1,13 +1,14 @@ +BDEPEND=virtual/pkgconfig dev-util/intltool >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 DEFINED_PHASES=configure prepare -DEPEND=>=media-libs/libmpd-0.17 gnome-base/libglade x11-libs/gtk+:2 cover? ( net-libs/libnxml net-misc/curl ) lyrics? ( net-libs/libnxml net-misc/curl ) taglib? ( >=media-libs/taglib-1.5 ) virtual/pkgconfig dev-util/intltool >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DEPEND=media-libs/libmpd:= gnome-base/libglade:= x11-libs/gtk+:2 cover? ( net-libs/libnxml:= net-misc/curl:= ) lyrics? ( net-libs/libnxml:= net-misc/curl:= ) taglib? ( media-libs/taglib:= ) DESCRIPTION=a graphical music player daemon (MPD) client using GTK+2 -EAPI=4 +EAPI=7 HOMEPAGE=https://launchpad.net/gimmix IUSE=cover lyrics taglib KEYWORDS=amd64 ~ppc x86 LICENSE=GPL-2 -RDEPEND=>=media-libs/libmpd-0.17 gnome-base/libglade x11-libs/gtk+:2 cover? ( net-libs/libnxml net-misc/curl ) lyrics? ( net-libs/libnxml net-misc/curl ) taglib? ( >=media-libs/taglib-1.5 ) +RDEPEND=media-libs/libmpd:= gnome-base/libglade:= x11-libs/gtk+:2 cover? ( net-libs/libnxml:= net-misc/curl:= ) lyrics? ( net-libs/libnxml:= net-misc/curl:= ) taglib? ( media-libs/taglib:= ) SLOT=0 SRC_URI=mirror://gentoo/gimmix-0.5.7.2.tar.bz2 -_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=22ce36f6474390d37fadab6ddc9941d1 +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=d63c8b3bf2e59117c1a46f7a19520522 diff --git a/metadata/md5-cache/media-sound/podcatcher-3.1.6 b/metadata/md5-cache/media-sound/podcatcher-3.1.6 index f63c11dd3a3b..b05dbeed7e60 100644 --- a/metadata/md5-cache/media-sound/podcatcher-3.1.6 +++ b/metadata/md5-cache/media-sound/podcatcher-3.1.6 @@ -1,11 +1,11 @@ DEFINED_PHASES=install DEPEND=>=dev-lang/ruby-1.8.2 DESCRIPTION=Podcast client for the command-line written in Ruby -EAPI=4 +EAPI=7 HOMEPAGE=http://podcatcher.rubyforge.org/ KEYWORDS=~amd64 ~ppc ~x86 LICENSE=GPL-2 RDEPEND=>=dev-lang/ruby-1.8.2 SLOT=0 SRC_URI=http://rubyforge.org/frs/download.php/76053/podcatcher-3.1.6.tar.gz -_md5_=963b306155fd48d126cf9ace9027c290 +_md5_=533280cea24fc5820ef3aa6f0c296f00 diff --git a/metadata/md5-cache/media-sound/retrovol-0.13 b/metadata/md5-cache/media-sound/retrovol-0.13 index cd0dc4983cc2..5806027402ab 100644 --- a/metadata/md5-cache/media-sound/retrovol-0.13 +++ b/metadata/md5-cache/media-sound/retrovol-0.13 @@ -1,7 +1,8 @@ -DEFINED_PHASES=compile configure install postinst prepare unpack -DEPEND=x11-libs/gtk+:2 virtual/pkgconfig nls? ( sys-devel/gettext ) +BDEPEND=virtual/pkgconfig nls? ( sys-devel/gettext ) +DEFINED_PHASES=configure postinst +DEPEND=x11-libs/gtk+:2 DESCRIPTION=Systemtray volume mixer applet from PuppyLinux -EAPI=4 +EAPI=7 HOMEPAGE=http://puppylinux.org/wikka/Retrovol IUSE=nls KEYWORDS=~amd64 ~x86 @@ -9,5 +10,4 @@ LICENSE=GPL-3 LGPL-3 public-domain RDEPEND=x11-libs/gtk+:2 SLOT=0 SRC_URI=http://www.browserloadofcoolness.com/software/puppy/PETget/retrovol-0.13.tar.gz -_eclasses_=base 2ec5c64f5de125f0c65a927c4c128fef desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 l10n 97f2753e3f1f3753d53d856c7c0bbb0b ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=bc789c6d4a46b5185db1b3c694063a0f +_md5_=4f3afb943d9728134d190d8f3da17946 diff --git a/metadata/md5-cache/media-sound/ttaenc-3.4.1-r1 b/metadata/md5-cache/media-sound/ttaenc-3.4.1-r1 index 9223af95ef6f..5b2f7de78808 100644 --- a/metadata/md5-cache/media-sound/ttaenc-3.4.1-r1 +++ b/metadata/md5-cache/media-sound/ttaenc-3.4.1-r1 @@ -1,11 +1,10 @@ -DEFINED_PHASES=compile install prepare -DEPEND=sys-apps/sed +DEFINED_PHASES=configure install DESCRIPTION=True Audio Compressor Software -EAPI=4 +EAPI=7 HOMEPAGE=http://tta.sourceforge.net KEYWORDS=amd64 x86 LICENSE=GPL-2 SLOT=0 SRC_URI=mirror://sourceforge/tta/ttaenc-3.4.1-src.tgz _eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c -_md5_=3e38c08a3279638fa3d8dd90ad2d5fd4 +_md5_=994b8ee0614e921377a04965f5bc84bd diff --git a/metadata/md5-cache/media-sound/volumeicon-0.4.6 b/metadata/md5-cache/media-sound/volumeicon-0.4.6 deleted file mode 100644 index 6166b0fa6b50..000000000000 --- a/metadata/md5-cache/media-sound/volumeicon-0.4.6 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=configure prepare -DEPEND=>=dev-libs/glib-2 media-libs/alsa-lib >=x11-libs/gtk+-2.16:2 x11-libs/libX11 libnotify? ( >=x11-libs/libnotify-0.7 ) virtual/pkgconfig -DESCRIPTION=A lightweight volume control that sits in your systray -EAPI=4 -HOMEPAGE=http://softwarebakery.com/maato/volumeicon.html -IUSE=libnotify -KEYWORDS=amd64 x86 -LICENSE=GPL-3 -RDEPEND=>=dev-libs/glib-2 media-libs/alsa-lib >=x11-libs/gtk+-2.16:2 x11-libs/libX11 libnotify? ( >=x11-libs/libnotify-0.7 ) -SLOT=0 -SRC_URI=http://softwarebakery.com/maato/files/volumeicon/volumeicon-0.4.6.tar.gz -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=354434b9d0a9dbf7b46e0080eee25028 diff --git a/metadata/md5-cache/media-sound/wavbreaker-0.11 b/metadata/md5-cache/media-sound/wavbreaker-0.11 index a3ec21d41ccf..dd0a7c309a88 100644 --- a/metadata/md5-cache/media-sound/wavbreaker-0.11 +++ b/metadata/md5-cache/media-sound/wavbreaker-0.11 @@ -1,13 +1,14 @@ +BDEPEND=virtual/pkgconfig nls? ( sys-devel/gettext ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 DEFINED_PHASES=configure prepare -DEPEND=dev-libs/libxml2 >=x11-libs/gtk+-2:2 alsa? ( media-libs/alsa-lib ) pulseaudio? ( media-sound/pulseaudio ) nls? ( sys-devel/gettext ) virtual/pkgconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DEPEND=dev-libs/libxml2:= x11-libs/gtk+:2 alsa? ( media-libs/alsa-lib:= ) pulseaudio? ( media-sound/pulseaudio:= ) DESCRIPTION=wavbreaker/wavmerge GTK+ utility to break or merge WAV files -EAPI=4 +EAPI=7 HOMEPAGE=http://wavbreaker.sourceforge.net IUSE=alsa nls oss pulseaudio KEYWORDS=amd64 x86 LICENSE=GPL-2 -RDEPEND=dev-libs/libxml2 >=x11-libs/gtk+-2:2 alsa? ( media-libs/alsa-lib ) pulseaudio? ( media-sound/pulseaudio ) +RDEPEND=dev-libs/libxml2:= x11-libs/gtk+:2 alsa? ( media-libs/alsa-lib:= ) pulseaudio? ( media-sound/pulseaudio:= ) SLOT=0 SRC_URI=mirror://sourceforge/wavbreaker/wavbreaker-0.11.tar.gz -_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=dcf6367176912146fec29db649caa295 +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=f67354edcae693b85e7451a0650bd984 diff --git a/metadata/md5-cache/media-sound/wavplay-2.0 b/metadata/md5-cache/media-sound/wavplay-2.0 index 01c7776801e9..091c1af3dc5a 100644 --- a/metadata/md5-cache/media-sound/wavplay-2.0 +++ b/metadata/md5-cache/media-sound/wavplay-2.0 @@ -1,11 +1,11 @@ +BDEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 DEFINED_PHASES=configure prepare -DEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 DESCRIPTION=A command line player/recorder for wav files -EAPI=4 +EAPI=7 HOMEPAGE=https://sourceforge.net/projects/wavplay/ KEYWORDS=~amd64 x86 LICENSE=GPL-2 SLOT=0 SRC_URI=mirror://sourceforge/wavplay/wavplay-2.0.tar.gz _eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c -_md5_=0dfcf51b1c212fb31df78641c564323d +_md5_=fc0d39e6ff776cc7e3ac57ee79fd60ea diff --git a/metadata/md5-cache/sci-biology/augustus-2.5.5 b/metadata/md5-cache/sci-biology/augustus-2.5.5 index a830a548cb02..8b5104561aff 100644 --- a/metadata/md5-cache/sci-biology/augustus-2.5.5 +++ b/metadata/md5-cache/sci-biology/augustus-2.5.5 @@ -1,11 +1,11 @@ -DEFINED_PHASES=compile install prepare +DEFINED_PHASES=compile configure install DESCRIPTION=Eukaryotic gene predictor -EAPI=4 +EAPI=7 HOMEPAGE=http://augustus.gobics.de/ IUSE=examples KEYWORDS=amd64 x86 LICENSE=Artistic SLOT=0 SRC_URI=http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=5660f556708e8c3b5d43c9ef832e66ec +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=80962b244c7531e320f35904727b5bd5 diff --git a/metadata/md5-cache/sci-biology/gibbs-3.1 b/metadata/md5-cache/sci-biology/gibbs-3.1 index a25c3f3552eb..e4d0e8b42fa6 100644 --- a/metadata/md5-cache/sci-biology/gibbs-3.1 +++ b/metadata/md5-cache/sci-biology/gibbs-3.1 @@ -1,7 +1,8 @@ -DEFINED_PHASES=compile configure install postinst prepare test -DEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +BDEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 +DEFINED_PHASES=configure install postinst prepare +DEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 ) DESCRIPTION=Identify motifs, conserved regions, in DNA or protein sequences -EAPI=4 +EAPI=7 HOMEPAGE=http://bayesweb.wadsworth.org/gibbs/gibbs.html IUSE=mpi KEYWORDS=amd64 x86 @@ -9,5 +10,5 @@ LICENSE=GPL-2 RDEPEND=mpi? ( virtual/mpi sys-cluster/mpe2 ) SLOT=0 SRC_URI=mirror://gentoo/gibbs-3.1.tar.gz -_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c autotools-utils 95db0904ad0f62535e18e5ccb67cce5e desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=e28918ff8ca46c8b8254e4e36f8d0bcf +_eclasses_=autotools ea7865c8fba1ea8d3639f355fffe1a3c libtool f143db5a74ccd9ca28c1234deffede96 multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=8d48efee68d1063803fccbc4c73a0f5d diff --git a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 index 6f39e8c26c79..de218b00d488 100644 --- a/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 +++ b/metadata/md5-cache/sci-biology/glimmerhmm-3.0.1-r1 @@ -1,10 +1,10 @@ -DEFINED_PHASES=compile install prepare unpack +DEFINED_PHASES=compile configure install DESCRIPTION=A eukaryotic gene finding system from TIGR -EAPI=4 +EAPI=7 HOMEPAGE=http://www.cbcb.umd.edu/software/GlimmerHMM/ KEYWORDS=amd64 x86 LICENSE=Artistic SLOT=0 SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.1.tar.gz -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=addae30e588a0c7a05baea53d553af0f +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=9fc33629a982f35b93c18da772894fdd diff --git a/metadata/md5-cache/sci-biology/last-230 b/metadata/md5-cache/sci-biology/last-230 deleted file mode 100644 index 5c13aee8fe43..000000000000 --- a/metadata/md5-cache/sci-biology/last-230 +++ /dev/null @@ -1,11 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=app-arch/unzip -DESCRIPTION=Genome-scale comparison of biological sequences -EAPI=4 -HOMEPAGE=http://last.cbrc.jp/ -KEYWORDS=amd64 x86 -LICENSE=GPL-3 -SLOT=0 -SRC_URI=http://last.cbrc.jp/archive/last-230.zip -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=5da658e6779591b0d1b9ad3413a0e7b2 diff --git a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 b/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 deleted file mode 100644 index 57e1c5383c3e..000000000000 --- a/metadata/md5-cache/sci-biology/mrbayes-3.1.2-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) -DESCRIPTION=Bayesian Inference of Phylogeny -EAPI=4 -HOMEPAGE=http://mrbayes.csit.fsu.edu/ -IUSE=debug mpi readline -KEYWORDS=amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris -LICENSE=GPL-2 -RDEPEND=sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0 ) -SLOT=0 -SRC_URI=mirror://sourceforge/mrbayes/mrbayes-3.1.2.tar.gz -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=a082c9b1f1b5f9fa9b85e23eb7009a6d diff --git a/metadata/md5-cache/sci-biology/plink-1.07-r1 b/metadata/md5-cache/sci-biology/plink-1.07-r1 deleted file mode 100644 index 4f8d0b921d8a..000000000000 --- a/metadata/md5-cache/sci-biology/plink-1.07-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare -DEPEND=app-arch/unzip lapack? ( virtual/pkgconfig ) -DESCRIPTION=Whole genome association analysis toolset -EAPI=4 -HOMEPAGE=http://pngu.mgh.harvard.edu/~purcell/plink/ -IUSE=lapack -webcheck R -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -RDEPEND=sys-libs/zlib lapack? ( virtual/lapack ) -SLOT=0 -SRC_URI=http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=b659cc5ab8af123ceaf15f1349214345 diff --git a/metadata/md5-cache/sci-biology/shrimp-2.0.1 b/metadata/md5-cache/sci-biology/shrimp-2.0.1 deleted file mode 100644 index d86d2991f5ff..000000000000 --- a/metadata/md5-cache/sci-biology/shrimp-2.0.1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install prepare setup -DEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs -DESCRIPTION=SHort Read Mapping Package -EAPI=4 -HOMEPAGE=http://compbio.cs.toronto.edu/shrimp/ -IUSE=custom-cflags -KEYWORDS=amd64 x86 -LICENSE=shrimp -RDEPEND=!sci-biology/emboss !sci-mathematics/cado-nfs -SLOT=0 -SRC_URI=http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_0_1.src.tar.gz -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic 8a43b9830f1e64a7a5fc0a276afa0275 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=33caa30e4cdcb3e86f4b1be8c6c30c46 diff --git a/metadata/md5-cache/sci-biology/tree-puzzle-5.2 b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 index 56e0a3103673..a9f74c4889af 100644 --- a/metadata/md5-cache/sci-biology/tree-puzzle-5.2 +++ b/metadata/md5-cache/sci-biology/tree-puzzle-5.2 @@ -1,7 +1,7 @@ -DEFINED_PHASES=configure install prepare setup +DEFINED_PHASES=configure install setup DEPEND=mpi? ( virtual/mpi ) DESCRIPTION=Maximum likelihood analysis for nucleotide, amino acid, and two-state data -EAPI=4 +EAPI=7 HOMEPAGE=http://www.tree-puzzle.de IUSE=mpi KEYWORDS=~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos @@ -10,5 +10,5 @@ RDEPEND=mpi? ( virtual/mpi ) RESTRICT=test SLOT=0 SRC_URI=http://www.tree-puzzle.de/tree-puzzle-5.2.tar.gz -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=6f933fde60eb23f0e50fbe5e137bbc7e +_eclasses_=multilib 1d91b03d42ab6308b5f4f6b598ed110e toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c +_md5_=8bd164fc83c9bb1d9a2e9559a47ff526 diff --git a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 b/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 deleted file mode 100644 index c130d2b73700..000000000000 --- a/metadata/md5-cache/sci-biology/velvet-1.0.18-r1 +++ /dev/null @@ -1,13 +0,0 @@ -DEFINED_PHASES=compile install postinst prepare -DEPEND=sys-libs/zlib doc? ( virtual/latex-base ) -DESCRIPTION=A sequence assembler for very short reads -EAPI=4 -HOMEPAGE=https://www.ebi.ac.uk/~zerbino/velvet/ -IUSE=-doc -KEYWORDS=amd64 x86 -LICENSE=GPL-2 -RDEPEND=sys-libs/zlib -SLOT=0 -SRC_URI=https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.0.18.tgz -_eclasses_=desktop b1d22ac8bdd4679ab79c71aca235009d epatch a1bf4756dba418a7238f3be0cb010c54 estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic 8a43b9830f1e64a7a5fc0a276afa0275 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 1d91b03d42ab6308b5f4f6b598ed110e preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 512eb3367f507ebaa1d1d43ab7d66e6c vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf -_md5_=81d9bd82f6f3df3f4b73fa7d65b5d95e diff --git a/metadata/pkg_desc_index b/metadata/pkg_desc_index index 4cc1f7e7f96e..afbdcc6ac4a8 100644 --- a/metadata/pkg_desc_index +++ b/metadata/pkg_desc_index @@ -14067,7 +14067,7 @@ media-sound/vlevel 0.5-r1: Dynamic compressor to amplify quiet parts of music media-sound/vlorb 1.2: A high quality Audio CD to audio file encoder media-sound/vmpk 0.6.2a: Virtual MIDI Piano Keyboard media-sound/volti 0.2.3-r1: GTK+ application for controlling audio volume from system tray/notification area -media-sound/volumeicon 0.4.6 0.5.1-r1: A lightweight volume control that sits in your systray +media-sound/volumeicon 0.5.1-r1: A lightweight volume control that sits in your systray media-sound/volwheel 0.2.8-r1: A volume control trayicon with mouse wheel support media-sound/vorbis-tools 1.4.0-r5: Tools for using the Ogg Vorbis sound file format media-sound/vorbisgain 0.37-r2: Calculator of perceived sound level for Ogg Vorbis files @@ -15963,7 +15963,7 @@ sci-biology/iqpnni 3.3.2-r1: Important Quartet Puzzling and NNI Operation sci-biology/kalign 2.03-r2: Global and progressive multiple sequence alignment sci-biology/kallisto 0.43.1 9999: Near-optimal RNA-Seq quantification sci-biology/lagan 2.0-r3: The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA -sci-biology/last 230 299-r1: Genome-scale comparison of biological sequences +sci-biology/last 299-r1: Genome-scale comparison of biological sequences sci-biology/libgtextutils 0.6.1: Gordon Text utils Library sci-biology/mafft 7.050 7.215 7.305: Multiple sequence alignments using a variety of algorithms sci-biology/maq 0.7.1-r2: Mapping and Assembly with Qualities, mapping NGS reads to reference genomes @@ -15973,7 +15973,7 @@ sci-biology/meme 4.11.2_p2: The MEME/MAST system - Motif discovery and search sci-biology/mira 4.0.2: Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina sci-biology/mosaik 2.2.30: A reference-guided aligner for next-generation sequencing technologies sci-biology/mothur 1.27.0-r1: A suite of algorithms for ecological bioinformatics -sci-biology/mrbayes 3.1.2-r1 3.1.2-r2: Bayesian Inference of Phylogeny +sci-biology/mrbayes 3.1.2-r2: Bayesian Inference of Phylogeny sci-biology/mummer 3.23: A rapid whole genome aligner sci-biology/muscle 3.8.31: Multiple sequence comparison by log-expectation sci-biology/ncbi-tools 2.2.26-r2: Development toolkit and applications for computational biology, including BLAST @@ -15988,7 +15988,7 @@ sci-biology/phyml 2.4.5-r3: Estimation of large phylogenies by maximum likelihoo sci-biology/picard 1.103: Java-based command-line utilities that manipulate SAM files sci-biology/piler 1.0-r1: Analysis of repetitive DNA found in genome sequences sci-biology/pilercr 1.0-r1: Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) -sci-biology/plink 1.07-r1 1.90_pre140514: Whole genome association analysis toolset +sci-biology/plink 1.90_pre140514: Whole genome association analysis toolset sci-biology/poa 2-r1: Fast multiple sequence alignments using partial-order graphs sci-biology/prank 140603: Probabilistic Alignment Kit sci-biology/primer3 2.3.7: Primer Design for PCR reactions @@ -16010,7 +16010,7 @@ sci-biology/rnaview 20040713-r4: Generates 2D displays of RNA/DNA secondary stru sci-biology/samtools 0.1.20-r3 1.5 1.9: Utilities for analysing and manipulating the SAM/BAM alignment formats sci-biology/seaview 4.3.5 4.5.4 4.6: A graphical multiple sequence alignment editor sci-biology/seqan 1.4.2-r1 2.2.0-r1 2.4.0 9999: C++ Sequence Analysis Library -sci-biology/shrimp 2.0.1 2.2.3: SHort Read Mapping Package +sci-biology/shrimp 2.2.3: SHort Read Mapping Package sci-biology/sibsim4 0.20: A rewrite and improvement upon sim4, a DNA-mRNA aligner sci-biology/sim4 20030921-r2: A program to align cDNA and genomic DNA sci-biology/stride 20011129-r1: Protein secondary structure assignment from atomic coordinates @@ -16026,7 +16026,7 @@ sci-biology/ucsc-genome-browser 260-r1: The UCSC genome browser suite, also know sci-biology/unafold 3.8-r1: Unified Nucleic Acid Folding and hybridization package sci-biology/update-blastdb 12.0.0: update_blastdb.pl for local blast db maintainance sci-biology/vcftools 0.1.14: Tools for working with VCF (Variant Call Format) files -sci-biology/velvet 1.0.18-r1 1.2.10: A sequence assembler for very short reads +sci-biology/velvet 1.2.10: A sequence assembler for very short reads sci-biology/vienna-rna 2.1.1 2.1.8: RNA secondary structure prediction and comparison sci-biology/wgs-assembler 7.0-r2: The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG sci-biology/wise 2.4.0_alpha: Intelligent algorithms for DNA searches diff --git a/metadata/timestamp.chk b/metadata/timestamp.chk index 420808085bb8..745c47046d0d 100644 --- a/metadata/timestamp.chk +++ b/metadata/timestamp.chk @@ -1 +1 @@ -Tue, 10 Dec 2019 23:48:37 +0000 +Wed, 11 Dec 2019 00:26:11 +0000 diff --git a/profiles/use.local.desc b/profiles/use.local.desc index a4398ac42809..4691c9ff6932 100644 --- a/profiles/use.local.desc +++ b/profiles/use.local.desc @@ -7233,8 +7233,6 @@ sci-biology/clustalw-mpi:static_pairalign - Use static (as opposed to dynamic) s sci-biology/exonerate:utils - Install all utilities sci-biology/fasttree:double-precision - use double precision instead of single-precision floating point (2x memroy required) sci-biology/mcl:blast - Add support for NCBI BLAST data -sci-biology/plink:R - add support R language -sci-biology/plink:webcheck - add support for online update checking every time the program starts sci-biology/seqan:tools - Build and install SeqAn commandline tools, such as the Yara aligner sci-biology/ucsc-genome-browser:server - Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed. sci-biology/yass:dmalloc - Enable debugging with the dmalloc library |