Drop "CCP4: Software for Macromolecular Crystallography"

obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=160190 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=324059 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=332485 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367771 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367773 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=383227 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=448756 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460502 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460504 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=466936 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467040 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467048 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=476580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478586 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478588 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478594 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478604 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521646 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=528512 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=530878 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=540760 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=555614 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=556498 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=557038 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=561196 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=562780 Signed-off-by: Justin Lecher <jlec@gentoo.org>
2026-09-24 04:59:14 -07:00 · 2015-10-26 08:29:56 +01:00
parent 42f1475e45
commit 7d62034735
207 changed files with 8 additions and 11262 deletions
--- a/app-office/sc/sc-7.16-r1.ebuild
+++ b/app-office/sc/sc-7.16-r1.ebuild
@@ -3,6 +3,7 @@
 # $Id$

 EAPI=5
+
 inherit eutils multilib toolchain-funcs

 DESCRIPTION="sc is a free curses-based spreadsheet program that uses key bindings similar to vi and less"
@@ -17,9 +18,7 @@ COMMON_DEPEND=">=sys-libs/ncurses-5.2"
 DEPEND="virtual/pkgconfig"
 RDEPEND="
 	${COMMON_DEPEND}
-	!dev-lang/stratego
-	!<sci-chemistry/ccp4-apps-6.1.3-r4
-"
+	!dev-lang/stratego"

 src_prepare() {
 	epatch \
--- a/dev-libs/libjwc_c/Manifest
+++ b/dev-libs/libjwc_c/Manifest
@@ -1 +0,0 @@
-DIST libjwc_c-1.1.tar.gz 253637 SHA256 4e3c5406347356ac4549b2b977c8011391926470cc3556e54148070b929d9ea9 SHA512 5a095fdbf4f70d012f718d2bcd2a9689bf788801df3f3f97bead70861d08d5f6b5a9ac879e02c260974b755906d35de168646947900bcb18dad40839846d87ad WHIRLPOOL bca0bb19e2898c18f29a275c1997bf55058f5efbbc1147cb7e7a967f2eafb346c0d74975208dc6dd749ba60b256dca3c1548d9a58bd938fb19d77946a1aaa85a
--- a/dev-libs/libjwc_c/files/612-gentoo.patch
+++ b/dev-libs/libjwc_c/files/612-gentoo.patch
@@ -1,20 +0,0 @@
-diff -Nu libjwc_c-1.1/imglib.c libjwc_c/imglib.c
--- libjwc_c-1.1/imglib.c	1999-08-17 15:58:11.000000000 +0200
-+++ libjwc_c/imglib.c	2004-06-03 14:24:05.000000000 +0200
-@@ -4259,7 +4259,7 @@
- {
- 
- /* Note: In this routine the first local axis is called 'x' and the
-         second logal axi is called 'y' */
-+         second local axis is called 'y' */
- 
-    int mxcent;                  /* Current max no. of elements in active 
-                                    spots array */
-@@ -4469,6 +4469,7 @@
- 
- /* skipping condition */
- 
-+               iymid = (actspots[j].iyend+actspots[j].iybeg)/2;
-                itmp = abs(iymid-actspots[j].iycent);
-                if (abs((actspots[j].iyend+actspots[j].iybeg) -(iel+ibl))>
-                    abs((actspots[j].iyend-actspots[j].iybeg) +(iel-ibl))&&
--- a/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild
+++ b/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild
@@ -1,31 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils
-
-PATCH="612"
-
-DESCRIPTION="additional c library for ccp4"
-HOMEPAGE="http://www.ccp4.ac.uk/main.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="static-libs"
-
-DEPEND="sci-libs/ccp4-libs"
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/${PATCH}-gentoo.patch )
-
-src_prepare() {
-	rm missing || die
-	echo "libjwc_c_la_LIBADD = -lm -lccp4f" >> Makefile.am || die
-	autotools-utils_src_prepare
-}
--- a/dev-libs/libjwc_c/metadata.xml
+++ b/dev-libs/libjwc_c/metadata.xml
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci</herd>
-	<maintainer>
-		<email>sci@gentoo.org</email>
-	</maintainer>
-</pkgmetadata>
--- a/dev-libs/libjwc_f/Manifest
+++ b/dev-libs/libjwc_f/Manifest
@@ -1 +0,0 @@
-DIST libjwc_f-1.1.tar.gz 170973 SHA256 9c05d5bac2a2e75d5fd490665c795ae31280da886e30f66cf39b3a32f2981199 SHA512 6d947e1513c137a23a4b6c2525e2a2f71c31a41f37455b9b3c97bd4c82128d5b3f4a7bfdd14aba57fbc258dcdcb8fa55e420a8573576992d0ae164bfe394f8d1 WHIRLPOOL 2652f3f43451cfb378d931ccff22a20131f2f44c40c2fe4c51ea45ef08f2e08306c1362f256c0c13014b9db3418ccbce437e4ccea41faae066c800a2ece02551
--- a/dev-libs/libjwc_f/files/612-gentoo.patch
+++ b/dev-libs/libjwc_f/files/612-gentoo.patch
@@ -1,100 +0,0 @@
-diff -Nu libjwc_f-1.1/configure.in ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in
--- libjwc_f-1.1/configure.in	1999-10-21 16:07:14.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in	2004-03-11 17:31:45.000000000 +0100
-@@ -8,6 +8,7 @@
- AC_CANONICAL_SYSTEM
- 
- AM_INIT_AUTOMAKE(libjwc_f, 1.1)
-+AM_MAINTAINER_MODE
- 
- case ${with_g77} in
-   "yes" ) CC="gcc" GCC=yes F77=g77 ;;
-@@ -17,7 +18,7 @@
- AC_PROG_F77
- 
- AC_PROG_INSTALL
-AC_PROG_RANLIB
-+AC_PROG_LIBTOOL
- 
- case "$target" in
-   *irix6* )
-@@ -26,8 +27,9 @@
-       case "$FFLAGS" in
-       *-64* ) ;;   # assume they meant it
-       *-o32* | *-32* ) ;;   # presumably OK
-      * ) FFLAGS="$FFLAGS -o32 -O -g3"
-          CFLAGS=-32
-+      *-n32* ) ;;
-+      * ) FFLAGS="$FFLAGS -n32 -O -g3"
-+          CFLAGS=-n32
-           AC_MSG_WARN([
- 
- *** Using compiler flag -o32 for probable compatibility with
-@@ -47,8 +49,33 @@
- *** See the INSTALL file for more info.
- ])
-     fi ;;
-+  *linux*  )
-+    case $F77 in
-+    g77*)
-+     case "$FFLAGS" in
-+      *no-second-underscore* ) ;; # presumably OK
-+      * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;;
-+      esac
-+    esac ;;
-+  *darwin* ) 
-+    case $F77 in
-+    g77*)
-+     case "$FFLAGS" in
-+      *no-second-underscore* ) ;; # presumably OK
-+      * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;;
-+      esac
-+#mac g77 currently goes not handle -fno-common
-+    enable_shared=no;
-+    esac ;;
-   * ) 
- esac
-+# efc, version 7.1 at least does not support soname, so use CC
-+case "$F77" in
-+ *efc ) F77LD=${F77LD:-'${CC}'} ;;
-+ * ) F77LD=${F77LD:-'${F77}'}
-+esac
-+
-+AC_SUBST(F77LD)
- 
- AM_PROG_LIBTOOL
- 
-Common subdirectories: libjwc_f-1.1/doc and ccp4-6.1.2/x-windows/libjwc/libjwc_f/doc
-diff -Nu libjwc_f-1.1/opn_scr.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f
--- libjwc_f-1.1/opn_scr.f	1999-09-07 12:50:13.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f	2000-10-25 13:03:09.000000000 +0200
-@@ -16,6 +16,6 @@
- C
- C====== Open the file
- C
-      OPEN (IUN_SCR, STATUS='SCRATCH')
-      RETURN
-+C     OPEN (IUN_SCR, STATUS='SCRATCH')
-+      CALL CCPDPN(IUN_SCR,'JWCSCR','SCRATCH','U',0, IFAIL) 
-       END
-diff -Nu libjwc_f-1.1/rpf_dstar.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f
--- libjwc_f-1.1/rpf_dstar.f	1999-07-09 13:39:38.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f	2004-06-04 12:10:59.000000000 +0200
-@@ -376,7 +376,8 @@
-              INR_FLAG = 2
-              PHIW = 0.0
-           END IF
-        ELSE
-+          RETURN
-+        ENDIF
- C
- C---- Calculate distance of edge of spot from sphere at end of rotation
- Crotgen.for
-@@ -418,7 +419,6 @@
-             INR_FLAG = 4
-  40         RETURN
-           END IF
-        END IF
-       END IF
-       RETURN
-       END
--- a/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild
+++ b/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild
@@ -1,38 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils fortran-2
-
-PATCH="612"
-
-DESCRIPTION="Additional fortran library for ccp4"
-HOMEPAGE="http://www.ccp4.ac.uk/main.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="static-libs"
-
-RDEPEND="
-	dev-libs/libjwc_c
-	sci-libs/ccp4-libs"
-DEPEND="${RDEPEND}"
-
-PATCHES=( "${FILESDIR}"/${PATCH}-gentoo.patch )
-
-src_prepare() {
-	rm missing || die
-	echo "libjwc_f_la_LIBADD = -ljwc_c -lccp4f" >> Makefile.am || die
-	autotools-utils_src_prepare
-}
-
-src_install() {
-	autotools-utils_src_install
-	dohtml doc/*
-}
--- a/dev-libs/libjwc_f/metadata.xml
+++ b/dev-libs/libjwc_f/metadata.xml
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci</herd>
-	<maintainer>
-		<email>sci@gentoo.org</email>
-	</maintainer>
-</pkgmetadata>
--- a/profiles/arch/powerpc/package.use.force
+++ b/profiles/arch/powerpc/package.use.force
@@ -15,5 +15,4 @@ net-p2p/sancho-bin java
 # sci-chemistry/arp-warp-bin is not available for ppc
 # sci-chemistry/solve-resolve-bin is not available for ppc
 # sci-chemistry/cns is not available for ppc
-sci-chemistry/oasis minimal
 sci-libs/cctbx minimal
--- a/profiles/arch/powerpc/package.use.mask
+++ b/profiles/arch/powerpc/package.use.mask
@@ -291,12 +291,6 @@ mail-client/claws-mail pda
 # No media-sound/lilypond here, yet (bug #356069)
 app-text/asciidoc test

-# Kacper Kowalik <xarthisius@gentoo.org> (16 Jan 2011)
-# bug 303931
-# dev-lang/icc is not available for ppc
-# sci-chemistry/arp-warp-bin is not available for ppc
-sci-chemistry/ccp4 arpwarp
-
 # Justin Lecher <jlec@gentoo.org> (01 Nov 2010)
 # Deps not Keyworded
 sci-chemistry/apbs fetk
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -241,41 +241,6 @@ net-firewall/shorewall6-lite
 =app-emulation/vmware-workstation-9*
 =app-emulation/vmware-modules-271*

-# Justin Lecher <jlec@gentoo.org> (15 Sep 2015)
-# Outdated and multiple bugs
-# Use upstream installer for up to version
-dev-libs/libjwc_c
-dev-libs/libjwc_f
-sci-chemistry/arp-warp-bin
-sci-chemistry/balbes
-sci-chemistry/ccp4
-sci-chemistry/ccp4-apps
-sci-chemistry/ccp4i
-<sci-chemistry/coot-0.8
-sci-chemistry/imosflm
-sci-chemistry/makecif
-sci-chemistry/molrep
-sci-chemistry/mosflm
-sci-chemistry/mrbump
-sci-chemistry/oasis
-sci-chemistry/pdb-extract
-sci-chemistry/pointless
-sci-chemistry/refmac
-sci-chemistry/scala
-sci-chemistry/sfcheck
-sci-chemistry/solve-resolve-bin
-sci-chemistry/xdsi
-sci-chemistry/xia2
-sci-libs/balbes-db
-sci-libs/cctbx
-<sci-libs/coot-data-3
-sci-libs/ccp4-libs
-<=sci-libs/clipper-2.1_p100511-r1
-<sci-libs/mmdb-1.25.5-r1:0
-<sci-libs/monomer-db-5.41
-<sci-libs/ssm-1.4
-x11-libs/libxdl_view
-
 # Michał Górny <mgorny@gentoo.org> (09 Sep 2015)
 # Package to be used with gentoo-x86 CVS, so pretty much defunct now.
 # Removal in 30 days. Bug #560056.
--- a/sci-chemistry/arp-warp-bin/Manifest
+++ b/sci-chemistry/arp-warp-bin/Manifest
@@ -1 +0,0 @@
-DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532
--- a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild
+++ b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild
@@ -1,81 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils prefix
-
-MY_P="arp_warp_${PV}"
-
-DESCRIPTION="Improvement and interpretation of crystallographic electron density maps"
-SRC_URI="${MY_P}.tar.gz"
-HOMEPAGE="http://www.embl-hamburg.de/ARP/"
-
-LICENSE="ArpWarp"
-SLOT="0"
-KEYWORDS="-* amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse2"
-
-REQUIRED_USE="cpu_flags_x86_sse2"
-
-RDEPEND="
-	app-shells/tcsh
-	sci-chemistry/refmac
-	virtual/awk
-	virtual/jre
-	virtual/opengl
-	x11-libs/libX11"
-DEPEND=""
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${MY_P}"
-
-QA_PREBUILT="opt/arp-warp-bin/bin/*"
-
-pkg_nofetch(){
-	elog "Fill out the form at http://www.embl-hamburg.de/ARP/"
-	elog "and place ${A} in ${DISTDIR}"
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/7.3-setup.patch
-	eprefixify "${S}"/share/arpwarp_setup_base.*
-
-	sed -e '/exit/d' -i "${S}"/share/arpwarp_setup_base.* || die
-}
-
-src_install(){
-	m_type=$(uname -m)
-	os_type=$(uname)
-
-	exeinto /opt/${PN}/bin/bin-${m_type}-${os_type}
-	doexe "${S}"/bin/bin-${m_type}-${os_type}/* "${S}"/share/*{pl,sh}
-
-	insinto /opt/${PN}/bin/bin-${m_type}-${os_type}
-	doins "${S}"/share/*{gif,bmp,XYZ,bash,csh,dat,lib,tbl,llh,prm}
-
-	insinto /etc/profile.d/
-	newins "${S}"/share/arpwarp_setup_base.csh 90arpwarp_setup.csh
-	newins "${S}"/share/arpwarp_setup_base.bash 90arpwarp_setup.sh
-
-	dodoc "${S}"/README manual/UserGuide${PV}.pdf
-	dohtml -r "${S}"/manual/html/*
-}
-
-pkg_postinst(){
-	testcommand=$(echo 3 2 | awk '{printf"%3.1f",$1/$2}')
-	if [ $testcommand == "1,5" ];then
-	  ewarn "*** ERROR ***"
-	  ewarn "   3/2=" $testcommand
-	  ewarn "Invalid decimal separator (must be ".")"
-	  ewarn "You need to set this correctly!!!"
-	  echo
-	  ewarn "One way of setting the decimal separator is:"
-	  ewarn "setenv LC_NUMERIC C' in your .cshrc file"
-	  ewarn "\tor"
-	  ewarn "export LC_NUMERIC=C' in your .bashrc file"
-	  ewarn "Otherwise please consult your system manager"
-	fi
-}
--- a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch
+++ b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch
@@ -1,30 +0,0 @@
-diff --git a/share/arpwarp_setup_base.bash b/share/arpwarp_setup_base.bash
-index 29e769c..0b8a51e 100644
--- a/share/arpwarp_setup_base.bash
-+++ b/share/arpwarp_setup_base.bash
-@@ -13,10 +13,10 @@ else
-     identifier=${nameprocessor}'-'${namesystem}
- fi
- #
-arpwarphome="$1X"
-+arpwarphome="@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin"
- #
- export warpbin=${arpwarphome}/bin/bin-${identifier}
-export warpdoc=${arpwarphome}/manual
-+export warpdoc=@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/arp-warp-bin-7.1/html/
- export PATH=${warpbin}:${PATH}
- #
- # Checks for existence of $warpbin directory
-diff --git a/share/arpwarp_setup_base.csh b/share/arpwarp_setup_base.csh
-index 41b11e9..a4edcff 100644
--- a/share/arpwarp_setup_base.csh
-+++ b/share/arpwarp_setup_base.csh
-@@ -13,7 +13,7 @@ else
-     set identifier = ${nameprocessor}'-'${namesystem}
- endif
- #
-set arpwarphome = '$1X'
-+set arpwarphome = '@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin'
- #
- setenv warpbin ${arpwarphome}/bin/bin-${identifier}
- #
--- a/sci-chemistry/arp-warp-bin/metadata.xml
+++ b/sci-chemistry/arp-warp-bin/metadata.xml
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
--- a/sci-chemistry/balbes/Manifest
+++ b/sci-chemistry/balbes/Manifest
@@ -1,2 +0,0 @@
-DIST balbes-1.0.0_p100317.tar.gz 506464 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c SHA512 0029e459877113de212574daec8532f0d225e96772c6a777d34af94e5f11c1253ca941266e68da79e0a5c5a96416a824f76c6f1d8652d9a60a34756989cae41e WHIRLPOOL 9024490eea43ef526f00aff9f2045e2689dd6d9e7575c9fd3de2a23fc4af3ad784660df4c78c9aa6380df1dac9fbf46c8b6be105a3094761ebdd43c5cb541beb
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
--- a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
+++ b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
@@ -1,79 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-CCP4VER="6.1.3"
-PYTHON_DEPEND="2"
-
-inherit eutils fortran-2 python toolchain-funcs
-
-DESCRIPTION="Automated molecular replacement (MR) pipeline"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/index.html"
-SRC_URI="
-	mirror://gentoo/${P}.tar.gz
-	ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-core-src.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-# bundled PyXML is modified and cannot be replaced
-
-COMMON_DEPEND="sci-libs/ccp4-libs"
-RDEPEND="${COMMON_DEPEND}
-	~sci-libs/balbes-db-${CCP4VER}
-	!<=sci-chemistry/ccp4-apps-6.1.3-r1"
-DEPEND="${COMMON_DEPEND}"
-
-S="${WORKDIR}"/src
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_set_active_version 2
-}
-
-src_unpack() {
-	unpack ${P}.tar.gz
-	tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz \
-		ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \
-		ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4
-	python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes
-}
-
-src_prepare() {
-	mkdir "${WORKDIR}"/bin || die
-	epatch "${FILESDIR}"/${PV}-makefile.patch
-	cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/
-	epatch "${FILESDIR}"/pyxml-0.8.4-python-2.6.patch
-}
-
-src_compile() {
-	emake \
-		BLANC_FORT="$(tc-getFC) ${FFLAGS}" || die
-	cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4
-	find build -delete
-	$(PYTHON) setup.py build
-	find xml/xslt test -delete
-}
-
-src_install() {
-	insinto /usr/share/balbes/BALBES_0.0.1/
-	doins -r \
-		 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \
-		 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 || die
-	dobin \
-		"${WORKDIR}"/bin/* \
-		"${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \
-		|| die
-}
-
-pkg_postinst() {
-	python_mod_optimize /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4}
-}
-
-pkg_postrm() {
-	python_mod_cleanup /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4}
-}
--- a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch
+++ b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch
@@ -1,107 +0,0 @@
-diff --git a/makefile b/makefile
-index baaceb5..85a7baf 100755
--- a/makefile
-+++ b/makefile
-@@ -70,6 +70,15 @@ OBJDB_G =  get_pdb_list.o
- 
- #OBJDB_Z =  blanc2mtz.o libutils.o
- 
-+# incomplete targets:
-+# dimer_search_db domain_search_db domain align3
-+all: search_db get_structure_db manage_db search_dm dom2ch \
-+            save_si get_pdb_list_db update_db \
-+            update_dom_db bl2mtz check_file_db fobs2cif sol_check \
-+            get_trns p2s check_cell alt_sg \
-+            align cell_list create_bins \
-+            get_pdb_list_db get_ch get_nm get_mod
-+
- search_db: sdb_l
- 
- get_structure_db: tdb_l
-@@ -201,58 +210,58 @@ save_seg_id.o: save_seg_id.f
- 	$(BLANC_FORT) -c save_seg_id.f 
- 
- sdb_l: $(OBJDB_S)
-	$(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S)
- tdb_l: $(OBJDB_T)
-	$(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T)
- mdb_l: $(OBJDB_M)
-	$(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M)
- mdm_l: $(OBJDB_MD)
-	$(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD)
- d2c_l: $(OBJDB_A)
-	$(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A)
- upd_l: $(OBJDB_U)
-	$(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U)
- dom_l: $(OBJDB_V)
-	$(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V)
- ddb_l: $(OBJDB_D)
-	$(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D)
- dmdb_l: $(OBJDB_N)
-	$(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N)
- gdb_l: $(OBJDB_G)
-	$(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G)
- b2m_l: blanc2mtz.o libutils.o
-	$(BLANC_FORT) -o ../bin/blanc2mtz  blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz  blanc2mtz.o libutils.o -lccp4f -lccp4c
- f2c_l: f2cif.o libutils.o
-	$(BLANC_FORT) -o ../bin/f2cif  f2cif.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif  f2cif.o libutils.o
- chf_l: check_file_DB.o libutils.o
-	$(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o
- chc_l: check_cell_sg.o libutils.o
-	$(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o
- asl_l: alt_sg_list.o libutils.o
-	$(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o
- sc_l: $(OBJDB_C)
-	$(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C)
- gt_l: $(OBJDB_R)
-	$(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R)
- dmn_l: domain.o libutils.o
-	$(BLANC_FORT) -o ../bin/domain domain.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o
- pack: pdb_pack.o libutils.o
-	$(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o
- p2s_l: $(OBJDB_P)
-	$(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P)
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P)
- aln_l: align_DB.o  DB_subr.o libutils.o
-	$(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o
- aln3_l: align_DB_new.o  DB_subr.o libutils.o
-	$(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o
- cell_l: create_cell_list.o  DB_subr.o libutils.o
-	$(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o
- getch_l: get_chain.o  DB_subr.o libutils.o
-	$(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o
- getnmr_l: get_nmr.o  DB_subr.o libutils.o
-	$(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o
- getmod_l: get_model.o libutils.o
-	$(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o
- crb_l: create_binaries.o  DB_subr.o libutils.o
-	$(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o
- save_si_l: save_seg_id.o  DB_subr.o libutils.o
-	$(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o
--- a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch
+++ b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch
@@ -1,28 +0,0 @@
-diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py
--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py	2008-12-15 16:54:36.000000000 +0900
-+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py	2008-12-15 16:57:02.000000000 +0900
-@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP
-         self._rel = rel
-         nt = ParsedNodeTest.ParsedNodeTest('node', '')
-         ppl = ParsedPredicateList.ParsedPredicateList([])
-        as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
-        self._step = ParsedStep.ParsedStep(as, nt, ppl)
-+        as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
-+        self._step = ParsedStep.ParsedStep(as_, nt, ppl)
-         return
- 
-     def evaluate(self, context):
-diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py
--- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py	2008-12-15 16:54:36.000000000 +0900
-+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py	2008-12-15 16:58:58.000000000 +0900
-@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP
-         self._right = right
-         nt = ParsedNodeTest.ParsedNodeTest('node','')
-         ppl = ParsedPredicateList.ParsedPredicateList([])
-        as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
-        self._middle = ParsedStep.ParsedStep(as, nt, ppl)
-+        as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self')
-+        self._middle = ParsedStep.ParsedStep(as_, nt, ppl)
- 
-     def evaluate(self, context):
-         res = []
--- a/sci-chemistry/balbes/metadata.xml
+++ b/sci-chemistry/balbes/metadata.xml
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<longdescription>
-	BALBES is a system for solving protein structures using x-ray 
-	crystalographic data. Molecular Replacement(MR) is its core 
-	scientific method. BALBES aims to integrate all components, 
-	necessary for finding a solution structure by MR, into one system. 
-	It consists of a database, scientific programs and a python 
-	pipeline. The system is automated so that it needs no user's 
-	intervention when running complicated combination of jobs such 
-	as model searching, molecular replacement and refinement.
-</longdescription>
-</pkgmetadata>
--- a/sci-chemistry/ccp4-apps/Manifest
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -1,2 +0,0 @@
-DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
@@ -1,395 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs
-
-MY_P="${PN/-apps}-${PV}"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-SRC_URI="
-	${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="examples X"
-
-X11DEPS="
-	x11-libs/libX11
-	x11-libs/libXaw
-	x11-libs/libXt
-	x11-libs/libxdl_view"
-
-TKDEPS="
-	>=dev-lang/tk-8.3:0=
-	>=dev-tcltk/blt-2.4
-	dev-tcltk/iwidgets
-	dev-tcltk/itcl
-	dev-tcltk/itk
-	>=dev-tcltk/tdom-0.8
-	dev-tcltk/tktreectrl"
-
-SCILIBS="
-	~sci-libs/ccp4-libs-${PV}
-	>=sci-libs/ccp4-libs-${PV}-r7
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/ssm
-	virtual/blas
-	virtual/lapack"
-
-SCIAPPS="
-	sci-chemistry/pdb-extract
-	sci-chemistry/pymol
-	sci-chemistry/rasmol
-	>=sci-chemistry/oasis-4.0-r1"
-
-RDEPEND="
-	${TKDEPS}
-	${SCILIBS}
-	app-shells/tcsh
-	dev-python/pyxml
-	dev-libs/libxml2:2
-	dev-libs/libjwc_c
-	dev-libs/libjwc_f
-	dev-libs/boehm-gc
-	!app-office/sc
-	!<sci-chemistry/ccp4-6.1.3
-	X? ( ${X11DEPS} )"
-DEPEND="${RDEPEND}
-	X? (
-		x11-misc/imake
-		x11-proto/inputproto
-		x11-proto/xextproto
-	)"
-PDEPEND="${SCIAPPS}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# We already have sci-chemistry/rasmol
-	# Also remember to create the bindir.
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# We have seperate ebuilds for those
-	for bin in molref xia scala imosflm balbes; do
-		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
-	done
-
-	# don't configure what is not build
-	ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# Not renaming, but unbundling libs
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
-
-	# Use pkg-config to detect BLAS/LAPCK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# unbundle libs
-	ccp_patch "${FILESDIR}"/${PV}-unbundle.patch
-
-	# tcl-8.6
-	ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch
-
-	# Update things for oasis 4 usage
-	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
-	sed 's: oasis : :g' -i src/Makefile.in || die
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \
-		-e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \
-		-e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \
-		-e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \
-		-i configure || die
-
-	sed \
-		-e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \
-		-i src/Makefile* || die
-
-	find "${S}" -name "Makefile.*" \
-		-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
-
-	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-		eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-
-	python_fix_shebang -f .
-}
-
-src_configure() {
-	# Build system is broken if we set LDFLAGS
-	export GENTOOLDFLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# These are broken with ./src/procheck/ps.f
-	filter-flags "-floop-*"
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-	export BINSORT_SCR="${T}"
-	export CCP4_MASTER="${WORKDIR}"
-	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
-	export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-diffractionImg \
-		--disable-clipper \
-		--disable-ssm \
-		--disable-mosflm \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "configure failed"
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--bindir="${ED}"/usr/libexec/ccp4/bin \
-		--with-ccp4="${S}" \
-		--with-clipper="${EPREFIX}/usr" \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-mmdb="${EPREFIX}/usr" \
-		CXX=$(tc-getCXX)
-	popd 2>/dev/null
-}
-
-src_compile() {
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-		emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-		emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	# if we don't make this, a ton of programs fail to install
-	mkdir "${S}"/bin || die
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd "${S}"/src/clipper_progs 2>/dev/null
-		emake install || die
-	popd 2>/dev/null
-
-	einstall || die "install failed"
-
-	# Collision with sci-chemistry/mrbump
-	rm -f "${S}"/bin/{mrbump,pydbviewer} || die
-
-	# Bins
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${S}"/bin/* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file} || die
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file} || die
-		fi
-	done
-
-	rm -f "${S}"/include/ccp4.setup*
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-	local _man
-	pushd "${S}"/man/cat1 > /dev/null
-	for _man in *; do
-		newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2}
-	done
-	popd > /dev/null
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc manual/* README CHANGES doc/* examples/README || die
-
-	rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${ED}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${i}
-			dodoc "${S}"/examples/${i}/*
-		done
-
-		docinto examples/tutorial
-		dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
-		for i in data results; do
-			docinto examples/tutorial/${i}
-			dodoc "${S}"/examples/tutorial/${i}/*
-		done
-
-		for i in non-runnable runnable; do
-			docinto examples/unix/${i}
-			dodoc "${S}"/examples/unix/${i}/*
-		done
-	fi
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
-
-	cat >> "${T}"/baubles <<- EOF
-	#!${EPREFIX}/bin/bash
-	exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py"
-	EOF
-
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${T}"/baubles || die
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
--- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
@@ -1,70 +0,0 @@
--- src/clipper_progs/src/intensity_target.h.orig	2010-01-21 11:27:13.236795886 -0600
-+++ src/clipper_progs/src/intensity_target.h	2010-01-21 11:31:33.450686927 -0600
-@@ -70,9 +70,31 @@
-   {
-   public:
-     //! constructor: takes the datalist against which to calc target
-    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ );
-+    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
-+    {
-+      hkl_data1 = &hkl_data1_;
-+      hkl_data2 = &hkl_data2_;
-+    }
-     //! return the value and derivatives of the target function
-    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const;
-+    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
-+    {
-+      Rderiv result;
-+      result.r = result.dr = result.dr2 = 0.0;
-+      const T1& it1 = (*hkl_data1)[ih];
-+      const T2& it2 = (*hkl_data2)[ih];
-+      if ( !it1.missing() && !it2.missing() )
-+        if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
-+          const ftype eps = ih.hkl_class().epsilon();
-+          const ftype i1 = it1.I() / eps;
-+          const ftype i2 = it2.I() / eps;
-+          const ftype w = sqrt( i1 * i2 );    
-+          const ftype d = intensityh + log(i1) - log(i2);
-+          result.r   =       w * d * d;
-+          result.dr  = 2.0 * w * d;
-+          result.dr2 = 2.0 * w;
-+      }
-+      return result;
-+    }
-     //! the type of the function: optionally used to improve convergence
-     FNtype type() const { return QUADRATIC; }
-   private:
-@@ -109,33 +131,4 @@
-     return result;
-   }
- 
-  // Log I1-I2 scaling
-
-  template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
-  {
-    hkl_data1 = &hkl_data1_;
-    hkl_data2 = &hkl_data2_;
-  }
-
-  template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
-  {
-    Rderiv result;
-    result.r = result.dr = result.dr2 = 0.0;
-    const T1& it1 = (*hkl_data1)[ih];
-    const T2& it2 = (*hkl_data2)[ih];
-    if ( !it1.missing() && !it2.missing() )
-      if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
-	const ftype eps = ih.hkl_class().epsilon();
-	const ftype i1 = it1.I() / eps;
-	const ftype i2 = it2.I() / eps;
-	const ftype w = sqrt( i1 * i2 );    
-	const ftype d = intensityh + log(i1) - log(i2);
-	result.r   =       w * d * d;
-	result.dr  = 2.0 * w * d;
-	result.dr2 = 2.0 * w;
-    }
-    return result;
-  }
-
-
- #endif
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch
@@ -1,14 +0,0 @@
-diff --git a/share/Makefile.in b/share/Makefile.in
-index 2d4f20b..4500993 100755
--- a/share/Makefile.in
-+++ b/share/Makefile.in
-@@ -18,9 +18,6 @@ install :
- 	for i in $(MRBUMP_TARGETS); do \
- 	   test -s $(MRBUMP_BINDIR)/$$i  &&  $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\
- 	done
-	for i in $(BALBES_TARGETS); do \
-	  test -s $(BALBES_BINDIR)/$$i  &&  $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\
-	done
- 
- clean : ; -rm -f core *.o *~ a.out 
- 
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch
@@ -1,24 +0,0 @@
--- ccp4-6.1.1/x-windows/Makefile.in	2008-08-11 19:20:01.000000000 +0200
-+++ ccp4-6.1.1/x-windows/Makefile.in.new	2009-02-27 14:32:25.000000000 +0100
-@@ -35,7 +35,7 @@
- #
- # all
- #
-all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm
-+all : rotgen_ hklview xjiffy
- #
- # xdl_view
- #
-@@ -157,11 +157,10 @@
- #
- install_obj = hklview rotgen ipmosflm
- install: all
-+	mkdir -p $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
- 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install
-	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
- 	cd $(rotgen_dir); $(MAKE) install
-	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
- #
- # clean
- #
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch
@@ -1,11 +0,0 @@
--- ccp4i/Makefile.in	2009-06-19 15:08:53.000000000 +0200
-+++ ccp4i/Makefile.in.new	2009-08-04 21:10:14.000000000 +0200
-@@ -9,7 +9,7 @@
- SHELL = /bin/sh
- DESTDIR = $(prefix)
- CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin
-CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer
-+CCP4I_TARGETS = ccp4i loggraph crank mapslicer
- 
- install :
- 	for i in $(CCP4I_TARGETS); do \
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch
@@ -1,35 +0,0 @@
--- Makefile.in	2009-06-19 15:13:29.000000000 +0200
-+++ Makefile.in.new	2009-08-02 23:06:41.000000000 +0200
-@@ -2,7 +2,7 @@
- # $Id$
- 
- SHELL = /bin/sh
-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
-+DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
- # this is for the benefit of makes that don't pass variable values in
- # recursive invocations, so that you can override these values on the
- # command line at the top level
-@@ -69,19 +69,19 @@
- 	$(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \
- 	$(MAKE) install
- 
-srcdir :  FORCE libdir
-+srcdir :  FORCE 
- 	if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi
- 
- supported : srcdir
- 
-unsupported :  FORCE libdir
-+unsupported :  FORCE
- 	if test -d unsupported/src; then cd unsupported/src;  \
- 	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi
- 
-datadir : FORCE libdir
-+datadir : FORCE
- 	cd lib/data; $(MAKE) $(MFLAGS) $(MVARS)
- 
-xwindir : FORCE libdir
-+xwindir : FORCE
- 	if test -f x-windows/Makefile; then cd x-windows; \
- 	   $(MAKE) -i $(MFLAGS) ; else true; fi
- 
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch
@@ -1,19 +0,0 @@
--- src/pisa/Makefile.am	2007-07-10 10:56:05.000000000 +0200
-+++ src/pisa/Makefile.am.new	2009-06-11 21:16:51.000000000 +0200
-@@ -1,4 +1,4 @@
-SUBDIRS = molref pisastore sbase
-+SUBDIRS = pisastore sbase
- 
- pkgdatadir = $(datadir)/pisa
- 
--- src/pisa/Makefile.in	2009-06-12 21:12:08.000000000 +0200
-+++ src/pisa/Makefile.in.new	2009-06-12 21:41:52.000000000 +0200
-@@ -82,7 +82,7 @@
- am__quote = @am__quote@
- install_sh = @install_sh@
- pisa_LDFLAGS = @pisa_LDFLAGS@
-SUBDIRS = molref pisastore sbase
-+SUBDIRS = pisastore sbase
- 
- dist_pkgdata_DATA = pisa.cfg
- 
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch
@@ -1,42 +0,0 @@
--- ./src/Makefile.in	2009-03-20 15:06:41.000000000 +0100
-+++ ./src/Makefile.in.new	2009-07-31 23:46:13.000000000 +0200
-@@ -50,7 +50,7 @@
- 
- # these live in subdirectories and have more than one dependency:
- OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \
-         scala dm dmmulti stereo mapmask maprot ncsmask \
-+         dm dmmulti stereo mapmask maprot ncsmask \
-          sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \
-          anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat 
- 
-@@ -637,7 +637,7 @@
- 
- ### scala, mapmask, maprot, ncsmask, combat
- 
-scala mapmask maprot ncsmask combat sc dyndom: # dependencies below
-+mapmask maprot ncsmask combat sc dyndom: # dependencies below
- 	@$(SETFLAGS) pwd=`pwd` ; rm -f $@; \
- 	  cd $(srcdir)/$@_; \
- 	  echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\
-@@ -1002,21 +1002,6 @@
- proclean:	$(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par
- rmsdev:		$(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc
- 
-scaladir = $(srcdir)/scala_
-scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \
-	$(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \
-	$(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \
-	$(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \
-	$(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \
-	$(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \
-        $(scaladir)/axes.fh $(scaladir)/bigarg.fh \
-        $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \
-        $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \
-        $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \
-        $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \
-        $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \
-        $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh
-
- freemask.o:	$(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \
- 		$(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \
- 		$(dmdir)/params.fh $(dmdir)/uvwdata.fh
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch
@@ -1,14 +0,0 @@
--- src/Makefile.in	2009-07-05 16:50:25.000000000 +0200
-+++ src/Makefile.in.new	2009-07-05 19:38:06.000000000 +0200
-@@ -50,9 +50,9 @@
- 
- # these live in subdirectories and have more than one dependency:
- OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \
-         scala dm dmmulti stereo mapmask maprot ncsmask chef \
-+         scala dm dmmulti stereo mapmask maprot ncsmask \
-          sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \
-         anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat 
-+         anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf 
- 
- # targets built from .c sources:
- CSIMPLE = pltdev binsort
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
@@ -1,111 +0,0 @@
--- configure	2009-08-07 12:11:28.000000000 +0200
-+++ configure.new.nolib	2009-08-17 22:30:39.000000000 +0200
-@@ -3113,41 +3113,6 @@
-     RX_L="$configdir/lib/rxdispencer/rx"
-     export RX_H RX_L
-   fi
-  echo 
-  echo "Running separate configure for CCIF library."
-  echo
-  cd lib/ccif
-  echo "Updating modification times for configuration files"
-  echo "Please wait..."
-  for i in configure.in aclocal.m4 configure Makefile.in; do
-    touch $i && sleep 1   
-  done
-  echo "...done."      
-
-  if [ "X$LIBFOPTIM" != "X" ]; then
-    FOPTIM_save=$FOPTIM
-    FOPTIM=$LIBFOPTIM
-    FFLAGS="${FOPTIM} ${XFFLAGS}"
-  fi
-  if [ "X$LIBCOPTIM" != "X" ]; then
-    COPTIM_save=$COPTIM
-    COPTIM=$LIBCOPTIM
-    CFLAGS="${COPTIM} ${XCFLAGS}"
-  fi
-  ( touch /tmp/$$.cache_file 2>/dev/null && \
-    cat /dev/null > /tmp/$$.cache_file && \
-    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \
-    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
-  rm -f /tmp/$$.cache_file
-  if [ "X$LIBFOPTIM" != "X" ]; then
-    FOPTIM=$FOPTIM_save
-    FFLAGS="${FOPTIM} ${XFFLAGS}"
-  fi
-  if [ "X$LIBCOPTIM" != "X" ]; then
-    COPTIM=$COPTIM_save
-    CFLAGS="${COPTIM} ${XCFLAGS}"
-  fi
-  cd ../..
-   echo
-   echo "Returning to main configure."
-   echo
-@@ -5094,53 +5059,6 @@
-   echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-   ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} 
-   echo
-  echo "CCP4 configure: Running separate configure for libjwc_c library."
-  echo
-  cd ${srcdir}/${xwindir}/libjwc/libjwc_c
-  echo "Updating modification times for configuration files in libjwc_c"
-  echo "Please wait..."
-  for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do
-    touch $i && sleep 1
-  done
-  echo "...done."
-  echo
-  echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-  ( touch /tmp/$$.cache_file 2>/dev/null && \
-    cat /dev/null > /tmp/$$.cache_file && \
-    ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
-    ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-  rm -f /tmp/$$.cache_file
-  echo
-  echo "CCP4 configure: Running separate configure for libjwc_f library."
-  echo
-  cd ${srcdir}/${xwindir}/libjwc/libjwc_f
-  # for g77 3.1 some builds do not have no-common for system libs,
-  # so disable for now
-  echo "Updating modification times for configuration files in libjwc_f"
-  echo "Please wait..."
-  for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do
-    touch $i && sleep 1
-  done
-  echo "...done."
-  echo
-  # for g77 3.1 some builds do not have no-common for system libs,
-  # so disable for now
-  case $system in
-  Darwin* )
-    echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-    ( touch /tmp/$$.cache_file 2>/dev/null && \
-      cat /dev/null > /tmp/$$.cache_file && \
-      ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
-      ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-    ;;
-  * )
-    echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-    ( touch /tmp/$$.cache_file 2>/dev/null && \
-      cat /dev/null > /tmp/$$.cache_file && \
-      ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
-      ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-  esac
-  rm -f /tmp/$$.cache_file
- 
-   if test "$non_shared" = yes; then
- #this is a bit of a cheat/fudge but that's life!
-@@ -5210,12 +5128,6 @@
-   fi
- 
-   echo
-  echo "CCP4 configure: Running separate configure for Mosflm"
-  echo
-  cd ${srcdir}/${mosflmdir}
-  echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-  ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-  echo
-   cd ../..
-   echo "Returning to main configure."
-   echo
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch
@@ -1,87 +0,0 @@
--- ccp4-6.0.99e.orig/configure	2008-07-31 10:37:22.000000000 -0700
-+++ ccp4-6.0.99e/configure	2008-07-31 10:39:18.000000000 -0700
-@@ -643,45 +643,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
-if test -z "$onlylibs" ; then 
-   for i in CCP4_SCR BINSORT_SCR; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the value of $i."
-       badvar=1
-     fi
-   done
-
-   for i in libdir bindir includedir; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the argument of --$i."
-       badvar=1
-     fi
-   done
-
-   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-     if test -d $i || mkdir $i; then :
-     else
-       eval echo "! No directory $i and can\'t create it."
-       badvar=1
-     fi
-   done
-else
-   # Kludge to fool the "Makefile" target in the top-level CCP4
-   # Makefile into not trying to remake src/Makefile.in
-   for i in $srcdir/src $srcdir/lib/src ; do
-     if test -d $i || mkdir $i; then
-       if ! test -f $i/Makefile.in ; then
-         echo
-         echo "onlylibs: making dummy file $i/Makefile.in"
-	 touch $i/Makefile.in
-       fi
-     fi
-   done
-fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir includedir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
--- a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
@@ -1,152 +0,0 @@
-diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c
-index bfda882..f821e04 100755
--- a/lib/DiffractionImage/Bruker/FRM_LIB.c
-+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c
-@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files.
- #include "sys/types.h"  /* _open, etc. */
- #include "sys/stat.h"   /* _open, etc. */
- 
-+#include <unistd.h>
-+
- #ifndef _MSC_VER
- int min(int a, int b)
- 	{
-diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c
-index 1a933de..1c40c32 100755
--- a/lib/DiffractionImage/MAR/mar300_header.c
-+++ b/lib/DiffractionImage/MAR/mar300_header.c
-@@ -23,6 +23,9 @@
-  */
- #include "mar300_header.h"
- 
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
-  * Local functions
-  */
-diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c
-index a8351ea..16d0f7b 100755
--- a/lib/DiffractionImage/MAR/mar345_header.c
-+++ b/lib/DiffractionImage/MAR/mar345_header.c
-@@ -32,6 +32,9 @@
-  */
- #include "mar345_header.h"
- 
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
-  * Definitions
-  */
-diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c
-index 07f2741..6364ca4 100755
--- a/lib/DiffractionImage/MAR/nb_header.c
-+++ b/lib/DiffractionImage/MAR/nb_header.c
-@@ -20,6 +20,8 @@
- #include <io.h>
- #endif
- 
-+#include <sys/types.h>
-+#include <unistd.h>
- /*
-  * mar software include files
-  */
-diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c
-index 443bb8c..0d96b3f 100755
--- a/lib/DiffractionImage/MAR/swap.c
-+++ b/lib/DiffractionImage/MAR/swap.c
-@@ -10,6 +10,9 @@
-  *
-  **********************************************************************/
- 
-+#define _XOPEN_SOURCE
-+#include <unistd.h>
-+
- void swaplong();
- void swapshort();
- 
-diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c
-index 0f6a6b7..a09dc48 100755
--- a/lib/ccif/f_interface.c
-+++ b/lib/ccif/f_interface.c
-@@ -25,6 +25,7 @@
- ********************************************************************/
- 
- #include "stdpccts.h"
-+#include <sys/mman.h>
- 
- /* This file is terribly organised, and badly needs re-doing. There is probably
-  * scope for splitting this into three modules:
-diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c
-index 8b5d04f..74ee3f7 100755
--- a/lib/src/ccp4_general_f.c
-+++ b/lib/src/ccp4_general_f.c
-@@ -26,6 +26,7 @@
- #include <string.h>
- #include <stdlib.h>
- #include <math.h>
-+#include <time.h>
- #include "ccp4_errno.h"
- #include "ccp4_fortran.h"
- #include "ccp4_parser.h"
-diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c
-index 3e83d4d..bb3e975 100755
--- a/lib/src/ccp4_program.c
-+++ b/lib/src/ccp4_program.c
-@@ -25,6 +25,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
-+#include <time.h>
- #include "ccp4_program.h"
- #include "ccp4_parser.h"
- #include "ccp4_utils.h"
-diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c
-index ee8af24..c6fb3cd 100755
--- a/lib/src/fsplit.c
-+++ b/lib/src/fsplit.c
-@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c	5.5 (Berkeley) 3/12/91";
- #include <string.h>
- #include <sys/types.h>
- #include <sys/stat.h>
-+#include <unistd.h>
- 
- /*
-  *	usage:		fsplit [-e efile] ... [file]
-diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c
-index ea52e96..30dbd56 100755
--- a/src/clipper_progs/src/pirate/compress42.c
-+++ b/src/clipper_progs/src/pirate/compress42.c
-@@ -142,6 +142,7 @@
- #include	<sys/types.h>
- #include	<sys/stat.h>
- #include	<errno.h>
-+#include	<unistd.h>
- 
- #ifdef DIRENT
- #	include	<dirent.h>
-diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c
-index e224430..c7b82f4 100755
--- a/src/mtz2cif_/mtz2cif.c
-+++ b/src/mtz2cif_/mtz2cif.c
-@@ -28,6 +28,7 @@
- #include "cmtzlib.h"
- #include "ccp4_parser.h"
- #include "ccp4_general.h"
-+#include "ccp4_program.h"
- #include "csymlib.h"
- #include "mtz2cif_lib.h"
- 
-diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c
-index 67e0bf1..76526ab 100755
--- a/x-windows/XCCPJIFFY/xplot84driver.c
-+++ b/x-windows/XCCPJIFFY/xplot84driver.c
-@@ -11,6 +11,7 @@
- 
- #include <stdio.h>
- #include <sys/types.h>
-+#include <stdlib.h>
- 
- #include <X11/StringDefs.h>
- #include <X11/Intrinsic.h>
--- a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
@@ -1,597 +0,0 @@
-diff --git a/configure b/configure
-index 833f483..bcfa62d 100755
--- a/configure
-+++ b/configure
-@@ -3226,574 +3226,14 @@ else
-   echo
-   echo "Warning: this option has not been extensively tested!"
-   echo "Please report problems to ccp4@ccp4.ac.uk"
-  # Search for vendor LAPACK/BLAS first
-  if test ! "$with_netlib_lapack" ; then
-    # Initialise variables to blank
-    lapackdir=
-    XLAPACK_LIB=
-    # Possible directories to check for vendor or pre-existing LAPACK or
-    # BLAS - add to these if you want to test others
-    trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib"
-    # Possible library names
-    # These are the names like xxxx where the library will be libxxxx.a
-    # or libxxxx.so
-    echo
-    echo "Guessing names for native/vendor LAPACK and/or BLAS libraries"
-    echo "on this system"
-    case $system in
-      linux | linux64 | linux32 )
-        # linux users will usually have them in /usr/lib but don't call it
-        trylapack="lapack"
-        tryblas="blas"
-        # if code is non_shared then this can lead to problems. both blas and lapack
-        # need to be resolved even if they are not called!
-        if test "$non_shared" = yes; then
-          echo "You are compiling linux non_shared. This sometimes causes problems "
-          echo "  so checking for requirements." 
-          echo "Checking: try to link library against test program"
-          if test -f testlink.f || test -f testlink ; then
-            rm -f testlink*
-          fi 
-          cat > testlink.f <<EOF
-      PROGRAM TESTLINK
-C A bit of scala code to test the linking
-      real bf(3), bnorm
-c
-      integer maxbmt
-      parameter (maxbmt = 2)
-      double precision B(maxbmt,maxbmt), eigval(maxbmt),
-     $   eigvec(maxbmt,maxbmt), w(5*maxbmt)
-      integer m, ia, ix, istat
-c
-      B(1,1) = 1.00
-      B(1,2) = 1.00
-      B(2,1) = 1.00
-      B(2,2) = 1.00
-c
-      m = maxbmt
-      ia = maxbmt
-      ix = maxbmt
-      call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat)
-      end
-EOF
-          #firstly test without -lblas
-          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
-          echo $test_compile
-          if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
-            # Compilation was okay
-            echo "... only -llapack needed"
-            XLAPACK_LIB="-llapack"
-            # Set the next two variables so that configure
-            # doesn't try to build netlib libraries
-            LAPACKLIB="lapack"
-            noblas=yes
-            trylapack=
-            tryblas=
-          else
-	    echo "more than just -llapack needed...."
-            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
-            echo $test_compile
-            if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-              # Compilation was okay
-              echo "...-llapack and -lblas were needed"
-              XLAPACK_LIB="-llapack -lblas"
-              # Set the next two variables so that configure
-              # doesn't try to build netlib libraries
-              LAPACKLIB="lapack blas"
-              noblas=no
-              trylapack=
-              tryblas=
-	    else
-              echo "....could not find either lapack or blas."
-	    fi
-          fi
-        fi
-        # add 64 bit libs
-        case $system in
-          linux64 ) trydirs="/usr/lib64 ${trydirs}" ;;
-        esac
-
-        ;;
-      osf1)
-        # OSF1 has dxml (old version) and cxml
-        # which should have both lapack and blas 
-        trylapack="dxml cxml"
-        tryblas=
-        trydirs="${trydirs} /usr/shlib"
-        ;;
-      irix)
-        # Additional search paths for IRIX
-        trydirs="${trydirs} /usr/lib32"
-        # SCSL should have both LAPACK and BLAS
-        trylapack="scs"
-        tryblas="blas"
-        ;;
-      irix64)
-        # Additional search paths for IRIX64
-        trydirs="${trydirs} /usr/lib64"
-        # SCSL should have both LAPACK and BLAS
-        trylapack="scs"
-        tryblas="blas"
-        # Extra compiler flags?
-        #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON"
-        ;;
-      aix)
-        # Additional search paths for AIX
-        trydirs="${trydirs}" 
-        # AIX might have ESSL library - blas only I think
-        trylapack=
-        tryblas="essl"
-        ;;
-      hpux)
-        # Additional search paths for HPUX
-        trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0"
-        # HPUX should have both LAPACK (part of mlib) and BLAS
-        trylapack="lapack"
-        tryblas="blas"
-        # Extra compiler flags?
-        # +U77 required for ETIME function - this is already in XFFLAGS
-        #XLAPACKFLAGS="+U77"
-        ;;
-
-      sunos | sunos64)
-        # Sun has libraries with BLAS and LAPACK invoked using
-        # -xlic_lib=sunperf
-        trylapack=
-        tryblas=
-        echo "SunOs can use the Sun Performance Library (if installed)"
-        echo "which has both BLAS and LAPACK 3.0"
-        echo 
-        echo "Looking for a valid library to use..."
-        echo
-	# Loop over the possible library names
-        try_libs="sunperf"
-        for testlib in $try_libs
-        do
-          if test ! "$XLAPACK_LIB" ; then
-            # Try running a test compile to see if this a valid library
-            if test -f testlink.f || test -f testlink ; then
-              rm -f testlink*
-            fi
-            cat > testlink.f <<EOF
-c Test fortran program to link against library
-      PROGRAM TESTLINK
-      IMPLICIT NONE
-      INTEGER A
-      A = 1
-      STOP
-      END
-EOF
-            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib"
-            echo $test_compile
-            if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-              # Compilation was okay
-              echo "... -xlic_lib=$testlib is okay"
-              XLAPACK_LIB="-dalign -xlic_lib=$testlib"
-              # Set the next two variables so that configure
-              # doesn't try to build netlib libraries
-              LAPACKLIB="$testlib"
-              noblas=yes
-            else
-              # Compilation failed
-              echo "... cannot use -xlic_lib=$testlib"
-            fi
-            # End of test for testlib
-          fi
-          # End of loop over possible lib names
-        done
-	# Report if no suitable library was found
-        if test ! "$XLAPACK_LIB" ; then
-          echo
-          echo "No suitable LAPACK library was found."
-          echo "This may be because the Sun Performance Library is not"
-          echo "installed on your system"
-          echo "Contact your system administrator or Sun vendor"
-        fi
-        ;;
-      Darwin | Darwin32 | Darwin64 )
-        # Darwin has libraries with BLAS and LAPACK invoked using 
-        # -framework vecLib
-        echo "Darwin can use the vecLib Library (if installed)"
-        echo "which has both BLAS and LAPACK 3.0"
-        echo
-        # This is a special case so try running a test compile
-        echo "Checking: try to link library against test program"
-        if test -f testlink.f || test -f testlink ; then
-          rm -f testlink*
-        fi
-        cat > testlink.f <<EOF
-c Test fortran program to link against library
-      PROGRAM TESTLINK
-      IMPLICIT NONE     
-      INTEGER A
-      A = 1
-      STOP
-      END
-EOF
-        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib"
-        echo $test_compile
-        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-          # Compilation was okay
-          echo "... -framework vecLib is okay"
-          XLAPACK_LIB="-framework vecLib"
-          # Set the next two variables so that configure
-          # doesn't try to build netlib libraries
-          LAPACKLIB="vecLib"
-          noblas=yes
-        else
-#alternative linking for vecLib libraries
-          case `uname -sr` in
-            *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;;
-            * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;;
-          esac
-
-        echo $test_compile
-        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-          # Compilation was okay
-          echo "... -framework vecLib is okay"
-          XLAPACK_LIB="-Wl,-framework -Wl,vecLib"
-          # Set the next two variables so that configure
-          # doesn't try to build netlib libraries
-          LAPACKLIB="-Wl,-framework -Wl,vecLib"
-          noblas=yes
-        else
-          # Compilation failed
-          echo "... cannot use -framework vecLib"
-          echo
-         fi
-        fi
-        trylapack=
-        tryblas=
-# try the fink installation
-        trydirs="${trydirs} /sw"
-        ;;
-      Darwin_ibm_compilers )
-        # Darwin has libraries with BLAS and LAPACK invoked using
-        # -framework vecLib
-        echo "Darwin can use the vecLib Library (if installed)"
-        echo "which has both BLAS and LAPACK 3.0"
-        echo
-        # This is a special case so try running a test compile
-        echo "Checking: try to link library against test program"
-        if test -f testlink.f || test -f testlink ; then
-          rm -f testlink*
-        fi
-        cat > testlink.f <<EOF
-c Test fortran program to link against library
-      PROGRAM TESTLINK
-      IMPLICIT NONE
-      INTEGER A
-      A = 1
-      STOP
-      END
-EOF
-      case `uname -sr` in
-        Darwin\ 8* )
-        XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
-        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
-        ;;
-        Darwin\ 7* )
-        XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
-        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB"
-        ;;
-        *)
-        XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib"
-        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
-        esac
-        echo $test_compile
-        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-          # Compilation was okay
-          echo "... -framework vecLib is okay"
-          # Set the next two variables so that configure
-          # doesn't try to build netlib libraries
-          LAPACKLIB="vecLib"
-          noblas=yes
-        else
-          # Compilation failed
-          XLAPACK_LIB=""
-          echo "... cannot use -framework vecLib"
-          echo
-        fi
-        trylapack=
-        tryblas=
-# try the fink installation
-        trydirs="${trydirs} /sw"
-        ;;
-
-      Darwin_intel_compilers)
-        # Darwin has libraries with BLAS and LAPACK invoked using
-        # -F vecLib
-        echo "Darwin can use the vecLib Library (if installed)"
-        echo "which has both BLAS and LAPACK 3.0"
-        echo
-        # This is a special case so try running a test compile
-        echo "Checking: try to link library against test program"
-        if test -f testlink.f || test -f testlink ; then
-          rm -f testlink*
-        fi
-        cat > testlink.f <<EOF
-c Test fortran program to link against library
-      PROGRAM TESTLINK
-      IMPLICIT NONE
-      INTEGER A
-      A = 1
-      STOP
-      END
-EOF
-        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib"
-        echo $test_compile
-        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-          # Compilation was okay
-          # doesn't try to build netlib libraries
-          XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib"
-          LAPACKLIB="vecLib"
-          noblas=yes
-        else
-          # Compilation failed
-          echo "... cannot use -framework vecLib"
-          echo
-         fi
-        trylapack=
-        tryblas=
-# try the fink installation
-        trydirs="${trydirs} /sw"
-        ;;
-
-#       linux_ia64_sgi_altix)
-# SGI Japan
-      ia64_linux_intel) 
-        # Additional search paths for Linux/IA64
-        trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib"
-        # SCSL and MKL should have both LAPACK and BLAS
-        trylapack="mkl_lapack scs lapack"
-        tryblas="mkl scs blas"
-        ;;
-      linux_ibm_compilers )
-        trylapack="lapack"
-        tryblas="blas"
-        ;;
-      linux64_ibm_compilers )
-        trydirs="/usr/lib64 ${trydirs}"
-        trylapack="lapack"
-        tryblas="blas"
-        ;;
-      linux_intel_compilers )
-        trydirs="/usr/lib64 ${trydirs}"
-        trylapack="mkl_lapack lapack"
-        tryblas="mkl blas"
-        ;;
-      *)
-        echo "The guesses for this system may not be correct - please"
-        echo "e-mail ccp4@ccp4.ac.uk if you have any extra information"
-	echo
-        # Default guess is just libblas
-        trylapack="lapack"
-        tryblas="blas"
-        ;;
-    esac
-    #
-    # Search for LAPACK libraries
-    #
-    # Write out what the guesses are
-    if test "$trylapack" ; then
-      echo "Possible LAPACK library names for this system:"
-      for libname in $trylapack
-      do
-        echo "   lib$libname"
-      done
-      # Possible library name extensions
-      tryexts="a so dylib"
-      # Now loop over all the possibilities and see if anything
-      # turns up
-      echo
-      echo "Searching for libraries with LAPACK and BLAS:"
-      for testdir in $trydirs
-      do
-        for testlib in $trylapack
-        do
-          for ext in $tryexts
-          do
-            if test ! "$LAPACKLIB"; then
-              if test -s "$testdir/lib$testlib.$ext" ; then
-                echo "...found LAPACK library: $testdir/lib$testlib.$ext"
-                # Now try and link to a test program
-                # This is really for IRIX where libraries can be
-                # o32 or n32
-                echo "   Testing: try to link library against test program"
-                if test -f testlink.f || test -f testlink ; then
-                  rm -f testlink*
-                fi
-                cat > testlink.f <<EOF
-c Test fortran program to link against library
-      PROGRAM TESTLINK
-      IMPLICIT NONE
-      INTEGER A
-      A = 1
-      STOP
-      END
-EOF
-                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
-                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-                echo $test_compile
-                if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-                  have_lapack=yes
-                else
-# cover clapack option
-                  echo $test_ccompile
-                  if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then
-                    have_lapack=yes
-                  fi
-                fi
-                if test x$have_lapack = xyes ; then
-                # This one is okay
-                  LAPACKLIB="$testlib"
-                  LAPACKDIR="$testdir"
-                  echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
-		  #
-		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
-                  #
-                  # Test to see if we need BLAS too
-                  # Do this by trying to compile a test program
-                  # Use the LSAME test for now
-                  echo
-                  echo "   * Checking whether we need a separate BLAS library *"
-                  echo "   Testing: try linking library against test program"
-                  cd lib/lapack/test
-                  if test -f testlsame ; then
-                    rm -f testsame testlsame.o
-                  fi
-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
-                  echo $test_compile
-                  if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
-                    have_blas=yes
-                  else
-#cblas route
-                    echo $test_ccompile
-                    if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then
-                      have_blas=yes
-                    fi
-                  fi
-                  if test x$have_blas = xyes ; then
-                    echo "Test program okay - additional separate BLAS not required"
-                    noblas=yes
-                  else
-                    echo "Test program failed - need a separate BLAS library"
-                  fi
-                  cd ../../..
-                else
-                # Keep looking
-                  echo "   link failed - cannot use lib$testlib"
-                fi
-              fi
-            fi
-          done
-        done
-        if test ! "$LAPACKLIB"; then
-          echo "...nothing in $testdir"
-        fi
-      done
-    fi
-
-    # If LAPACKLIB hasn't been set at this point then no LAPACK library
-    # was found 
-    if test ! "$LAPACKLIB" ; then
-      echo
-      echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead"
-      make_lapack=lapacklib
-    fi
-    # Look for possible BLAS
-    if test ! "$noblas" ; then
-      if test "$tryblas" ; then
-        echo
-        echo "Possible BLAS library names for this system:"
-        for libname in $tryblas
-        do
-          echo "   lib$libname"
-        done
-        # Possible library name extensions
-        tryexts="a so"
-        # Now loop over all the possibilities and see if anything
-        # turns up
-        echo
-        echo "Searching for libraries with BLAS:"
-        for testdir in $trydirs
-        do
-          for testlib in $tryblas
-          do
-            for ext in $tryexts
-            do
-              if test ! "$BLASLIB"; then
-                if test -s "$testdir/lib$testlib.$ext" ; then
-                  echo "...found BLAS library: $testdir/lib$testlib.$ext"
-                  # Now try and link to a test program
-                  # This is really for IRIX where libraries can be
-                  # o32 or n32
-                  echo "   Testing: try to link library against test program"
-                  if test -f testlink.f || test -f testlink ; then
-                    rm -f testlink*
-                  fi
-                  cat > testlink.f <<EOF
-c Test fortran program to link against library
-      PROGRAM TESTLINK
-      IMPLICIT NONE
-      INTEGER A
-      A = 1
-      STOP
-      END
-EOF
-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-                  echo $test_compile
-                  if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
-                    have_blas=yes
-                  else
-                    echo $test_ccompile
-                    if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
-                      have_blas=yes
-                    fi
-                  fi
-                  if test x$have_blas = xyes ; then
-                    # This one is okay
-                    BLASLIB="$testlib"
-                    BLASDIR="$testdir"
-                    BLASEXT="$ext"
-                    echo "Link ok - using lib$BLASLIB from $BLASDIR"
-		    XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB"
-                  else
-                  # Keep looking
-                    echo "   link failed - cannot use lib$testlib"
-                  fi
-                fi
-              fi
-            done
-          done
-          if test ! "$BLASLIB"; then
-            echo "...nothing in $testdir"
-          fi
-        done
-      fi
-      # Do we need to build BLAS too?      
-      if test ! "$BLASLIB" ; then
-        echo
-        echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead"
-        echo "This may result in poorer performance of the LAPACK routines"
-        make_blas=blaslib
-        BLASLIB=blas
-        BLASDIR="$srcdir/lib/lapack"
-        BLASEXT="a"
-      fi
-    fi
-+  # gentoo is clever
-+  make_blas=
-+  make_lapack=
-+  BLASLIB=$(${PKG_CONFIG} --libs blas)
-+  LAPACKLIB=$(${PKG_CONFIG} --libs lapack)
-+  XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}"
-+  XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)"
-   # Otherwise force building of NetLib BLAS and LAPACK libs
-  else
-    echo
-    echo "! Force building of NetLib BLAS and LAPACK..."
-    make_blas=blaslib
-    make_lapack=lapacklib
-    BLASLIB=blas
-    BLASDIR="$srcdir/lib/lapack"
-    BLASEXT="a"
-  fi
-   # need to know if we the lapack library was linked using the C or
-   # fortran linker
-   if test -f testlink.f || test -f testlink || test -f testlink.c ; then
-@@ -3916,8 +3356,8 @@ RANLIB   = ${RANLIB}
- INSTALL_DATA = ${INSTALL_DATA}
- libdir   = $libdir
- #
-BLASLIB     = lib${BLASLIB}.${BLASEXT}
-LAPACKLIB   = liblapack.a
-+BLASLIB     = ${BLASLIB}
-+LAPACKLIB   = ${LAPACKLIB}
- #
- # These variables define targets in the main Makefile
- blaslib   = ${make_blas}
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
@@ -1,23 +0,0 @@
-diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am
-index 053e83a..4ff3394 100755
--- a/src/pisa/sbase/Makefile.am
-+++ b/src/pisa/sbase/Makefile.am
-@@ -1,4 +1,4 @@
-pkgdatadir = $(datadir)/sbase
-+pkgdatadir = $(datadir)/pisa/sbase
- dist_pkgdata_DATA = \
- graph.sbase     index.sbase     struct.sbase
- 
-diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in
-index faa3f7f..8630bd7 100755
--- a/src/pisa/sbase/Makefile.in
-+++ b/src/pisa/sbase/Makefile.in
-@@ -62,7 +62,7 @@ POST_UNINSTALL = :
- EXEEXT = @EXEEXT@
- OBJEXT = @OBJEXT@
- PATH_SEPARATOR = @PATH_SEPARATOR@
-pkgdatadir = $(datadir)/sbase
-+pkgdatadir = $(datadir)/pisa/sbase
- AMTAR = @AMTAR@
- AR_FLAGS = @AR_FLAGS@
- AWK = @AWK@
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
@@ -1,65 +0,0 @@
-diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash
-index 9848101..cea8ae6 100755
--- a/ccp4-6.1.2/include/ccp4.setup-bash
-+++ b/ccp4-6.1.2/include/ccp4.setup-bash
-@@ -188,9 +188,9 @@ fi
- #Python path for the subprocess fixed module
- 
- if [ $ccp4_first_in_path -eq 1 ]; then
-    setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
-+    setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
- else
-    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
-+    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
- fi
- 
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
-diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh
-index 42f0820..93c2cf3 100755
--- a/ccp4-6.1.2/include/ccp4.setup-csh
-+++ b/ccp4-6.1.2/include/ccp4.setup-csh
-@@ -180,9 +180,9 @@ endif
- #Python path for the subprocess fixed module
- if (${?PYTHONPATH}) then
-   if ($ccp4_first_in_path) then
-      setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
-+      setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
-   else
-      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
-+      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
-   endif
- else
-     setenv PYTHONPATH ${CCP4}/share/python
-diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh
-index 4396ebf..a0455bd 100755
--- a/ccp4-6.1.2/include/ccp4.setup-sh
-+++ b/ccp4-6.1.2/include/ccp4.setup-sh
-@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
- #Python path for the subprocess fixed module
- 
- if test $ccp4_first_in_path -eq 1; then
-    export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
-+    export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
- else
-    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
-+    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
- fi
- 
- ################### THE REST SHOULDN'T NEED EDITING #####################
-diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh
-index 0e5c2ce..53523f3 100755
--- a/ccp4-6.1.2/include/ccp4.setup-zsh
-+++ b/ccp4-6.1.2/include/ccp4.setup-zsh
-@@ -157,10 +157,10 @@ export CLASSPATH
- #Python path for the subprocess fixed module
- 
- if ($ccp4_first_in_path) then
-    PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
-+    PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
-     export PYTHONPATH
- else
-    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
-+    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
-     export PYTHONPATH
- fi
- 
--- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
@@ -1,60 +0,0 @@
-diff --git a/src/Makefile.in b/src/Makefile.in
-index 70781f3..b2dcc25 100755
--- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o
- pdbcur : $(pdbcurobjs)
- 	@$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS)
- ncont : $(ncontobjs)
-	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS)
-+	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb
- coord_format : $(coord_formatobjs)
- 	@$(SETFLAGS) xxx=1 ; \
- 	rm -f coord_format; \
-diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am
-index 85f212e..2608c6d 100755
--- a/src/rapper/LOOP/Makefile.am
-+++ b/src/rapper/LOOP/Makefile.am
-@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains.
- hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \
- residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp
- 
-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
-+rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@
- 
- pkgdatadir = $(datadir)/rapper
- dist_pkgdata_DATA = params.xml
- 
-INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
-+INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@
- #SUBDIRS = \
- #@PYTHON_USE_TRUE@ python
- 
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
-index e78b10d..486b931 100755
--- a/src/rapper/Makefile.am
-+++ b/src/rapper/Makefile.am
-@@ -1,3 +1,3 @@
-SUBDIRS = libxml2 gc7.0 LOOP data
-+SUBDIRS = LOOP data
- 
- EXTRA_DIST =
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
-index 5e4ef69..268a579 100755
--- a/src/rapper/configure.ac
-+++ b/src/rapper/configure.ac
-@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
- 
- AC_SUBST(rapper_LDFLAGS)
- 
-AC_CONFIG_SUBDIRS([gc7.0 libxml2])
-+PKG_CHECK_MODULES([LIBXML],[libxml-2.0])
-+AC_SUBST([LIBXML_CFLAGS])
-+AC_SUBST([LIBXML_LIBS])
-+
-+PKG_CHECK_MODULES([GC],[bdw-gc])
-+AC_SUBST([GC_CFLAGS])
-+AC_SUBST([GC_LIBS])
-+
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
--- a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
@@ -1,131 +0,0 @@
- src/Makefile.in       |   14 +++++-----
- src/pisa/configure.ac |   67 +++++++++----------------------------------------
- 2 files changed, 19 insertions(+), 62 deletions(-)
-
-diff --git a/src/Makefile.in b/src/Makefile.in
-index 70781f3..b11db04 100755
--- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs)
- 	eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS)
- pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end
- 	@$(SETFLAGS) xxx=1 ; \
-	echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; 
-	eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
-+	echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; 
-+	eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
- 
- ### bp3, afro, gcx
- 
-@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs)
- 
- $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end
- 	@$(SETFLAGS) xxx=1 ; \
-	echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
-	eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
-+	echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
-+	eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
- 
- ### crunch2 pmf
- 
-@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs)
- cross_validate : $(cross_validateobjs)
- 	@$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS)
- cif2xml.o cross_validate.o : # dependencies at end
-	@$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
-+	@$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
- 
- pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract
- pdb_extract_suite :
-@@ -873,8 +873,8 @@ $(dev_tools_ctargets) :
- $(dev_tools_cxxtargets) :
- 	@$(SETFLAGS) xxx=1; \
- 	  rm -f $@; \
-	  echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\
-	  eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS)
-+	  echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\
-+	  eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS)
- 
- ### mlphare
- mlphare:
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
-index 81afdda..044b6f8 100755
--- a/src/pisa/configure.ac
-+++ b/src/pisa/configure.ac
-@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- # test for function in m
- AC_CHECK_LIB([m], [sqrt])
- 
-dnl Optional: Check for MMDB.
-AM_PATH_MMDB(,
-  [ if test "x$mmdb_prefix" != x ; then
-      if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then 
-        case "$ac_MMDB_CXXFLAGS" in
-        *src/mmdb )
-        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
-        ;;
-        *include/mmdb )
-        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
-        ;;
-        *)
-        esac
-	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
-        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
-        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
-      else
-        MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb"
-        MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb"
-        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
-      fi
-    else
-     AC_MSG_ERROR([mmdb not found])
-    fi
-  ]
-)
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+PKG_CHECK_MODULES([SSM],[ssm])
-+
-+MMDB_CXXFLAGS=${MMDB_CFLAGS}
-+
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_CXXFLAGS])
-+AC_SUBST([SSM_CFLAGS])
-+
-+AC_SUBST([MMDB_LIBS])
-+AC_SUBST([SSM_LIBS])
- 
-ac_saved_CXXFLAGS=$CXXFLAGS
-ac_saved_LIBS=$LIBS
- CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
- LIBS="$MMDB_LIBS $LIBS"
-AM_PATH_SSM(,
-  [ if test "x$ssm_prefix" != x ; then
-      if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then 
-        case "$ac_SSM_CXXFLAGS" in
-        *lib/ssm )
-        ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g`
-        ;;
-        *include/ssm )
-        ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g`
-        ;;
-        *)
-        esac
-        SSM_CXXFLAGS="$ac_SSM_CXXFLAGS"
-        SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#`
-        AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
-      else
-        SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm"
-        SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm"
-        AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
-      fi
-    else
-     AC_MSG_ERROR([ssm not found])
-    fi
-  ]
-)
-CXXFLAGS=$ac_saved_CXXFLAGS
-LIBS=$ac_saved_LIBS
-+
- 
- # Checks for typedefs, structures, and compiler characteristics.
- #
--- a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
+++ b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
@@ -1,130 +0,0 @@
- src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++---------------
- 1 file changed, 17 insertions(+), 17 deletions(-)
-
-diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-index 2c9f02f..98d814a 100755
--- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-+++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags,
-     puts("canvas_draw_line: about to evaluate the command...");
-   }
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     return 0;
-   }
-   if (CCP4MAPWISH_CANVAS_DIAG)
-@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y,
-     puts("canvas_draw_rectangle: about to evaluate the command...");
-   }
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units);
-     return 0;
-   }
-@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y,
-   /* Execute the command which draws the label */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale)
-   /* Execute the command which scales the canvas */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas)
-   /* Execute the command which resizes the canvas */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty)
-   /* Execute the command which resizes the canvas */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag)
-   /* Execute the command which deletes the tagged items */
-   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command);
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-@@ -892,15 +892,15 @@ int canvas_exists(char *canvas)
- 
-   sprintf(tmpstr,"winfo exists %s",canvas);
-   if (Tcl_Eval(interp,tmpstr) != TCL_OK) {
-    printf("canvas_exists: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     return 0;
-   }
-   /* Extract a long int using strtol
-      If no conversion takes place then "endptr" will be equal
-      to "result" */
-  istatus = (int) strtol(interp->result,&endptr,10);
-  if (strcmp(interp->result,endptr) == 0) {
-    printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result);
-+  istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10);
-+  if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
-+    printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
-   if (!istatus) {
-@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units)
- 
-   /* Execute the tk scaling command */
-   if (Tcl_Eval(interp,"tk scaling") != TCL_OK) {
-    printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result);
-+    printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
-     return (float) 0.0;
-   }
- 
-   /* Extract a float from the result */
-  tkscale = ((float) strtod(interp->result,&endptr));
-  if (strcmp(interp->result,endptr) == 0) {
-+  tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr));
-+  if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
-     printf("canvas_get_tk_scaling: couldn't extract scale factor\n");
-     return (float) 0.0;
-   }
-@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4])
- 
-   /* Evaluate the command */
-   if (Tcl_Eval(interp,command) != TCL_OK) {
-    printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result);
-+    printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
-     return 0;
-   }
- 
-   /* Process the result - it should consist of 4 integers */
-   /* Use strtok which can split the string based on tokens
-      set by the programmer - in this case a space */
-  if (!interp->result) {
-+  if (!Tcl_GetStringResult(interp)) {
-     puts("canvas_get_limits: failed to fetch canvas limits");
-     return TCL_ERROR;
-   }
-   i = 0;
-  p = strtok(interp->result," ");
-+  p = strtok(Tcl_GetStringResult(interp)," ");
-   if (p == NULL) {
-     return 0;
-   }
--- a/sci-chemistry/ccp4-apps/metadata.xml
+++ b/sci-chemistry/ccp4-apps/metadata.xml
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
--- a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild
+++ b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild
@@ -1,38 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit fortran-2
-
-DESCRIPTION="Protein X-ray crystallography toolkit -- meta package"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI=""
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="X arpwarp +balbes"
-
-RDEPEND="
-	~sci-chemistry/ccp4-apps-${PV}[X?]
-	!<=sci-chemistry/ccp4-apps-${PV}-r2
-	>=sci-chemistry/molrep-11.0.00-r1
-	>=sci-chemistry/mosflm-7.0.6-r2
-	sci-chemistry/mrbump[X?]
-	>=sci-chemistry/oasis-4.0-r1
-	>=sci-chemistry/pdb-extract-3.004-r2
-	>=sci-chemistry/refmac-5.5.0110-r1
-	>=sci-chemistry/scala-3.3.18-r1
-	>=sci-chemistry/sfcheck-7.03.18-r1
-	sci-chemistry/xia2
-	arpwarp? ( sci-chemistry/arp-warp-bin )
-	balbes? ( sci-chemistry/balbes )
-	X? (
-		~sci-chemistry/ccp4i-${PV}
-		sci-chemistry/imosflm
-		sci-chemistry/pymol
-		sci-chemistry/rasmol
-		)"
-DEPEND=""
--- a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
+++ b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
@@ -1,87 +0,0 @@
--- ccp4-6.0.1.orig/configure	2006-06-10 17:30:02.000000000 -0700
-+++ ccp4-6.0.1/configure	2006-06-10 17:45:43.000000000 -0700
-@@ -623,45 +623,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
-if test -z "$onlylibs" ; then 
-   for i in CCP4_SCR BINSORT_SCR; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the value of $i."
-       badvar=1
-     fi
-   done
-
-   for i in libdir bindir; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the argument of --$i."
-       badvar=1
-     fi
-   done
-
-   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-     if test -d $i || mkdir $i; then :
-     else
-       eval echo "! No directory $i and can\'t create it."
-       badvar=1
-     fi
-   done
-else
-   # Kludge to fool the "Makefile" target in the top-level CCP4
-   # Makefile into not trying to remake src/Makefile.in
-   for i in $srcdir/src $srcdir/lib/src ; do
-     if test -d $i || mkdir $i; then
-       if ! test -f $i/Makefile.in ; then
-         echo
-         echo "onlylibs: making dummy file $i/Makefile.in"
-	 touch $i/Makefile.in
-       fi
-     fi
-   done
-fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
--- a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
+++ b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
@@ -1,11 +0,0 @@
--- ccp4-6.0.1.orig/lib/src/library_f.c	2006-06-12 07:06:22.000000000 -0700
-+++ ccp4-6.0.1/lib/src/library_f.c	2006-06-12 07:21:56.000000000 -0700
-@@ -716,7 +716,7 @@
- 
- #endif /* end of apple xlf support */
- 
-#if ( defined (__linux__) && defined (_CALL_SYSV) )
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
- /* linuxppc xlf support */
- void gerror_ (str, Lstr)
- char *str;
--- a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
+++ b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
@@ -1,87 +0,0 @@
--- ccp4-6.0.1.orig/configure	2006-06-10 17:30:02.000000000 -0700
-+++ ccp4-6.0.1/configure	2006-06-10 17:45:43.000000000 -0700
-@@ -623,45 +623,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
-if test -z "$onlylibs" ; then 
-   for i in CCP4_SCR BINSORT_SCR; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the value of $i."
-       badvar=1
-     fi
-   done
-
-   for i in libdir bindir; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the argument of --$i."
-       badvar=1
-     fi
-   done
-
-   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-     if test -d $i || mkdir $i; then :
-     else
-       eval echo "! No directory $i and can\'t create it."
-       badvar=1
-     fi
-   done
-else
-   # Kludge to fool the "Makefile" target in the top-level CCP4
-   # Makefile into not trying to remake src/Makefile.in
-   for i in $srcdir/src $srcdir/lib/src ; do
-     if test -d $i || mkdir $i; then
-       if ! test -f $i/Makefile.in ; then
-         echo
-         echo "onlylibs: making dummy file $i/Makefile.in"
-	 touch $i/Makefile.in
-       fi
-     fi
-   done
-fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
--- a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch
+++ b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch
@@ -1,14 +0,0 @@
-https://bugs.gentoo.org/show_bug.cgi?id=175630
-JTRiley
-
--- ccp4-6.0.2.orig/src/refmac5_/make_unix_ccp4.f	2005-09-06 07:29:56.000000000 -0400
-+++ ccp4-6.0.2.new/src/refmac5_/make_unix_ccp4.f	2007-05-02 20:03:46.000000000 -0400
-@@ -97,7 +97,7 @@
- 
-       READ(CID,'(I2,1X,I2,1X,I2,2X)') IH(4),IH(3),IH(2)
- 
-      CALL IDATE(IMON,IDAY,IYR)
-+      CALL UIDATE(IMON,IDAY,IYR)
-       IF(IYR.GE.99) THEN
-         IYR=IYR+1900
-       ELSE
--- a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch
+++ b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch
@@ -1,11 +0,0 @@
--- ccp4-6.0.1.orig/lib/src/library_f.c	2006-06-12 07:06:22.000000000 -0700
-+++ ccp4-6.0.1/lib/src/library_f.c	2006-06-12 07:21:56.000000000 -0700
-@@ -716,7 +716,7 @@
- 
- #endif /* end of apple xlf support */
- 
-#if ( defined (__linux__) && defined (_CALL_SYSV) )
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
- /* linuxppc xlf support */
- void gerror_ (str, Lstr)
- char *str;
--- a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
+++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
@@ -1,13 +0,0 @@
--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist	2006-01-06 17:54:17.000000000 -0800
-+++ ccp4-5.99.5/ccp4i/etc/configure.def.dist	2006-01-06 17:54:47.000000000 -0800
-@@ -54,8 +54,8 @@
- MESSAGE                   _text				""
- BLT_LIBRARY               _text                     ""
- MENU_LENGTH               _positiveint              25
-HYPERTEXT_VIEWER          _text                     netscape
-START_NETSCAPE	          _text			    netscape
-+HYPERTEXT_VIEWER          _text                     firefox
-+START_NETSCAPE	          _text			    firefox
- O_MAPMAN                  _text                     mapman
- MAPMAN_MAXSIZE		  _positiveint		    4194304
- QUANTA_MBKALL             _text                     mbkall
--- a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
+++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
@@ -1,103 +0,0 @@
--- ccp4-5.99.5.orig/configure	2006-01-17 00:35:36.000000000 -0800
-+++ ccp4-5.99.5/configure	2006-01-17 10:44:39.000000000 -0800
-@@ -2410,12 +2410,12 @@
-       end
- EOF
-           #firslty test without -lblas
-          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
-+          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread"
-           echo $test_compile
-           if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
-             # Compilation was okay
-            echo "... only -llapack needed"
-            XLAPACK_LIB="-llapack"
-+            echo "... only -llapack -lpthread needed"
-+            XLAPACK_LIB="-llapack -lpthread"
-             # Set the next two variables so that configure
-             # doesn't try to build netlib libraries
-             LAPACKLIB="lapack"
-@@ -2424,12 +2424,12 @@
-             tryblas=
-           else
- 	    echo "more than just -llapack needed...."
-            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
-+            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread"
-             echo $test_compile
-             if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-               # Compilation was okay
-              echo "...-llapack and -lblas were needed"
-              XLAPACK_LIB="-llapack -lblas"
-+              echo "...-llapack, -lpthread and -lblas were needed"
-+              XLAPACK_LIB="-llapack -lpthread -lblas"
-               # Set the next two variables so that configure
-               # doesn't try to build netlib libraries
-               LAPACKLIB="lapack blas"
-@@ -2720,8 +2720,8 @@
-       STOP
-       END
- EOF
-                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
-                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-+                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
-+                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
-                 echo $test_compile
-                 if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-                   have_lapack=yes
-@@ -2738,7 +2738,7 @@
-                   LAPACKDIR="$testdir"
-                   echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
- 		  #
-		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
-+		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread"
-                   #
-                   # Test to see if we need BLAS too
-                   # Do this by trying to compile a test program
-@@ -2750,8 +2750,8 @@
-                   if test -f testlsame ; then
-                     rm -f testsame testlsame.o
-                   fi
-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
-+                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread"
-+                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread"
-                   echo $test_compile
-                   if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
-                     have_blas=yes
-@@ -2830,8 +2830,8 @@
-       STOP
-       END
- EOF
-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-+                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
-+                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
-                   echo $test_compile
-                   if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
-                     have_blas=yes
-@@ -3033,7 +3033,7 @@
-         if test -f testlsame ; then
-           rm -f testsame testlsame.o
-         fi
-        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB"
-+        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread"
-         echo $test_compile
-         if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
-           echo "Found LSAME in lib$BLASLIB"
-@@ -3046,7 +3046,7 @@
-         if test -f testxerbla ; then
-           rm -f testxerbla testxerbla.o
-         fi
-        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB"
-+        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread"
-         echo $test_compile
-         if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then
-           # Found lsame
-@@ -3080,7 +3080,7 @@
-     cd ../..
-     #
-     lapackdir=lib/lapack
-    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB"
-+    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread"
- # netlib lapack is in fortran, so we may need the fortran libraries when
- # we are linking using the C or C++ compilers
-     case $system in 
--- a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
+++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
@@ -1,11 +0,0 @@
--- ccp4-5.99.5/lib/clipper/configure.orig	2006-01-07 16:54:13.000000000 -0800
-+++ ccp4-5.99.5/lib/clipper/configure	2006-01-07 16:54:31.000000000 -0800
-@@ -21751,7 +21751,7 @@
- 
- if test "x$mccp4_prefix" != x; then
-  # ie. mccp4=thing was given (thing is what we're checking for)
- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include"
-+ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4"
-  ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4"
- else
-  # treat as standard lib/include
--- a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
+++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
@@ -1,10 +0,0 @@
--- ccp4-5.99.5.orig/x-windows/Makefile.in	2006-01-06 12:31:02.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Makefile.in	2006-01-06 12:31:30.000000000 -0800
-@@ -158,6 +158,7 @@
- install_obj = ipdisp.exe hklview xdldataman xdlmapman \
- rotgen ipmosflm
- install: all
-+	mkdir -p $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
--- a/sci-chemistry/ccp4/files/dont-build-rasmol.patch
+++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch
@@ -1,19 +0,0 @@
--- ccp4-5.99.5.orig/x-windows/Makefile.in	2005-12-05 03:06:57.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Makefile.in	2005-12-05 03:07:23.000000000 -0800
-@@ -35,7 +35,7 @@
- #
- # all
- #
-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm
-+all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm
- #
- # xdl_view
- #
-@@ -161,7 +161,6 @@
- 	$(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir)
- 	$(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir)
- 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) install
-	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
- 	cd $(rotgen_dir); $(MAKE) install
- 	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
- 	cd $(xdlview_dir); $(MAKE) install
--- a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
+++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
@@ -1,10 +0,0 @@
--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:12.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:41.000000000 -0800
-@@ -37,6 +37,7 @@
- 	${F77} ${FFLAGS} -o $@ $<
- 
- ipmosflm:	${OBJS}
-+		mkdir -p ${DPSBIN}
- 		${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \
-                 -o ${DPSBIN}/ipmosflm ${LDFLAGS}
- 
--- a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
+++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
@@ -1,11 +0,0 @@
--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:42:19.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:43:35.000000000 -0800
-@@ -132,7 +132,7 @@
- #
- # CBF library
- #
-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
-+$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
- 	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
- 	$(AR) cr $@ *.o
- 	$(RANLIB) $@
--- a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
+++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
@@ -1,10 +0,0 @@
--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:09.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:30.000000000 -0800
-@@ -76,6 +76,7 @@
- 
- # local version of libdps_index.a
- ${LIB}/dps_index.a: ${IOBJS} ${HOBJS}
-+	mkdir -p ${LIB}
- 	ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS}
- 
- ${LIB}/libpeak.a: 
--- a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
+++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
@@ -1,10 +0,0 @@
--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:48:47.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:49:02.000000000 -0800
-@@ -42,6 +42,7 @@
- 	$(LOCALLIBS) $(LIBS) 
- 
- index: $(IOBJS) 
-+	mkdir -p $(LIBDIR)
- 	${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS)
- 	chmod 644 $(LIBDIR)/libdps_index.a
- 
--- a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
+++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
@@ -1,11 +0,0 @@
--- ccp4-5.99.5.orig/configure	2006-01-06 11:45:43.000000000 -0800
-+++ ccp4-5.99.5/configure	2006-01-06 11:46:53.000000000 -0800
-@@ -3210,7 +3210,7 @@
- #ccp4 setup
-   xopts="${xopts} --with-ccp4=${srcdir}"
- #interface setup
-  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol"
-+  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr"
-   echo   
-   echo "********* CLIPPER CONFIGURATION ***********"
-   echo
--- a/sci-chemistry/ccp4/metadata.xml
+++ b/sci-chemistry/ccp4/metadata.xml
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<use>
-		<flag name="balbes">Install sci-chemistry/balbes</flag>
-		<flag name="arpwarp">Add binary arp-warp for molecular replacement</flag>
-	</use>
-</pkgmetadata>
--- a/sci-chemistry/ccp4i/Manifest
+++ b/sci-chemistry/ccp4i/Manifest
@@ -1,3 +0,0 @@
-DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
-DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687 SHA512 0bf18d9768b722c553e79eed04de316f6b0b4695f7678e1d850d5e22735ecc79cdb961ea76b6482457fff232892b81ce191cd48fa588ded8058184a871dffb65 WHIRLPOOL f24625941e31e951f13c94cf31e2ca061840b016aa3fd038d29710d9ca400d364467dc3fa1e42a55944d63ac7e42a0a6baa39a596c55b18610eeb552d232d1b8
--- a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
+++ b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
@@ -1,99 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib python-single-r1 virtualx
-
-MY_PN="${PN%i}"
-MY_P="${MY_PN}-${PV}"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="
-	${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	mirror://gentoo/${P}-arpwarp.patch.bz2
-	https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-LICENSE="ccp4"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	media-gfx/graphviz
-	>=dev-lang/tk-8.3:0
-	>=dev-tcltk/blt-2.4
-	sci-libs/ccp4-libs"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-fix-baubles.patch
-	"${WORKDIR}"/${P}-arpwarp.patch
-	)
-
-src_prepare() {
-	epatch ${PATCHES[@]}
-
-	[[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
-	python_fix_shebang ccp4i/ share/dbccp4i/
-}
-
-src_configure() {
-	:
-}
-
-src_compile() {
-	:
-}
-
-src_install() {
-	# rm imosflm stuff
-	rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} || die
-
-	rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS || die
-
-	# This is installed by mrbump
-	rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} || die
-
-	# CCP4Interface - GUI
-	insinto /usr/$(get_libdir)/ccp4
-	doins -r "${S}"/ccp4i
-	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
-	doexe "${S}"/ccp4i/bin/*
-	dosym ../$(get_libdir)/ccp4/ccp4i/bin/ccp4i /usr/bin/ccp4i
-
-	dodir /usr/$(get_libdir)/ccp4/ccp4i/unix
-
-	# dbccp4i
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/dbccp4i
-}
-
-pkg_postinst() {
-	_ccp4-setup() {
-		source "${EPREFIX}/etc/profile"
-		export USER=root
-		bash "${EPREFIX}"/usr/$(get_libdir)/ccp4/ccp4i/bin/ccp4i -h > /dev/null
-	}
-	VIRTUALX_COMMAND="_ccp4-setup" virtualmake
-	echo ""
-	elog "ccp4i needs some enviromental settings. So please"
-	elog "\t source ${EPREFIX}/etc/profile"
-	echo ""
-}
--- a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
+++ b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
@@ -1,22 +0,0 @@
--- ccp4i/etc/configure.def.dist	2009-01-09 16:45:08.000000000 +0100
-+++ ccp4i/etc/configure.def.dist.new	2009-07-07 23:17:26.000000000 +0200
-@@ -53,8 +53,8 @@
- RUN_IMOSFLM               _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]"
- RUN_CCP4MG                _text                     "ccp4mg"
- RUN_COOT                  _text                     "coot"
-RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share smartie baubles.py]"
-RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]"
-+RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]"
-+RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]"
- ENABLE_BUBBLE_HELP        _logical                  1
- DISABLE_TASKS             _logical                  1
- CCP4_SETUP_COMMAND        _text                     setup_ccp4
-@@ -62,7 +62,7 @@
- BLT_LIBRARY               _text                     ""
- MENU_LENGTH               _positiveint              25
- HYPERTEXT_VIEWER          _text                     firefox
-START_NETSCAPE	          _text			    netscape
-+START_NETSCAPE	          _text			    firefox
- O_MAPMAN                  _text                     mapman
- MAPMAN_MAXSIZE		  _positiveint		    4194304
- QUANTA_MBKALL             _text                     mbkall
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
@@ -1,61 +0,0 @@
-diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script
-index def44bc..dd4bb7e 100755
--- a/ccp4i/scripts/check.script
-+++ b/ccp4i/scripts/check.script
-@@ -24,7 +24,7 @@
-   if $RUN_RAMPAGE {
- 
-     # Generate command line
-    set cmd "[BinPath rapper]"
-+    set cmd "[BinPath rappermc]"
- 
-     set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
-     set paramsfile [FileJoin $rapperdatadir params.xml]
-diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script
-index cdae1e2..faae226 100755
--- a/ccp4i/scripts/rapper.script
-+++ b/ccp4i/scripts/rapper.script
-@@ -17,7 +17,7 @@
- 
- #set up command line 
- 
-set cmd "[BinPath rapper]"
-+set cmd "[BinPath rappermc]"
- 
- set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
- set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml]
-@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT"
- 
- # Run RAPPER to join loop back to framework and out put to defined pdb file
- # Also need to sort out multimodel files join - FIX ME
-set cmd2 "[BinPath rapper]"
-+set cmd2 "[BinPath rappermc]"
- append cmd2 " $paramsfile joinpdb "
- append cmd2 " --pdb2 \"$root\-loop.pdb\" "
- append cmd2 " --pdb  \"$root\-framework.pdb\" "
-diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl
-index ae88ff2..ee3307b 100755
--- a/ccp4i/tasks/check.tcl
-+++ b/ccp4i/tasks/check.tcl
-@@ -46,7 +46,7 @@ proc check_run { arrayname } {
-  # Check for Rampage program. If it is not found, we switch off the option.
-  # If it was the only option, script will fail with next check.
-  if { $array(RUN_RAMPAGE) == 1 } {
-   if { [FindExecutable "rapper"] == "" } {
-+   if { [FindExecutable "rappermc"] == "" } {
-       WarningMessage "Input Error: Rapper_Rampage program not found in system path."
-       set array(RUN_RAMPAGE) 0
-     }
-diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl
-index e299057..8843a3f 100755
--- a/ccp4i/tasks/rapper.tcl
-+++ b/ccp4i/tasks/rapper.tcl
-@@ -28,7 +28,7 @@ proc rapper_run { arrayname } {
-  # Check for RAPPER program. If it is not found, we switch off the option.
-  # If it was the only option, script will fail with next check.
-   if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} {
-   if { [FindExecutable "rapper"] == "" } {
-+   if { [FindExecutable "rappermc"] == "" } {
-       WarningMessage "Input Error: RAPPER program not found in system path."
-       set build_type 0
-     }
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
@@ -1,26 +0,0 @@
-diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script
-index 3483c97..5027536 100755
--- a/ccp4i/scripts/superpose.script
-+++ b/ccp4i/scripts/superpose.script
-@@ -21,7 +21,7 @@
- 
-   if { [regexp SSM $SUPERPOSE_MODE ] } {
- 
-    set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
-+    set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
-     set status [Execute $cmd "" program_status report ]
- 
-   } elseif { [regexp TOP $SUPERPOSE_MODE ] } {
-diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl
-index 748bf6e..c92122a 100755
--- a/ccp4i/tasks/superpose.tcl
-+++ b/ccp4i/tasks/superpose.tcl
-@@ -100,7 +100,7 @@ proc superpose_run { arrayname } {
- # If user is match equivalent named residues/atoms then fit in the match fields
-   switch [GetValue $arrayname SUPERPOSE_MODE] \
-   SSM {
-    if { ![file exists [FindExecutable superpose]] } {
-+    if { ![file exists [FindExecutable superpose-ccp4]] } {
-        WarningMessage "The program \"superpose\" is not on your path. 
- Check your installation for \"superpose\" program and \"ssm\" library."
-        return 0
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
@@ -1,91 +0,0 @@
-diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl
-index 7d05905..d01f1dc 100755
--- a/ccp4i/crank/plugins/prep/crank_prep.tcl
-+++ b/ccp4i/crank/plugins/prep/crank_prep.tcl
-@@ -226,7 +226,7 @@ proc run_truncate { i j } {
-     set script "$script\n$labout"
-     set script "$script\nEND\n"
- 	
-    set run_command "truncate $command << \"$script\""
-+    set run_command "ftruncate $command << \"$script\""
-     puts $run_command
-     catch {eval exec $run_command } output 
-     puts $output
-diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script
-index e74aa0d..a2a1adb 100755
--- a/ccp4i/scripts/dtrek2mtz.script
-+++ b/ccp4i/scripts/dtrek2mtz.script
-@@ -36,7 +36,7 @@
-     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
- 
-     CreateComScript truncate truncate_script
-    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-+    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-     set status [Execute $cmd $truncate_script program_status report]
- 
-     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
-diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script
-index 90cba83..1c90c33 100755
--- a/ccp4i/scripts/import.script
-+++ b/ccp4i/scripts/import.script
-@@ -144,7 +144,7 @@ if { $FORMAT ==  "MTZ" } {
- 
-     set truncatemtz [GetTmpFileName -ext mtz ]
-     CreateComScript truncate truncate_script
-    set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
-+    set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
-     set status [Execute $cmd $truncate_script program_status report]
- 
- 
-diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script
-index dcc619b..7250513 100755
--- a/ccp4i/scripts/import_scaled.script
-+++ b/ccp4i/scripts/import_scaled.script
-@@ -62,7 +62,7 @@
- 
-     } else {
-       CreateComScript truncate truncate_script
-      set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-+      set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-       set status [Execute $cmd $truncate_script program_status report]
- 
-       HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
-diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script
-index 6940ccd..bde10d6 100755
--- a/ccp4i/scripts/scala.script
-+++ b/ccp4i/scripts/scala.script
-@@ -275,7 +275,7 @@ END"
- 
-       } else {
-         CreateComScript truncate truncate_script
-        set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
-+        set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
-         set status [Execute $cmd $truncate_script $LOG_FILE  program_status report  ]
-       }
-           
-diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script
-index 986e06c..a1947a6 100755
--- a/ccp4i/scripts/scalepack2mtz.script
-+++ b/ccp4i/scripts/scalepack2mtz.script
-@@ -35,7 +35,7 @@
- 
-     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
-     CreateComScript truncate truncate_script
-    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-+    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
-     set status [Execute $cmd $truncate_script program_status report]
- 
-     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
-diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script
-index e0e09ce..2d448a2 100755
--- a/ccp4i/scripts/truncate.script
-+++ b/ccp4i/scripts/truncate.script
-@@ -45,7 +45,7 @@
- 
-   CreateComScript truncate truncate_script
- 
-  set cmd "[BinPath truncate] HKLIN \"$HKLIN\""
-+  set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\""
-   if { ![StringSame $INPUT_DATA AMPLITUDES] } {
-     append cmd " HKLOUT \"$HKL_TRUNCATE\""
-   }
--- a/sci-chemistry/ccp4i/metadata.xml
+++ b/sci-chemistry/ccp4i/metadata.xml
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
--- a/sci-chemistry/coot/coot-0.7.1-r1.ebuild
+++ b/sci-chemistry/coot/coot-0.7.1-r1.ebuild
@@ -1,167 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils python-single-r1 toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
-SRC_URI="
-	http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz
-	test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+openmp static-libs test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23:0
-	sci-libs/ssm
-	sci-libs/monomer-db
-	sci-chemistry/reduce
-	sci-chemistry/refmac
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	${PYTHON_DEPS}
-	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=dev-libs/gmp-4.2.2-r2
-	>=net-misc/curl-7.19.6
-	net-dns/libidn"
-DEPEND="${RDEPEND}
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python-single-r1_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.7-clipper-config.patch
-	"${FILESDIR}"/${PN}-0.7-goocanvas.patch
-	"${FILESDIR}"/${PN}-0.7-mmdb-config.patch
-	"${FILESDIR}"/${PN}-0.7-ssm.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
-
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-gtk2
-		--with-pygtk
-		$(use_enable openmp)
-		)
-	autotools-utils_src_configure
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
-}
-
-src_install() {
-	autotools-utils_src_install
-	insinto /usr/share/${PN}
-	doins syminfo.lib
-}
--- a/sci-chemistry/coot/coot-0.7.2.ebuild
+++ b/sci-chemistry/coot/coot-0.7.2.ebuild
@@ -1,165 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils python-single-r1 toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
-SRC_URI="
-	http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz
-	test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="+openmp static-libs test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23:0
-	sci-libs/ssm
-	sci-libs/monomer-db
-	sci-chemistry/reduce
-	sci-chemistry/refmac
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	${PYTHON_DEPS}
-	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=dev-libs/gmp-4.2.2-r2
-	>=net-misc/curl-7.19.6
-	net-dns/libidn"
-DEPEND="${RDEPEND}
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python-single-r1_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.7-clipper-config.patch
-	"${FILESDIR}"/${PN}-0.7-goocanvas.patch
-	"${FILESDIR}"/${PN}-0.7-mmdb-config.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
-
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-gtk2
-		--with-pygtk
-		$(use_enable openmp)
-		)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	cp "${S}"/src/coot_gtk2.py python/coot.py || die
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
-}
--- a/sci-chemistry/coot/coot-0.7.ebuild
+++ b/sci-chemistry/coot/coot-0.7.ebuild
@@ -1,159 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-PYTHON_DEPEND="2"
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils python toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
-SRC_URI="
-	http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
-	test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="+openmp static-libs test"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23:0
-	sci-libs/ssm
-	<sci-libs/monomer-db-1
-	sci-chemistry/reduce
-	<sci-chemistry/refmac-5.6
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	dev-python/pygtk:2
-	>=dev-libs/gmp-4.2.2-r2
-	>=net-misc/curl-7.19.6
-	net-dns/libidn"
-DEPEND="${RDEPEND}
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python_set_active_version 2
-	python_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-clipper-config.patch
-	"${FILESDIR}"/${P}-goocanvas.patch
-	"${FILESDIR}"/${P}-mmdb-config.patch
-	"${FILESDIR}"/${P}-ssm.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
-
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-gtk2
-		--with-pygtk
-		$(use_enable openmp)
-		)
-	autotools-utils_src_configure
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
-}
--- a/sci-chemistry/imosflm/Manifest
+++ b/sci-chemistry/imosflm/Manifest
@@ -1 +0,0 @@
-DIST imosflm-1.0.7.zip 941784 SHA256 b067261b4d7ef2f1f7581ddeaa08252d29f889acf89ce190eb0d8b30aa94b107 SHA512 f3163e1f71c5b1e24d6b3fbd5a040bbcebae25485d1258eef4b2725821f5f96c1260adb2bcc3ab57179d7b9b9e538ddf0494ab9b5be259b98d138fddacec8c77 WHIRLPOOL bd2b6bcdcc241fde41fe2ba99bd1e2f47bc444c46ee36a5b332d5c018b81a9d649378110a8bffa48ffc67a19b04ede7e61846b53a250e5fe3058ec0313fda80c
--- a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch
+++ b/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch
@@ -1,12 +0,0 @@
-diff --git a/c/tkImageLoad.c b/c/tkImageLoad.c
-index e7c46f0..1496a15 100755
--- a/c/tkImageLoad.c
-+++ b/c/tkImageLoad.c
-@@ -12,6 +12,7 @@
- #include <tcl.h>
- #include <tk.h>
- #include <assert.h>
-+#include <stdlib.h>
- 
- #define HEADER_LINE_LENGTH 512
- #define BYTES_PER_PIXEL 2
--- a/sci-chemistry/imosflm/files/1.0.4-tk.patch
+++ b/sci-chemistry/imosflm/files/1.0.4-tk.patch
@@ -1,50 +0,0 @@
--- c/tkImageLoad.c	2009-08-14 21:10:19.000000000 +0200
-+++ c/tkImageLoad.c.new	2009-08-14 21:10:55.000000000 +0200
-@@ -19,6 +19,7 @@
- //#define BLOCKED 1
- //#define UNBLOCKED 1
- #define IN_BLOCK_FLIP 1
-+#define USE_COMPOSITELESS_PHOTO_PUT_BLOCK
- 
- /* *********************************************************************/
- 
--- c/tkImageLoad.c	2009-08-14 21:13:29.000000000 +0200
-+++ c/tkImageLoad.c.new	2009-08-14 21:14:59.000000000 +0200
-@@ -272,9 +272,11 @@
-   }
-   /* put the photo block into the image */
- #ifdef __alpha
-  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height);
-+  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height,
-+  TK_PHOTO_COMPOSITE_OVERLAY);
- #else
-  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET);
-+  Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET,
-+  TK_PHOTO_COMPOSITE_OVERLAY);
- #endif
- 
-   /* Free the photo block's memory now it is finished with */
-@@ -417,9 +419,11 @@
- 
-   /* put the photo block back into the image */
- #ifdef __alpha
- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height);
-+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,
-+ TK_PHOTO_COMPOSITE_OVERLAY);
- #else
- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET);
-+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET,
-+ TK_PHOTO_COMPOSITE_OVERLAY);
- #endif
-   /* Free the photo block's memory now it is finished with */
-   if (block.pixelPtr) {
--- c/tkImageLoad.c	2009-08-14 21:15:06.000000000 +0200
-+++ c/tkImageLoad.c.new	2009-08-14 21:16:53.000000000 +0200
-@@ -9,6 +9,7 @@
- \************************************************************************/
- 
- #include <stdio.h>
-+#include <string.h>
- #include <tcl.h>
- #include <tk.h>
- #include <assert.h>
--- a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch
+++ b/sci-chemistry/imosflm/files/1.0.7-libpng16.patch
@@ -1,13 +0,0 @@
-http://bugs.gentoo.org/467036
-
--- src/contrast.tcl
-+++ src/contrast.tcl
-@@ -3,7 +3,7 @@
- 
- package require palette
- 
-image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUKJGtVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPlXtupMAAAAASUVORK5CYII="
-+image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUeJytVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPv4fGP4AAAAASUVORK5CYII="
- 
- class Contrast {
-     inherit Palette
--- a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild
+++ b/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils multilib toolchain-funcs versionator
-
-MY_PV="$(delete_all_version_separators ${PV})"
-
-DESCRIPTION="A new GUI for the Mosflm crystallographic data processing tool"
-HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/imosflm"
-SRC_URI="${HOMEPAGE}/ver${MY_PV}/downloads/${P}.zip"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-lang/tcl:0=
-	>=dev-tcltk/itcl-3.3
-	>=dev-tcltk/itk-3.3
-	>=dev-tcltk/iwidgets-4
-	>=dev-tcltk/tdom-0.8
-	>=dev-tcltk/tkimg-1.3
-	>=dev-tcltk/tktreectrl-2.1
-	dev-tcltk/anigif
-	dev-tcltk/combobox
-	dev-tcltk/tablelist
-	>=sci-chemistry/mosflm-7.0.9"
-DEPEND="app-arch/unzip"
-
-S=${WORKDIR}/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-libpng16.patch
-}
-
-src_install(){
-	rm -rf lib/{*.so,anigif,combobox}
-
-	insinto /usr/$(get_libdir)/${PN}
-	doins -r "${S}"/{src,bitmaps,lib}
-	fperms 775 /usr/$(get_libdir)/${PN}/src/imosflm
-
-	cat >> "${T}"/23imosflm <<- EOF
-	IMOSFLM_VERSION="${PV}"
-	EOF
-
-	doenvd "${T}"/23imosflm
-
-	make_wrapper imosflm /usr/$(get_libdir)/${PN}/src/imosflm
-}
--- a/sci-chemistry/imosflm/metadata.xml
+++ b/sci-chemistry/imosflm/metadata.xml
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
--- a/sci-chemistry/makecif/Manifest
+++ b/sci-chemistry/makecif/Manifest
@@ -1 +0,0 @@
-DIST makecif-5.6.6.tar.gz 3797710 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f SHA512 874c69d85b55ef22057c1113418218d7fd0a1e795f04673f3d64cd015230ab47ad8bdb0277ca9b389cc3edf397dc63c2c1cdd35837a86bc5d2a595d9ae534dbc WHIRLPOOL 5ecc1f7d06445d34e1d5d97ad98fd4c9d21db1e1611a9d89e25f0228a7b2cce5fa631b470687b3e6f7085c932cee6c5d8d4da2e6473406a22d63a26645f56be7
--- a/sci-chemistry/makecif/files/5.6.6-makefile.patch
+++ b/sci-chemistry/makecif/files/5.6.6-makefile.patch
@@ -1,49 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index 6c8264a..acdec20 100755
--- a/src/makefile
-+++ b/src/makefile
-@@ -22,6 +22,8 @@ MAKEDIC = $(MAKECIF)/dic/
- # setenv BLANC_FORT "f77  -O1" 
- #
- 
-+all: makecif_all libcheck_all modcheck_all emin_all
-+
- clean:
- 	rm -f temp_makecif_path.fh
- 	rm -f ../bin/*
-@@ -118,7 +120,7 @@ makecif.o: makecif.f  lib_com.fh crd_com.fh
- 	$(BLANC_FORT) -c makecif.f  
- 
- mkcif: main_makecif.o make_lib11.o make_lib12.o make_lib2.o make_vdw.o make_CIF.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o 
-	$(BLANC_FORT) -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o  libcheck.o 
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o  libcheck.o 
- # -------------
- libcheck.o: libcheck.f  lib_com.fh crd_com.fh 
- 	$(BLANC_FORT) -c libcheck.f
-@@ -130,7 +132,7 @@ main_libcheck.o: main_libcheck.f libcheck_version.fh
- 	$(BLANC_FORT) -c main_libcheck.f
- 
- lbcheck: main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o libcheck.o  make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_unix.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o
-	$(BLANC_FORT) -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o  mol2_file.o sdf_files.o 
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o  mol2_file.o sdf_files.o 
- # ------------
- 
- emin.o: emin.f crd_com.fh atom_com.fh
-@@ -143,7 +145,7 @@ main_emin.o: main_emin.f
- 	$(BLANC_FORT) -c main_emin.f 
- 
- emn: main_emin.o emin_new.o angle_subr.o make_unix.o make_CIF.o make_subr_2.o make_subr.o
-	$(BLANC_FORT) -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o
- 
- # -------------
- 
-@@ -155,7 +157,7 @@ main_modcheck.o: main_modcheck.f
- 	$(BLANC_FORT) -c main_modcheck.f 
- 
- mdcheck: main_modcheck.o modcheck.o mod_subr.o make_CIF.o make_unix.o make_subr_2.o make_subr.o 
-	$(BLANC_FORT) -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o  
-+	$(BLANC_FORT) ${LDFLAGS} -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o  
- 
- 
- # ======================================
--- a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild
+++ b/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild
@@ -1,40 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="PDB --> CIF convertor"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-LICENSE="ccp4"
-IUSE=""
-
-S="${WORKDIR}"/${PN}
-
-DEPEND=""
-RDEPEND="
-	!>=sci-chemistry/refmac-5.6
-	sci-libs/monomer-db"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-makefile.patch
-}
-
-src_compile() {
-	emake -C src clean
-	emake \
-		-C src \
-		BLANC_FORT="$(tc-getFC) ${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin bin/*
-	dodoc readme
-}
--- a/sci-chemistry/makecif/makecif-5.6.6.ebuild
+++ b/sci-chemistry/makecif/makecif-5.6.6.ebuild
@@ -1,39 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="PDB --> CIF convertor"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-LICENSE="ccp4"
-IUSE=""
-
-S="${WORKDIR}"/${PN}
-
-DEPEND=""
-RDEPEND="
-	!>=sci-chemistry/refmac-5.6
-	sci-libs/monomer-db"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-makefile.patch
-}
-
-src_compile() {
-	cd src && emake clean
-	emake \
-		BLANC_FORT="$(tc-getFC) ${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin bin/*
-	dodoc readme
-}
--- a/sci-chemistry/makecif/metadata.xml
+++ b/sci-chemistry/makecif/metadata.xml
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<longdescription>
-PDB - CIF convertor
-check and create correct structure description
-create the list of restraints
-create dictionary description of new ligands
-rebuild missing atoms
-create tree like structure
-also the part of REFMAC
-can use additional user's dictionary
-</longdescription>
-</pkgmetadata>
--- a/sci-chemistry/molrep/Manifest
+++ b/sci-chemistry/molrep/Manifest
@@ -1,2 +0,0 @@
-DIST molrep-11.0.02.tar.gz 3594084 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce SHA512 e22636e2d6b5558b66877960a64c0b990bb50d9e1b42016981b64e1311f83d5942fde7c1cd2dc8462ef1be814ce94ef566028079a7a091c9b3d7300f2d6ce03f WHIRLPOOL e507108a38be703e882ab3fd25e817c53c2d57b76fce578de3d308f10a85fce7a9febed39f748667a01c631b35787955d7d0290c944d4bfabfc936eab620daaf
-DIST molrep-11.0.03.tar.gz 3643087 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392 SHA512 d9ff351e3754871d100c41aa9b8af48e3588768320f5ed92e536fac5e24114ca5df6497103d0b077455fc4e30e2d3d085aeb63854eb88dc8e74259b4e1683dc8 WHIRLPOOL b16e128e3ca7f1734ca79f70decab3e262d47b6a37c49e46c4c7d51f3fd8093cd3a0f20e487caeb5e9aa0a37a9fd050588cad3e99ad46e1866d05ff4a8ed0bb6
--- a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
+++ b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
@@ -1,61 +0,0 @@
--- src/makefile	2009-02-27 16:51:46.492890717 +0100
-+++ src/makefile.new	2009-02-27 16:52:18.295619642 +0100
-@@ -5,8 +5,8 @@
- 
- BIN = $(MOLREP)/bin
- 
-OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o
-OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o
-+OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o
-+OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o
- 
- 
- all: molrep
-@@ -19,31 +19,31 @@
- # -----------------------------
- 
- molrep.o: molrep.f 
-	$(MR_FORT) -c molrep.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep.f
- molrep1.o: molrep1.f 
-	$(MR_FORT) -c molrep1.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep1.f
- molrep2.o: molrep2.f 
-	$(MR_FORT) -c molrep2.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep2.f
- molrep3.o: molrep3.f 
-	$(MR_FORT) -c molrep3.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep3.f
- molrep_prog.o: molrep_prog.f 
-	$(MR_FORT) -c molrep_prog.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog.f
- molrep_prog1.o: molrep_prog1.f 
-	$(MR_FORT) -c molrep_prog1.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog1.f
- molrep_prog2.o: molrep_prog2.f 
-	$(MR_FORT) -c molrep_prog2.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_prog2.f
- molrep_subr.o: molrep_subr.f  
-	$(MR_FORT) -c molrep_subr.f 
-molrep_sym.o: molrep_sym.f  
-	$(MR_FORT) -c molrep_sym.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_subr.f
-+molrep_sym_ccp4.o: molrep_sym.f  
-+	$(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f 
- main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh 
-	$(MR_FORT) -c main_molrep_mtz.f 
-molrep_unix.o: molrep_unix.f 
-	$(MR_FORT) -c molrep_unix.f 
-+	$(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f 
-+molrep_unix_ccp4.o: molrep_unix.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f 
- molrep_dummy.o: molrep_dummy.f 
-	$(MR_FORT) -c molrep_dummy.f 
-+	$(MR_FORT) $(FFLAGS) -c molrep_dummy.f 
- 
- molrep: $(OBJS)
-	$(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-+	$(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
- 
- # --------------------------------
-
--- a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
+++ b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
@@ -1,12 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index 30d0de7..10dd68f 100755
--- a/src/makefile
-+++ b/src/makefile
-@@ -46,6 +46,6 @@ molrep_dummy.o: molrep_dummy.f
- 	$(MR_FORT) -c molrep_dummy.f 
- 
- molrep: $(OBJS)
-	$(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
-+	$(MR_FORT) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
- 
- # --------------------------------
--- a/sci-chemistry/molrep/files/11.0.00-test.patch
+++ b/sci-chemistry/molrep/files/11.0.00-test.patch
@@ -1,191 +0,0 @@
-diff --git a/molrep_check/em.bat b/molrep_check/em.bat
-index 2f0f992..96ddd75 100755
--- a/molrep_check/em.bat
-+++ b/molrep_check/em.bat
-@@ -8,6 +8,8 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- _NMON  6
- stop
-+echo $?
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 2. Atomic model --> EM map
-@@ -20,6 +22,7 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- _NMON  6
- _prf  y
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 3. Atomic model --> EM map
-@@ -36,6 +39,7 @@ _ncs  322
- _centre  0.500 0.490 0.490
- _angles  0.0 0.0 90.0  
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- cp out/molrep.pdb hexamer.pdb
-@@ -52,6 +56,7 @@ $MR_TEST/molrep -mx hexamer.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- _DOM s
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 5. EM --> X-ray     
-@@ -60,6 +65,7 @@ stop
- $MR_TEST/molrep -f ../em/p2.cif  -m ../em/pel.map -po out/ -ps scr/ -i <<stop
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- # --------------------------------
- #
- # 6. Placing  the model to a particular orientation and position.
-@@ -72,4 +78,5 @@ $MR_TEST/molrep -f ../em/p2.cif  -m ../em/pel.map -po out/ -ps scr/ -i <<stop
- _fun  s
- _file_t ../em/tab
- stop
-+[[ $? ]] || exit 1
- #==========================================
-diff --git a/molrep_check/mr.bat b/molrep_check/mr.bat
-index 284a4cd..6e00695 100755
--- a/molrep_check/mr.bat
-+++ b/molrep_check/mr.bat
-@@ -10,6 +10,7 @@
- $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i <<stop
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -26,6 +27,7 @@ _nmon   2
- _COMPL  .5
- _SIM    .7
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -46,6 +48,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -mx ../data/test_mod
- # --------------------------------
- _NP    3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -67,6 +70,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -po out/ -ps scr/ -i
- _NMON   2
- _NP     3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -85,6 +89,7 @@ _NPT    3
- _NPTD   3
- _DYAD   D
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -103,6 +108,7 @@ _NP    3
- _NPT   10
- _NMR   3
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -118,6 +124,7 @@ _PRF Y
- _compl 1.
- _sim   .2
- stop
-+[[ $? ]] || exit 1
- #
- # =================================================================
- #
-@@ -136,6 +143,7 @@ _ph   PH
- _fom  FOM
- #
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   9. use sequence
-@@ -145,6 +153,7 @@ stop
- $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -s ../data/s100.seq -po out/ -ps scr/ -i <<stop 
- # --------------------------------
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   10. Locked RF
-@@ -157,6 +166,7 @@ _lock y
- _file_tsrf ../data/srf.tab
- _nsrf 1
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   11. Multi-monomer search using NCS, SELF = 'A' means to compute Self RF and 
-@@ -169,6 +179,7 @@ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -m2 ../data/monomer.p
- _self a
- _nsrf 1
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   12.  use pst
-@@ -179,6 +190,7 @@ $MR_TEST/molrep -f ../data/pst.mtz -m ../data/model_pst.pdb -po out/ -ps scr/ -i
- # --------------------------------
- #
- stop
-+[[ $? ]] || exit 1
- # =================================================================
- #
- #   13. space group check
-@@ -189,7 +201,8 @@ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i
- # --------------------------------
- _sg all
- #
-stop
-+s[[ $? ]] || exit 1
-+top
- # ==========================================================
- #  
- #  14. Example for finding HA position by MR solution.
-@@ -206,6 +219,7 @@ _SIGFD  SIGFD3
- #
- _FUN   d
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #  
- #  15. Example for HA search by multi-copy search
-@@ -225,6 +239,7 @@ _diff h
- _dyad y
- _nmon 4
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #  
- #  16. Example HA for search by translation function
-@@ -242,6 +257,7 @@ _FUN  t
- _diff  h
- _nmon  4
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
- #  
- #  17. Example for Self RF for Heavy Atom structure in derivative.
-@@ -258,4 +274,5 @@ _SIGFD  SIGFD3
- _FUN  r
- _diff  h
- stop
-+[[ $? ]] || exit 1
- # ==========================================================
--- a/sci-chemistry/molrep/files/11.0.03-EOR.patch
+++ b/sci-chemistry/molrep/files/11.0.03-EOR.patch
@@ -1,16 +0,0 @@
- src/molrep.f |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/src/molrep.f b/src/molrep.f
-index eac0cfc..94f74c6 100755
--- a/src/molrep.f
-+++ b/src/molrep.f
-@@ -1257,7 +1257,7 @@ C         CHECK_DENS_FILE( 2 )
-         LEN1 = 1
-         IF(LEN.GT.60) LEN1 = LEN - 59
-         WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)') 
-     *                                 NAME2(LEN11:LEN)
-+     *                                 NAME2(LEN1:LEN)
-         CALL MSGDOC(MDoc,LINE)
- 
-       ENDIF
--- a/sci-chemistry/molrep/metadata.xml
+++ b/sci-chemistry/molrep/metadata.xml
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-</pkgmetadata>
--- a/sci-chemistry/molrep/molrep-11.0.02.ebuild
+++ b/sci-chemistry/molrep/molrep-11.0.02.ebuild
@@ -1,57 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="molecular replacement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3
-	sci-libs/mmdb
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/11.0.00-respect-FLAGS.patch \
-		"${FILESDIR}"/11.0.00-test.patch
-}
-
-src_compile() {
-	cd "${S}"/src
-	emake clean
-	emake \
-		MR_FORT="$(tc-getFC) ${FFLAGS}" \
-		FFLAGS="${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
-}
-
-src_test() {
-	export MR_TEST="${S}/bin/"
-	cd "${S}"/molrep_check/work
-	mkdir out scr
-	cp ../*.bat .
-	bash em.bat || die
-	bash mr.bat || die
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/${PN}
-	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
-	dodoc readme doc/${PN}.rtf
-}
--- a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
+++ b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
@@ -1,59 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="molecular replacement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3
-	sci-libs/mmdb
-	virtual/lapack"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/11.0.00-respect-FLAGS.patch \
-		"${FILESDIR}"/11.0.00-test.patch \
-		"${FILESDIR}"/${PV}-EOR.patch
-	[[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore
-}
-
-src_compile() {
-	cd "${S}"/src
-	emake clean
-	emake \
-		MR_FORT="$(tc-getFC) ${FFLAGS}" \
-		FFLAGS="${FFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
-}
-
-src_test() {
-	export MR_TEST="${S}/bin/"
-	cd "${S}"/molrep_check/work
-	mkdir out scr
-	cp ../*.bat .
-	bash em.bat || die
-	bash mr.bat || die
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/${PN}
-	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
-	dodoc readme doc/${PN}.rtf
-}
--- a/sci-chemistry/mosflm/Manifest
+++ b/sci-chemistry/mosflm/Manifest
@@ -1 +0,0 @@
-DIST mosflm709.tgz 3324010 SHA256 d22b05211f274b50c284d4c14fcb456c52b13344e2a48d5f45855fe87f82f6d1 SHA512 aa85f8459f280e0e1d2d54041029ef072346ecef3ffcc7724eb524469e1b77dfbd95aac8b46f2b9682d605a4e5931d9c13f1162d5f3bcff08644db7e79a6316c WHIRLPOOL b3a82858a8d2a3162bc0fcfb3bf7fb7b01cfc6bca80b34643e7c6caae54b1ef1e2b24a58617ffe2b0423ca6626d51e31b49c0dba6a82ed5c61fa10d044e0d3b8
--- a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch
+++ b/sci-chemistry/mosflm/files/7.0.6-Makefile.patch
@@ -1,13 +0,0 @@
--- Makefile	2008-10-17 16:15:30.000000000 +0200
-+++ Makefile.new	2009-02-20 21:52:34.000000000 +0100
-@@ -22,7 +22,7 @@
- CBFLIBS = cbf/lib/libcbf.a
- JPGLIBS = jpg/libjpeg.a
- 
-all:	$(DPSLIBS) $(CBFLIBS) $(JPGLIBS)
-	cd mosflm ; make
-+all:	dpslibs cbflibs
-+	+make -C mosflm
- 
- ##########################################################################
-
--- a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch
+++ b/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch
@@ -1,36 +0,0 @@
-diff --git a/mosflm/bravais_fortran.c b/mosflm/bravais_fortran.c
-index 3d68cad..800bd0e 100644
--- a/mosflm/bravais_fortran.c
-+++ b/mosflm/bravais_fortran.c
-@@ -2,6 +2,7 @@
- #include <stdlib.h>
- #include <math.h>
- #include "../util/util.h"
-+#include "../util/bravais.h"
- 
- /* bravais_fortran_(): This routine converts array from FORTRAN program
-                        to structure for call to bravais
-diff --git a/mosflm/chelp.c b/mosflm/chelp.c
-index b2aaefc..fa44ab0 100644
--- a/mosflm/chelp.c
-+++ b/mosflm/chelp.c
-@@ -5,6 +5,7 @@
- /* modified for Linux by Joachim Meyer jmeyer@embl-heidelberg.de 1998.05.19 */
- 
- #include "chelp.h"
-+#include <stdio.h>
- 
- #if CALL_LIKE_HPUX
-   void chelp ()
-diff --git a/mosflm/pck.c b/mosflm/pck.c
-index ec094fc..288671d 100644
--- a/mosflm/pck.c
-+++ b/mosflm/pck.c
-@@ -17,6 +17,7 @@
- #include <math.h>
- #include <ctype.h>
- #include <string.h>
-+#include <unistd.h>
- 
- #define BYTE char
- #define WORD short int
--- a/sci-chemistry/mosflm/files/7.0.6-parallel.patch
+++ b/sci-chemistry/mosflm/files/7.0.6-parallel.patch
@@ -1,28 +0,0 @@
--- cbf/Makefile	2009-08-31 09:35:06.000000000 +0200
-+++ cbf/Makefile.new	2009-08-31 10:44:46.000000000 +0200
-@@ -362,6 +362,8 @@
-              $(EXAMPLES)/img.h               \
-              $(INCLUDE)/md5.h
- 
-+OBJ = $(subst .c,.o,$(SOURCE))
-+
- #
- # Compile the library and examples
- #
-@@ -379,11 +381,14 @@
- $(LIB):
- 	mkdir $(LIB)
- 
-+
-+.c.o: $(SOURCE) $(HEADERS)
-+	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $<
-+
- #
- # CBF library
- #
-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
-	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP)
- 	$(AR) cr $@ *.o
- 	rm *.o
- 	if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi
--- a/sci-chemistry/mosflm/files/7.0.7-parallel.patch
+++ b/sci-chemistry/mosflm/files/7.0.7-parallel.patch
@@ -1,92 +0,0 @@
- Makefile     |   21 ++++++++++-----------
- cbf/Makefile |    9 +++++++--
- 2 files changed, 17 insertions(+), 13 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 37f4c7e..51d4164 100644
--- a/Makefile
-+++ b/Makefile
-@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a
- CBFLIBS = cbf/lib/libcbf.a
- JPGLIBS = jpg/libjpeg.a
- 
-all:	$(DPSLIBS) $(CBFLIBS) $(JPGLIBS)
-	cd mosflm ; make
-+all:	$(DPSLIBS)
-+	$(MAKE) -C mosflm
- 
- ##########################################################################
- #                                                                        #
-@@ -47,22 +47,21 @@ dpslibs:
- 
- cbflibs: 
- 	rm -f `find ./cbf -name "*.a" -print`
-	cd cbf ; make all ; if [ -f $(RANLIB) ]; \
-	then $(RANLIB) lib/libcbf.a; fi
-+	$(MAKE) -C cbf all
- 
- jpglibs: 
-	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a
-+	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a
- 
- ${DPSLIBS}:
-	make dpslibs
-+	$(MAKE) dpslibs
- 
- ${CBFLIBS}:
-	make cbflibs
-+	$(MAKE) cbflibs
- 
- ${JPGLIBS}:
-	make jpglibs
-+	$(MAKE) jpglibs
- 
-libs:	${DPSLIBS} ${CBFLIBS} ${JPGLIBS}
-+libs:	${DPSLIBS} ${CBFLIBS}
- 	@echo "****************************************************************"
- 	@echo "             Making libraries for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
-@@ -71,11 +70,11 @@ ipmosflm: libs
- 	@echo "****************************************************************"
- 	@echo "           Making IPMOSFLM for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
-	cd mosflm ; make ipmosflm
-+	$(MAKE) -C mosflm ipmosflm
- 
- force:
- 	rm bin/ipmosflm
-	make ipmosflm
-+	$(MAKE) ipmosflm
- 
- install:
- 	@echo "the executable is in ${MOSHOME}/bin/ipmosflm"
-diff --git a/cbf/Makefile b/cbf/Makefile
-index e61497c..c3c94ac 100644
--- a/cbf/Makefile
-+++ b/cbf/Makefile
-@@ -362,6 +362,8 @@ HEADERS   =  $(INCLUDE)/cbf.h                  \
-              $(EXAMPLES)/img.h               \
-              $(INCLUDE)/md5.h
- 
-+OBJ = $(subst .c,.o,$(SOURCE))
-+
- #
- # Compile the library and examples
- #
-@@ -379,11 +381,14 @@ $(INSTALLDIR):
- $(LIB):
- 	mkdir $(LIB)
- 
-+
-+.c.o: $(SOURCE) $(HEADERS)
-+	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $<
-+
- #
- # CBF library
- #
-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
-	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP)
- 	$(AR) cr $@ *.o
- 	rm *.o
- 	if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi
--- a/sci-chemistry/mosflm/files/7.0.9-parallel.patch
+++ b/sci-chemistry/mosflm/files/7.0.9-parallel.patch
@@ -1,92 +0,0 @@
- Makefile     |   21 ++++++++++-----------
- cbf/Makefile |    9 +++++++--
- 2 files changed, 17 insertions(+), 13 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 3d2f543..2219d8d 100644
--- a/Makefile
-+++ b/Makefile
-@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a
- CBFLIBS = cbf/lib/libcbf.a
- JPGLIBS = jpg/libjpeg.a
- 
-all:	$(DPSLIBS) $(CBFLIBS) $(JPGLIBS)
-	cd mosflm ; make
-+all:	$(DPSLIBS)
-+	$(MAKE) -C mosflm
- 
- dpslibs:
- 	@-find . -name "*a" -delete
-@@ -32,22 +32,21 @@ dpslibs:
- 
- cbflibs: 
- 	@-find ./cbf -name "*.a" -delete
-	cd cbf ; make all ; if [ -f $(RANLIB) ]; \
-	then $(RANLIB) lib/libcbf.a; fi
-+	$(MAKE) -C cbf all
- 
- jpglibs: 
-	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a
-+	cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a
- 
- ${DPSLIBS}:
-	make dpslibs
-+	$(MAKE) dpslibs
- 
- ${CBFLIBS}:
-	make cbflibs
-+	$(MAKE) cbflibs
- 
- ${JPGLIBS}:
-	make jpglibs
-+	$(MAKE) jpglibs
- 
-libs:	${DPSLIBS} ${CBFLIBS} ${JPGLIBS}
-+libs:	${DPSLIBS} ${CBFLIBS}
- 	@echo "****************************************************************"
- 	@echo "             Making libraries for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
-@@ -56,11 +55,11 @@ ipmosflm: libs
- 	@echo "****************************************************************"
- 	@echo "           Making IPMOSFLM for system ${HOSTTYPE}"
- 	@echo "****************************************************************"
-	cd mosflm ; make ipmosflm
-+	$(MAKE) -C mosflm ipmosflm
- 
- force:
- 	@-rm -f bin/ipmosflm
-	make ipmosflm
-+	$(MAKE) ipmosflm
- 
- install:
- 	@echo "the executable is in ${MOSHOME}/bin/ipmosflm"
-diff --git a/cbf/Makefile b/cbf/Makefile
-index e61497c..c3c94ac 100644
--- a/cbf/Makefile
-+++ b/cbf/Makefile
-@@ -362,6 +362,8 @@ HEADERS   =  $(INCLUDE)/cbf.h                  \
-              $(EXAMPLES)/img.h               \
-              $(INCLUDE)/md5.h
- 
-+OBJ = $(subst .c,.o,$(SOURCE))
-+
- #
- # Compile the library and examples
- #
-@@ -379,11 +381,14 @@ $(INSTALLDIR):
- $(LIB):
- 	mkdir $(LIB)
- 
-+
-+.c.o: $(SOURCE) $(HEADERS)
-+	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $<
-+
- #
- # CBF library
- #
-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
-	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP)
- 	$(AR) cr $@ *.o
- 	rm *.o
- 	if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
+++ b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
@@ -1,16 +0,0 @@
- mosflm/pilatus_c.c |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c
-index 1eaae26..cce5a02 100644
--- a/mosflm/pilatus_c.c
-+++ b/mosflm/pilatus_c.c
-@@ -34,7 +34,7 @@ delete them later */
-   int cbf_int[16];
-   long cbf_int4[16];
-   double cbf_double[16];
-  char cbf_char[16][24];
-+  char cbf_char[16][32];
-   /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll 
- delete them later */
-   int id, index, iindex;
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
+++ b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
@@ -1,29 +0,0 @@
- mosflm/mosflm_jpeg.c           |    1 +
- src/dps/index/ind_gen_direct.c |    2 ++
- 2 files changed, 3 insertions(+), 0 deletions(-)
-
-diff --git a/mosflm/mosflm_jpeg.c b/mosflm/mosflm_jpeg.c
-index 2b32b2e..54684d0 100644
--- a/mosflm/mosflm_jpeg.c
-+++ b/mosflm/mosflm_jpeg.c
-@@ -76,6 +76,7 @@ G. Winter
- #include <fcntl.h>
- #include <stdio.h>
- #include <stdlib.h>
-+#include <string.h>
- #if (defined _MSC_VER) 
- /* no need to do this for __MINGW_ (Mingw gcc) this is just about unique!*/
- #define S_IRWXU S_IREAD|S_IWRITE|S_IEXEC
-diff --git a/src/dps/index/ind_gen_direct.c b/src/dps/index/ind_gen_direct.c
-index 6e143df..2eea61b 100644
--- a/src/dps/index/ind_gen_direct.c
-+++ b/src/dps/index/ind_gen_direct.c
-@@ -41,6 +41,8 @@
- /* #include <malloc.h> */
- #include "util.h"
- #include "ind_gen_direct.h"
-+#include "ind_help.h"
-+#include "ind_sort_merge.h"
- /* char *strcat( char *, const char *); */
- 
- 
--- a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch
+++ b/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch
@@ -1,16 +0,0 @@
- mosflm/pilatus_c.c |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c
-index 4a85b26..9893e0c 100644
--- a/mosflm/pilatus_c.c
-+++ b/mosflm/pilatus_c.c
-@@ -34,7 +34,7 @@ delete them later */
-   int cbf_int[16] = {0};
-   long cbf_int4[16] = {0};
-   double cbf_double[16] = {0};
-  char cbf_char[16][24] = {' '};
-+  char cbf_char[16][32] = {' '};
-   /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll 
- delete them later */
-   int id, index, iindex;
--- a/sci-chemistry/mosflm/metadata.xml
+++ b/sci-chemistry/mosflm/metadata.xml
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-</pkgmetadata>
--- a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild
+++ b/sci-chemistry/mosflm/mosflm-7.0.9.ebuild
@@ -1,74 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils fortran-2 toolchain-funcs versionator
-
-MY_PV="$(delete_all_version_separators)"
-MY_P="${PN}${MY_PV}"
-
-DESCRIPTION="A program for integrating single crystal diffraction data from area detectors"
-HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/mosflm/"
-SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	sci-libs/cbflib
-	sci-libs/ccp4-libs
-	sys-libs/ncurses
-	virtual/jpeg:0=
-	x11-libs/libxdl_view"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	sed \
-		-e "s:../cbf/lib/libcbf.a:-lcbf -limg:g" \
-		-e "s:../jpg/libjpeg.a:-ljpeg:g" \
-		-i ${PN}/Makefile || die
-
-	sed \
-		-e '/jinclude.h/d' \
-		-i mosflm/mosflm_jpeg.c || die
-
-	cp DATETIME.C mosflm/datetime.c || die
-
-	epatch \
-		"${FILESDIR}"/${PV}-parallel.patch \
-		"${FILESDIR}"/7.0.6-impl-dec.patch \
-		"${FILESDIR}"/${P}-buffer-overflow.patch \
-		"${FILESDIR}"/${PN}-7.0.7-impl-dec.patch
-
-	rm -rf test.f {cbf,jpg}/*.{h,c} || die
-}
-
-src_compile() {
-	emake \
-		MOSHOME="${S}" \
-		DPS="${S}" \
-		FC=$(tc-getFC) \
-		FLINK=$(tc-getFC) \
-		CC=$(tc-getCC) \
-		AR_FLAGS=vru \
-		MOSLIBS="-lccp4f -lccp4c -lxdl_view $($(tc-getPKG_CONFIG) --libs ncurses) -lXt -lmmdb -lccif -lstdc++" \
-		MCFLAGS="-O0 -fno-second-underscore" \
-		MOSFLAGS="${FFLAGS} -fno-second-underscore" \
-		FFLAGS="${FFLAGS} -fno-second-underscore" \
-		CFLAGS="${CFLAGS}" \
-		MOSCFLAGS="${CFLAGS}" \
-		LFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/ipmosflm
-	dosym ../libexec/ccp4/bin/ip${PN} /usr/bin/ip${PN}
-}
--- a/sci-chemistry/mrbump/Manifest
+++ b/sci-chemistry/mrbump/Manifest
@@ -1 +0,0 @@
-DIST mrbump-0.4.4.tar.gz 9220116 SHA256 499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a SHA512 3a39159d78c4310f5a04efc7bb10ed81f6f260baa65db3615d5065c94175e33de3dbe2073de057a699efe541d59674cc927699229a4af5e8102600caea4c03d3 WHIRLPOOL adb8c583b81cce8ec7e29f203b0a33de41f42c0fae77317671593f661db8c06c56106ed4fcfdeb503c9594c8802dc1dd1a0c7da290b7d3046e8f3d8d6911f60d
--- a/sci-chemistry/mrbump/files/0.4.4-superpose.patch
+++ b/sci-chemistry/mrbump/files/0.4.4-superpose.patch
@@ -1,11 +0,0 @@
--- share/mrbump/include/mr/Ensemble.py	2008-07-28 16:40:47.000000000 +0200
-+++ share/mrbump/include/mr/Ensemble.py.new	2009-08-26 22:26:44.000000000 +0200
-@@ -29,7 +29,7 @@
-          self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose.exe') 
-          self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset.exe') 
-       else:
-         self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose') 
-+         self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose-ccp4') 
-          self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset') 
-  
-       self.SPxyz_template=''
--- a/Show More
+++ b/Show More
				`@@ -1 +0,0 @@`
				`DIST libjwc_c-1.1.tar.gz 253637 SHA256 4e3c5406347356ac4549b2b977c8011391926470cc3556e54148070b929d9ea9 SHA512 5a095fdbf4f70d012f718d2bcd2a9689bf788801df3f3f97bead70861d08d5f6b5a9ac879e02c260974b755906d35de168646947900bcb18dad40839846d87ad WHIRLPOOL bca0bb19e2898c18f29a275c1997bf55058f5efbbc1147cb7e7a967f2eafb346c0d74975208dc6dd749ba60b256dca3c1548d9a58bd938fb19d77946a1aaa85a`
				`@@ -1 +0,0 @@`
				`DIST libjwc_f-1.1.tar.gz 170973 SHA256 9c05d5bac2a2e75d5fd490665c795ae31280da886e30f66cf39b3a32f2981199 SHA512 6d947e1513c137a23a4b6c2525e2a2f71c31a41f37455b9b3c97bd4c82128d5b3f4a7bfdd14aba57fbc258dcdcb8fa55e420a8573576992d0ae164bfe394f8d1 WHIRLPOOL 2652f3f43451cfb378d931ccff22a20131f2f44c40c2fe4c51ea45ef08f2e08306c1362f256c0c13014b9db3418ccbce437e4ccea41faae066c800a2ece02551`
				`@@ -1 +0,0 @@`
				`DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532`
				`@@ -1 +0,0 @@`
				`DIST imosflm-1.0.7.zip 941784 SHA256 b067261b4d7ef2f1f7581ddeaa08252d29f889acf89ce190eb0d8b30aa94b107 SHA512 f3163e1f71c5b1e24d6b3fbd5a040bbcebae25485d1258eef4b2725821f5f96c1260adb2bcc3ab57179d7b9b9e538ddf0494ab9b5be259b98d138fddacec8c77 WHIRLPOOL bd2b6bcdcc241fde41fe2ba99bd1e2f47bc444c46ee36a5b332d5c018b81a9d649378110a8bffa48ffc67a19b04ede7e61846b53a250e5fe3058ec0313fda80c`
				`@@ -1 +0,0 @@`
				`DIST makecif-5.6.6.tar.gz 3797710 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f SHA512 874c69d85b55ef22057c1113418218d7fd0a1e795f04673f3d64cd015230ab47ad8bdb0277ca9b389cc3edf397dc63c2c1cdd35837a86bc5d2a595d9ae534dbc WHIRLPOOL 5ecc1f7d06445d34e1d5d97ad98fd4c9d21db1e1611a9d89e25f0228a7b2cce5fa631b470687b3e6f7085c932cee6c5d8d4da2e6473406a22d63a26645f56be7`
				`@@ -1 +0,0 @@`
				`DIST mosflm709.tgz 3324010 SHA256 d22b05211f274b50c284d4c14fcb456c52b13344e2a48d5f45855fe87f82f6d1 SHA512 aa85f8459f280e0e1d2d54041029ef072346ecef3ffcc7724eb524469e1b77dfbd95aac8b46f2b9682d605a4e5931d9c13f1162d5f3bcff08644db7e79a6316c WHIRLPOOL b3a82858a8d2a3162bc0fcfb3bf7fb7b01cfc6bca80b34643e7c6caae54b1ef1e2b24a58617ffe2b0423ca6626d51e31b49c0dba6a82ed5c61fa10d044e0d3b8`
				`@@ -1 +0,0 @@`
				`DIST mrbump-0.4.4.tar.gz 9220116 SHA256 499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a SHA512 3a39159d78c4310f5a04efc7bb10ed81f6f260baa65db3615d5065c94175e33de3dbe2073de057a699efe541d59674cc927699229a4af5e8102600caea4c03d3 WHIRLPOOL adb8c583b81cce8ec7e29f203b0a33de41f42c0fae77317671593f661db8c06c56106ed4fcfdeb503c9594c8802dc1dd1a0c7da290b7d3046e8f3d8d6911f60d`