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Kent Fredric 29bb345f1e dev-perl/Bio-SamTools: Bump to version 1.430.0 
- Links against samtools:0.1-legacy series, as even though this code
  previously attempted to use 1.0+, closer inspection indicated
  incomplete linking, missing symbols, and failing tests introduced
  by this attempt. Additionally, upstream EXPLICITLY STATE the lack of
  current support for samtools 1.0

- Restores DIST_TEST as I can now test they work

- Fold swathe of sed commands into patch

Upstream:
- Ship some test files requried for tests to pass

Closes: https://bugs.gentoo.org/611970
Closes: https://bugs.gentoo.org/604950
Package-Manager: Portage-2.3.6, Repoman-2.3.2
2017-09-10 15:22:39 +12:00
app-accessibility
app-accessibility/caribou: remove old
2017-08-28 00:25:39 +03:00
app-admin
app-admin/puppet-agent: 1.10.6 stable amd64 and x86 with cleanup
2017-09-09 18:16:45 -05:00
app-antivirus
app-antivirus/skyldav: use HTTPS for links to dev.gentoo.org
2017-09-06 22:59:34 +02:00
app-arch
app-arch/bzip2: Add sublot
2017-09-09 23:06:47 +02:00
app-backup
app-backup/dar: amd64 stable #629702
2017-09-02 19:37:36 -04:00
app-benchmarks
app-benchmarks/i7z: remove suspicious subslot operators
2017-08-13 00:48:35 +10:00
app-cdr
app-cdr/burncdda: Update HOMEPAGE
2017-09-05 18:33:18 +02:00
app-crypt
app-crypt/certbot-apache: 0.18.1 bup
2017-09-09 16:47:13 -05:00
app-dicts
app-dicts/myspell-ru: Update HOMEPAGE
2017-09-06 10:59:22 +02:00
app-doc
app-doc/diveintopython: avoid mixing tabs/spaces in metadata.xml.
2017-09-04 23:56:36 +02:00
app-editors
app-editors/focuswriter: version bump 1.6.7
2017-09-10 01:55:53 +10:00
app-emacs
app-emacs/with-editor: add 2.6.0
2017-09-07 08:21:53 +02:00
app-emulation
app-emulation/virt-what: arm stable, bug #629424
2017-09-09 12:24:45 +02:00
app-eselect
app-eselect/eselect-repository: Fix <remote-id/>
2017-09-09 13:02:26 +02:00
app-forensics
app-forensics/chkrootkit: arm stable, bug #629390
2017-09-09 12:24:25 +02:00
app-i18n
app-i18n/ibus: add ~arm, bug #626804
2017-09-08 22:09:35 +02:00
app-laptop
app-laptop/mbpfan: update the live ebuild
2017-08-23 14:43:36 -04:00
app-leechcraft
net-libs/telepathy-qt: Prepare rdeps for dropping USE=qt5
2017-08-31 22:53:50 +02:00
app-misc
app-misc/pal: Make repoman happier
2017-09-07 10:10:19 +02:00
app-mobilephone
app-mobilephone/obexftp: remove unused patches
2017-09-03 00:46:01 +10:00
app-office
media-libs/phonon: Prepare rdeps for dropping USE=qt5
2017-08-31 22:53:49 +02:00
app-officeext
app-officeext/ooofbtools: version bump
2017-07-26 15:44:34 +03:00
app-pda
app-pda/fusepod: Remove last-rited pkg, #596602
2017-08-14 22:00:04 +02:00
app-portage
app-portage/elt-patches: arm stable, bug #627824
2017-09-08 07:04:39 +02:00
app-shells
app-shells/thefuck: Remove old
2017-09-09 00:11:39 +02:00
app-text
app-text/xapian-omega: punt 1.4.3 for bug #630540
2017-09-09 21:30:46 -04:00
app-vim
app-vim/ctrlp: clean up old.
2017-09-08 23:12:44 +02:00
app-xemacs
app-xemacs/emerge: keyword ~mips
2017-08-09 08:15:24 -04:00
dev-ada
dev-ada/gps-bin: inherit toolchain-funcs. Fix bug #628958
2017-08-31 16:03:06 +02:00
dev-cpp
dev-cpp/tclap: add ~arm64, bug #624102
2017-09-07 21:27:17 +02:00
dev-db
dev-db/pgadmin4: Initial Commit
2017-09-09 19:26:55 -04:00
dev-dotnet
dev-dotnet/gtk-sharp: keyword ~arm64
2017-07-08 11:18:59 +02:00
dev-embedded
dev-embedded/gpsim: remove old
2017-09-05 03:22:14 -04:00
dev-erlang
…
dev-games
dev-games/tiled: version bump 1.0.3
2017-09-02 23:54:06 +10:00
dev-go
dev-go/gogo-protobuf: Initial version
2017-08-23 14:47:06 +02:00
dev-haskell
dev-haskell/stack: block against dev-haskell/stack-bin[symlink]
2017-08-26 12:32:36 +01:00
dev-java
dev-java/javatoolkit: remove broken versions.
2017-09-09 00:27:32 +02:00
dev-lang
dev-lang/php: stable 7.0.23 for ppc/ppc64, bug #629452
2017-09-09 20:02:06 +01:00
dev-libs
dev-libs/mpfr: version bump to 3.1.6
2017-09-09 21:51:58 -04:00
dev-lisp
dev-lisp/sbcl: Bumps version to 1.3.21
2017-09-02 16:58:19 +02:00
dev-lua
dev-lua/luacheck: new package
2017-09-02 10:45:22 +02:00
dev-ml
dev-ml/llvm-ocaml: Bump to 5.0.0
2017-09-08 19:30:31 +02:00
dev-perl
dev-perl/Bio-SamTools: Bump to version 1.430.0
2017-09-10 15:22:39 +12:00
dev-php
dev-php/pecl-ncurses: use HTTPS for links to dev.gentoo.org
2017-09-06 22:52:41 +02:00
dev-python
dev-python/oauthlib: version bump to 2.0.3
2017-09-09 22:16:46 -04:00
dev-qt
dev-qt/qtlocation: arm stable, bug #627542
2017-09-08 07:04:21 +02:00
dev-ros
dev-ros/rospack: backport upstream patch to build with boost 1.65, bug #629900
2017-09-08 09:16:10 +02:00
dev-ruby
dev-ruby/rails: add rails 5.0.6
2017-09-09 09:07:13 +02:00
dev-scheme
Remove masked for removal packages
2017-09-04 11:11:45 +02:00
dev-tcltk
dev-tcltk/tclpython: x86 stable
2017-08-05 18:22:35 +10:00
dev-tex
dev-tex/vc: use HTTPS for links to dev.gentoo.org
2017-09-06 22:52:42 +02:00
dev-texlive
Drop dev-lang/ruby to ~sparc, bug 615822
2017-08-14 19:15:42 +02:00
dev-util
dev-util/pkgconfig: stable 0.29.2 for ppc/ppc64, bug #629968
2017-09-09 19:45:24 +01:00
dev-vcs
dev-vcs/git: stable 2.13.5 for hppa/sparc, bug #627488 (thanks to Dakon)
2017-09-08 23:12:46 +01:00
eclass
toolchain-glibc.eclass: Do not export any phases in EAPI=6. Well. Nearly.
2017-09-09 23:21:23 +02:00
games-action
games-action/minetest_game: version bump to 0.4.16
2017-09-02 10:16:02 +02:00
games-arcade
games-arcade/opentyrian: remove deprecated games eclass
2017-09-05 13:32:26 -05:00
games-board
games-board/pokerth: Fully qualify std::advance
2017-09-07 09:13:20 +02:00
games-emulation
games-emulation/mekanix: remove deprecated games eclass
2017-09-05 13:32:26 -05:00
games-engines
games-engines/renpy: x86 stable (bug #625624)
2017-08-30 01:15:37 +02:00
games-fps
games-fps/wolfgl: remove deprecated games eclass
2017-09-06 18:28:35 -05:00
games-kids
*games*/*: Dekeyword ppc/ia64/sparc
2017-07-08 15:32:31 -07:00
games-misc
games-misc/lolcat: add ruby23, ruby24
2017-08-22 07:01:54 +02:00
games-mud
games-mud/gnome-mud: remove old
2017-08-22 15:16:38 +03:00
games-puzzle
games-puzzle/angrydd: HOMEPAGE and SRC_URI 301 redirect to HTTPS
2017-08-22 23:37:51 +02:00
games-roguelike
games-roguelike/angband: fix build on pie gcc, bug #617982
2017-09-09 21:41:24 +01:00
games-rpg
games-rpg/comi: use HTTPS for links to dev.gentoo.org
2017-09-06 22:58:45 +02:00
games-server
*games*/*: Dekeyword ppc/ia64/sparc
2017-07-08 15:32:31 -07:00
games-simulation
games-simulation/openrct2: drop old
2017-08-12 00:12:24 +02:00
games-sports
games-sports/trigger: Fix building with GCC-6
2017-07-30 11:08:42 +02:00
games-strategy
games-strategy/defcon-demo: remove deprecated games eclass
2017-09-07 16:04:16 -05:00
games-util
games-util/wit: use https for HOMEPAGE
2017-09-08 08:45:05 -04:00
gnome-base
gnome-base/librsvg: stable 2.40.18 for sparc, bug #625860 (thank to Dakon)
2017-09-09 20:41:04 +01:00
gnome-extra
gnome-extra/cinnamon-screensaver: New upstream version 3.4.2
2017-09-05 22:05:18 +02:00
gnustep-apps
gnustep-apps/pikopixel: use HTTPS for links to dev.gentoo.org
2017-09-06 22:58:47 +02:00
gnustep-base
gnustep-base/mknfonts: drop old
2017-08-30 23:22:45 +02:00
gnustep-libs
gnustep-libs/renaissance: drop old
2017-08-30 23:22:46 +02:00
java-virtuals
java-virtuals/servlet-api: Remove old EAPI 4 versions
2017-08-28 23:01:42 +01:00
kde-apps
kde-apps/step: Fix configure with USE=-nls
2017-09-09 13:53:37 +02:00
kde-frameworks
kde-frameworks/kdelibs: Fix build with app-text/enchant-2.1.0
2017-09-09 21:29:10 +02:00
kde-misc
kde-misc/kdiff3: use HTTPS for links to dev.gentoo.org
2017-09-06 22:58:50 +02:00
kde-plasma
kde-plasma/kwallet-pam: Drop old
2017-09-09 18:34:55 +02:00
licenses
licenses: Remove unused GMGPL license.
2017-09-06 08:42:26 +02:00
lxde-base
lxde-base/lxpanel: update HOMEPAGE.
2017-07-14 23:07:00 +02:00
lxqt-base
sys-auth/polkit-qt: Prepare rdeps for dropping USE=qt5
2017-09-01 23:34:03 +02:00
mail-client
mail-client/mutt: version bump to 1.9.0, bug #629748
2017-09-09 21:14:04 +02:00
mail-filter
mail-filter/libspf2: fix building with GCC5, bug #570486
2017-09-08 13:24:34 +02:00
mail-mta
mail-mta/exim: proxy no longer is experimental, thanks Eugene O Alexeyev
2017-09-05 11:24:11 +02:00
mate-base
…
mate-extra
…
media-fonts
media-fonts/terminus-font-4.40-r0: alpha stable
2017-09-04 09:25:52 +02:00
media-gfx
media-gfx/imagemagick: stable 6.9.9.0 for ppc/ppc64, bug #625404
2017-09-09 18:04:54 +01:00
media-libs
media-libs/libraw: Removed old.
2017-09-09 23:03:12 +02:00
media-plugins
media-plugins/kipi-plugins: Remove 5.6.0
2017-09-06 20:50:19 +02:00
media-radio
media-radio/flrig: Version bump
2017-09-07 19:41:52 +02:00
media-sound
media-sound/quodlibet: update dependencies
2017-09-05 20:44:45 -05:00
media-tv
media-tv/plex-media-server: version bump to 1.8.1
2017-09-04 11:48:12 -04:00
media-video
media-video/ffmpeg: arm stable, bug #627018
2017-09-07 21:12:14 +02:00
metadata
metdata/repoman/*: Add current API version and minimum repoman version info
2017-08-17 02:11:52 +00:00
net-analyzer
net-analyzer/tcpdump: stable 4.9.2 for ia64, bug #630110
2017-09-09 12:53:02 +01:00
net-dialup
net-dialup/accel-ppp: use HTTPS for links to dev.gentoo.org
2017-09-06 22:58:59 +02:00
net-dns
net-dns/dnsmasq: Stabilize 2.77-r1 on amd64
2017-09-07 18:51:40 -07:00
net-firewall
net-firewall/firehol: Bump to 3.1.4
2017-09-08 22:38:53 +03:00
net-fs
net-fs/samba: Removed old.
2017-09-01 22:54:40 +02:00
net-ftp
net-ftp/tftp-hpa: remove old
2017-08-31 13:37:29 -04:00
net-im
net-im/qutim: Fix manifest
2017-09-09 14:54:53 +02:00
net-irc
net-irc/atheme-services: Revbump to 7.2.9-r1
2017-09-06 12:58:30 +02:00
net-libs
net-libs/gnutls: cleanup 3.3 series
2017-09-09 22:34:22 +03:00
net-mail
net-mail/amavis-logwatch: new revision with yet another bugfix patch.
2017-09-07 07:42:55 -04:00
net-misc
net-misc/quagga: arm stable, bug #630088
2017-09-09 12:26:56 +02:00
net-nds
net-nds/openldap: update link to wiki
2017-09-03 00:14:59 +10:00
net-news
net-news/newsbeuter: remove old
2017-08-24 05:22:10 -04:00
net-nntp
net-nntp/nzbget: remove old
2017-09-03 00:55:11 +02:00
net-p2p
net-p2p/classified-ads: remove bogus dev-qt/qt-mobility dependency
2017-09-10 02:13:39 +10:00
net-print
net-print/cups-filters: Removed old.
2017-09-08 12:08:48 +02:00
net-proxy
net-proxy/dante: use https for HOMEPAGE and SRC_URI
2017-08-31 10:30:41 -04:00
net-voip
net-voip/telepathy-gabble: fix build with USE=-jingle, bug #523230
2017-09-02 20:00:47 +02:00
net-vpn
net-vpn/wireguard: version bump
2017-09-07 16:51:19 +02:00
net-wireless
net-wireless/broadcom-sta: Remove myself as a maintainer
2017-09-09 13:33:43 -07:00
perl-core
perl-core/File-Path: arm stable, bug #620304
2017-08-08 22:39:40 +02:00
profiles
profiles: Mask vanilla use flag for sys-libs/glibc
2017-09-09 21:22:28 +02:00
ros-meta
ros-meta/rosbridge_suite: Bump to 0.8.1.
2017-09-01 13:18:38 +02:00
sci-astronomy
sci-astronomy/xephem: remove 3.7.6
2017-09-03 01:10:29 +10:00
sci-biology
sci-biology/pysam: Fix broken relative -I
2017-09-02 20:35:42 +02:00
sci-calculators
sci-calculators/datamash: Fix patch/drop autotools.eclass.
2017-08-24 00:09:31 +02:00
sci-chemistry
sci-chemistry/votca-ctp: add ref
2017-09-04 12:06:02 -06:00
sci-electronics
sci-electronics/klayout: switch to ruby22 due to ruby21 removal
2017-08-20 10:59:18 +02:00
sci-geosciences
sci-geosciences/qgis: Try to fix bug #612956
2017-09-10 01:17:57 +02:00
sci-libs
sci-libs/votca-moo: initial commit
2017-09-03 08:54:54 -06:00
sci-mathematics
sci-mathematics/isabelle: use HTTPS for links to dev.gentoo.org
2017-09-06 22:59:17 +02:00
sci-misc
sci-misc/boinc: New ebuild for series 7.8 client version 7.8.1
2017-08-19 21:01:29 +02:00
sci-physics
sci-physics/lammps: version bump
2017-09-08 10:38:29 -06:00
sci-visualization
sci-visualization/visit: remove unused patches
2017-09-02 12:13:11 +02:00
scripts
…
sec-policy
sec-policy: Release of SELinux policies 2.20170805-r1
2017-09-09 17:25:00 +08:00
sys-apps
sys-apps/sydbox: ptrace()-based sandbox from Exherbo
2017-09-09 23:11:23 +02:00
sys-auth
sys-auth/google-authenticator: Revision bump to distribute latest changes
2017-09-07 21:16:03 +00:00
sys-block
sys-block/partitionmanager: Cleanup ancient blocker
2017-09-06 18:58:00 +02:00
sys-boot
sys-boot/grub: update metadata to list me as the maintainer of grub-legacy
2017-09-01 16:17:43 -04:00
sys-cluster
sys-cluster/kubelet: Remove old
2017-09-08 23:41:34 +02:00
sys-devel
sys-devel/flex: allow user patches for cases like #628744
2017-09-09 09:28:14 +01:00
sys-fabric
sys-fabric/librdmacm: keyworded 1.0.18-r1 for ppc, bug #611280
2017-08-13 11:51:36 +01:00
sys-firmware
sys-firmware/seabios: stabilize on amd64, x86, bug #625614
2017-08-31 20:06:08 -05:00
sys-freebsd
…
sys-fs
sys-fs/quota: Add missing dependency
2017-09-09 21:19:57 +02:00
sys-kernel
sys-kernel/linux-headers: add ~arm, bug #626640
2017-09-08 22:08:45 +02:00
sys-libs
sys-libs/glibc: D'oh (1).
2017-09-09 23:43:23 +02:00
sys-power
sys-power/upower: stable 0.99.5 for ia64, bug #630358
2017-09-09 12:53:02 +01:00
sys-process
sys-process/vixie-cron: Fix SELinux support
2017-09-05 15:50:37 +08:00
virtual
Revert "virtual/mysql: Drop old"
2017-09-03 14:53:58 -04:00
www-apache
www-apache/mod_evasive: Update HOMEPAGE
2017-08-27 14:19:16 +02:00
www-apps
www-apps/gitea: Version bump to 1.1.4
2017-09-08 23:54:30 +02:00
www-client
www-client/opera-beta: Old.
2017-09-07 22:40:29 +02:00
www-misc
www-misc/multisort: Shorter DESCRIPTION
2017-08-06 15:41:52 +02:00
www-plugins
www-plugins/chrome-binary-plugins: automated update (61.0.3163.79, 61.0.3163.79)
2017-09-06 08:52:00 -04:00
www-servers
www-servers/caddy: Version bump to 0.10.7
2017-09-09 00:01:45 +02:00
x11-apps
x11-apps/fusion-icon: remove redundant long description
2017-09-10 00:14:19 +10:00
x11-base
x11-base/xorg-server: remove unused patch
2017-09-04 13:00:05 -07:00
x11-drivers
x11-drivers/xf86-video-ati: Removed old.
2017-09-08 12:53:58 +02:00
x11-libs
x11-libs/pango: stable 1.40.6 for sparc, bug #624312 (thank to Dakon)
2017-09-09 20:23:24 +01:00
x11-misc
x11-misc/compton: add missing maintainer-needed comment to metadata
2017-09-09 21:55:30 +03:00
x11-plugins
x11-plugins/compiz-plugins-unsupported: use HTTPS for links to dev.gentoo.org
2017-09-06 22:59:31 +02:00
x11-proto
x11-proto/evieext: Remove last-rited pkg, #615314
2017-08-16 12:21:40 +02:00
x11-terms
x11-terms/st: Switch to HTTPS.
2017-08-31 12:30:57 +02:00
x11-themes
x11-themes/adwaita-qt: Stabilize
2017-09-08 15:46:16 +02:00
x11-wm
x11-wm/muffin: New upstream version 3.4.1
2017-09-05 21:43:34 +02:00
xfce-base
xfce-base/xfconf: Run tests with -j1 due to race condition
2017-09-05 19:13:11 +02:00
xfce-extra
xfce-extra/xfce4-xkb-plugin: Bump to 0.8.1
2017-09-09 09:23:33 +02:00
.gitignore
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header.txt
…
skel.ebuild
…
skel.metadata.xml
…
S
Description
No description provided
9.8 GiB
Languages
Shell 98%
Roff 1.3%
Emacs Lisp 0.2%
C 0.1%