Merge remote-tracking branch 'github/master'

* github/master:
  sci-chemistry/freeon: Drop obsolete versions
  Moved to tree
  sci-physics/root: Fix compilation with USE="mysql" wrt bug #523996; fix die_compiler message
  sync with gx86
  net-libs/xrootd: version bump and fix bug 521496
  travis.yml: use newer portage version
  fixed bash-comp (bug #526320)
  version bump

39 files changed, 657 insertions, 749 deletions

diff --git a/.travis.yml b/.travis.yml
index ec1e792da..84e0f787d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,18 +2,18 @@ before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
-    - wget "http://distfiles.gentoo.org/distfiles/portage-2.2.10.tar.bz2"
+    - wget "http://distfiles.gentoo.org/distfiles/portage-2.2.12.tar.bz2"
     - wget "http://distfiles.gentoo.org/snapshots/portage-latest.tar.xz"
     - sudo chmod 777 /etc/passwd /etc/group /etc /usr
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
     - mkdir -p /etc/portage/ /usr/portage/distfiles
-    - tar xjf portage-2.2.10.tar.bz2
+    - tar xjf portage-2.2.12.tar.bz2
     - tar xJf portage-latest.tar.xz -C /usr/
-    - cp portage-2.2.10/cnf/repos.conf /etc/portage/
+    - cp portage-2.2.12/cnf/repos.conf /etc/portage/
     - rsync --recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --checksum --quiet rsync://rsync.gentoo.org/gentoo-portage /usr/portage
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
     - cd travis-overlay
-    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.10/bin/repoman
+    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.12/bin/repoman
 script: 
-    - "./../portage-2.2.10/bin/repoman full -d -v"
+    - "./../portage-2.2.12/bin/repoman full -d -v"
diff --git a/dev-lang/ispc/ChangeLog b/dev-lang/ispc/ChangeLog
index e81a15906..529d48d08 100644
--- a/dev-lang/ispc/ChangeLog
+++ b/dev-lang/ispc/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Oct 2014; Christoph Junghans <ottxor@gentoo.org> ispc-9999.ebuild:
+  sync with gx86
+
   12 May 2014; Christoph Junghans <ottxor@gentoo.org> ispc-9999.ebuild:
   sync with gx86
 
diff --git a/dev-lang/ispc/ispc-9999.ebuild b/dev-lang/ispc/ispc-9999.ebuild
index c859a817b..793182dca 100644
--- a/dev-lang/ispc/ispc-9999.ebuild
+++ b/dev-lang/ispc/ispc-9999.ebuild
@@ -36,6 +36,7 @@ DEPEND="
 	"
 
 src_compile() {
+	sed -i '/^\t@/s/@//' Makefile || die #make all slient commands ("@") verbose
 	emake LDFLAGS="${LDFLAGS}" OPT="${CXXFLAGS}" CXX="$(tc-getCXX)" CPP="$(tc-getCPP)"
 }
 
diff --git a/net-libs/xrootd/ChangeLog b/net-libs/xrootd/ChangeLog
new file mode 100644
index 000000000..0c0326fcd
--- /dev/null
+++ b/net-libs/xrootd/ChangeLog
@@ -0,0 +1,118 @@
+# ChangeLog for net-libs/xrootd
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/ChangeLog,v 1.19 2014/06/19 18:13:17 bicatali Exp $
+
+*xrootd-4.0.0 (19 Jun 2014)
+
+  19 Jun 2014; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-4.0.0.ebuild:
+  Version bump
+
+  11 Mar 2014; Patrick Lauer <patrick@gentoo.org> xrootd-3.3.6.ebuild:
+  Whitespace
+
+*xrootd-3.3.6 (10 Mar 2014)
+
+  10 Mar 2014; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.6.ebuild:
+  Version bump
+
+  20 Nov 2013; Patrick Lauer <patrick@gentoo.org> xrootd-3.3.4.ebuild:
+  Whitespace
+
+*xrootd-3.3.4 (19 Nov 2013)
+
+  19 Nov 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.4.ebuild,
+  -xrootd-3.3.1.ebuild, metadata.xml:
+  Version bump
+
+*xrootd-3.3.2 (04 Jun 2013)
+
+  04 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.2.ebuild,
+  -xrootd-3.2.7.ebuild, files/cmsd.initd, files/frm_purged.initd,
+  files/frm_xfrd.initd:
+  Version bump. Keyword amd64-linux and x86-linux. Fixed non-bashism in init
+  scripts
+
+*xrootd-3.3.1 (23 Mar 2013)
+
+  23 Mar 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.1.ebuild,
+  -xrootd-3.2.6.ebuild:
+  Version bump
+
+*xrootd-3.2.7 (24 Jan 2013)
+
+  24 Jan 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.7.ebuild:
+  Version bump
+
+  05 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> xrootd-3.2.6.ebuild:
+  add user eclass
+
+*xrootd-3.2.6 (05 Dec 2012)
+
+  05 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.6.ebuild,
+  -xrootd-3.2.2.ebuild, -xrootd-3.2.4.ebuild, files/cmsd.initd,
+  files/frm_purged.initd, files/frm_xfrd.initd, files/xrootd.initd,
+  metadata.xml, xrootd-3.2.1.ebuild:
+  Version bump. Transfering checks on /var/run and /var/spool at install time to
+  run-time (bug #445882)
+
+*xrootd-3.2.4 (29 Sep 2012)
+
+  29 Sep 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.4.ebuild:
+  Version bump
+
+  24 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/xrootd-3.2.2-glibc216.patch, xrootd-3.2.2.ebuild:
+  fixed for glibc-2.16, bug #426300
+
+*xrootd-3.2.2 (09 Jul 2012)
+
+  09 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.2.ebuild:
+  Version bump
+
+  09 Jul 2012; Justin Lecher <jlec@gentoo.org> -xrootd-3.1.0.ebuild,
+  -xrootd-3.1.1.ebuild, xrootd-3.2.1.ebuild, metadata.xml:
+  Cleaned old, add missing eclass
+
+  08 Jul 2012; Jeff Horelick <jdhore@gentoo.org> xrootd-3.2.1.ebuild:
+  marked x86 per bug 425054
+
+  06 Jul 2012; Agostino Sarubbo <ago@gentoo.org> xrootd-3.2.1.ebuild:
+  Stable for amd64, wrt bug #425054
+
+*xrootd-3.2.1 (22 May 2012)
+
+  22 May 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.1.ebuild:
+  Version bump
+
+*xrootd-3.1.1 (06 Mar 2012)
+
+  06 Mar 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.1.1.ebuild:
+  Version bump
+
+  19 Dec 2011; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.1.0.ebuild,
+  +files/cmsd.confd, +files/cmsd.initd, +files/frm_purged.initd,
+  +files/frm_xfrd.initd, +files/xrootd.confd, +files/xrootd.initd,
+  +metadata.xml:
+  Initial import to the main tree
+
+*xrootd-3.1.0 (03 Dec 2011)
+
+  03 Dec 2011; Andrew Savchenko <bircoph@gmail.com> +xrootd-3.1.0.ebuild,
+  +files/cmsd.initd, +files/frm_purged.initd, +files/frm_xfrd.initd,
+  +files/xrootd.confd, +files/xrootd.initd, +metadata.xml:
+  XRootD isn't really a new program in this overlay. It was
+  previously bundled within sci-physics/root, but now it is unbundled
+  upstream and needs to be installed as a separate package in order
+  to be used from ROOT.
+
+  Aside from standard xrootd distribution, this ebuild may install
+  useful pdf documentation from the official web site.
+
+  Program was tested on ~x86 and ~amd64 with some basic setup, though
+  no real production tests were done. Please note, that xrootd and
+  accompany daemons do not work with root privileges any longer, so
+  special xrootd user was used.
+
+  Another note: all daemons MUST use the same config (-c
+  /etc/xrootd/your._config), that's why there is only one conf.d file
+  for all four daemons.
diff --git a/net-libs/xrootd/Manifest b/net-libs/xrootd/Manifest
new file mode 100644
index 000000000..c6ff158bb
--- /dev/null
+++ b/net-libs/xrootd/Manifest
@@ -0,0 +1,11 @@
+AUX cmsd.confd 193 SHA256 50e9c05d9090498853f8d34a7676228a1670a8c8512254151139ae6de876bee3 SHA512 f2e1b55eb27a59f32211eb5d839428fd4155c59898a38949bc4013be6b5f560fed795623e9401c4540382243314c257ca1007a089a57a5610b97e89f676f1408 WHIRLPOOL d377fc399aecc760d610ce34984647dca1364c051ff7dacd9cb8d7a23e4dadf7ca96c546d44cf294cbbee19c91464b2042907ff660e6158399baddff937b1093
+AUX cmsd.initd 993 SHA256 3aad47f4949da37d97ef08068435121b7e861a5b89fe13ad7633a065e2954ec8 SHA512 eaef2f79b0b999935ae68e2ecb391cb335550f32e0325661e84ef86c600d930874fff3893d3c0debc751dac843eaccda7d02a40c00d3e38b1087891dd61d36e7 WHIRLPOOL 32c8a21ca06bccd59c5cf7e9ace354e41c588e7df68d3ca82bef160cfc5ee876a401b4cdd4c0418b5e433cd6392ccb98fbf37341855f5527ec77c3a19daf3bde
+AUX frm_purged.initd 1009 SHA256 948236ba61ab7d3c932a2a8159bf2da4864c3ce4ee3900ec3f2ac596dff7c1cf SHA512 945080c25b30ab9d82cf60134631f6fcbb7cd19708115ee5efc988386f7a198888e5328bd053ab4541d8d14003a3e96894834e7284344dae22021723576a802a WHIRLPOOL 2f46a6b856c35df4e33c1cfc800f55676c72c57f616afa60bab01f672638d1691641f3eae23a23113f9d9ab16cad47ea7cc2c153d784c77eb48b4877f1c3685f
+AUX frm_xfrd.initd 1011 SHA256 04d3395ebfe826e22e4c48fb5c6861f07807ed85204f28020f8fe5a622c31e09 SHA512 abe8dda53a6750959fa250c0d2aba32564c99f2585910332f2d9c3daf8187bbcaca7e5673648e96f385ac2b8c8b871ce1546f8b34c5be65f522d5e3a2afc177d WHIRLPOOL 17e5922c3da70bbd0083d9c51ea08a50669c9ae122df737535d37196f7cf2e5a39abfd8f590dbc62fe688304f58986a924a53c7758f1d0c5cff463691f51053d
+AUX xrootd-no-werror.patch 559 SHA256 ce4eb50998227d239437c76c993a691c3b04cd88e86ee100e5d1e578b2d0a4ed SHA512 993b18aaf851fb7115073acfd2f653c0e8e2df77ca9c4f7daf17d62e57d1ff7a8d1e548466c1a3cb014a563761a02b27ded3e2fdddd6be97570a8086c7e7da58 WHIRLPOOL 8bf01d9bef5601153e5442b58825cf9722e7e7f755a1abf24f1a12f030ee3c2fffbb6819d8ea25fc674734c23dc3dfffb989925fc1de63887b41eebc5cf79dce
+AUX xrootd.confd 651 SHA256 c0bec135fc63da3000a520ebe1cffec7e507f4f31e9038f7ef4350f973548785 SHA512 60ab5b6d77cf79437960044bf201127c8adf5134e7f61a18dcccd2e474a4e41eda971e3ada71dea987716080fb308af98a5237bab2a0b82f50f932ff59e3fdea WHIRLPOOL ca35a9ce16b7d82839ca6ef1989b5b40177c93ff52379a2296e4bd99483422f2f49c57eb0b646673f84bc09f9b3b8f1298c906311367711f60170394c0dee6c6
+AUX xrootd.initd 968 SHA256 ba83e4bb99a7a236e3131019c5c3775e0c22bc180ef5791dc7d60cc0e0891efe SHA512 3b2d92f15907dbec4eea071018d8fb9ad5d091a59f49bacc80e2882f6b57d26485a34c5869979f842aac4ff08fa4a5206c09ecb921e859a83360058d5c42f361 WHIRLPOOL 84bbeea7013f512f383708f5b76814bbfa35fb785e8619f8d78ad34ec4a99a3caf293f00d23dccc30149356fa7fe62459f2a5201d756722cd0778cbf31fa7bfd
+DIST xrootd-4.0.4.tar.gz 1920380 SHA256 17091c1de35b06fccc0acbf2f2084d697e3cebea09dc4056338da5e11458b5f7 SHA512 6419c6d70d2e481963b74a9f23808ca889530079dc6e8bc6aa47ff888b6cc5613a1c6702dd3fb86f6e416255206f9db14f9d775896feae6ba70907c666615a79 WHIRLPOOL 0f3422ebf254750d2ca9e122b0eb4f00bd802d378f3d520006b3772cd511ec385a79dced9e111b46ce4296a1ca339fc71425b0a5877385084f0870707b45664b
+EBUILD xrootd-4.0.4.ebuild 1927 SHA256 608768ca1abda33c0143f45a97cebbb910976c5b64e6844640d0bf31dee22ffd SHA512 a40f18570f1f55b146a285d1b70775447ef7b662833b6a1f9557a1fc8044e29ce231dc2ce0481dc883a30892b9c96da8394fe9c17301a66beac2203891f8b9f0 WHIRLPOOL 9e90cb014689d89ccf2a22704463d8cbdd452198b274f36e0810249f0ca28a66646f9c15251ddf3d9366abf974ed17e2d70432d03fc9d25ad5c5a5de06ded20f
+MISC ChangeLog 4044 SHA256 a14476f27e2bf31549ab297b1882dbd4616ab00d121bcb527a371b92ce00027e SHA512 adb356be9167bd50f5e79af2711cb4c2860820c28c4de0ddf6dec74765b4a6b4ad59edaec3f28cae0dcfbe1314120b1e1d41cd33a4841a34ade43f9571c5d217 WHIRLPOOL 9f904690858fa1f1dc743a46011e851ec7568cc5f51b0b9a68cbdfaea23fb10a1e418f064cacb5edf02370eb64232ec99a41aa70cc5fe3bf1833b68ed9c6fc25
+MISC metadata.xml 671 SHA256 4b7fe955de34a52ccb81772aeb326674c3c8f371abd550676cbed5bb7f27e76f SHA512 1b7f5c9ea11cfc6e8a5d91b6d28450b783b685bce95d07cb2e023a14af42ec4e2affc8ff1e80b5a973d574499d63c1390fda599ff69b0838b29c3951810bf940 WHIRLPOOL ff405df291dba6dfe4b83d51b23730e1ab39d433c57aae1937467fbe47b07870262e07f4d49b65fc0e989a3748346ae65ae0ca31c2a546b98a346a547af71fe7
diff --git a/net-libs/xrootd/files/cmsd.confd b/net-libs/xrootd/files/cmsd.confd
new file mode 100644
index 000000000..ab5aa8c61
--- /dev/null
+++ b/net-libs/xrootd/files/cmsd.confd
@@ -0,0 +1,9 @@
+# conf.d file for cmsd daemon
+
+# User to run as (default is root)
+CMSD_USER="root"
+
+#
+# Please refer to the cmsd(1) man(1) page for more
+# information on command line parameters. 
+CMSD_OPTS=""
diff --git a/net-libs/xrootd/files/cmsd.initd b/net-libs/xrootd/files/cmsd.initd
new file mode 100644
index 000000000..b04ca579c
--- /dev/null
+++ b/net-libs/xrootd/files/cmsd.initd
@@ -0,0 +1,35 @@
+#!/sbin/runscript
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/cmsd.initd,v 1.3 2013/06/04 15:51:34 bicatali Exp $
+
+. /etc/conf.d/xrootd
+
+depend() {
+    need net
+    use logger dns
+    provide root-file-server
+}
+
+start_pre() {
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd
+}
+
+start() {
+    ebegin "Starting Cluster Management Service daemon"
+    start-stop-daemon --start --quiet --user ${XROOTD_USER} \
+	--make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \
+	--exec /usr/bin/${RC_SVCNAME} --background -- \
+        -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \
+        ${CMSD_OPTS}
+    eend $?
+}
+
+stop() {
+    ebegin "Stopping Cluster Management Service daemon"
+    start-stop-daemon --stop --quiet \
+	--pidfile /var/run/${RC_SVCNAME}.pid \
+	--exec /usr/bin/${RC_SVCNAME}
+    eend $?
+}
diff --git a/net-libs/xrootd/files/frm_purged.initd b/net-libs/xrootd/files/frm_purged.initd
new file mode 100644
index 000000000..1e95d5c8c
--- /dev/null
+++ b/net-libs/xrootd/files/frm_purged.initd
@@ -0,0 +1,35 @@
+#!/sbin/runscript
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/frm_purged.initd,v 1.3 2013/06/04 15:51:34 bicatali Exp $
+
+. /etc/conf.d/xrootd
+
+depend() {
+    need net
+    use logger dns
+    provide root-file-server
+}
+
+start_pre() {
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd
+}
+
+start() {
+    ebegin "Starting File Residency Manager purge daemon"
+    start-stop-daemon --start --quiet --user ${XROOTD_USER} \
+	--make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \
+	--exec /usr/bin/${RC_SVCNAME} --background -- \
+        -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \
+        ${FRM_PURGED_OPTS}
+    eend $?
+}
+
+stop() {
+    ebegin "Stopping File Residency Manager purge daemon"
+    start-stop-daemon --stop --quiet \
+	--pidfile /var/run/${RC_SVCNAME}.pid \
+	--exec /usr/bin/${RC_SVCNAME}
+    eend $?
+}
diff --git a/net-libs/xrootd/files/frm_xfrd.initd b/net-libs/xrootd/files/frm_xfrd.initd
new file mode 100644
index 000000000..0b28f873a
--- /dev/null
+++ b/net-libs/xrootd/files/frm_xfrd.initd
@@ -0,0 +1,35 @@
+#!/sbin/runscript
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/frm_xfrd.initd,v 1.3 2013/06/04 15:51:34 bicatali Exp $
+
+. /etc/conf.d/xrootd
+
+depend() {
+    need net
+    use logger dns
+    provide root-file-server
+}
+
+start_pre() {
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd
+}
+
+start() {
+    ebegin "Starting File Residency Manager transfer daemon"
+    start-stop-daemon --start --quiet --user ${XROOTD_USER} \
+	--make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \
+	--exec /usr/bin/${RC_SVCNAME} --background -- \
+        -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \
+        ${FRM_XFRD_OPTS}
+    eend $?
+}
+
+stop() {
+    ebegin "Stopping File Residency Manager transfer daemon"
+    start-stop-daemon --stop --quiet \
+	--pidfile /var/run/${RC_SVCNAME}.pid \
+	--exec /usr/bin/${RC_SVCNAME}
+    eend $?
+}
diff --git a/net-libs/xrootd/files/xrootd-no-werror.patch b/net-libs/xrootd/files/xrootd-no-werror.patch
new file mode 100644
index 000000000..d9f3b1c52
--- /dev/null
+++ b/net-libs/xrootd/files/xrootd-no-werror.patch
@@ -0,0 +1,11 @@
+--- cmake/XRootDOSDefs.cmake.orig	2014-06-04 20:31:15.000000000 +0400
++++ cmake/XRootDOSDefs.cmake	2014-08-21 12:12:55.397368485 +0400
+@@ -15,7 +15,7 @@
+ # GCC
+ #-------------------------------------------------------------------------------
+ if( CMAKE_COMPILER_IS_GNUCXX )
+-  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Werror" )
++  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra" )
+   set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-parameter" )
+   # gcc 4.1 is retarded
+   execute_process( COMMAND ${CMAKE_C_COMPILER} -dumpversion
diff --git a/net-libs/xrootd/files/xrootd.confd b/net-libs/xrootd/files/xrootd.confd
new file mode 100644
index 000000000..0e847e53e
--- /dev/null
+++ b/net-libs/xrootd/files/xrootd.confd
@@ -0,0 +1,21 @@
+# conf.d file for xroot, cmsd, frm_purged, frm_xfrd daemons
+
+# User to run as, please note that:
+# 1) daemons will refuse to run as root;
+# 2) several dirs must be created with an appropriate permissions
+# and ownership, so be careful when changing default 'xrootd' user.
+XROOTD_USER="xrootd"
+
+# Configuration file MUST be the same for all four daemons.
+# See /etc/xrootd for available simple defaults.
+XROOTD_CONF="/etc/xrootd/xrootd-clustered.cfg"
+
+# Logdir for all daemons
+XROOTD_LOGDIR="/var/log/xrootd"
+
+# Additional options for each daemon, please refer to their
+# documentation for details
+XROOTD_OPTS=""
+CMSD_OPTS=""
+FRM_PURGED=""
+FRM_XFRD=""
diff --git a/net-libs/xrootd/files/xrootd.initd b/net-libs/xrootd/files/xrootd.initd
new file mode 100644
index 000000000..1685ccc5c
--- /dev/null
+++ b/net-libs/xrootd/files/xrootd.initd
@@ -0,0 +1,33 @@
+#!/sbin/runscript
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/xrootd.initd,v 1.2 2012/12/05 18:19:15 bicatali Exp $
+
+depend() {
+    need net
+    use logger dns
+    provide root-file-server
+}
+
+start_pre() {
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool
+    checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd
+}
+
+start() {
+    ebegin "Starting extended ROOTD file server"
+    start-stop-daemon --start --quiet --user ${XROOTD_USER} \
+	--make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \
+        --exec /usr/bin/${RC_SVCNAME} --background -- \
+        -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \
+        ${XROOTD_OPTS}
+    eend $?
+}
+
+stop() {
+    ebegin "Stopping extended ROOTD file server"
+    start-stop-daemon --stop --quiet \
+	--pidfile /var/run/${RC_SVCNAME}.pid \
+	--exec /usr/bin/${RC_SVCNAME}
+    eend $?
+}
diff --git a/net-libs/xrootd/metadata.xml b/net-libs/xrootd/metadata.xml
new file mode 100644
index 000000000..604e38963
--- /dev/null
+++ b/net-libs/xrootd/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-physics</herd>
+<longdescription lang="en">
+  XROOTD software framework is a fully generic suite for fast, low latency
+  and scalable data access, which can serve natively any kind of data,
+  organized as a hierarchical filesystem-like namespace, based on the
+  concept of directory. 
+  It is usually used with <pkg>sci-physics/root</pkg> and its PROOF
+  facilities for cluster computing in high energy physics.
+</longdescription>
+<use>
+  <flag name="fuse">Enable the <pkg>sys-fs/fuse</pkg> filesystem driver</flag>
+</use>
+</pkgmetadata>
diff --git a/net-libs/xrootd/xrootd-4.0.4.ebuild b/net-libs/xrootd/xrootd-4.0.4.ebuild
new file mode 100644
index 000000000..ef02d4502
--- /dev/null
+++ b/net-libs/xrootd/xrootd-4.0.4.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/xrootd-4.0.0.ebuild,v 1.1 2014/06/19 18:13:17 bicatali Exp $
+
+EAPI=5
+
+inherit cmake-utils eutils user multilib
+
+DURI="http://xrootd.slac.stanford.edu/doc/prod"
+
+DESCRIPTION="Extended ROOT remote file server"
+HOMEPAGE="http://xrootd.org/"
+SRC_URI="${HOMEPAGE}/download/v${PV}/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc fuse kerberos perl readline ssl test"
+
+RDEPEND="
+	!<sci-physics/root-5.32[xrootd]
+	sys-libs/zlib:0=
+	fuse? ( sys-fs/fuse:0= )
+	kerberos? ( virtual/krb5 )
+	perl? (
+		dev-lang/perl
+		readline? ( dev-perl/Term-ReadLine-Perl )
+	)
+	readline? ( sys-libs/readline:0= )
+	ssl? ( dev-libs/openssl:0= )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen[dot] )
+	perl? ( dev-lang/swig )
+	test? ( dev-util/cppunit )"
+
+pkg_setup() {
+	enewgroup xrootd
+	enewuser xrootd -1 -1 "${EPREFIX}"/var/spool/xrootd xrootd
+}
+
+src_prepare() {
+	epatch "${FILESDIR}/${PN}-no-werror.patch"
+}
+
+src_configure() {
+	local mycmakeargs=(
+		$(cmake-utils_use_enable fuse)
+		$(cmake-utils_use_enable kerberos KRB5)
+		$(cmake-utils_use_enable perl)
+		$(cmake-utils_use_enable readline)
+		$(cmake-utils_use_enable ssl CRYPTO)
+		$(cmake-utils_use_enable test TESTS)
+	)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	use doc && doxygen Doxyfile
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# base configs
+	insinto /etc/xrootd
+	doins packaging/common/*.cfg
+
+	fowners root:xrootd /etc/xrootd
+	keepdir /var/log/xrootd
+	fowners xrootd:xrootd /var/log/xrootd
+
+	local i
+	for i in cmsd frm_purged frm_xfrd xrootd; do
+		newinitd "${FILESDIR}"/${i}.initd ${i}
+	done
+	# all daemons MUST use single master config file
+	newconfd "${FILESDIR}"/xrootd.confd xrootd
+
+	dodoc docs/ReleaseNotes.txt
+	use doc && dohtml -r doxydoc/html/*
+}
diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
deleted file mode 100644
index 4bbf7b913..000000000
--- a/sci-biology/consed/ChangeLog
+++ /dev/null
@@ -1,41 +0,0 @@
-# ChangeLog for sci-biology/consed
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  05 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
-  consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
-  consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
-  sci-biology/consed: add a stub file for consedrc; refer to it via
-  CONSED_PARAMETERS
-
-  05 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
-  consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
-  consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
-  sci-biology/consed: fix more hardcoded paths
-
-  02 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
-  consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
-  consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
-  sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl
-  scripts to fix situations when user has for some reason an empty CONSED_HOME
-
-*consed-27 (23 Mar 2014)
-*consed-26 (23 Mar 2014)
-*consed-25 (23 Mar 2014)
-*consed-24 (23 Mar 2014)
-*consed-23 (23 Mar 2014)
-*consed-22 (23 Mar 2014)
-*consed-21 (23 Mar 2014)
-
-  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  consed-20-r1.ebuild, +consed-21.ebuild, +consed-22.ebuild,
-  files/nLine.h.patch, files/nextPhredPipeline.cpp.patch, metadata.xml:
-  Added versions 21, 22, 23, 24, 25, 26, 27. None of them need the two
-  patches anymore but all of them need samtools for BAM support.
-  Compiled with x86_64-pc-linux-gnu-4.3.6.
-
-  31 Oct 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  consed-20-r1.ebuild:
-  renamed dependency from openmotif to motif consed-20-r1.ebuild,
-  added some extra patches files/nLine.h.patch,
-  files/nextPhredPipeline.cpp.patch
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
deleted file mode 100644
index d9a8e8ba6..000000000
--- a/sci-biology/consed/Manifest
+++ /dev/null
@@ -1,16 +0,0 @@
-DIST consed-20-linux.tar.gz 31407408 SHA256 ebde602163743d018ac8bf49f04ff0afbd0cccb3b7ef065a154943a68e95ad27 SHA512 57c1a90410d9c8e47fc725e28ae3a7ecbc369d287917072f6ebcc0ee78113f9c7083b9f92c9dc4a3837fe0400716e4e8b5fd9de5a41b00656a66443b786287e7 WHIRLPOOL 82643dfce4da8782ef69506cacac5f75fbe8b64fadef82339d664a93fcaf9f3378c99e82cc19e43c6a5500943ecb4e876d80926a0aa8fc422314c2811c0c6ca5
-DIST consed-20-sources.tar.gz 7418118 SHA256 8d12191e08d9dfc73c3284a057b7fd80d1aefe4a60d11a0de1db6ba9ce9ba4b7 SHA512 59487531e1557bb9757c713428daa4c98e55b6a07bcd639c86d98aa653cb0bc2fae5124b5b85ee29a8fe45ea7d962f21242ab89eb8e02f1ce7f4c38d9ba7c26a WHIRLPOOL 0c01775503dfa70b44a30be956872566759bfb76c22ed8db8ccb039df625f5391bdc9090ecb4de1ed33662ecc36d1abc20ee3fd092eae53f930f641decc9b46e
-DIST consed-21-linux.tar.gz 34018168 SHA256 1117083c07f8c5f8ca017b82065cc6d567d155b21d2c5d4d1e44da9f15fd77ca SHA512 b8e6aebc9c82901bdc41f22b500ff4600b1188a6db1abd76e3306c093cdf507399670a02f362993d29a6ee1eaddee8ab90a0e2cd06167c725b62716eab8a9266 WHIRLPOOL abe42c45e9643473c81d8524db1d5d3e6f1bfe1bf95553a5e7eb980b0bf9adb2aa53be94d7f88eebc57d037d6444b8b0da53f5162f244c41538395f20e505d06
-DIST consed-21-sources.tar.gz 3026753 SHA256 b9f963c1f325c714b124ccdeaca703952fd1b978e4a72a0bca8abe733d05dc73 SHA512 a82c0ec9622f7b4f53f90a3092ad4fa58dcd2acd55f4304ad3a71bfaaba0efd7db01c5b820e115b63a2853425d7fb17278762ad24b012cc3cf420a7cb2305f56 WHIRLPOOL 566b7e227bbf6d35bc99d6fccfbb90b97c157ff1ffcfedfa3e7a88578e4d0ece3662181819cb3129a55a9164f084ed0b9366d9e17e3cdceb5fc61a538ada892c
-DIST consed-22-linux.tar.gz 34018168 SHA256 1117083c07f8c5f8ca017b82065cc6d567d155b21d2c5d4d1e44da9f15fd77ca SHA512 b8e6aebc9c82901bdc41f22b500ff4600b1188a6db1abd76e3306c093cdf507399670a02f362993d29a6ee1eaddee8ab90a0e2cd06167c725b62716eab8a9266 WHIRLPOOL abe42c45e9643473c81d8524db1d5d3e6f1bfe1bf95553a5e7eb980b0bf9adb2aa53be94d7f88eebc57d037d6444b8b0da53f5162f244c41538395f20e505d06
-DIST consed-22-sources.tar.gz 3026753 SHA256 b9f963c1f325c714b124ccdeaca703952fd1b978e4a72a0bca8abe733d05dc73 SHA512 a82c0ec9622f7b4f53f90a3092ad4fa58dcd2acd55f4304ad3a71bfaaba0efd7db01c5b820e115b63a2853425d7fb17278762ad24b012cc3cf420a7cb2305f56 WHIRLPOOL 566b7e227bbf6d35bc99d6fccfbb90b97c157ff1ffcfedfa3e7a88578e4d0ece3662181819cb3129a55a9164f084ed0b9366d9e17e3cdceb5fc61a538ada892c
-DIST consed-23-linux.tar.gz 34018168 SHA256 1117083c07f8c5f8ca017b82065cc6d567d155b21d2c5d4d1e44da9f15fd77ca SHA512 b8e6aebc9c82901bdc41f22b500ff4600b1188a6db1abd76e3306c093cdf507399670a02f362993d29a6ee1eaddee8ab90a0e2cd06167c725b62716eab8a9266 WHIRLPOOL abe42c45e9643473c81d8524db1d5d3e6f1bfe1bf95553a5e7eb980b0bf9adb2aa53be94d7f88eebc57d037d6444b8b0da53f5162f244c41538395f20e505d06
-DIST consed-23-sources.tar.gz 3026753 SHA256 b9f963c1f325c714b124ccdeaca703952fd1b978e4a72a0bca8abe733d05dc73 SHA512 a82c0ec9622f7b4f53f90a3092ad4fa58dcd2acd55f4304ad3a71bfaaba0efd7db01c5b820e115b63a2853425d7fb17278762ad24b012cc3cf420a7cb2305f56 WHIRLPOOL 566b7e227bbf6d35bc99d6fccfbb90b97c157ff1ffcfedfa3e7a88578e4d0ece3662181819cb3129a55a9164f084ed0b9366d9e17e3cdceb5fc61a538ada892c
-DIST consed-24-linux.tar.gz 34018168 SHA256 1117083c07f8c5f8ca017b82065cc6d567d155b21d2c5d4d1e44da9f15fd77ca SHA512 b8e6aebc9c82901bdc41f22b500ff4600b1188a6db1abd76e3306c093cdf507399670a02f362993d29a6ee1eaddee8ab90a0e2cd06167c725b62716eab8a9266 WHIRLPOOL abe42c45e9643473c81d8524db1d5d3e6f1bfe1bf95553a5e7eb980b0bf9adb2aa53be94d7f88eebc57d037d6444b8b0da53f5162f244c41538395f20e505d06
-DIST consed-24-sources.tar.gz 3026753 SHA256 b9f963c1f325c714b124ccdeaca703952fd1b978e4a72a0bca8abe733d05dc73 SHA512 a82c0ec9622f7b4f53f90a3092ad4fa58dcd2acd55f4304ad3a71bfaaba0efd7db01c5b820e115b63a2853425d7fb17278762ad24b012cc3cf420a7cb2305f56 WHIRLPOOL 566b7e227bbf6d35bc99d6fccfbb90b97c157ff1ffcfedfa3e7a88578e4d0ece3662181819cb3129a55a9164f084ed0b9366d9e17e3cdceb5fc61a538ada892c
-DIST consed-25-linux.tar.gz 34018168 SHA256 1117083c07f8c5f8ca017b82065cc6d567d155b21d2c5d4d1e44da9f15fd77ca SHA512 b8e6aebc9c82901bdc41f22b500ff4600b1188a6db1abd76e3306c093cdf507399670a02f362993d29a6ee1eaddee8ab90a0e2cd06167c725b62716eab8a9266 WHIRLPOOL abe42c45e9643473c81d8524db1d5d3e6f1bfe1bf95553a5e7eb980b0bf9adb2aa53be94d7f88eebc57d037d6444b8b0da53f5162f244c41538395f20e505d06
-DIST consed-25-sources.tar.gz 3026753 SHA256 b9f963c1f325c714b124ccdeaca703952fd1b978e4a72a0bca8abe733d05dc73 SHA512 a82c0ec9622f7b4f53f90a3092ad4fa58dcd2acd55f4304ad3a71bfaaba0efd7db01c5b820e115b63a2853425d7fb17278762ad24b012cc3cf420a7cb2305f56 WHIRLPOOL 566b7e227bbf6d35bc99d6fccfbb90b97c157ff1ffcfedfa3e7a88578e4d0ece3662181819cb3129a55a9164f084ed0b9366d9e17e3cdceb5fc61a538ada892c
-DIST consed-26-linux.tar.gz 34018168 SHA256 1117083c07f8c5f8ca017b82065cc6d567d155b21d2c5d4d1e44da9f15fd77ca SHA512 b8e6aebc9c82901bdc41f22b500ff4600b1188a6db1abd76e3306c093cdf507399670a02f362993d29a6ee1eaddee8ab90a0e2cd06167c725b62716eab8a9266 WHIRLPOOL abe42c45e9643473c81d8524db1d5d3e6f1bfe1bf95553a5e7eb980b0bf9adb2aa53be94d7f88eebc57d037d6444b8b0da53f5162f244c41538395f20e505d06
-DIST consed-26-sources.tar.gz 3026753 SHA256 b9f963c1f325c714b124ccdeaca703952fd1b978e4a72a0bca8abe733d05dc73 SHA512 a82c0ec9622f7b4f53f90a3092ad4fa58dcd2acd55f4304ad3a71bfaaba0efd7db01c5b820e115b63a2853425d7fb17278762ad24b012cc3cf420a7cb2305f56 WHIRLPOOL 566b7e227bbf6d35bc99d6fccfbb90b97c157ff1ffcfedfa3e7a88578e4d0ece3662181819cb3129a55a9164f084ed0b9366d9e17e3cdceb5fc61a538ada892c
-DIST consed-27-linux.tar.gz 34390726 SHA256 8038d2b94078ba918e97785fc7497252139029281000f1c54ff9dd1ec70e05fc SHA512 0cffbdf09dff3a2252cef29b62ae8d3216af9690ea372f3748fdfdfeefc7b24dd4d78a7701354ec35b13dee582f0b622eee17c8162339da58e55282db3c92106 WHIRLPOOL 65b79247a43600db3978ba3faf6ac03f2ec480c38d3dd76935a485e2a181fb33ef8626119d02f89653133944a687f3686ec9062de9a6523724071e72a30c55e2
-DIST consed-27-sources.tar.gz 3078907 SHA256 369159d75e451a2bc520aabe9347a5bbe055a8e868527253c848a0b00f9a416d SHA512 f70830f6ed4efe3512baa66714ee08af266116173d774e72b1f2abe83e94521091794a782e2fd42bc9a54cffc7aeea59cfd5ff7edb36dff1e30db1d1b7a17608 WHIRLPOOL 595d7aba1ee2628bd1c21ff49dacdbbabf67439e327128eeaf614ab13a92d496e6e6fef67e4d921feef70a59b01a7824df262c4bc308b1b0b372133ce3502d3a
diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
deleted file mode 100644
index 30ba8661a..000000000
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-	epatch "${FILESDIR}"/nextPhredPipeline.cpp.patch || die
-	epatch "${FILESDIR}"/nLine.h.patch || die
-}
-
-src_compile() {
-	emake || die "If you have gcc-4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild
deleted file mode 100644
index b7993b760..000000000
--- a/sci-biology/consed/consed-21.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	sci-biology/samtools
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	doenvd "${S}/99consed" || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild
deleted file mode 100644
index 4c8dd7fb1..000000000
--- a/sci-biology/consed/consed-22.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	sci-biology/samtools
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild
deleted file mode 100644
index 4c8dd7fb1..000000000
--- a/sci-biology/consed/consed-23.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	sci-biology/samtools
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild
deleted file mode 100644
index 4c8dd7fb1..000000000
--- a/sci-biology/consed/consed-24.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	sci-biology/samtools
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild
deleted file mode 100644
index 4c8dd7fb1..000000000
--- a/sci-biology/consed/consed-25.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	sci-biology/samtools
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild
deleted file mode 100644
index 4c8dd7fb1..000000000
--- a/sci-biology/consed/consed-26.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	sci-biology/samtools
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
deleted file mode 100644
index 4c8dd7fb1..000000000
--- a/sci-biology/consed/consed-27.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-RDEPEND="${DEPEND}
-	sci-biology/samtools
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please visit ${HOMEPAGE} and obtain the file"
-	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
-	einfo "and place it in ${DISTDIR},"
-	einfo "obtain the file"
-	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_prepare() {
-	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
-	sed -i \
-		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
-}
-
-src_compile() {
-	emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
-	emake -C misc/mktrace || die
-	emake -C misc/phd2fasta || die
-	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
-	dobin scripts/* contributions/* || die
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq} || die
-	insinto /usr/share/${PN}/examples
-	doins -r standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer || die
-	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
-	mkdir -p "${D}"/etc/consedrc
-	touch "${D}"/etc/consedrc
-	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
-	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
-	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt || die
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}
diff --git a/sci-biology/consed/files/nLine.h.patch b/sci-biology/consed/files/nLine.h.patch
deleted file mode 100644
index 9b6779e33..000000000
--- a/sci-biology/consed/files/nLine.h.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- nLine.h.ori 2011-04-28 02:12:58.000000000 +0200
-+++ nLine.h     2011-04-28 02:13:43.000000000 +0200
-@@ -44,11 +44,11 @@
- 
- #ifdef DEFINE_nLine
- 
--int nLine;
-+long nLine;
- 
- #else
- 
--extern int nLine;
-+extern long nLine;
- 
- #endif
- 
-
diff --git a/sci-biology/consed/files/nextPhredPipeline.cpp.patch b/sci-biology/consed/files/nextPhredPipeline.cpp.patch
deleted file mode 100644
index 92d4fc05a..000000000
--- a/sci-biology/consed/files/nextPhredPipeline.cpp.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- nextPhredPipeline.cpp.ori	2011-01-08 20:44:45.000000000 +0100
-+++ nextPhredPipeline.cpp	2011-01-08 20:47:29.000000000 +0100
-@@ -476,7 +476,7 @@
- void nextPhredPipeline :: openAndLockControlFile() {
- 
- 
--   nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR );
-+   nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600 );
-    if ( nFDControlFile_ == -1 ) {
-       THROW_FILE_ERROR( filControlFile_ );
-    }
diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
deleted file mode 100644
index 3302123e5..000000000
--- a/sci-biology/consed/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog
index 8a6cf13c2..509aa1acc 100644
--- a/sci-chemistry/freeon/ChangeLog
+++ b/sci-chemistry/freeon/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Oct 2014; Justin Lecher <jlec@gentoo.org> ChangeLog:
+  Drop obsolete versions
+
   17 Sep 2014; Christoph Junghans <ottxor@gentoo.org> metadata.xml:
   updated metadata.xml
 
diff --git a/sci-chemistry/votca-csg/ChangeLog b/sci-chemistry/votca-csg/ChangeLog
index 9fff6d440..621aa69bc 100644
--- a/sci-chemistry/votca-csg/ChangeLog
+++ b/sci-chemistry/votca-csg/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  24 Oct 2014; Christoph Junghans <ottxor@gentoo.org> votca-csg-9999.ebuild:
+  fixed bash-comp (bug #526320)
+
   01 Sep 2014; Christoph Junghans <ottxor@gentoo.org> votca-csg-9999.ebuild:
   sync with gx86
 
diff --git a/sci-chemistry/votca-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
index 6fc1afe24..94f2fc005 100644
--- a/sci-chemistry/votca-csg/votca-csg-9999.ebuild
+++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild
@@ -86,8 +86,12 @@ src_configure() {
 }
 
 src_install() {
-	newbashcomp scripts/csg-completion.bash ${PN}
 	cmake-utils_src_install
+	newbashcomp scripts/csg-completion.bash csg_call
+	for i in "${ED}"/usr/bin/csg_*; do
+		[[ ${i} = *csg_call ]] && continue
+		bashcomp_alias csg_call "${i##*/}"
+	done
 	if use doc; then
 		if [[ ${PV} = *9999* ]]; then
 			pushd "${WORKDIR}"/manual
diff --git a/sci-libs/trilinos/ChangeLog b/sci-libs/trilinos/ChangeLog
index 394f9fbb4..d6c571df8 100644
--- a/sci-libs/trilinos/ChangeLog
+++ b/sci-libs/trilinos/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*trilinos-11.10.2 (21 Oct 2014)
+
+  21 Oct 2014; Matthias Maier <tamiko@gentoo.org> +trilinos-11.10.2.ebuild,
+  trilinos-11.4.2.ebuild:
+  version bump
+
   06 Jan 2014; Justin Lecher <jlec@gentoo.org> trilinos-11.0.3.ebuild:
   Don't use plain pkg-config
 
diff --git a/sci-libs/trilinos/Manifest b/sci-libs/trilinos/Manifest
index 357d5de0d..be2c62aeb 100644
--- a/sci-libs/trilinos/Manifest
+++ b/sci-libs/trilinos/Manifest
@@ -1,3 +1,4 @@
 DIST trilinos-11.0.3-Source.tar.gz 107076534 SHA256 4e9d68d23eac1076200a3224fab14cd3a63a77574f1456d1bff931b2887b5c63 SHA512 9c449c6f9b2bc6346867bc68c29f83edc81790889d483129a98d149e1ff79d32b13310e8fcb3b4412b2f722b5d7efedd2a65f2e882b38629d4a1d50ecfc9783f WHIRLPOOL 7af72bd92cb4aa72ec8d98065570c9af2cc04187b7b2cce5d701e25d2c25efdc8826a4359b035008b8cf086026b88126bcfa6e807cac4f18d5fb745a48568f10
+DIST trilinos-11.10.2-Source.tar.bz2 110633685 SHA256 d3a39b7ad5c61d1e1413f9e550f0a81832a36e4a3072b8b99cebed6900d2d0ea SHA512 0147ed8d4483765ef03114eaed8098b0b41f81dde09147e584ce4e3f8fd2465ad11a6edd288f9ed857bfc163ed45d1a728989a185c22c819434cbb1ffdadd7cb WHIRLPOOL 7229a984a2c894f8edab01ec675fc5582553ca4ef652bda3006318b91d1d56f581ecc5eaed4a023e20cb25e9969a57e61735e415f6c734d41796b905fa9978ae
 DIST trilinos-11.2.3-Source.tar.bz2 101522486 SHA256 e8c7a899b9cbb1a8b168b3da5621eb34c9e48c2d48dfbf651366a50a465772c2 SHA512 9a64fd092012a67e0c317fb242a5e6378e543f8aa11d0f9e0bb45569c5f7e146f97e85a462305fe3c92436cc2540b95597c2ffc9bbcfc4b7ee08d9a09dbcdb80 WHIRLPOOL ac27521c7c5ca2e4337ff1aa9f18e68bcde8c5130821dfc8cda5af10c91e2e79e20017c2b76773ca412234b43885df30d781a0cb67ae2c15c47c091f548bdb8e
 DIST trilinos-11.4.2-Source.tar.bz2 104205684 SHA256 9bbf33936c5c1e83e0c5a5e336fbdac8e59d0bebf766a4369ad32bfdf15f4199 SHA512 06e8d6873409b8aae3660890a1d3f05467f137a9ec28780ec600531907627e3f123a97e2d3681510d18762beea8dca4fa859308797d75c1862c51c06890ae1da WHIRLPOOL 1b774b77d4efbc582012240290aa7d03df0ae12e87530da1b87be3ce591db60b793941c9f6b70df596fb1e29c33208d1a0c4353c278bc394711477e9a9e47d23
diff --git a/sci-libs/trilinos/trilinos-11.10.2.ebuild b/sci-libs/trilinos/trilinos-11.10.2.ebuild
new file mode 100644
index 000000000..39f3a44ac
--- /dev/null
+++ b/sci-libs/trilinos/trilinos-11.10.2.ebuild
@@ -0,0 +1,202 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils toolchain-funcs multilib toolchain-funcs
+
+DESCRIPTION="Scientific library collection for large scale problems"
+HOMEPAGE="http://trilinos.sandia.gov/"
+SRC_URI="${P}-Source.tar.bz2"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+LICENSE="BSD LGPL-2.1"
+SLOT="0"
+
+IUSE="
+	adolc arprec boost clp cppunit cuda eigen glpk gtest
+	hdf5 hwloc hypre metis mkl mumps netcdf petsc qd qt4
+	scalapack scotch sparse superlu taucs tbb test threads
+	tvmet yaml zlib
+"
+
+# TODO: fix export cmake function for tests
+RESTRICT="test fetch"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	virtual/mpi
+	adolc? ( sci-libs/adolc )
+	arprec? ( sci-libs/arprec )
+	boost? ( dev-libs/boost )
+	clp? ( sci-libs/coinor-clp )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-3.2 )
+	eigen? ( dev-cpp/eigen:3 )
+	gtest? ( dev-cpp/gtest )
+	hdf5? ( sci-libs/hdf5[mpi] )
+	hypre? ( sci-libs/hypre )
+	hwloc? ( sys-apps/hwloc )
+	mkl? ( sci-libs/mkl )
+	metis? ( || ( sci-libs/parmetis sci-libs/metis ) )
+	mumps? ( sci-libs/mumps )
+	netcdf? ( sci-libs/netcdf )
+	petsc? ( sci-mathematics/petsc )
+	qd? ( sci-libs/qd )
+	qt4? ( dev-qt/qtgui:4 )
+	scalapack? ( virtual/scalapack )
+	scotch? ( sci-libs/scotch )
+	sparse? ( sci-libs/cxsparse sci-libs/umfpack )
+	superlu? ( sci-libs/superlu )
+	taucs? ( sci-libs/taucs )
+	tbb? ( dev-cpp/tbb )
+	tvmet? ( dev-libs/tvmet )
+	yaml? ( dev-cpp/yaml-cpp )
+	zlib? ( sys-libs/zlib )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${P}-Source"
+
+trilinos_conf() {
+	local dirs libs d
+	for d in $($(tc-getPKG_CONFIG) --libs-only-L $1); do
+		dirs="${dirs};${d:2}"
+	done
+	[[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_DIRS=${dirs:1}" )
+	for d in $($(tc-getPKG_CONFIG) --libs-only-l $1); do
+		libs="${libs};${d:2}"
+	done
+	[[ -n ${libs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_NAMES=${libs:1}" )
+	dirs=""
+	for d in $($(tc-getPKG_CONFIG) --cflags-only-I $1); do
+		dirs="${dirs};${d:2}"
+	done
+	[[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_INCLUDE_DIRS=${dirs:1}" )
+}
+
+trilinos_enable() {
+	cmake-utils_use $1 TPL_ENABLE_${2:-${1^^}}
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-11.4.2-fix-install-paths.patch
+}
+
+src_configure() {
+
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"
+		-DTrilinos_ENABLE_ALL_PACKAGES=ON
+		-DTrilinos_INSTALL_INCLUDE_DIR="${EPREFIX}/usr/include/trilinos"
+		-DTrilinos_INSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)/trilinos"
+		-DTrilinos_INSTALL_CONFIG_DIR="${EPREFIX}/usr/$(get_libdir)/cmake"
+		-DTPL_ENABLE_BinUtils=ON
+		-DTPL_ENABLE_MPI=ON
+		-DTPL_ENABLE_BLAS=ON
+		-DTPL_ENABLE_LAPACK=ON
+		$(cmake-utils_use test Trilinos_ENABLE_TESTS)
+		$(trilinos_enable adolc)
+		$(trilinos_enable arprec)
+		$(trilinos_enable boost Boost)
+		$(trilinos_enable boost BoostLib)
+		$(trilinos_enable cppunit Cppunit)
+		$(trilinos_enable clp Clp)
+		$(trilinos_enable cuda)
+		$(trilinos_enable cuda CUSPARSE)
+		$(trilinos_enable cuda Thrust)
+		$(trilinos_enable eigen Eigen)
+		$(trilinos_enable gtest gtest)
+		$(trilinos_enable glpk)
+		$(trilinos_enable hdf5)
+		$(trilinos_enable hwloc)
+		$(trilinos_enable hypre)
+		$(trilinos_enable metis)
+		$(trilinos_enable mkl)
+		$(trilinos_enable mkl PARDISO_MKL)
+		$(trilinos_enable mumps)
+		$(trilinos_enable netcdf Netcdf)
+		$(trilinos_enable petsc)
+		$(trilinos_enable qd)
+		$(trilinos_enable qt4 QT)
+		$(trilinos_enable scalapack)
+		$(trilinos_enable scalapack BLACS)
+		$(trilinos_enable scotch Scotch)
+		$(trilinos_enable sparse AMD)
+		$(trilinos_enable sparse CSparse)
+		$(trilinos_enable sparse UMFPACK)
+		$(trilinos_enable superlu SuperLU)
+		$(trilinos_enable taucs)
+		$(trilinos_enable tbb)
+		$(trilinos_enable threads Pthread)
+		$(trilinos_enable tvmet)
+		$(trilinos_enable yaml yaml-cpp)
+		$(trilinos_enable zlib Zlib)
+	)
+
+	use eigen && \
+		mycmakeargs+=(
+		-DEigen_INCLUDE_DIRS="${EPREFIX}/usr/include/eigen3"
+	)
+	use hypre && \
+		mycmakeargs+=(
+		-DHYPRE_INCLUDE_DIRS="${EPREFIX}/usr/include/hypre"
+	)
+	use scotch && \
+		mycmakeargs+=(
+		-DScotch_INCLUDE_DIRS="${EPREFIX}/usr/include/scotch"
+	)
+
+	# cxsparse is a rewrite of csparse + extras
+	use sparse && \
+		mycmakeargs+=(
+		-DCSparse_LIBRARY_NAMES="cxsparse"
+	)
+
+	# mandatory blas and lapack
+	trilinos_conf blas BLAS
+	trilinos_conf lapack LAPACK
+	use superlu && trilinos_conf superlu SuperLU
+	use metis && trilinos_conf metis METIS
+
+	# blacs library is included in scalapack these days
+	if use scalapack; then
+		trilinos_conf scalapack SCALAPACK
+		mycmakeargs+=(
+			-DBLACS_LIBRARY_NAMES="scalapack"
+			-DBLACS_INCLUDE_DIRS="${EPREFIX}/usr/include/blacs"
+		)
+	fi
+
+	# TODO: do we need that line?
+	export CC=mpicc CXX=mpicxx && tc-export CC CXX
+
+	# cmake-utils eclass patches the base directory CMakeLists.txt
+	# which does not work for complex Trilinos CMake modules
+	CMAKE_BUILD_TYPE=RELEASE cmake-utils_src_configure
+
+	# TODO:
+	# python bindings with python-r1
+	# fix hypre bindings
+	# fix hdf5
+	# cuda/thrust is untested
+	# do we always need mpi? and for all packages: blah[mpi] ?
+	# install docs, examples
+	# see what packages are related, do we need REQUIRED_USE
+	# proper use flags description
+	# add more use flags/packages ?
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# register $(get_libdir)/trilinos in LDPATH so that the dynamic linker
+	# has a chance to pick up the libraries...
+	cat >> "${T}"/99trilinos <<- EOF
+	LDPATH="${EPREFIX}/usr/$(get_libdir)/trilinos"
+	EOF
+	doenvd "${T}"/99trilinos
+}
diff --git a/sci-libs/trilinos/trilinos-11.4.2.ebuild b/sci-libs/trilinos/trilinos-11.4.2.ebuild
index dcd7983a1..51734a4e3 100644
--- a/sci-libs/trilinos/trilinos-11.4.2.ebuild
+++ b/sci-libs/trilinos/trilinos-11.4.2.ebuild
@@ -23,7 +23,7 @@ IUSE="
 "
 
 # TODO: fix export cmake function for tests
-RESTRICT="test"
+RESTRICT="test fetch"
 
 RDEPEND="
 	virtual/blas
diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog
index 9b455b6c3..aff13e158 100644
--- a/sci-physics/root/ChangeLog
+++ b/sci-physics/root/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.96 2012/03/29 18:21:49 bicatali Exp $
 
+  25 Oct 2014; Matthias Maier <tamiko@gentoo.org> root-5.34.18-r2.ebuild,
+  root-6.00.01-r1.ebuild, root-6.00.02.ebuild, root-9999.ebuild:
+  sci-physics/root: Fix compilation with USE="mysql" wrt bug #523996; fix
+  die_compiler message
+
   29 Sep 2014; Justin Lecher <jlec@gentoo.org> root-6.00.02.ebuild,
   +files/root-6.00.02-tm_zone.patch, metadata.xml:
   Backport fix for build failure
diff --git a/sci-physics/root/root-5.34.18-r2.ebuild b/sci-physics/root/root-5.34.18-r2.ebuild
index 072b81d9c..7ce12fd96 100644
--- a/sci-physics/root/root-5.34.18-r2.ebuild
+++ b/sci-physics/root/root-5.34.18-r2.ebuild
@@ -260,6 +260,8 @@ src_configure() {
 			$(use_enable math tmva)
 			$(use_enable math unuran)
 			$(use_enable mysql)
+			$(usex mysql \
+				"--with-mysql-incdir=${EPREFIX}/usr/include/mysql" "")
 			$(use_enable odbc)
 			$(use_enable opengl)
 			$(use_enable oracle)
diff --git a/sci-physics/root/root-6.00.01-r1.ebuild b/sci-physics/root/root-6.00.01-r1.ebuild
index ebc10e1ed..6fe0c162f 100644
--- a/sci-physics/root/root-6.00.01-r1.ebuild
+++ b/sci-physics/root/root-6.00.01-r1.ebuild
@@ -322,6 +322,8 @@ src_configure() {
 			$(use_enable math vdt)
 			$(use_enable math unuran)
 			$(use_enable mysql)
+			$(usex mysql \
+				"--with-mysql-incdir=${EPREFIX}/usr/include/mysql" "")
 			$(use_enable odbc)
 			$(use_enable opengl)
 			$(use_enable oracle)
diff --git a/sci-physics/root/root-6.00.02.ebuild b/sci-physics/root/root-6.00.02.ebuild
index 5208cc9f3..e53ed3d7c 100644
--- a/sci-physics/root/root-6.00.02.ebuild
+++ b/sci-physics/root/root-6.00.02.ebuild
@@ -128,10 +128,10 @@ PDEPEND="doc? ( ~app-doc/root-docs-${PV}[http=,math=] )"
 DOC_DIR="/usr/share/doc/${P}"
 
 die_compiler() {
-	die "Need one of the following C++11 capable compilers:"
-	die "    >=sys-devel/gcc[cxx]-4.8"
-	die "    >=sys-devel/clang-3.4"
-	die "    >=dev-lang/icc-13"
+	die "Need one of the following C++11 capable compilers:"\
+		"    >=sys-devel/gcc[cxx]-4.8"\
+		"    >=sys-devel/clang-3.4"\
+		"    >=dev-lang/icc-13"
 }
 
 pkg_setup() {
@@ -322,6 +322,8 @@ src_configure() {
 			$(use_enable math vdt)
 			$(use_enable math unuran)
 			$(use_enable mysql)
+			$(usex mysql \
+				"--with-mysql-incdir=${EPREFIX}/usr/include/mysql" "")
 			$(use_enable odbc)
 			$(use_enable opengl)
 			$(use_enable oracle)
diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild
index b2074ac3f..00f49462a 100644
--- a/sci-physics/root/root-9999.ebuild
+++ b/sci-physics/root/root-9999.ebuild
@@ -128,10 +128,10 @@ PDEPEND="doc? ( ~app-doc/root-docs-${PV}[http=,math=] )"
 DOC_DIR="/usr/share/doc/${P}"
 
 die_compiler() {
-	die "Need one of the following C++11 capable compilers:"
-	die "    >=sys-devel/gcc[cxx]-4.8"
-	die "    >=sys-devel/clang-3.4"
-	die "    >=dev-lang/icc-13"
+	die "Need one of the following C++11 capable compilers:"\
+		"    >=sys-devel/gcc[cxx]-4.8"\
+		"    >=sys-devel/clang-3.4"\
+		"    >=dev-lang/icc-13"
 }
 
 pkg_setup() {
@@ -320,6 +320,8 @@ src_configure() {
 			$(use_enable math vdt)
 			$(use_enable math unuran)
 			$(use_enable mysql)
+			$(usex mysql \
+				"--with-mysql-incdir=${EPREFIX}/usr/include/mysql" "")
 			$(use_enable odbc)
 			$(use_enable opengl)
 			$(use_enable oracle)