gentoo resync : 15.09.2019

8 files changed, 133 insertions, 156 deletions

diff --git a/profiles/Manifest.gz b/profiles/Manifest.gz
index 65a5bc3f2fa2..070f740b8652 100644
--- a/profiles/Manifest.gz
+++ b/profiles/Manifest.gz
diff --git a/profiles/arch/arm/make.defaults b/profiles/arch/arm/make.defaults
index 3da266c294fb..972d7a5a46af 100644
--- a/profiles/arch/arm/make.defaults
+++ b/profiles/arch/arm/make.defaults
@@ -23,6 +23,3 @@ VIDEO_CARDS="exynos fbdev omap"
 # Unhide the ARM-specific USE_EXPANDs.
 USE_EXPAND_HIDDEN="-CPU_FLAGS_ARM"
 
-# Hans de Graaff <graaff@gentoo.org) (2019-07-17)
-# Temporary RUBY_TARGETS for bug 688976
-RUBY_TARGETS="ruby24 -ruby25"
diff --git a/profiles/arch/arm/use.stable.mask b/profiles/arch/arm/use.stable.mask
index 08dc0f3696fe..6f5daaad02d2 100644
--- a/profiles/arch/arm/use.stable.mask
+++ b/profiles/arch/arm/use.stable.mask
@@ -8,10 +8,6 @@
 # Dependencies not yet stable.
 ayatana
 
-# Hans de Graaff <graaff@gentoo.org> (2019-07-17)
-# Temporary mask for stable bug 688976
-ruby_targets_ruby25
-
 # Thomas Deutschmann <whissi@gentoo.org> (2019-06-08)
 # Needs dev-lang/php:7.3 stable
 php_targets_php7-3
diff --git a/profiles/arch/arm64/package.use.mask b/profiles/arch/arm64/package.use.mask
index a3e5b667dbe5..250a9f78ce22 100644
--- a/profiles/arch/arm64/package.use.mask
+++ b/profiles/arch/arm64/package.use.mask
@@ -1,18 +1,6 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-# Andreas Sturmlechner <asturm@gentoo.org> (2019-09-06)
-# dev-qt/qtgamepad is not keyworded yet
-dev-qt/qt3d gamepad
-
-# Andreas Sturmlechner <asturm@gentoo.org> (2019-08-18)
-# media-video/pipewire is not keyworded yet
-dev-libs/weston pipewire
-kde-apps/krfb wayland
-kde-plasma/xdg-desktop-portal-kde screencast
-sys-apps/xdg-desktop-portal screencast
-x11-wm/mutter screencast
-
 # Aaron Bauman <bman@gentoo.org> (2019-08-05)
 # dep not keyworded here
 media-gfx/gnome-photos upnp-av
diff --git a/profiles/arch/arm64/package.use.stable.mask b/profiles/arch/arm64/package.use.stable.mask
index 91094955c621..dfeac18eaec8 100644
--- a/profiles/arch/arm64/package.use.stable.mask
+++ b/profiles/arch/arm64/package.use.stable.mask
@@ -1,6 +1,14 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
+# Andreas Sturmlechner <asturm@gentoo.org> (2019-09-14)
+# media-video/pipewire is not stable yet
+dev-libs/weston pipewire
+kde-apps/krfb wayland
+kde-plasma/xdg-desktop-portal-kde screencast
+sys-apps/xdg-desktop-portal screencast
+x11-wm/mutter screencast
+
 # Aaron Bauman (2019-08-01)
 # app-text/docbook2X fails test
 dev-cpp/libcmis man
diff --git a/profiles/base/package.use.mask b/profiles/base/package.use.mask
index 83f2781aa51a..bb2dc3c56112 100644
--- a/profiles/base/package.use.mask
+++ b/profiles/base/package.use.mask
@@ -7,6 +7,11 @@
 # This file is only for generic masks. For arch-specific masks (i.e.
 # mask everywhere, unmask on arch/*) use arch/base.
 
+# Craig Andrews <candrews@gentoo.org> (2019-09-12)
+# OpenSSL (as of version 1.1.1) doesn't have APIs for QUIC support
+# see https://github.com/openssl/openssl/pull/8797
+net-libs/ngtcp2 ssl
+
 # Michał Górny <mgorny@gentoo.org> (2019-09-08)
 # LLVM 5 is being removed.
 ~dev-ada/gps-2018 gnat_2017
diff --git a/profiles/package.mask b/profiles/package.mask
index 24d40d50d64d..0f3d726bf5a2 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,6 +29,106 @@
 
 #--- END OF EXAMPLES ---
 
+# Zac Medico <zmedico@gentoo.org> (2019-09-14)
+# No reverse dependencies.
+# Removal in 30 days.  Bug #694390.
+dev-go/go-oauth2
+
+# Zac Medico <zmedico@gentoo.org> (2019-09-14)
+# No reverse dependencies.
+# Removal in 30 days.  Bug #694392.
+dev-go/go-protobuf
+
+# Michał Górny <mgorny@gentoo.org> (2019-09-14)
+# Unmaintained.  All of them were not bumped since 2016.  No reverse
+# dependencies.
+# Removal in 30 days.  Bug #694398.
+dev-go/cli
+dev-go/go-gitlab-client
+dev-go/toml
+
+# Michał Górny <mgorny@gentoo.org> (2019-09-14)
+# sci-biology/goby has been removed.  This package makes little sense
+# without it.
+# Removal in 30 days.
+sci-biology/goby-cpp
+
+# Michał Górny <mgorny@gentoo.org> (2019-09-14)
+# Unmaintained.  Vulnerable to arbitrary code execution.  Debian (being
+# its current upstream) removed it.  The recommended replacement
+# is net-misc/dhcpcd.
+# Removal in 30 days.  Bug #694314.
+net-misc/pump
+
+# Thomas Sachau <tommy@gentoo.org> (2019-09-14)
+# Freemail has been completly rewritten so the current
+# ebuild does no longer work for it. In addition the source
+# has moved. So masking for removal.
+# Removal in 30 days. Bug #628914
+net-mail/Freemail
+
+# Michał Górny <mgorny@gentoo.org> (2019-09-14)
+# The following packages are unmaintained and have not been tested
+# with Python 3.7.  Most of them are either in need of version bumps,
+# a few have been declared discontinued upstream.  None of them has
+# any reverse dependency.
+# Removal in 30 days.  Bug #694280.
+dev-python/attrdict
+dev-python/behave
+dev-python/cfgio
+dev-python/django-opensearch
+dev-python/django-otp-yubikey
+dev-python/django-phonenumber-field
+dev-python/grafanalib
+dev-python/libasyncns-python
+dev-python/maybe
+dev-python/mockredispy
+dev-python/parse
+dev-python/parse-type
+dev-python/pyClamd
+dev-python/pycallgraph
+dev-python/pyroma
+dev-python/pytest-raisesregexp
+dev-python/python-consul
+dev-python/python-ptrace
+dev-python/pyuv
+dev-python/safety
+dev-python/sphinxcontrib-cheeseshop
+dev-python/structlog
+dev-python/torment
+dev-python/twilio
+dev-python/xonsh
+dev-python/yubiotp
+
+# Michał Górny <mgorny@gentoo.org> (2019-09-14)
+# The following packages are unmaintained and do not declare support
+# for Python 3.  Most of them are either in need of version bumps,
+# or are dead upstream (haven't had a release since 2009-2015).
+# None of them have any reverse dependencies.
+# Removal in 30 days.  Bug #694280.
+dev-python/Ming
+dev-python/casuarius
+dev-python/imdbpy
+dev-python/kaa-base
+dev-python/kaa-display
+dev-python/kaa-imlib2
+dev-python/kaa-metadata
+dev-python/larch
+dev-python/pybloomfiltermmap
+dev-python/pylirc
+dev-python/pyringe
+dev-python/pystdf
+dev-python/python-dsv
+dev-python/python-gudev
+dev-python/python-spidermonkey
+dev-python/python-virtkey
+dev-python/rtf2xml
+dev-python/tmdb3
+dev-python/tracing
+dev-python/txsocksx
+dev-python/wsgilog
+dev-python/xmpppy
+
 # Michał Górny <mgorny@gentoo.org> (2019-09-13)
 # Last bumped in 2017.  Newer version fails to fetch.  Pending bump.
 # Unresolved license issues.
@@ -218,11 +318,6 @@ dev-libs/libmongo-client
 dev-libs/libmail
 
 # Michał Górny <mgorny@gentoo.org> (2019-09-12)
-# Unmaintained.  Last release in 2010.  No reverse dependencies.
-# Removal in 30 days.  Bug #694190.
-dev-libs/liblzw
-
-# Michał Górny <mgorny@gentoo.org> (2019-09-12)
 # Unmaintained.  Last release in 2009.  No reverse dependencies.
 # Removal in 30 days.  Bug #694188.
 dev-libs/libidmef
@@ -651,12 +746,8 @@ sys-cluster/lspbs
 # sci-mathematics/kodkod: reported to fail to build.  Last bumped
 # in 2012.  Homepage is gone, and sources are nowhere to be found.
 #
-# sci-mathematics/kodkodi: the only revdep of the above.  Last release
-# in 2012.  No reverse dependencies.
-#
 # Removal in 30 days.  Bug #685802.
 sci-mathematics/kodkod
-sci-mathematics/kodkodi
 
 # Michał Górny <mgorny@gentoo.org> (2019-09-07)
 # Unmaintained.  Not bumped since 2011.
@@ -958,12 +1049,6 @@ dev-tcltk/tkTheme
 # Removal in 30 days.  Bug #681044.
 net-misc/tokyotyrant
 
-# Michał Górny <mgorny@gentoo.org> (2019-08-27)
-# Live ebuild committed in Oct 2018, and not updated since.  Suffers
-# from numerous QA violations.  Never had a keyworded version.
-# Removal in 14 days.  Bug #692048.
-net-misc/hblink
-
 # Ulrich Müller <ulm@gentoo.org> (2019-08-26)
 # A more recent version of thumbs.el is distributed
 # as part of GNU Emacs proper.
@@ -1008,12 +1093,6 @@ virtual/ruby-ffi
 # Depends on >=virtual/{jdk,jre}-11 which is masked
 =www-servers/tomcat-9.0.24
 
-# Michael Orlitzky <mjo@gentoo.org> (2019-08-18)
-# Ebuilds contain a two-year old root exploit. Less-than-maintained
-# since robbat2's announcement on 2017-11-30. Binary package to begin
-# with. Masked for removal eventually, https://bugs.gentoo.org/630808
-app-misc/dnetc
-
 # Mart Raudsepp <leio@gentoo.org> (2019-08-18)
 # Fails to dbus activate properly for me. Help welcome figuring it out.
 net-misc/gnome-remote-desktop
@@ -1035,95 +1114,6 @@ net-misc/openrdate
 # Lots of new versions upstream. Removal in 30 days.
 dev-embedded/bitbake
 
-# Michał Górny <mgorny@gentoo.org> (2019-08-15)
-# Unmaintained, PPC-only.  The Gentoo version is outdated, ebuild
-# is still EAPI=0 and has QA violations.  Last upstream release in 2009,
-# declared EOL since then.
-# Removal in 30 days.  Bug #692202.
-dev-lang/pasm
-
-# Aaron Bauman <bman@gentoo.org> (2019-08-14)
-# sec bug #636976, unmaintained in Gentoo, license
-# forked multiple times. Removal in 30 days.
-dev-java/itext
-app-text/jpdftweak
-dev-util/deskzilla
-media-sound/tuxguitar
-sci-mathematics/isabelle
-sci-chemistry/jmol
-sci-mathematics/cvc3
-sci-mathematics/e
-sci-mathematics/kodkodi
-sci-mathematics/spass
-
-# Michał Górny <mgorny@gentoo.org> (2019-08-14)
-# No longer builds.  Homepage is gone, and its keep-alive fork is also
-# dead.
-# Removal in 30 days.  Bug #691840.
-sys-apps/lomoco
-
-# Aaron Bauman <bman@gentoo.org> (2019-08-14)
-# open sec bug #622428, unmaintained
-# list includes rdeps. Removal in 30 days.
-dev-java/xstream
-dev-java/jsap
-net-misc/java-wakeonlan
-sci-biology/goby
-
-# Aaron Bauman <bman@gentoo.org> (2019-08-14)
-# longstanding sec vulns, unpatched, not maintained
-# bug #509354, #519216, #603440
-# list includes rdeps. Removal in 30 days.
-dev-java/smack
-dev-java/netbeans-ide
-dev-java/netbeans-apisupport
-dev-java/netbeans-cnd
-dev-java/netbeans-dlight
-dev-java/netbeans-enterprise
-dev-java/netbeans-enterprise
-dev-java/netbeans-ergonomics
-dev-java/netbeans-extide
-dev-java/netbeans-groovy
-dev-java/netbeans-java
-dev-java/netbeans-java
-dev-java/netbeans-javacard
-dev-java/netbeans-javadoc
-dev-java/netbeans-javafx
-dev-java/netbeans-mobility
-dev-java/netbeans-nb
-dev-java/netbeans-php
-dev-java/netbeans-profiler
-dev-java/netbeans-webcommon
-dev-java/netbeans-websvccommon
-dev-util/netbeans
-
-# Aaron Bauman <bman@gentoo.org> (2019-08-14)
-# open sec bug #612914, unmaintained
-# Removal in 30 days
-dev-java/logback
-
-# Aaron Bauman <bman@gentoo.org> (2019-08-14)
-# open sec bug #607720, unmaintained
-# Removal in 30 days
-dev-java/svgsalamander
-dev-java/flyingsaucer
-
-# Aaron Bauman <bman@gentoo.org> (2019-08-14)
-# open sec bug #605690, unmaintained
-# Removal in 30 days
-dev-java/groovy
-app-misc/freemind
-
-# Aaron Bauman <bman@gentoo.org> (2019-08-14)
-# open sec bug #576874, unmaintained in Gentoo
-# no rdeps. Removal in 30 days
-dev-java/kryo
-
-# Andreas K. Hüttel <dilfridge@gentoo.org> (2019-08-14)
-# EAPI=2, ages old, effectively unmaintained. Gone in
-# 30 days. Bug 688154
-dev-java/jlayer
-
 # Mike Gilbert <floppym@gentoo.org> (2019-08-13)
 # Dev channel releases are only for people who
 # are developers or want more experimental features
diff --git a/profiles/use.local.desc b/profiles/use.local.desc
index 112da19b9d8b..5c72dce571c9 100644
--- a/profiles/use.local.desc
+++ b/profiles/use.local.desc
@@ -942,10 +942,6 @@ app-misc/digitemp:ds9097u - Build support for the ds9097u sensor
 app-misc/elasticsearch:x-pack - Enable additional features (may need a license)
 app-misc/emelfm2:ansi - Add support for ANSI escape sequences
 app-misc/emelfm2:gtk3 - Use x11-libs/gtk+:3 instead of x11-libs/gtk+:2
-app-misc/freemind:groovy - Build plugin for scripting via Groovy
-app-misc/freemind:latex - Build plugin for inserting mathematical formulas in LaTeX syntax
-app-misc/freemind:pdf - Build plugin for exporting mindmaps to SVG and PDF
-app-misc/freemind:svg - Build plugin for exporting mindmaps to SVG and PDF
 app-misc/g810-led:hidapi - Use dev-libs/hidapi instead of virtual/libusb for talking to the device (advertised to be faster)
 app-misc/gcstar:stats - Enable statistics reporting
 app-misc/gcstar:tellico - Enable support for kde-misc/tellico files
@@ -1894,8 +1890,6 @@ dev-java/icedtea-bin:webstart - Provide javaws command through symlink to icedte
 dev-java/icedtea-web:javascript - Enable support for using proxy auto config (PAC) files.
 dev-java/icedtea-web:nsplugin - Enable the browser plugin (NPPlugin).
 dev-java/icedtea-web:tagsoup - Depend on dev-java/tagsoup which allows parsing malformed .jnlp files
-dev-java/itext:rtf - Build and provide libraries for rich text format
-dev-java/itext:rups - Build and provide GUI for Reading/Updating PDF Syntax
 dev-java/jdbc-mysql:c3p0 - Enable c3p0 support
 dev-java/jdbc-mysql:log4j - Enable log4 support
 dev-java/jfreesvg:debug - Enable debugging during compilation.
@@ -1903,7 +1897,6 @@ dev-java/jna:awt - Enables support for Java AWT
 dev-java/jna:nio-buffers - Enables support for NIO buffers
 dev-java/log4j:javamail - Build the SMTPAppender
 dev-java/log4j:jms - Build the JMSAppender
-dev-java/logback:tomcat - Builds Apache Tomcat support
 dev-java/lucene:contrib - Include extra functionality from contrib/
 dev-java/miglayout:swt - Add support for the SWT toolkit.
 dev-java/openjdk:gentoo-vm - Allow this JDK to be recognised by Gentoo (package manager, eselect, java-config, EXPERIMENTAL!)
@@ -3842,6 +3835,8 @@ kde-apps/spectacle:share - Enable support for a share menu using kde-frameworks/
 kde-apps/step:qalculate - Enable the libqalculate library for unit conversion
 kde-apps/yakuake:absolute-position - Use kde-frameworks/kwayland for absolute window positioning in KWin
 kde-frameworks/frameworkintegration:appstream - Enable AppStream software metadata support
+kde-frameworks/kcompletion:designer - Build plugins for dev-qt/designer
+kde-frameworks/kconfigwidgets:designer - Build plugins for dev-qt/designer
 kde-frameworks/kconfigwidgets:man - Build and install man pages
 kde-frameworks/kded:man - Build and install man pages
 kde-frameworks/kdesignerplugin:designer - Build KF5 widgets plugin for QtDesigner
@@ -3849,25 +3844,33 @@ kde-frameworks/kdesignerplugin:webkit - Build kdewebkit plugin for QtDesigner
 kde-frameworks/kdewebkit:designer - Build plugins for dev-qt/designer
 kde-frameworks/kfilemetadata:epub - Enable support for reading EPUB ebook metadata
 kde-frameworks/kfilemetadata:office - Enable support for reading ODF and OOXML metadata
+kde-frameworks/kiconthemes:designer - Build plugins for dev-qt/designer
 kde-frameworks/kimageformats:eps - Support the EPS graphics file format
 kde-frameworks/kinit:caps - Capabilities support for improved security and better OOM handling
 kde-frameworks/kinit:man - Build and install man pages
+kde-frameworks/kio:designer - Build plugins for dev-qt/designer
 kde-frameworks/kio:kwallet - Enable permanent storage of passwords for kpasswdserver with kde-frameworks/kwallet
+kde-frameworks/kitemviews:designer - Build plugins for dev-qt/designer
 kde-frameworks/knotifications:phonon - Play notification sounds via media-libs/phonon instead of media-libs/libcanberra
 kde-frameworks/knotifications:speech - Enable text-to-speech notification support
 kde-frameworks/knotifyconfig:phonon - Add sound support via media-libs/phonon
 kde-frameworks/kpackage:man - Build and install man pages
+kde-frameworks/kplotting:designer - Build plugins for dev-qt/designer
 kde-frameworks/kservice:man - Build and install man pages
 kde-frameworks/ktexteditor:editorconfig - Enable support for EditorConfig configuration files
+kde-frameworks/ktextwidgets:designer - Build plugins for dev-qt/designer
 kde-frameworks/ktextwidgets:speech - Enable text-to-speech support
 kde-frameworks/kwallet:gpg - Support wallets with GnuPG encryption in addition to the default blowfish-encrypted file
 kde-frameworks/kwallet:man - Build and install man pages
+kde-frameworks/kwidgetsaddons:designer - Build plugins for dev-qt/designer
 kde-frameworks/kxmlgui:attica - Enable support for kde-frameworks/attica
+kde-frameworks/kxmlgui:designer - Build plugins for dev-qt/designer
 kde-frameworks/networkmanager-qt:teamd - Enable Teamd control support
 kde-frameworks/plasma:gles2 - Use GLES 2.0 or later instead of full OpenGL
 kde-frameworks/prison:qml - Enable QML/QtQuick support via dev-qt/qtdeclarative
 kde-frameworks/purpose:kaccounts - Enable support for system-wide defined KAccounts
 kde-frameworks/sonnet:aspell - Enable the app-text/aspell spell-checking backend
+kde-frameworks/sonnet:designer - Build plugins for dev-qt/designer
 kde-frameworks/sonnet:hunspell - Enable the app-text/hunspell spell-checking backend
 kde-misc/kdeconnect:app - Enable experimental kcapp frontend
 kde-misc/kdeconnect:mousepad - Enable remote mousepad plugin using x11-libs/libfakekey
@@ -4330,7 +4333,7 @@ media-gfx/graphviz:X - Builds lefty front-end, builds plugin -Txlib, and enables
 media-gfx/graphviz:devil - Enables DevIL output plugin -Tdevil
 media-gfx/graphviz:gdk-pixbuf - Enables gdk-pixbuf2 plugin
 media-gfx/graphviz:gtk - Enables gtk+ output plugin -Tgtk (needs cairo)
-media-gfx/graphviz:gts - Enables support for gts
+media-gfx/graphviz:gts - Enables support for GNU Triangulated Surface Library (required for sfdp to work)
 media-gfx/graphviz:lasi - Enables PostScript output via media-libs/lasi, for plugin -Tlasi (needs cairo)
 media-gfx/gthumb:http - Enable webservice integration through net-libs/libsoup
 media-gfx/gthumb:json - Compile code that uses the libjson-glib library
@@ -5023,10 +5026,6 @@ media-sound/supercollider:vim - Enable the SCVIM user interface
 media-sound/teamspeak-server:tsdns - Install TeamSpeaks own DNS service for handling multiple virtual servers.
 media-sound/tomahawk:telepathy - Enable support for the real-time communication framework telepathy
 media-sound/traverso:lv2 - Add support for Ladspa V2
-media-sound/tuxguitar:fluidsynth - Enables Fluidsynth MIDI software synthesis (with external sound fonts). JSA must be disabled in the plug-ins menu to use this.
-media-sound/tuxguitar:lilypond - Exports the score in a lilypond compatible format.
-media-sound/tuxguitar:pdf - Exports the score as a PDF file using dev-java/itext.
-media-sound/tuxguitar:tray - Adds an icon to the tray that controls midi playback.
 media-sound/umurmur:mbedtls - Use net-libs/mbedtls as TLS provider
 media-sound/umurmur:shm - Enable shared memory support
 media-sound/upmpdcli:thirdparty - Enable streaming from Qobuz and Tidal external services
@@ -6579,6 +6578,7 @@ net-misc/cgminer:minion - Enable support for mining with BlackArrow Bitfury
 net-misc/cgminer:modminer - Enable support for mining with ModMiner FPGAs
 net-misc/cgminer:sp10 - Enable support for Spondoolies SP10
 net-misc/cgminer:sp30 - Enable support for Spondoolies SP30
+net-misc/chrome-remote-desktop:xrandr - Enable support for the XRandR extension for dynamic desktop resizing
 net-misc/chrony:adns - Support for asynchronous DNS
 net-misc/chrony:cmdmon - Support for command and monitoring
 net-misc/chrony:html - Install HTML documentation
@@ -6602,6 +6602,7 @@ net-misc/connman:wispr - Enable support for WISPr hotspot logins.
 net-misc/connman-gtk:openconnect - Support easier authentication to AnyConnect VPNs
 net-misc/crossbar:tor - include tor services connections support
 net-misc/csync:sftp - Enable sftp transfer support via net-libs/libssh
+net-misc/curl:alt-svc - Enable alt-svc support
 net-misc/curl:brotli - Enable brotli compression support
 net-misc/curl:http2 - Enabled HTTP/2.0 support
 net-misc/curl:metalink - Enable metalink support
@@ -6981,6 +6982,7 @@ net-p2p/eiskaltdcpp:libcanberra - Enable sound notifications support over libcan
 net-p2p/eiskaltdcpp:minimal - Don't install headers
 net-p2p/fms:frost - Add support for frost boards
 net-p2p/fms:ssl - Add support for FCP connection over SSL
+net-p2p/freenet:nss - Use nss for crypto operations, if it is the fastest way
 net-p2p/go-ethereum:devtools - Build Ethereum development tools (evm, abigen, puppeth, ...)
 net-p2p/go-ethereum:opencl - Add OpenCL GPU mining support
 net-p2p/ktorrent:bwscheduler - Schedule upload and download limits over a period of a week
@@ -7354,7 +7356,6 @@ sci-biology/clustalw-mpi:mpi_njtree - Use MPI (as opposed to serial) code for co
 sci-biology/clustalw-mpi:static_pairalign - Use static (as opposed to dynamic) scheduling for pair alignments
 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/goby:cpp - Compile C/C++ API
 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
@@ -7385,7 +7386,6 @@ sci-chemistry/gromacs:offensive - Enable gromacs partly offensive quotes
 sci-chemistry/gromacs:opencl - Enable opencl non-bonded kernels
 sci-chemistry/gromacs:single-precision - Single precision version of gromacs (default)
 sci-chemistry/gromacs:tng - Enable new trajectory format - tng
-sci-chemistry/jmol:client-only - Install the viewer only, no applet files for httpd
 sci-chemistry/molequeue:client - Build the client application
 sci-chemistry/molequeue:server - Build the serve application
 sci-chemistry/molequeue:zeromq - Build with net-libs/zeromq support
@@ -7717,14 +7717,14 @@ sci-libs/vtk:boost - Add support for boost
 sci-libs/vtk:cg - Use nvidia's cg shaders
 sci-libs/vtk:gdal - Support for gdal formated data
 sci-libs/vtk:imaging - Building Imaging modules
-sci-libs/vtk:json - Support for json formated data
+sci-libs/vtk:json - Support for json formatted data
 sci-libs/vtk:kaapi - Use sci-libs/xkaapi to handle smp support
 sci-libs/vtk:offscreen - Offscreen rendering through OSMesa
 sci-libs/vtk:rendering - Building Redering modules
 sci-libs/vtk:tbb - Use dev-cpp/tbb to handle smp support
 sci-libs/vtk:views - Building Views modules
 sci-libs/vtk:web - Install web component
-sci-libs/vtk:xdmf2 - Support for xdmf2 formated data
+sci-libs/vtk:xdmf2 - Support for xdmf2 formatted data
 sci-libs/xkaapi:blas - Kaapi BLAS tasks for PLASMA
 sci-libs/xkaapi:gpu - Build library for gpu threading
 sci-mathematics/Macaulay2:optimization - Accept upstream's choices for -O option, i.e. -O3 almost everywhere.
@@ -7736,13 +7736,10 @@ sci-mathematics/bertini:optimization - Accept upstream's choices for -O option.
 sci-mathematics/cgal:mpfi - Enable support for multiple recision interval arithmetic via sci-libs/mpfi
 sci-mathematics/cgal:ntl - Enable support for dev-libs/ntl
 sci-mathematics/coq:camlp5 - Build using camlp5. This is required for some plugins like Ssreflect.
-sci-mathematics/cvc3:isabelle - Add integration support for the Isabelle/HOL theorem prover.
-sci-mathematics/cvc3:zchaff - Use the SAT solver zchaff whose copyright is owned by Princeton University and is more restrictive (see zchaff license).
 sci-mathematics/cvc4:cln - Use sci-libs/cln
 sci-mathematics/cvc4:proofs - Support for proof generation
 sci-mathematics/cvc4:replay - Turn on the replay feature
 sci-mathematics/cvc4:statistics - Include statistics
-sci-mathematics/e:isabelle - Add integration support for the Isabelle/HOL theorem prover.
 sci-mathematics/flint:gc - Enable garbage collection support via dev-libs/boehm-gc
 sci-mathematics/flint:ntl - Build NTL interface
 sci-mathematics/form:devref - Build and install developers reference
@@ -7757,10 +7754,6 @@ sci-mathematics/geomview:motionaveraging - Enable experimental motion averaging
 sci-mathematics/gmp-ecm:custom-tune - Improve performance of some operations by selecting machine-specific defaults
 sci-mathematics/gretl:R - Enable support for dev-lang/R
 sci-mathematics/gsl-shell:fox - Build a x11-libs/fox GUI
-sci-mathematics/isabelle:graphbrowsing - Generate theory browsing information, including HTML documents that show a theory's definition, the theorems proved in its ML file and the relationship with its ancestors and descendants.
-sci-mathematics/isabelle:ledit - Use ledit for the isabelle tty line editor
-sci-mathematics/isabelle:readline - Use readline (rlwrap) for the isabelle tty line editor
-sci-mathematics/kodkodi:isabelle - Add integration support for the Isabelle/HOL theorem prover.
 sci-mathematics/maxima:clisp - Compile maxima with GNU CLISP (dev-lisp/clisp)
 sci-mathematics/maxima:clozurecl - Compile maxima with Clozure Common Lisp (dev-lisp/clozurecl)
 sci-mathematics/maxima:cmucl - Compile maxima with CMU Common Lisp (dev-lisp/cmucl)
@@ -7800,7 +7793,6 @@ sci-mathematics/rstudio:server - Build and install the RStudio server
 sci-mathematics/rw:executable - Build the 'rw' program.
 sci-mathematics/singular:boost - Compile against external boost headers (dev-libs/boost)
 sci-mathematics/slepc:complex-scalars - Make scalars complex
-sci-mathematics/spass:isabelle - Add integration support for the Isabelle/HOL theorem prover.
 sci-mathematics/unuran:prng - Use sci-mathematics/prng library
 sci-mathematics/unuran:rngstreams - Use sci-mathematics/rngstreams library
 sci-mathematics/why3-for-spark:coq - Add sci-mathematics/coq support
@@ -7913,7 +7905,7 @@ sci-visualization/veusz:fits - Add FITS format via dev-python/astropy
 sci-visualization/veusz:minuit - Use Minuit during fitting viadev-python/pyminuit
 sci-visualization/visit:cgns - Builds the reader for the CFD General Notation System file format.
 sci-visualization/visit:silo - Adds support for reading .silo files.
-sci-visualization/visit:xdmf2 - Support for xdmf2 formated data.
+sci-visualization/visit:xdmf2 - Support for xdmf2 formatted data.
 sci-visualization/yt:hub - Connect to the yt hub with dev-python/girder-client
 sec-policy/selinux-base:open_perms - Enable the open permissions for file object classes (SELinux policy capability).
 sec-policy/selinux-base:peer_perms - Enable the labeled networking peer permissions (SELinux policy capability).
@@ -8858,6 +8850,9 @@ www-apps/postfixadmin:vacation - Install vacation.pl script and dependencies
 www-apps/radicale:bcrypt - Depend on passlib to enable bcrypt and md5 authentication methods
 www-apps/redmine:markdown - Enable support for Markdown
 www-apps/redmine:passenger - Enable support for www-apache/passenger
+www-apps/roundup:tz - Enable full support of timezone
+www-apps/roundup:whoosh - Enable Whoosh full-text indexer
+www-apps/roundup:xapian - Enable Xapian full-text indexer
 www-apps/rt:lighttpd - Add www-servers/lighttpd support
 www-apps/sitebar:plugins - Install optional plugins
 www-apps/trac:highlight - Enable syntax highlighting
@@ -9111,11 +9106,9 @@ x11-libs/libfm:automount - Use gnome-base/gvfs for automounting
 x11-libs/libfm:udisks - Use libfm's udisks-based volume monitor implementation instead of using the one from gvfs
 x11-libs/libfm:vala - Support custom actions in menus
 x11-libs/libva:drm - Enables VA/DRM API support.
-x11-libs/libva:egl - Enables EGL support.
 x11-libs/libva:utils - Install VA-API utility programs.
 x11-libs/libva-compat:drm - Enables VA/DRM API support.
 x11-libs/libva-compat:egl - Enables EGL support.
-x11-libs/libva-intel-driver:drm - Enables VA/DRM API support.
 x11-libs/libwnck:tools - Install wnckprop-3 and wnck-urgency-monitor-3 command-line tools
 x11-libs/libxcb:xkb - Enable the XCB keyboard extension
 x11-libs/motif:motif22-compatibility - Compatibility with Open Motif 2.2