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authorJustin Lecher <jlec@gentoo.org>2015-10-26 08:29:56 +0100
committerJustin Lecher <jlec@gentoo.org>2015-10-26 08:32:25 +0100
commit7d62034735e700ca67e977470d79f5571b15b221 (patch)
tree78d45bafd1284caf0c06b4b98131677301303cbb
parentadd co-maintainer Coacher to metadata (diff)
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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>
-rw-r--r--app-office/sc/sc-7.16-r1.ebuild5
-rw-r--r--dev-libs/libjwc_c/Manifest1
-rw-r--r--dev-libs/libjwc_c/files/612-gentoo.patch20
-rw-r--r--dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild31
-rw-r--r--dev-libs/libjwc_c/metadata.xml8
-rw-r--r--dev-libs/libjwc_f/Manifest1
-rw-r--r--dev-libs/libjwc_f/files/612-gentoo.patch100
-rw-r--r--dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild38
-rw-r--r--dev-libs/libjwc_f/metadata.xml8
-rw-r--r--profiles/arch/powerpc/package.use.force1
-rw-r--r--profiles/arch/powerpc/package.use.mask6
-rw-r--r--profiles/package.mask35
-rw-r--r--sci-chemistry/arp-warp-bin/Manifest1
-rw-r--r--sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild81
-rw-r--r--sci-chemistry/arp-warp-bin/files/7.3-setup.patch30
-rw-r--r--sci-chemistry/arp-warp-bin/metadata.xml5
-rw-r--r--sci-chemistry/balbes/Manifest2
-rw-r--r--sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild79
-rw-r--r--sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch107
-rw-r--r--sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch28
-rw-r--r--sci-chemistry/balbes/metadata.xml18
-rw-r--r--sci-chemistry/ccp4-apps/Manifest2
-rw-r--r--sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild395
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch70
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch14
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch24
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch11
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch35
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch19
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch42
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch14
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch111
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch152
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch597
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch23
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch65
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch60
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch131
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-rw-r--r--sci-chemistry/ccp4-apps/metadata.xml5
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-rw-r--r--sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch11
-rw-r--r--sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch14
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-rw-r--r--sci-chemistry/ccp4/files/create-mosflm-bindir.patch10
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-rw-r--r--sci-chemistry/ccp4/files/make-ipmosflm-dir.patch10
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-rw-r--r--sci-chemistry/ccp4/files/pass-clipper-enablevals.patch11
-rw-r--r--sci-chemistry/ccp4/metadata.xml9
-rw-r--r--sci-chemistry/ccp4i/Manifest3
-rw-r--r--sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild99
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch22
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch61
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch26
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch91
-rw-r--r--sci-chemistry/ccp4i/metadata.xml5
-rw-r--r--sci-chemistry/coot/coot-0.7.1-r1.ebuild167
-rw-r--r--sci-chemistry/coot/coot-0.7.2.ebuild165
-rw-r--r--sci-chemistry/coot/coot-0.7.ebuild159
-rw-r--r--sci-chemistry/imosflm/Manifest1
-rw-r--r--sci-chemistry/imosflm/files/1.0.4-impl-dec.patch12
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-rw-r--r--sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild54
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-rw-r--r--sci-chemistry/molrep/Manifest2
-rw-r--r--sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch61
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-rw-r--r--sci-chemistry/mosflm/Manifest1
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-rw-r--r--sci-chemistry/oasis/Manifest1
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-rw-r--r--sci-chemistry/pdb-extract/Manifest2
-rw-r--r--sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch46
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-rw-r--r--sci-chemistry/phaser/Manifest1
-rw-r--r--sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch13
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-rw-r--r--sci-chemistry/phaser/phaser-2.1.4.ebuild115
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-rw-r--r--sci-chemistry/pointless/files/1.5.1-gcc4.4.patch12
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-rw-r--r--sci-chemistry/pointless/pointless-1.6.14-r1.ebuild56
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-rw-r--r--sci-chemistry/refmac/Manifest2
-rw-r--r--sci-chemistry/refmac/files/5.5-test.log.patch32
-rw-r--r--sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch84
-rw-r--r--sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch17
-rw-r--r--sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch341
-rw-r--r--sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch341
-rw-r--r--sci-chemistry/refmac/metadata.xml9
-rw-r--r--sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild85
-rw-r--r--sci-chemistry/scala/Manifest1
-rw-r--r--sci-chemistry/scala/files/3.3.18-gcc4.6.patch17
-rw-r--r--sci-chemistry/scala/files/Makefile.am7
-rw-r--r--sci-chemistry/scala/files/configure.ac14
-rw-r--r--sci-chemistry/scala/metadata.xml13
-rw-r--r--sci-chemistry/scala/scala-3.3.20.ebuild38
-rw-r--r--sci-chemistry/sfcheck/Manifest1
-rw-r--r--sci-chemistry/sfcheck/files/7.03.17-ldflags.patch12
-rw-r--r--sci-chemistry/sfcheck/metadata.xml5
-rw-r--r--sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild42
-rw-r--r--sci-chemistry/solve-resolve-bin/Manifest2
-rw-r--r--sci-chemistry/solve-resolve-bin/metadata.xml8
-rw-r--r--sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild68
-rw-r--r--sci-chemistry/xdsi/Manifest1
-rw-r--r--sci-chemistry/xdsi/files/0.92-gentoo.patch27
-rw-r--r--sci-chemistry/xdsi/metadata.xml17
-rw-r--r--sci-chemistry/xdsi/xdsi-0.92-r1.ebuild54
-rw-r--r--sci-chemistry/xia2/Manifest6
-rw-r--r--sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch28
-rw-r--r--sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch28
-rw-r--r--sci-chemistry/xia2/metadata.xml5
-rw-r--r--sci-chemistry/xia2/xia2-0.3.1.0.ebuild59
-rw-r--r--sci-chemistry/xia2/xia2-0.3.1.6.ebuild66
-rw-r--r--sci-chemistry/xia2/xia2-0.3.1.7.ebuild66
-rw-r--r--sci-chemistry/xia2/xia2-0.3.3.1.ebuild70
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-rw-r--r--sci-chemistry/xia2/xia2-0.3.4.0.ebuild70
-rw-r--r--sci-libs/balbes-db/Manifest1
-rw-r--r--sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild47
-rw-r--r--sci-libs/balbes-db/metadata.xml5
-rw-r--r--sci-libs/ccp4-libs/Manifest1
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-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch33
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch24
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch22
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch140
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-lapack.patch597
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch230
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch87
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-rw-r--r--sys-apps/coreutils/coreutils-8.20.ebuild2
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207 files changed, 8 insertions, 11262 deletions
diff --git a/app-office/sc/sc-7.16-r1.ebuild b/app-office/sc/sc-7.16-r1.ebuild
index d9e0962abbb..3c3083ee7a3 100644
--- 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 \
diff --git a/dev-libs/libjwc_c/Manifest b/dev-libs/libjwc_c/Manifest
deleted file mode 100644
index 91e153d94c9..00000000000
--- a/dev-libs/libjwc_c/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libjwc_c-1.1.tar.gz 253637 SHA256 4e3c5406347356ac4549b2b977c8011391926470cc3556e54148070b929d9ea9 SHA512 5a095fdbf4f70d012f718d2bcd2a9689bf788801df3f3f97bead70861d08d5f6b5a9ac879e02c260974b755906d35de168646947900bcb18dad40839846d87ad WHIRLPOOL bca0bb19e2898c18f29a275c1997bf55058f5efbbc1147cb7e7a967f2eafb346c0d74975208dc6dd749ba60b256dca3c1548d9a58bd938fb19d77946a1aaa85a
diff --git a/dev-libs/libjwc_c/files/612-gentoo.patch b/dev-libs/libjwc_c/files/612-gentoo.patch
deleted file mode 100644
index af4a691febb..00000000000
--- a/dev-libs/libjwc_c/files/612-gentoo.patch
+++ /dev/null
@@ -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))&&
diff --git a/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild b/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild
deleted file mode 100644
index cc9feb0c8f9..00000000000
--- a/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/dev-libs/libjwc_c/metadata.xml b/dev-libs/libjwc_c/metadata.xml
deleted file mode 100644
index d747d72a25b..00000000000
--- a/dev-libs/libjwc_c/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/dev-libs/libjwc_f/Manifest b/dev-libs/libjwc_f/Manifest
deleted file mode 100644
index 65e6fb796fb..00000000000
--- a/dev-libs/libjwc_f/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libjwc_f-1.1.tar.gz 170973 SHA256 9c05d5bac2a2e75d5fd490665c795ae31280da886e30f66cf39b3a32f2981199 SHA512 6d947e1513c137a23a4b6c2525e2a2f71c31a41f37455b9b3c97bd4c82128d5b3f4a7bfdd14aba57fbc258dcdcb8fa55e420a8573576992d0ae164bfe394f8d1 WHIRLPOOL 2652f3f43451cfb378d931ccff22a20131f2f44c40c2fe4c51ea45ef08f2e08306c1362f256c0c13014b9db3418ccbce437e4ccea41faae066c800a2ece02551
diff --git a/dev-libs/libjwc_f/files/612-gentoo.patch b/dev-libs/libjwc_f/files/612-gentoo.patch
deleted file mode 100644
index e687d8bec6e..00000000000
--- a/dev-libs/libjwc_f/files/612-gentoo.patch
+++ /dev/null
@@ -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
diff --git a/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild b/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild
deleted file mode 100644
index 69a97bf28d9..00000000000
--- a/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild
+++ /dev/null
@@ -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/*
-}
diff --git a/dev-libs/libjwc_f/metadata.xml b/dev-libs/libjwc_f/metadata.xml
deleted file mode 100644
index d747d72a25b..00000000000
--- a/dev-libs/libjwc_f/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/profiles/arch/powerpc/package.use.force b/profiles/arch/powerpc/package.use.force
index d011e8fff45..846a4b60dbf 100644
--- 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
diff --git a/profiles/arch/powerpc/package.use.mask b/profiles/arch/powerpc/package.use.mask
index 4a791e4a4d2..cf9c1541c08 100644
--- 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
diff --git a/profiles/package.mask b/profiles/package.mask
index ace39767c6f..cdbcb01f77a 100644
--- 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.
diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest
deleted file mode 100644
index 739b86dac83..00000000000
--- a/sci-chemistry/arp-warp-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532
diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild
deleted file mode 100644
index ef10d0ab3d5..00000000000
--- a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild
+++ /dev/null
@@ -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=" $testcommand
- ewarn "Invalid decimal separator (must be ".")"
- ewarn "You need to set this correctly!!!"
- echo
- ewarn "One way of setting the decimal separator is:"
- ewarn "setenv LC_NUMERIC C' in your .cshrc file"
- ewarn "\tor"
- ewarn "export LC_NUMERIC=C' in your .bashrc file"
- ewarn "Otherwise please consult your system manager"
- fi
-}
diff --git a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch
deleted file mode 100644
index faed9c1102f..00000000000
--- a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff --git a/share/arpwarp_setup_base.bash b/share/arpwarp_setup_base.bash
-index 29e769c..0b8a51e 100644
---- a/share/arpwarp_setup_base.bash
-+++ b/share/arpwarp_setup_base.bash
-@@ -13,10 +13,10 @@ else
- identifier=${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}
- #
diff --git a/sci-chemistry/arp-warp-bin/metadata.xml b/sci-chemistry/arp-warp-bin/metadata.xml
deleted file mode 100644
index 51fdedab1b3..00000000000
--- a/sci-chemistry/arp-warp-bin/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest
deleted file mode 100644
index c5f8b274702..00000000000
--- a/sci-chemistry/balbes/Manifest
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
deleted file mode 100644
index 5334207c022..00000000000
--- a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild
+++ /dev/null
@@ -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}
-}
diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch
deleted file mode 100644
index da17240642d..00000000000
--- a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch
+++ /dev/null
@@ -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
diff --git 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
deleted file mode 100644
index d29b0b6a9eb..00000000000
--- a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch
+++ /dev/null
@@ -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 = []
diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml
deleted file mode 100644
index 4bb6be5e5d0..00000000000
--- a/sci-chemistry/balbes/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
deleted file mode 100644
index e56aec5512a..00000000000
--- a/sci-chemistry/ccp4-apps/Manifest
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
deleted file mode 100644
index 5e103213392..00000000000
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
+++ /dev/null
@@ -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}
-}
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
deleted file mode 100644
index 433a78dbd23..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
+++ /dev/null
@@ -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
diff --git 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
deleted file mode 100644
index f1df3e5e19f..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch
+++ /dev/null
@@ -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
-
diff --git 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
deleted file mode 100644
index e62ae12adfb..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch
+++ /dev/null
@@ -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
- #
diff --git 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
deleted file mode 100644
index f645643e1c6..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch
+++ /dev/null
@@ -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 \
diff --git 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
deleted file mode 100644
index 1d132300554..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch
+++ /dev/null
@@ -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
-
diff --git 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
deleted file mode 100644
index f16b0ecb938..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch
+++ /dev/null
@@ -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
-
diff --git 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
deleted file mode 100644
index af4fd8219c4..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch
+++ /dev/null
@@ -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
diff --git 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
deleted file mode 100644
index 3af4af503fa..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch
+++ /dev/null
@@ -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 $(REFMACTARGETS) dtrek2scala crunch2 pmf
-
- # targets built from .c sources:
- CSIMPLE = pltdev binsort
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
deleted file mode 100644
index 1e59578473f..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
+++ /dev/null
@@ -1,111 +0,0 @@
---- configure 2009-08-07 12:11:28.000000000 +0200
-+++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200
-@@ -3113,41 +3113,6 @@
- RX_L="$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
diff --git 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
deleted file mode 100644
index 583697cea0a..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -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
-
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
deleted file mode 100644
index db823606304..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
deleted file mode 100644
index 62892db0114..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
+++ /dev/null
@@ -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}
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
deleted file mode 100644
index 9d8fefe965e..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
+++ /dev/null
@@ -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@
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
deleted file mode 100644
index 7a012be6ef0..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
+++ /dev/null
@@ -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
-
diff --git 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
deleted file mode 100644
index a5144cfa5d3..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
+++ /dev/null
@@ -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)
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
deleted file mode 100644
index 107cfd74023..00000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
+++ /dev/null
@@ -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.
- #
diff --git 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
deleted file mode 100644
index 4b98545eec8..00000000000
--- a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
+++ /dev/null
@@ -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;
- }
diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml
deleted file mode 100644
index 51fdedab1b3..00000000000
--- a/sci-chemistry/ccp4-apps/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild
deleted file mode 100644
index eea4a408b47..00000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild
+++ /dev/null
@@ -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=""
diff --git 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
deleted file mode 100644
index 1420419ffab..00000000000
--- a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -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
-
diff --git 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
deleted file mode 100644
index a77d9494a05..00000000000
--- a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
+++ /dev/null
@@ -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;
diff --git 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
deleted file mode 100644
index 1420419ffab..00000000000
--- a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -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
-
diff --git 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
deleted file mode 100644
index c118cc53baf..00000000000
--- a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch
+++ /dev/null
@@ -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
diff --git 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
deleted file mode 100644
index a77d9494a05..00000000000
--- a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch
+++ /dev/null
@@ -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;
diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
deleted file mode 100644
index 106db895b77..00000000000
--- a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
deleted file mode 100644
index 02a2aa6d887..00000000000
--- a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
+++ /dev/null
@@ -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 $system in
diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
deleted file mode 100644
index 3bf5a065224..00000000000
--- a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800
-+++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800
-@@ -21751,7 +21751,7 @@
-
- if test "x$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
diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
deleted file mode 100644
index 34d6197572f..00000000000
--- a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
+++ /dev/null
@@ -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)
diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch
deleted file mode 100644
index 8da54fd26de..00000000000
--- a/sci-chemistry/ccp4/files/dont-build-rasmol.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
deleted file mode 100644
index 7813141b2ec..00000000000
--- a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
+++ /dev/null
@@ -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 ${LDFLAGS}
-
diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
deleted file mode 100644
index ae4b7633b10..00000000000
--- a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800
-+++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800
-@@ -132,7 +132,7 @@
- #
- # CBF library
- #
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
-+$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
- $(AR) cr $@ *.o
- $(RANLIB) $@
diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
deleted file mode 100644
index 97607b68967..00000000000
--- a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
+++ /dev/null
@@ -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:
diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
deleted file mode 100644
index eac1b9f1721..00000000000
--- a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
+++ /dev/null
@@ -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 $(LIBDIR)/libdps_index.a
-
diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
deleted file mode 100644
index 3e1a8b0e6be..00000000000
--- a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800
-+++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800
-@@ -3210,7 +3210,7 @@
- #ccp4 setup
- xopts="${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
diff --git a/sci-chemistry/ccp4/metadata.xml b/sci-chemistry/ccp4/metadata.xml
deleted file mode 100644
index d37774eb9ad..00000000000
--- a/sci-chemistry/ccp4/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <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>
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
deleted file mode 100644
index e082cb44f7f..00000000000
--- a/sci-chemistry/ccp4i/Manifest
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
deleted file mode 100644
index bdfba780049..00000000000
--- a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
+++ /dev/null
@@ -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 ""
-}
diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
deleted file mode 100644
index 2c5f659b801..00000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
deleted file mode 100644
index 9f5cfb4b635..00000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
+++ /dev/null
@@ -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
- }
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
deleted file mode 100644
index 74cd2b94660..00000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
+++ /dev/null
@@ -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 $arrayname SUPERPOSE_MODE] \
- SSM {
-- if { ![file exists [FindExecutable superpose]] } {
-+ if { ![file exists [FindExecutable superpose-ccp4]] } {
- WarningMessage "The program \"superpose\" is not on your path.
- Check your installation for \"superpose\" program and \"ssm\" library."
- return 0
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
deleted file mode 100644
index 9af60b7c515..00000000000
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
+++ /dev/null
@@ -1,91 +0,0 @@
-diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl
-index 7d05905..d01f1dc 100755
---- a/ccp4i/crank/plugins/prep/crank_prep.tcl
-+++ b/ccp4i/crank/plugins/prep/crank_prep.tcl
-@@ -226,7 +226,7 @@ proc run_truncate { i j } {
- set script "$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\""
- }
diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml
deleted file mode 100644
index 51fdedab1b3..00000000000
--- a/sci-chemistry/ccp4i/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/coot/coot-0.7.1-r1.ebuild b/sci-chemistry/coot/coot-0.7.1-r1.ebuild
deleted file mode 100644
index 001145ee18e..00000000000
--- a/sci-chemistry/coot/coot-0.7.1-r1.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/coot/coot-0.7.2.ebuild b/sci-chemistry/coot/coot-0.7.2.ebuild
deleted file mode 100644
index 0e14d446453..00000000000
--- a/sci-chemistry/coot/coot-0.7.2.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/coot/coot-0.7.ebuild b/sci-chemistry/coot/coot-0.7.ebuild
deleted file mode 100644
index f5cdfa54b52..00000000000
--- a/sci-chemistry/coot/coot-0.7.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/imosflm/Manifest b/sci-chemistry/imosflm/Manifest
deleted file mode 100644
index 2ce7d893b7f..00000000000
--- a/sci-chemistry/imosflm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST imosflm-1.0.7.zip 941784 SHA256 b067261b4d7ef2f1f7581ddeaa08252d29f889acf89ce190eb0d8b30aa94b107 SHA512 f3163e1f71c5b1e24d6b3fbd5a040bbcebae25485d1258eef4b2725821f5f96c1260adb2bcc3ab57179d7b9b9e538ddf0494ab9b5be259b98d138fddacec8c77 WHIRLPOOL bd2b6bcdcc241fde41fe2ba99bd1e2f47bc444c46ee36a5b332d5c018b81a9d649378110a8bffa48ffc67a19b04ede7e61846b53a250e5fe3058ec0313fda80c
diff --git a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch b/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch
deleted file mode 100644
index 5d0dd701091..00000000000
--- a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/imosflm/files/1.0.4-tk.patch b/sci-chemistry/imosflm/files/1.0.4-tk.patch
deleted file mode 100644
index a90175194eb..00000000000
--- a/sci-chemistry/imosflm/files/1.0.4-tk.patch
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch b/sci-chemistry/imosflm/files/1.0.7-libpng16.patch
deleted file mode 100644
index 27efc6f36f4..00000000000
--- a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild b/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild
deleted file mode 100644
index e49667e50dc..00000000000
--- a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/imosflm/metadata.xml b/sci-chemistry/imosflm/metadata.xml
deleted file mode 100644
index 51fdedab1b3..00000000000
--- a/sci-chemistry/imosflm/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/makecif/Manifest b/sci-chemistry/makecif/Manifest
deleted file mode 100644
index b489a33454f..00000000000
--- a/sci-chemistry/makecif/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST makecif-5.6.6.tar.gz 3797710 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f SHA512 874c69d85b55ef22057c1113418218d7fd0a1e795f04673f3d64cd015230ab47ad8bdb0277ca9b389cc3edf397dc63c2c1cdd35837a86bc5d2a595d9ae534dbc WHIRLPOOL 5ecc1f7d06445d34e1d5d97ad98fd4c9d21db1e1611a9d89e25f0228a7b2cce5fa631b470687b3e6f7085c932cee6c5d8d4da2e6473406a22d63a26645f56be7
diff --git a/sci-chemistry/makecif/files/5.6.6-makefile.patch b/sci-chemistry/makecif/files/5.6.6-makefile.patch
deleted file mode 100644
index 186abb92b7d..00000000000
--- a/sci-chemistry/makecif/files/5.6.6-makefile.patch
+++ /dev/null
@@ -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
-
-
- # ======================================
diff --git a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild b/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild
deleted file mode 100644
index 509117f300a..00000000000
--- a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/makecif/makecif-5.6.6.ebuild b/sci-chemistry/makecif/makecif-5.6.6.ebuild
deleted file mode 100644
index 3a5f70a8b25..00000000000
--- a/sci-chemistry/makecif/makecif-5.6.6.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/makecif/metadata.xml b/sci-chemistry/makecif/metadata.xml
deleted file mode 100644
index 993c1d1ffcd..00000000000
--- a/sci-chemistry/makecif/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
deleted file mode 100644
index d91b8a448ac..00000000000
--- a/sci-chemistry/molrep/Manifest
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
deleted file mode 100644
index d81ec793b51..00000000000
--- a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
+++ /dev/null
@@ -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)
-
- # --------------------------------
-
diff --git a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
deleted file mode 100644
index c18b9a1e3f0..00000000000
--- a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
+++ /dev/null
@@ -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)
-
- # --------------------------------
diff --git a/sci-chemistry/molrep/files/11.0.00-test.patch b/sci-chemistry/molrep/files/11.0.00-test.patch
deleted file mode 100644
index d90cfb8c7b3..00000000000
--- a/sci-chemistry/molrep/files/11.0.00-test.patch
+++ /dev/null
@@ -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
- # ==========================================================
diff --git a/sci-chemistry/molrep/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch
deleted file mode 100644
index 430629e8dcc..00000000000
--- a/sci-chemistry/molrep/files/11.0.03-EOR.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/molrep/metadata.xml b/sci-chemistry/molrep/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a..00000000000
--- a/sci-chemistry/molrep/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/molrep/molrep-11.0.02.ebuild b/sci-chemistry/molrep/molrep-11.0.02.ebuild
deleted file mode 100644
index 51ff6cb2652..00000000000
--- a/sci-chemistry/molrep/molrep-11.0.02.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
deleted file mode 100644
index 3373bbba6f9..00000000000
--- a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
+++ /dev/null
@@ -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
-}
diff --git a/sci-chemistry/mosflm/Manifest b/sci-chemistry/mosflm/Manifest
deleted file mode 100644
index 80df134c833..00000000000
--- a/sci-chemistry/mosflm/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mosflm709.tgz 3324010 SHA256 d22b05211f274b50c284d4c14fcb456c52b13344e2a48d5f45855fe87f82f6d1 SHA512 aa85f8459f280e0e1d2d54041029ef072346ecef3ffcc7724eb524469e1b77dfbd95aac8b46f2b9682d605a4e5931d9c13f1162d5f3bcff08644db7e79a6316c WHIRLPOOL b3a82858a8d2a3162bc0fcfb3bf7fb7b01cfc6bca80b34643e7c6caae54b1ef1e2b24a58617ffe2b0423ca6626d51e31b49c0dba6a82ed5c61fa10d044e0d3b8
diff --git a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch b/sci-chemistry/mosflm/files/7.0.6-Makefile.patch
deleted file mode 100644
index a35232f6e8c..00000000000
--- a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch
+++ /dev/null
@@ -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
-
- ##########################################################################
-
diff --git a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch b/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch
deleted file mode 100644
index da393eb93fe..00000000000
--- a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/mosflm/files/7.0.6-parallel.patch b/sci-chemistry/mosflm/files/7.0.6-parallel.patch
deleted file mode 100644
index f735c7ce5cf..00000000000
--- a/sci-chemistry/mosflm/files/7.0.6-parallel.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/mosflm/files/7.0.7-parallel.patch b/sci-chemistry/mosflm/files/7.0.7-parallel.patch
deleted file mode 100644
index df0a8b63273..00000000000
--- a/sci-chemistry/mosflm/files/7.0.7-parallel.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/mosflm/files/7.0.9-parallel.patch b/sci-chemistry/mosflm/files/7.0.9-parallel.patch
deleted file mode 100644
index 38c6fc45a5c..00000000000
--- a/sci-chemistry/mosflm/files/7.0.9-parallel.patch
+++ /dev/null
@@ -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
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
deleted file mode 100644
index 90158eb458d..00000000000
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
+++ /dev/null
@@ -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;
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
deleted file mode 100644
index 32f251f8e00..00000000000
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
+++ /dev/null
@@ -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 *); */
-
-
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch
deleted file mode 100644
index bb4a16bf30f..00000000000
--- a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch
+++ /dev/null
@@ -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;
diff --git a/sci-chemistry/mosflm/metadata.xml b/sci-chemistry/mosflm/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a..00000000000
--- a/sci-chemistry/mosflm/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild b/sci-chemistry/mosflm/mosflm-7.0.9.ebuild
deleted file mode 100644
index 3aa74ced3d9..00000000000
--- a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild
+++ /dev/null
@@ -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}
-}
diff --git a/sci-chemistry/mrbump/Manifest b/sci-chemistry/mrbump/Manifest
deleted file mode 100644
index f9887a6071b..00000000000
--- a/sci-chemistry/mrbump/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mrbump-0.4.4.tar.gz 9220116 SHA256 499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a SHA512 3a39159d78c4310f5a04efc7bb10ed81f6f260baa65db3615d5065c94175e33de3dbe2073de057a699efe541d59674cc927699229a4af5e8102600caea4c03d3 WHIRLPOOL adb8c583b81cce8ec7e29f203b0a33de41f42c0fae77317671593f661db8c06c56106ed4fcfdeb503c9594c8802dc1dd1a0c7da290b7d3046e8f3d8d6911f60d
diff --git a/sci-chemistry/mrbump/files/0.4.4-superpose.patch b/sci-chemistry/mrbump/files/0.4.4-superpose.patch
deleted file mode 100644
index c9941e9ece2..00000000000
--- a/sci-chemistry/mrbump/files/0.4.4-superpose.patch
+++ /dev/null
@@ -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=''
diff --git a/sci-chemistry/mrbump/metadata.xml b/sci-chemistry/mrbump/metadata.xml
deleted file mode 100644
index 4aaae064be7..00000000000
--- a/sci-chemistry/mrbump/metadata.xml
+++ /dev/null
@@ -1,10 +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>
- <name>Justin Lecher (jlec)</name>
- </maintainer>
-</pkgmetadata>
-
diff --git a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild b/sci-chemistry/mrbump/mrbump-0.4.4.ebuild
deleted file mode 100644
index 66ec9309e1c..00000000000
--- a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils multilib python
-
-DESCRIPTION="An automated scheme for Molecular Replacement"
-HOMEPAGE="http://www.ccp4.ac.uk/MrBUMP"
-SRC_URI="${HOMEPAGE}/release/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="X perl"
-
-RDEPEND=">=sci-chemistry/ccp4-apps-6.1.3[X?]
- || ( sci-biology/mafft
- sci-biology/clustalw:2
- sci-biology/probcons
- sci-biology/t-coffee )
- sci-biology/fasta
- X? ( media-gfx/graphviz )
- perl? ( dev-perl/SOAP-Lite )"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_unpack(){
- unpack ${A}
- cd "${S}"
- unpack ./"${PN}".tar.gz
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/${PV}-superpose.patch
- python_convert_shebangs 2 setup_lib/*
-}
-
-src_install(){
- insinto /usr/$(get_libdir)/ccp4/ccp4i
- doins -r ccp4i/{MrBUMP-ccp4i.tar.gz,MrBUMP/{help,scripts,tasks,templates}} || \
- die "failed to install interface"
-
- insinto /usr/share/${PN}
- doins -r share/${PN}/{data,include} || die "failed to install mrbump data"
-
- dobin share/${PN}/bin/* || die "failed to install binaries"
-
- dodoc README.txt || die
- dohtml html/mrbump_doc.html || die
-}
diff --git a/sci-chemistry/oasis/Manifest b/sci-chemistry/oasis/Manifest
deleted file mode 100644
index e87a831c1fe..00000000000
--- a/sci-chemistry/oasis/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST oasis4.0_Linux.zip 6714528 SHA256 56da70ce0c2750aaddf64ad2cd7852fc341d2022209484beb356b4e73dec61ba SHA512 b43b8315e8e3bc8531e11021605100f231635e2363256a19ed0f51015913221eb9e37b3891b9b1239bf83c9ada8f65a1bdc79ec5745201436f8c3b5019bd4bf7 WHIRLPOOL 24d337391997d036bd657ab22aecc77d36f7fa0af573d17433869a29640a8a10368c75ebee114071c577cc0cce34d838271147599d99e2c389088b8c6185f41b
diff --git a/sci-chemistry/oasis/files/4.0-makefile.patch b/sci-chemistry/oasis/files/4.0-makefile.patch
deleted file mode 100644
index f27a350a1fd..00000000000
--- a/sci-chemistry/oasis/files/4.0-makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/src/Makefile b/src/Makefile
-index 1e9128f..eb9edaf 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -20,8 +20,8 @@ IRIX:
- @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o oasis4-0 oasis4-0.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas
- @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o fnp2fp fnp2fp.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas
- Linux:
-- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB}
-- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB}
-+ ${F77} $(CFLAGS) $(LDFLAGS) -o oasis oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB}
-+ ${F77} $(CFLAGS) $(LDFLAGS) -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB}
- Darwin:
- @ ${F77} -O2 -fno-second-underscore -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm
- @ ${F77} -O2 -fno-second-underscore -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm
diff --git a/sci-chemistry/oasis/metadata.xml b/sci-chemistry/oasis/metadata.xml
deleted file mode 100644
index 8412c2f3d31..00000000000
--- a/sci-chemistry/oasis/metadata.xml
+++ /dev/null
@@ -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>
- <use>
- <flag name="minimal">Restricts functionality on free software</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-chemistry/oasis/oasis-4.0-r3.ebuild b/sci-chemistry/oasis/oasis-4.0-r3.ebuild
deleted file mode 100644
index 98c8aaef47b..00000000000
--- a/sci-chemistry/oasis/oasis-4.0-r3.ebuild
+++ /dev/null
@@ -1,70 +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 multilib toolchain-funcs
-
-MY_P="${PN}${PV}_Linux"
-
-DESCRIPTION="A direct-method program for SAD/SIR phasing"
-HOMEPAGE="http://cryst.iphy.ac.cn/Project/protein/protein-I.html"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${MY_P}.zip"
-
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-LICENSE="ccp4 oasis"
-IUSE="examples +minimal"
-
-RDEPEND="
- sci-chemistry/ccp4-apps
- sci-chemistry/pymol
- sci-libs/mmdb:0
- sci-visualization/gnuplot
- !minimal? (
- sci-chemistry/solve-resolve-bin
- sci-chemistry/arp-warp-bin
- )"
-DEPEND="${RDEPEND}
- sci-libs/ccp4-libs"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
- rm bin/{fnp2fp,gnuplot,oasis4-0,seq} || die
- epatch "${FILESDIR}"/${PV}-makefile.patch
-}
-
-src_compile() {
- emake \
- -C src \
- F77="$(tc-getFC)" \
- CFLAGS="${FFLAGS}" \
- CCP4_LIB="${EPREFIX}/usr/$(get_libdir)" \
- Linux
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin/
- doexe src/{${PN},fnp2fp}
-
- exeinto /usr/$(get_libdir)/${PN}
- doexe bin/*.*sh
-
- insinto /usr/share/doc/${PF}/html
- doins bin/html/*
- dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/html
- chmod 755 "${ED}"/usr/share/doc/${PF}/html/*.{*sh,awk} || die
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r examples
- fi
-
- cat >> "${T}"/25oasis <<- EOF
- oasisbin="${EPREFIX}/usr/$(get_libdir)/${PN}"
- EOF
-
- doenvd "${T}"/25oasis
-}
diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest
deleted file mode 100644
index 9036c79e3e7..00000000000
--- a/sci-chemistry/pdb-extract/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pdb-extract-v3.004-prod-src.tar.gz 942450 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953 SHA512 4505fd615324982e741a3656d8a36ffc2cd6524c825d254e0a1ff44b3464aaf63cbdbe4f614a6ace6c0e56af8f452634152edadd0ed5305f0148856affa8cb60 WHIRLPOOL b7077431d75a31a9ac4ea41f7cb76874aa49626a19c1290126405a8cdac4d210f56929f9213512ae4f542286be5cbedc972642b9ef07a4e461ac969c6c0d965f
-DIST pdb-extract-v3.11-prod-src.tar.gz 1016140 SHA256 cc56ab58e4b4f0914dcd61834cae673ade5b12688861ea5f0197a33f5939d131 SHA512 06ef4110f873d23bcf878877a8b9f714b895a5b269f8d33312387c0bcb569adb2b1d1577eebc30200d5f0d3648959450912911609dab3749e7d5eb4c84d7e12f WHIRLPOOL ea0e643e1d64f344fdd643348b0ce35143e29f27a64b9153d6645c8dbf914e193f700217c0caecb30ea300ae10f47ea09bed61811c3bb293ef63d9e45acf74d3
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
deleted file mode 100644
index 3a6f5498ffb..00000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
+++ /dev/null
@@ -1,46 +0,0 @@
---- Makefile 2008-12-05 14:36:44.000000000 +0100
-+++ Makefile.new 2008-12-05 14:37:21.000000000 +0100
-@@ -19,13 +19,7 @@
- CHECKOUT_SCRIPT_MODULE = util
- CHECKOUT_SCRIPT = checkout.sh
-
--LIBDIRS = cifobj-common-v4.1 \
-- tables-v8.0 \
-- regex-v2.2 \
-- cif-file-v1.0 \
-- misclib-v2.2 \
-- cifparse-obj-v7.0 \
-- $(EXTRACT)
-+LIBDIRS = $(EXTRACT)
-
- all: compile
-
---- pdb-extract-v3.0/Makefile 2008-12-05 14:42:58.000000000 +0100
-+++ pdb-extract-v3.0/Makefile.new 2008-12-05 14:42:15.510315392 +0100
-@@ -6,6 +6,7 @@
-
- M_INCL_DIR = ../include
- M_LIB_DIR = ../lib
-+M_LIB_DIR_GENTOO = @GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
- M_BIN_DIR = ../bin
-
- PROJ_DIR = .
-@@ -37,12 +38,12 @@
- include ../etc/Makefile.platform
-
- # Dependent libraries for the pdbml-parser
--CIF_FILE_LIB = $(M_LIB_DIR)/cif-file.a
--CIFPARSE_LIB = $(M_LIB_DIR)/cifparse-obj.a
--CIF_TABLE_LIB = $(M_LIB_DIR)/cif-table-obj.a
--CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a
--REGEX_LIB = $(M_LIB_DIR)/regex.a
--MISCLIB_LIB = $(M_LIB_DIR)/misclib.a
-+CIF_FILE_LIB = $(M_LIB_DIR_GENTOO)/cif-file.a
-+CIFPARSE_LIB = $(M_LIB_DIR_GENTOO)/cifparse-obj.a
-+CIF_TABLE_LIB = $(M_LIB_DIR_GENTOO)/tables.a
-+CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a
-+REGEX_LIB = $(M_LIB_DIR_GENTOO)/regex.a
-+MISCLIB_LIB = $(M_LIB_DIR_GENTOO)/misclib.a
-
- ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \
- $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB)
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
deleted file mode 100644
index cdf48e4784c..00000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
+++ /dev/null
@@ -1,199 +0,0 @@
-diff -Naur pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src.new/Makefile
---- pdb-extract-v3.004-prod-src/Makefile 2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/Makefile 2009-12-03 21:34:10.000000000 -0500
-@@ -52,7 +52,7 @@
- echo "------------------------------------------------------------"; \
- echo "**** Making $$libdir ****"; \
- echo "------------------------------------------------------------"; \
-- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
-+ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \
- done
-
- beta:
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3 2009-12-03 21:34:10.000000000 -0500
-@@ -91,7 +91,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -159,7 +159,7 @@
- STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4 2009-12-03 21:34:10.000000000 -0500
-@@ -92,7 +92,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -160,7 +160,7 @@
- STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3 2009-12-03 21:34:10.000000000 -0500
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
-
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
-
- # Lexer executable
-@@ -89,7 +91,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -107,8 +109,8 @@
- C_WARNINGS=$(WARNINGS)
-
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
- $(INCLUDES)
-
- ## C++ compiler
-@@ -128,9 +130,9 @@
- EXT=C
-
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
- $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
- $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -144,7 +146,7 @@
- F77=f77
-
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
-
- # Additional Fortran libraries
- F77LIBS=
-@@ -154,11 +156,11 @@
- #-----Linkers section----------------------------------------------------#
-
- # Static linking option. If not defined, dynamic linking is used.
--STATIC_LINKING=-static
-+STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
-
- # Fortran linker
- F77_LINKER=f77
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 2007-09-11 11:19:46.000000000 -0400
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4 2009-12-03 21:34:10.000000000 -0500
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
-
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
-
- # Lexer executable
-@@ -34,7 +36,7 @@
-
- # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
- # warnings as errors.
--WARNINGS_AS_ERRORS=-Werror
-+WARNINGS_AS_ERRORS=
-
- # ALL_WARNINGS defines flags to instruct all compilers to report all
- # warnings.
-@@ -90,7 +92,7 @@
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -108,8 +110,8 @@
- C_WARNINGS=$(WARNINGS)
-
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
- $(INCLUDES)
-
- ## C++ compiler
-@@ -129,9 +131,9 @@
- EXT=C
-
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
- $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
- $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -145,7 +147,7 @@
- F77=f77
-
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
-
- # Additional Fortran libraries
- F77LIBS=
-@@ -155,11 +157,11 @@
- #-----Linkers section----------------------------------------------------#
-
- # Static linking option. If not defined, dynamic linking is used.
--STATIC_LINKING=-static
-+STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
-
- # Fortran linker
- F77_LINKER=f77
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
deleted file mode 100644
index 6506713742b..00000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- pdb-extract-v3.0/src/extract.C 2007-09-11 17:19:48.000000000 +0200
-+++ pdb-extract-v3.0/src/extract.C.new 2008-12-05 17:49:59.000000000 +0100
-@@ -1689,7 +1689,7 @@
- open_file_error(inpfile, "get_mmcif");
- }
-
-- (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT");
-+ (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT");
- if(temp != NULL) {
- strcpy(pdb_extract, "");
- strcpy(pdb_extract_sf, "");
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
deleted file mode 100644
index 6907399c27d..00000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- cifobj-common-v4.1/src/GenString.C 2008-11-13 10:44:01.000000000 +0100
-+++ cifobj-common-v4.1/src/GenString.C.new 2008-11-13 10:43:54.000000000 +0100
-@@ -144,6 +144,7 @@
- #include <string>
- #include <algorithm>
- #include <sstream>
-+#include <string.h>
-
- #include "GenString.h"
-
---- tables-v8.0/src/ISTable.C 2007-09-11 17:19:47.000000000 +0200
-+++ tables-v8.0/src/ISTable.C.new 2008-11-13 10:48:18.000000000 +0100
-@@ -150,6 +150,7 @@
- #include <sstream>
- #include <iostream>
- #include <iomanip>
-+#include <limits.h>
-
- #include "Exceptions.h"
- #include "GenString.h"
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
deleted file mode 100644
index 7383811b5bf..00000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
+++ /dev/null
@@ -1,207 +0,0 @@
- Makefile | 2 +-
- etc/make.platform.darwin3 | 4 ++--
- etc/make.platform.darwin4 | 4 ++--
- etc/make.platform.gnu3 | 20 +++++++++++---------
- etc/make.platform.gnu4 | 20 +++++++++++---------
- 5 files changed, 27 insertions(+), 23 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 627d256..72c7e59 100644
---- a/Makefile
-+++ b/Makefile
-@@ -52,7 +52,7 @@ compile:
- echo "------------------------------------------------------------"; \
- echo "**** Making $$libdir ****"; \
- echo "------------------------------------------------------------"; \
-- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
-+ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \
- done
-
- beta:
-diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3
-index c5f7b06..4c1c97c 100644
---- a/etc/make.platform.darwin3
-+++ b/etc/make.platform.darwin3
-@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -159,7 +159,7 @@ F77LIBS=
- STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-
- # Fortran linker
- F77_LINKER=f77
-diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4
-index 4619b34..f481fdb 100644
---- a/etc/make.platform.darwin4
-+++ b/etc/make.platform.darwin4
-@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -160,7 +160,7 @@ F77LIBS=
- STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-
- # Fortran linker
- F77_LINKER=f77
-diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3
-index 7fd442e..9bec4dc 100644
---- a/etc/make.platform.gnu3
-+++ b/etc/make.platform.gnu3
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
-
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
-
- # Lexer executable
-@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG=
- C_WARNINGS=$(WARNINGS)
-
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
- $(INCLUDES)
-
- ## C++ compiler
-@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
- EXT=C
-
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
- $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
- $(DEFINES) $(INCLUDES)
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
- # source code that is not maintained by PDB
-@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
- F77=f77
-
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
-
- # Additional Fortran libraries
- F77LIBS=
-@@ -154,11 +156,11 @@ F77LIBS=
- #-----Linkers section----------------------------------------------------#
-
- # Static linking option. If not defined, dynamic linking is used.
--STATIC_LINKING=-static
-+STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
-
- # Fortran linker
- F77_LINKER=f77
-diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4
-index 78a0007..bc85308 100644
---- a/etc/make.platform.gnu4
-+++ b/etc/make.platform.gnu4
-@@ -6,6 +6,8 @@
- ##
- ##########################################################################
-
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
-+
- #-----Lexer and Parser section-------------------------------------------#
-
- # Lexer executable
-@@ -34,7 +36,7 @@ ABI=
-
- # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
- # warnings as errors.
--WARNINGS_AS_ERRORS=-Werror
-+WARNINGS_AS_ERRORS=
-
- # ALL_WARNINGS defines flags to instruct all compilers to report all
- # warnings.
-@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
- DEFINES=$(GDEFINES) $(LDEFINES)
-
- ## Global include directories
--GINCLUDES=
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
-
- # Collect all include directories from global include directories and
- # include directories specified in module makefile
-@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG=
- C_WARNINGS=$(WARNINGS)
-
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES)
-+CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES)
-
- ## C++ compiler
- ## This part defines C++ compiler information
-@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
- EXT=C
-
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
- $(DEFINES) $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
- $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
-
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
-@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
- F77=f77
-
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
-
- # Additional Fortran libraries
- F77LIBS=
-@@ -158,8 +160,8 @@ F77LIBS=
- STATIC_LINKING=
-
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
--LDFLAGS_NO_STATIC=$(ABI) -w
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
-
- # Fortran linker
- F77_LINKER=f77
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
deleted file mode 100644
index 5284bd745d5..00000000000
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
+++ /dev/null
@@ -1,64 +0,0 @@
- common-v4.5/src/mapped_ptr_vector.C | 14 +++++++-------
- 1 files changed, 7 insertions(+), 7 deletions(-)
-
-diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C
-index d7c61f3..e20a236 100644
---- a/common-v4.5/src/mapped_ptr_vector.C
-+++ b/common-v4.5/src/mapped_ptr_vector.C
-@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP,
- _vector.push_back(inP);
-
- typename tIndex::value_type valuePair(inP->GetName(),
-- make_pair(_vector.size() - 1, fileIndex));
-+ std::make_pair(_vector.size() - 1, fileIndex));
-
- _index.insert(valuePair);
-
- _currentName = inP->GetName();
-- _currentIndices = make_pair(_vector.size() - 1, fileIndex);
-+ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
-
- }
-
-@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name,
- _vector.push_back(NULL);
-
- typename tIndex::value_type valuePair(name,
-- make_pair(_vector.size() - 1, fileIndex));
-+ std::make_pair(_vector.size() - 1, fileIndex));
-
- _index.insert(valuePair);
-
- _currentName = name;
-- _currentIndices = make_pair(_vector.size() - 1, fileIndex);
-+ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
- }
-
-
-@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name)
- if (is_equal(_currentName, name, keyComp))
- {
- _currentName.clear();
-- _currentIndices = make_pair(_vector.size(), (unsigned int)0);
-+ _currentIndices = std::make_pair(_vector.size(), (unsigned int)0);
- }
-
- }
-@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
- if (_vector.empty())
- {
- // Empty container. Return invalid index.
-- return(make_pair(_vector.size(), (unsigned int)0));
-+ return(std::make_pair(_vector.size(), (unsigned int)0));
- }
-
- typename tIndex::key_compare keyComp = _index.key_comp();
-@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
- else
- {
- // Not found. Return invalid index.
-- return(make_pair(_vector.size(), (unsigned int)0));
-+ return(std::make_pair(_vector.size(), (unsigned int)0));
- }
- }
-
diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml
deleted file mode 100644
index e42d0af60f4..00000000000
--- a/sci-chemistry/pdb-extract/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
deleted file mode 100644
index 836d76f5c00..00000000000
--- a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit eutils toolchain-funcs multilib prefix
-
-MY_P="${PN}-v${PV}-prod-src"
-
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
-
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<app-text/html-xml-utils-5.3"
-DEPEND="${RDEPEND}
- >=sci-libs/cifparse-obj-7.025"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-cflags-install.patch \
- "${FILESDIR}"/${P}-gcc-4.3.patch \
- "${FILESDIR}"/${P}-Makefile.patch \
- "${FILESDIR}"/${P}-env.patch
-
- sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \
- pdb-extract-v3.0/Makefile \
- || die "Failed to fix libdir"
-
- # Get rid of unneeded directories, to make sure we use system files
- ebegin "Deleting redundant directories"
- rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \
- misclib-v2.2 regex-v2.2 tables-v8.0
- eend
-
- sed -i \
- -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
- -e "s:^\(CC=\).*:\1$(tc-getCC):g" \
- -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
- -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
- "${S}"/etc/make.* \
- || die "Failed to fix makefiles"
-
- eprefixify pdb-extract-v3.0/Makefile etc/*
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin
- doexe bin/pdb_extract{,_sf} bin/extract \
- || die "failed to install binaries"
- insinto /usr/include/rcsb
- doins include/* || die "failed to install include files"
- dodoc README* || die "failed to install docs"
- insinto /usr/share/rcsb/
- doins -r pdb-extract-data || die "failed to install data files"
-
- cat >> "${T}"/envd <<- EOF
- PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
- PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
- EOF
-
- newenvd "${T}"/envd 20pdb-extract \
- || die "failed to install env files"
-}
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
deleted file mode 100644
index 04351c8a125..00000000000
--- a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils toolchain-funcs multilib prefix
-
-MY_P="${PN}-v${PV}-prod-src"
-
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
-
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<app-text/html-xml-utils-5.3"
-DEPEND="${RDEPEND}
- >=sci-libs/cifparse-obj-7.025"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-cflags-install.patch \
- "${FILESDIR}"/${P}-gcc-4.7.patch \
- "${FILESDIR}"/${PN}-3.004-env.patch
-
- sed -i \
- -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
- -e "s:^\(CC=\).*:\1$(tc-getCC):g" \
- -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
- -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
- "${S}"/etc/make.* \
- || die "Failed to fix makefiles"
-
- eprefixify pdb-extract-v3.0/Makefile etc/*
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin
- doexe bin/pdb_extract{,_sf} bin/extract
- insinto /usr/include/rcsb
- doins include/*
- dodoc README*
- insinto /usr/share/rcsb/
- doins -r pdb-extract-data
-
- cat >> "${T}"/envd <<- EOF
- PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
- PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
- EOF
-
- newenvd "${T}"/envd 20pdb-extract
-}
diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest
deleted file mode 100644
index deb3ba972a7..00000000000
--- a/sci-chemistry/phaser/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 SHA512 cdf36572613a6e400af0f29da501ccfd2a9f1a7e2d89162aad3fe14929816b41790bb57ba1e77976b9046c6e06a29df2748999db93a2cd0a4d1fde95ac1f9e8b WHIRLPOOL 5aa1a1c6520be90ef02be0e9de9c111a9835cda05a3549c390f62ceef7e68c8392670d91941b823c0ee94f29e6aab9d34a61b90e8bd3d4820a83daa547463fdb
diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
deleted file mode 100644
index 5311cb33278..00000000000
--- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-index 3b1bd3a..8939a74 100755
---- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-+++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-@@ -802,8 +802,6 @@ class environment:
- else:
- action = self.write_bin_sh_dispatcher
- ext = ""
-- try: os.chmod(source_file, 0755)
-- except OSError: pass
- target_file_ext = target_file + ext
- remove_or_rename(target_file_ext)
- try: action(source_file, target_file_ext)
diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml
deleted file mode 100644
index 6b4826474da..00000000000
--- a/sci-chemistry/phaser/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- <description>ccp4 maintainer</description>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild
deleted file mode 100644
index 86fa57f5260..00000000000
--- a/sci-chemistry/phaser/phaser-2.1.4.ebuild
+++ /dev/null
@@ -1,115 +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 flag-o-matic python-single-r1 toolchain-funcs
-
-CCP4VER="6.1.13"
-
-DESCRIPTION="A program for phasing macromolecular crystal structures"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz"
-
-LICENSE="|| ( phaser phaser-com ccp4 )"
-SLOT="0"
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
-IUSE="openmp"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}"/ccp4-${CCP4VER}
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/phaser-2.1.4-chmod.patch \
- "${FILESDIR}"/phaser-2.1.4-ldflags.patch
-
- use openmp && append-flags -fopenmp
-
- for i in ${CXXFLAGS}; do
- OPTS="${OPTS} \"${i}\","
- done
-
- OPTS=${OPTS%,}
-
- sed -i \
- -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
- "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
- for i in ${LDFLAGS}; do
- OPTSLD="${OPTSLD} \"${i}\","
- done
-
- sed -i \
- -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \
- -e "s:\[\"-static:\[${OPTSLD} \"-static:g" \
- "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
-}
-
-src_configure() {
- local compiler
- local mtype
- local mversion
- local nproc
-
- # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc,
- # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC,
- # darwin_c++, darwin_gcc. The build systems seems to prepend
- # unix_ all by itself. Can this be derived from $(tc-getCC)?
- compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-
- # Breaks cross compilation.
- mtype=$(src/${PN}/bin/machine_type)
- mversion=$(src/${PN}/bin/machine_version)
-
- einfo "Creating build directory"
- mkdir build
- cd build
- ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons
- ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx
-
- einfo "Configuring phaser components"
- $(PYTHON) "libtbx/configure.py" \
- --build=release \
- --compiler=${compiler} \
- --repository="${S}"/src/${PN}/source \
- --repository="${S}"/lib/cctbx/cctbx_sources \
- --static_libraries \
- ccp4io="${S}" \
- mmtbx \
- phaser || die "configure.py failed"
-}
-
-src_compile() {
- nproc=`echo "-j1 ${MAKEOPTS}" \
- | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"`
-
- cd build
- einfo "Setting up build environment"
- source setpaths.sh
-
- einfo "Compiling phaser components"
- libtbx.scons -j ${nproc} || die "libtbx.scons failed"
-}
-
-src_install() {
- dobin build/exe/phaser || die
-
- cat >> "${T}"/53${PN} <<- EOF
- PHASER="${EPREFIX}/usr/bin"
- PHASER_ENVIRONMENT="1"
- PHASER_MTYPE="${mtype}"
- PHASER_MVERSION="${mversion}"
- PHASER_VERSION="${PV}"
- EOF
-
- doenvd "${T}"/53${PN} || die
-}
diff --git a/sci-chemistry/pointless/Manifest b/sci-chemistry/pointless/Manifest
deleted file mode 100644
index 911c4487511..00000000000
--- a/sci-chemistry/pointless/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pointless-1.6.14.tar.gz 423657 SHA256 68f0c1f65239b1451310fe885c2b9d51fc558de7b43af1e584750e05dc5635d8 SHA512 9dd524a7c842edc01206450c52ca1a01e8e3ee6f9ff71742789943ee10e006b5452b0be3aa509dd16bb85f1b9c3d7954616a78ec2fef2daea7c0ab42cdaa42b9 WHIRLPOOL 5085afbd88713384039ef2c2b4b2f7fddd8f078dca9df54062b0415e970791868c61df98f4044b4e061077a73b4e129b6e5db34852d64cace48108db9c6ae50f
-DIST pointless-1.6.2.tar.gz 412244 SHA256 5e09ca592ea565e8ace142fc0edff39d0ab723f4ac6e2cadd6ba571d667c80f6 SHA512 2e897a7302ba4d43da69c8ee91254b0632d8a0ae301140a144472f7e466078f0b1abd10362343d7d50d04bd86ae8b83265a20302f7aeae3dc8845f1581211ddd WHIRLPOOL 8953806f68684e882717673ec18263f0ac2093f3cb2cac573b20886f5f0d60c67b756f74bdb3555342bb3d287021b7c70b20c53f0e38e687a5914df935ae35cd
diff --git a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch b/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch
deleted file mode 100644
index ca67dbd3f33..00000000000
--- a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/string_util.hh b/string_util.hh
-index 66af6f3..047512b 100644
---- a/string_util.hh
-+++ b/string_util.hh
-@@ -3,6 +3,7 @@
-
- #include <string>
- #include <vector>
-+#include <stdio.h>
- #include "range.hh"
-
- //======================================================================
diff --git a/sci-chemistry/pointless/metadata.xml b/sci-chemistry/pointless/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a..00000000000
--- a/sci-chemistry/pointless/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild b/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild
deleted file mode 100644
index d983cb29024..00000000000
--- a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild
+++ /dev/null
@@ -1,56 +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 fortran-2 multilib python-single-r1 toolchain-funcs
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
- sci-chemistry/ccp4-apps
- >=sci-libs/ccp4-libs-6.1.3-r10
- sci-libs/clipper
- sci-libs/fftw:2.1
- sci-libs/mmdb
- >=sci-libs/cctbx-2010.03.29.2334-r3[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
- epatch "${FILESDIR}"/1.5.1-gcc4.4.patch
-}
-
-src_compile() {
- emake \
- -f Makefile.make \
- CC=$(tc-getCC) \
- CXX=$(tc-getCXX) \
- CFLAGS="${CFLAGS}" \
- CXXFLAGS="${CXXFLAGS}" \
- LFLAGS="${LDFLAGS}" \
- CLIB="${EPREFIX}/usr/$(get_libdir)" \
- CCTBX_VERSION=2010 \
- ICCP4=-I"${EPREFIX}/usr/include/ccp4" \
- ITBX="-I${EPREFIX}/usr/include" \
- ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \
- LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
- SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran"
-}
-
-src_install() {
- dobin pointless othercell
-}
diff --git a/sci-chemistry/pointless/pointless-1.6.14.ebuild b/sci-chemistry/pointless/pointless-1.6.14.ebuild
deleted file mode 100644
index 158bde017ae..00000000000
--- a/sci-chemistry/pointless/pointless-1.6.14.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils fortran-2 multilib python toolchain-funcs
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
- sci-chemistry/ccp4-apps
- >=sci-libs/ccp4-libs-6.1.3-r10
- sci-libs/clipper
- sci-libs/fftw:2.1
- sci-libs/mmdb
- >=sci-libs/cctbx-2010.03.29.2334-r3"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-pkg_setup() {
- fortran-2_pkg_setup
- python_set_active_version 2
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/1.5.1-gcc4.4.patch
-}
-
-src_compile() {
- emake \
- -f Makefile.make \
- CC=$(tc-getCC) \
- CXX=$(tc-getCXX) \
- CFLAGS="${CFLAGS}" \
- CXXFLAGS="${CXXFLAGS}" \
- LFLAGS="${LDFLAGS}" \
- CLIB="${EPREFIX}/usr/$(get_libdir)" \
- CCTBX_VERSION=2010 \
- ICCP4=-I"${EPREFIX}/usr/include/ccp4" \
- ITBX="-I${EPREFIX}/usr/include" \
- ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \
- LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
- SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" \
- || die
-}
-
-src_install() {
- dobin pointless othercell || die
-}
diff --git a/sci-chemistry/pointless/pointless-1.6.2.ebuild b/sci-chemistry/pointless/pointless-1.6.2.ebuild
deleted file mode 100644
index 2b9f0ad4faa..00000000000
--- a/sci-chemistry/pointless/pointless-1.6.2.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-PYTHON_DEPEND="2"
-
-inherit eutils fortran-2 multilib python toolchain-funcs
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
- sci-chemistry/ccp4-apps
- >=sci-libs/ccp4-libs-6.1.3-r10
- sci-libs/clipper
- sci-libs/fftw:2.1
- sci-libs/mmdb
- >=sci-libs/cctbx-2010.03.29.2334-r3"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-pkg_setup() {
- fortran-2_pkg_setup
- python_pkg_setup
- python_set_active_version 2
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/1.5.1-gcc4.4.patch
-}
-
-src_compile() {
- emake \
- -f Makefile.make \
- CC=$(tc-getCC) \
- CXX=$(tc-getCXX) \
- CFLAGS="${CFLAGS}" \
- CXXFLAGS="${CXXFLAGS}" \
- LFLAGS="${LDFLAGS}" \
- CLIB="${EPREFIX}/usr/$(get_libdir)" \
- CCTBX_VERSION=2010 \
- ICCP4=-I"${EPREFIX}/usr/include/ccp4" \
- ITBX="-I${EPREFIX}/usr/include" \
- ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \
- LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
- SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran"
-}
-
-src_install() {
- dobin pointless othercell
-}
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
deleted file mode 100644
index ba3def10302..00000000000
--- a/sci-chemistry/refmac/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST refmac_5.5.0110.tar.gz 1326832 SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca SHA512 7e7fd1a7d2d11ef5f2e08cae61da62ecfe6978730ce4ca80f8b00be9bdad5e7d0ad493e1b8d57d64f1393f2017a87b8342e2607b08bc4018def798038a111728 WHIRLPOOL 587260eebd2df3115ba01ee03c11ab773d7316100a09af1f259f7795a139f978d94c569b8e4ab85982c2eeda628e643376231bdca5311fc8c7d2de5b65a033ac
-DIST test-framework.tar.gz 130933173 SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 SHA512 3ef8253f472c5a481f836291afb80746ad73858e130130b848851b6b5dc53ada3b78c9f853af1c46fa22f469f2ce2f3248f5f760950e118610922c0429a7da16 WHIRLPOOL 022c1b493ecd35e769b44d1e52a351b4883682ef9759626bac36e26cc61078d95de0ec2531ed706897c683c38727139fa7a13d06b64c597026817ed79612d16d
diff --git a/sci-chemistry/refmac/files/5.5-test.log.patch b/sci-chemistry/refmac/files/5.5-test.log.patch
deleted file mode 100644
index 61858be357a..00000000000
--- a/sci-chemistry/refmac/files/5.5-test.log.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- test-framework/refmac5/test_refmac5.py 2009-06-29 15:45:37.000000000 +0200
-+++ test-framework/refmac5/test_refmac5.py.new 2009-06-29 15:48:05.000000000 +0200
-@@ -88,7 +88,8 @@
- 'make hydr no',
- 'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag',
- 'labout FC=FC PHIC=PHIC'],
-- working_directory = self.test_dir)
-+ working_directory = self.test_dir,
-+ log_file = 'test_twinned_refinement.log')
-
- self.assertEqual(status, 0)
-
-@@ -123,7 +124,8 @@
- 'weight auto',
- 'ncyc 20',
- 'labout FC=FC PHIC=PHIC'],
-- working_directory = self.test_dir)
-+ working_directory = self.test_dir,
-+ log_file = 'test_4_domain_tls.log')
-
- self.assertEqual(status, 0)
-
-@@ -156,7 +158,8 @@
- 'anomalous form SE -9.9 3.9',
- 'anomalous wavelength 0.97966',
- 'labout FC=FC PHIC=PHIC'],
-- working_directory = self.test_dir)
-+ working_directory = self.test_dir,
-+ log_file = 'test_sad_refinement.log')
-
- self.assertEqual(status, 0)
-
diff --git a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch
deleted file mode 100644
index 1efbaa04d9e..00000000000
--- a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-diff --git a/makefile b/makefile
-index 66d4cee..5270677 100644
---- a/makefile
-+++ b/makefile
-@@ -9,7 +9,7 @@ XFFLAGS = -fno-second-underscore -static
- XCFLAGS = -DGFORTRAN -DPROTOTYPE
- FFLAGS = $(FOPTIM) $(XFFLAGS)
- CFLAGS = $(COPTIM) $(XCFLAGS)
--CPPFLAGS = $(CFLAGS)
-+CPPFLAGS = $(CXXFLAGS) $(XCFLAGS)
-
- LLIBCIF =
- LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 371d84d..557077f 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -68,9 +68,7 @@ messy_pdb.o \
- bridge.o \
- i0.o \
- i1.o \
--chbevl.o \
--$(LLIBCIF) \
--$(LLIBLAPACK)
-+chbevl.o
- #$(LLIBCCP) \
- #crt0.o \
- #heavy.o \
-@@ -95,8 +93,7 @@ make_unix_ccp4.o \
- emin.o \
- libcheck_min.o \
- mol2_file.o \
--sdf_files.o \
--$(LLIBCCP)
-+sdf_files.o
-
- SUBM = \
- main_makecif.o \
-@@ -116,9 +113,7 @@ make_rst2.o \
- make_PDB.o \
- makecif.o \
- make_unix_ccp4.o \
--make_vdw.o \
--$(LLIBCCP) \
--$(LLIBCIF)
-+make_vdw.o
-
- SUBT = \
- tlsgroups.o \
-@@ -142,9 +137,7 @@ make_refmac_dummy.o \
- inout_routines.o \
- errwrt_1.o \
- linalgebra.o \
--subnumrec.o \
--$(LLIBCCP) \
--$(LLIBCIF)
-+subnumrec.o
- #--------------------------------------------------------------------------------
-
- ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s
-@@ -154,18 +147,19 @@ ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s
- all: refmac libcheck makecif
-
- refmac: $(SUBR)
-- $(FC) $(FFLAGS) $(LDFLAGF)-o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
-
- libcheck: $(SUBL)
-- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP)
-
- makecif: $(SUBM)
-- $(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF)
-
- tlsgroups: $(SUBT)
-- $(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF)
-
- clean:
- /bin/rm *.o
-
- bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
-+ $(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
deleted file mode 100644
index 3969cc9c858..00000000000
--- a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- hkon_secder_tch.f | 3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/hkon_secder_tch.f b/hkon_secder_tch.f
-index 31794b0..86d2cdf 100644
---- a/hkon_secder_tch.f
-+++ b/hkon_secder_tch.f
-@@ -3724,7 +3724,8 @@ c---External functions and subprutines
- INTEGER NWORKSPACE
- REAL*8 TOLER
- REAL*8 WORKSPACE(300)
-- REAL LSTLSQ,D2DF_WEIGHT
-+ REAL*8 D2DF_WEIGHT
-+ REAL LSTLSQ
- C
- INTEGER IBIN,IBIN_S
- INTEGER I,J,K
diff --git a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
deleted file mode 100644
index 9998b759c66..00000000000
--- a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,341 +0,0 @@
- makefile_refmac.inc1 | 215 ++++++++++++++++++++++++--------------------------
- 1 files changed, 104 insertions(+), 111 deletions(-)
-
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 0f8bd63..e59fbfb 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -96,9 +96,7 @@ bridge.o \
- i0.o \
- i1.o \
- chbevl.o \
--make_unix_ccp4.o \
--$(LLIBCIF) \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
-
-
- SUBL = \
-@@ -133,9 +131,7 @@ cell_symm_subrs.o \
- iheap_sort.o \
- linalgebra.o \
- math_refmac.o \
--subnumrec.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+subnumrec.o
-
- SUB_FREE = \
- freer_twin.o \
-@@ -145,9 +141,7 @@ subnumrec.o \
- libT.o \
- iheap_sort.o \
- cell_symm_subrs.o \
--math_refmac.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+math_refmac.o
-
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90
- twin77mod.o: twin77mod.f
- $(FC) $(FFLAGS) -c twin77mod.f
-
--gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90
-+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90
-+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90
-
--max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
-+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c max_with_twins.f
-
--merohedr_twin.o: restr_files.f90 merohedr_twin.f
-- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
-+merohedr_twin.o: restr_files.o merohedr_twin.f
-+ $(FC) $(FFLAGS) -c merohedr_twin.f
-
--ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f
-+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f
-
--ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f
-+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ml_params_refine.f
-
--optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
-+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
-+ $(FC) $(FFLAGS) -c optimise_solvent_all.f90
-
--ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
-+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
-+ $(FC) $(FFLAGS) -c ncs_rest.f
-
--ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
-- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
-+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
-+ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90
-
--lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
-+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c lsq_exp2.f
-
--vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
-+ $(FC) $(FFLAGS) -c vdw_and_contacts.f
-
- dist_routines.o: dist_routines.f90
- $(FC) $(FFLAGS) -c dist_routines.f90
-
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90
-+ $(FC) $(FFLAGS) -c ncs_simil.f90
-
- ridge.o: ridge.f90
- $(FC) $(FFLAGS) -c ridge.f90
-@@ -227,140 +221,138 @@ ridge.o: ridge.f90
- align_refmac.o: align_refmac.f90
- $(FC) $(FFLAGS) -c align_refmac.f90
-
--rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
-+ $(FC) $(FFLAGS) -c rigid_allocate.f
-
--tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c tls_allocate.f
-
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
-- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
-- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
-+ restr_files.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c hkon_secder_tch.f
-
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
-+ $(FC) $(FFLAGS) -c oppro_allocate.f
-
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
-+ $(FC) $(FFLAGS) -c read_extra_restraints.f
-
--coords.o: coords.f90 atomf77mod.f
-- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90
-+coords.o: coords.f90 atomf77mod.o
-+ $(FC) $(FFLAGS) -c coords.f90
-
-
--ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ls_scaling_double.f
-
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90
-- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
-+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f
-
--calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
-+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c calc_stats_twin.f
-
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c refpre_twin.f
-
-
--decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
-- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
-+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
-+ $(FC) $(FFLAGS) -c decide_twin_opers_0.f
-
- automorphism.o: automorphism.f90
- $(FC) $(FFLAGS) -c automorphism.f90
-
--mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o
-+ $(FC) $(FFLAGS) -c mtz_write_twin.f
-
- filter_params.o: filter_params.f90
- $(FC) $(FFLAGS) -c filter_params.f90
-
--rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f
-+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \
-+ agreem.o rharvest_mod.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c rcard_tor1.f
-
--inout_routines.o: restr_files.f90 inout_routines.f
-- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
-+inout_routines.o: restr_files.o inout_routines.f
-+ $(FC) $(FFLAGS) -c inout_routines.f
-
--local_tls.o: local_tls.f90 linalgebra_f90.f90
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
-+local_tls.o: local_tls.f90 linalgebra_f90.o
-+ $(FC) $(FFLAGS) -c local_tls.f90
-
- linalgebra_f90.o: linalgebra_f90.f90
- $(FC) $(FFLAGS) -c linalgebra_f90.f90
-
--make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c make_refmac_dummy.f
-
--ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
-+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c ml_scaling_double.f
-
--refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c refall_twin.f
-
--rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c rharvest_subr.f
-
--solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
-+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c solvent_contr_mask.f
-
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c subag_scale_hessian.f
-
--aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
-+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
-+ $(FC) $(FFLAGS) -c aniso_ref_eigen.f
-
--subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
-+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c subcf_scale1.f
-
--bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
-- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
-+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
-+ $(FC) $(FFLAGS) -c bvalue_routines.f90
-
--newentry_idealise.o:: newentry_idealise.f weights.f90
-- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
-+newentry_idealise.o:: newentry_idealise.f weights.o
-+ $(FC) $(FFLAGS) -c newentry_idealise.f
-
--occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
-+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c occupancy_only_refine.f
-
--refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
-- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
-+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
-+ $(FC) $(FFLAGS) -c refmac_completeness.f90
-
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c refmac_xml.f
-
- hkl_pack.o: hkl_pack.f90
- $(FC) $(FFLAGS) -c hkl_pack.f90
-
--extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
-+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c extra_eigen.f
-
--subvag.o: subvag.f hkl_pack.f90
-- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
-+subvag.o: subvag.f hkl_pack.o
-+ $(FC) $(FFLAGS) -c subvag.f
-
--make_PDB.o: make_PDB.f ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
-+make_PDB.o: make_PDB.f ncs_constr.o
-+ $(FC) $(FFLAGS) -c make_PDB.f
-
--make_CIF.o: make_CIF.f ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
-+make_CIF.o: make_CIF.f ncs_constr.o
-+ $(FC) $(FFLAGS) -c make_CIF.f
-
- refmac: $(SUBR)
-- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
-
--mol2_file.o: mol2_file.f odb_files.f90
-- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
-+mol2_file.o: mol2_file.f odb_files.o
-+ $(FC) $(FFLAGS) -c mol2_file.f
-
--odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f
-- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
-+odb_files.o: odb_files.f90 elements_module.o enerf77mod.o
-+ $(FC) $(FFLAGS) -c odb_files.f90
-
- elements_module.o: elements_module.f90
- $(FC) $(FFLAGS) -c elements_module.f90
-
--make_lib2.o: make_lib2.f odb_files.f90
-- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
-+make_lib2.o: make_lib2.f odb_files.o
-+ $(FC) $(FFLAGS) -c make_lib2.f
-
- pdb2libcheck.o: pdb2libcheck.f90
- $(FC) $(FFLAGS) -c pdb2libcheck.f90
-
--libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90
-- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
-+libcheck.o: libcheck.f elements_module.o pdb2libcheck.o
-+ $(FC) $(FFLAGS) -c libcheck.f
-
- header2matr.o: header2matr.f90
- $(FC) $(FFLAGS) -c header2matr.f90
-@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90
- $(FC) $(FFLAGS) -c freer_twin.f90
-
- libcheck: $(SUBL)
-- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
-
- free_twin: $(SUB_FREE)
-- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
-
-
- header2matr: $(SUB_HEADER)
-- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
-
- clean:
- /bin/rm *.o *.mod
-
- bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
-+ $(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
deleted file mode 100644
index 9998b759c66..00000000000
--- a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,341 +0,0 @@
- makefile_refmac.inc1 | 215 ++++++++++++++++++++++++--------------------------
- 1 files changed, 104 insertions(+), 111 deletions(-)
-
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 0f8bd63..e59fbfb 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -96,9 +96,7 @@ bridge.o \
- i0.o \
- i1.o \
- chbevl.o \
--make_unix_ccp4.o \
--$(LLIBCIF) \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
-
-
- SUBL = \
-@@ -133,9 +131,7 @@ cell_symm_subrs.o \
- iheap_sort.o \
- linalgebra.o \
- math_refmac.o \
--subnumrec.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+subnumrec.o
-
- SUB_FREE = \
- freer_twin.o \
-@@ -145,9 +141,7 @@ subnumrec.o \
- libT.o \
- iheap_sort.o \
- cell_symm_subrs.o \
--math_refmac.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+math_refmac.o
-
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90
- twin77mod.o: twin77mod.f
- $(FC) $(FFLAGS) -c twin77mod.f
-
--gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90
-+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90
-+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90
-
--max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
-+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c max_with_twins.f
-
--merohedr_twin.o: restr_files.f90 merohedr_twin.f
-- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
-+merohedr_twin.o: restr_files.o merohedr_twin.f
-+ $(FC) $(FFLAGS) -c merohedr_twin.f
-
--ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f
-+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f
-
--ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f
-+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ml_params_refine.f
-
--optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
-+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
-+ $(FC) $(FFLAGS) -c optimise_solvent_all.f90
-
--ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
-+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
-+ $(FC) $(FFLAGS) -c ncs_rest.f
-
--ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
-- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
-+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
-+ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90
-
--lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
-+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c lsq_exp2.f
-
--vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
-+ $(FC) $(FFLAGS) -c vdw_and_contacts.f
-
- dist_routines.o: dist_routines.f90
- $(FC) $(FFLAGS) -c dist_routines.f90
-
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90
-+ $(FC) $(FFLAGS) -c ncs_simil.f90
-
- ridge.o: ridge.f90
- $(FC) $(FFLAGS) -c ridge.f90
-@@ -227,140 +221,138 @@ ridge.o: ridge.f90
- align_refmac.o: align_refmac.f90
- $(FC) $(FFLAGS) -c align_refmac.f90
-
--rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
-+ $(FC) $(FFLAGS) -c rigid_allocate.f
-
--tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c tls_allocate.f
-
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
-- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
-- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
-+ restr_files.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c hkon_secder_tch.f
-
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
-+ $(FC) $(FFLAGS) -c oppro_allocate.f
-
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
-+ $(FC) $(FFLAGS) -c read_extra_restraints.f
-
--coords.o: coords.f90 atomf77mod.f
-- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90
-+coords.o: coords.f90 atomf77mod.o
-+ $(FC) $(FFLAGS) -c coords.f90
-
-
--ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ls_scaling_double.f
-
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90
-- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
-+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f
-
--calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
-+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c calc_stats_twin.f
-
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c refpre_twin.f
-
-
--decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
-- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
-+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
-+ $(FC) $(FFLAGS) -c decide_twin_opers_0.f
-
- automorphism.o: automorphism.f90
- $(FC) $(FFLAGS) -c automorphism.f90
-
--mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o
-+ $(FC) $(FFLAGS) -c mtz_write_twin.f
-
- filter_params.o: filter_params.f90
- $(FC) $(FFLAGS) -c filter_params.f90
-
--rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f
-+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \
-+ agreem.o rharvest_mod.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c rcard_tor1.f
-
--inout_routines.o: restr_files.f90 inout_routines.f
-- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
-+inout_routines.o: restr_files.o inout_routines.f
-+ $(FC) $(FFLAGS) -c inout_routines.f
-
--local_tls.o: local_tls.f90 linalgebra_f90.f90
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
-+local_tls.o: local_tls.f90 linalgebra_f90.o
-+ $(FC) $(FFLAGS) -c local_tls.f90
-
- linalgebra_f90.o: linalgebra_f90.f90
- $(FC) $(FFLAGS) -c linalgebra_f90.f90
-
--make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c make_refmac_dummy.f
-
--ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
-+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c ml_scaling_double.f
-
--refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c refall_twin.f
-
--rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c rharvest_subr.f
-
--solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
-+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c solvent_contr_mask.f
-
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c subag_scale_hessian.f
-
--aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
-+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
-+ $(FC) $(FFLAGS) -c aniso_ref_eigen.f
-
--subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
-+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c subcf_scale1.f
-
--bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
-- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
-+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
-+ $(FC) $(FFLAGS) -c bvalue_routines.f90
-
--newentry_idealise.o:: newentry_idealise.f weights.f90
-- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
-+newentry_idealise.o:: newentry_idealise.f weights.o
-+ $(FC) $(FFLAGS) -c newentry_idealise.f
-
--occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
-+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c occupancy_only_refine.f
-
--refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
-- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
-+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
-+ $(FC) $(FFLAGS) -c refmac_completeness.f90
-
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c refmac_xml.f
-
- hkl_pack.o: hkl_pack.f90
- $(FC) $(FFLAGS) -c hkl_pack.f90
-
--extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
-- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
-+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
-+ $(FC) $(FFLAGS) -c extra_eigen.f
-
--subvag.o: subvag.f hkl_pack.f90
-- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
-+subvag.o: subvag.f hkl_pack.o
-+ $(FC) $(FFLAGS) -c subvag.f
-
--make_PDB.o: make_PDB.f ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
-+make_PDB.o: make_PDB.f ncs_constr.o
-+ $(FC) $(FFLAGS) -c make_PDB.f
-
--make_CIF.o: make_CIF.f ncs_constr.f90
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
-+make_CIF.o: make_CIF.f ncs_constr.o
-+ $(FC) $(FFLAGS) -c make_CIF.f
-
- refmac: $(SUBR)
-- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
-
--mol2_file.o: mol2_file.f odb_files.f90
-- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
-+mol2_file.o: mol2_file.f odb_files.o
-+ $(FC) $(FFLAGS) -c mol2_file.f
-
--odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f
-- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
-+odb_files.o: odb_files.f90 elements_module.o enerf77mod.o
-+ $(FC) $(FFLAGS) -c odb_files.f90
-
- elements_module.o: elements_module.f90
- $(FC) $(FFLAGS) -c elements_module.f90
-
--make_lib2.o: make_lib2.f odb_files.f90
-- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
-+make_lib2.o: make_lib2.f odb_files.o
-+ $(FC) $(FFLAGS) -c make_lib2.f
-
- pdb2libcheck.o: pdb2libcheck.f90
- $(FC) $(FFLAGS) -c pdb2libcheck.f90
-
--libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90
-- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
-+libcheck.o: libcheck.f elements_module.o pdb2libcheck.o
-+ $(FC) $(FFLAGS) -c libcheck.f
-
- header2matr.o: header2matr.f90
- $(FC) $(FFLAGS) -c header2matr.f90
-@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90
- $(FC) $(FFLAGS) -c freer_twin.f90
-
- libcheck: $(SUBL)
-- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
-
- free_twin: $(SUB_FREE)
-- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
-
-
- header2matr: $(SUB_HEADER)
-- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
-
- clean:
- /bin/rm *.o *.mod
-
- bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
-+ $(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml
deleted file mode 100644
index c0432fefe85..00000000000
--- a/sci-chemistry/refmac/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- <name>Justin Lecher (jlec)</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
deleted file mode 100644
index eb8e8701821..00000000000
--- a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils fortran-2 flag-o-matic toolchain-funcs versionator
-
-DESCRIPTION="Macromolecular crystallographic refinement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
-SRC_URI="
- ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz
- test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
- sci-chemistry/makecif
- >=sci-libs/ccp4-libs-6.1.3-r7
- sci-libs/mmdb
- <sci-libs/monomer-db-1
- virtual/blas
- virtual/lapack"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-FORTRAN_STANDARD="77 90"
-
-S="${WORKDIR}"
-
-PATCHES=(
- "${FILESDIR}"/${PV}-allow-dynamic-linking.patch
- "${FILESDIR}"/${PV}-gcc4.6.patch
- )
-
-src_prepare() {
- epatch ${PATCHES[@]}
-
- use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch
- [[ ${FC} == *gfortran* ]] && \
- append-fflags -fno-second-underscore && \
- append-cflags -DGFORTRAN -DPROTOTYPE && \
- append-libs -lgfortran -lgfortranbegin -lstdc++
- [[ ${FC} == *ifort* ]] && \
- append-libs -lstdc++
-}
-
-src_compile() {
- emake \
- FC=$(tc-getFC) \
- CC=$(tc-getCC) \
- CXX=$(tc-getCXX) \
- COPTIM="${CFLAGS}" \
- FOPTIM="${FFLAGS:- -O2}" \
- VERSION="" \
- XFFLAGS="" \
- XCFLAGS="" \
- LLIBCCP="-lccp4f -lccp4c -lccif $($(tc-getPKG_CONFIG) --libs mmdb)" \
- LLIBLAPACK="$($(tc-getPKG_CONFIG) --libs lapack blas)" \
- LLIBOTHERS="${LIBS}" \
- ${PN} libcheck
-}
-
-src_test() {
- einfo "Starting tests ..."
- source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
- export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
- export CCP4_TEST="${WORKDIR}"/test-framework
- export CCP4_SCR="${T}"
- ln -sf refmac "${S}"/refmac5
- sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
- ccp4-run-thorough-tests -v test_refmac5 || die
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin/
- doexe ${PN}
- dosym refmac /usr/libexec/ccp4/bin/refmac5
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
- dosym refmac /usr/bin/refmac5
- dodoc refmac_keywords.pdf bugs_and_features.pdf
-}
diff --git a/sci-chemistry/scala/Manifest b/sci-chemistry/scala/Manifest
deleted file mode 100644
index e03416a2873..00000000000
--- a/sci-chemistry/scala/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scala-3.3.20.tar.gz 368628 SHA256 0efb108923a4d21fdc75d7ee92567e4bac4ae409f8798fbabd8142b5b026e976 SHA512 9f9812527013d87c80101333baf7ee646f6b3c665cdb477bb4e633c0a1fa57b31b6327913cf712e961c4484a9d9edf1aab5f3cfc66e6834aca1e970a4e0ca898 WHIRLPOOL 7d6082872a9f2f992186a2626dbf7ccd9f827b1322d1399b41ebc1b07267a46cfed5f7ea085403415c01eba4fc44e9d51983080537db04b227469d6871f8f1f9
diff --git a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch b/sci-chemistry/scala/files/3.3.18-gcc4.6.patch
deleted file mode 100644
index 0bb3d40d479..00000000000
--- a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- scala.f | 3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/scala.f b/scala.f
-index d7e1cbe..8ed6fd2 100644
---- a/scala.f
-+++ b/scala.f
-@@ -3955,7 +3955,8 @@ c line buffer
- character*40 key, value
- character*200 realfilename
-
-- integer intfp, i2swap, lenstr
-+ integer intfp, lenstr
-+ integer*2 i2swap
- external intfp, i2swap, lenstr
- logical litend
- external litend
diff --git a/sci-chemistry/scala/files/Makefile.am b/sci-chemistry/scala/files/Makefile.am
deleted file mode 100644
index 49fd61180ef..00000000000
--- a/sci-chemistry/scala/files/Makefile.am
+++ /dev/null
@@ -1,7 +0,0 @@
-
-LIBS = -lccp4f $(LAPACK_LIBS)
-
-bin_PROGRAMS = scala
-
-scala_SOURCES = scala.f
-
diff --git a/sci-chemistry/scala/files/configure.ac b/sci-chemistry/scala/files/configure.ac
deleted file mode 100644
index 35c4c7fdd19..00000000000
--- a/sci-chemistry/scala/files/configure.ac
+++ /dev/null
@@ -1,14 +0,0 @@
-# -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_PREREQ(2.59)
-AC_INIT(scala, https://bugs.gentoo.org/)
-AC_CONFIG_SRCDIR([scala.f])
-AM_INIT_AUTOMAKE([foreign])
-
-PKG_CHECK_MODULES([LAPACK],[lapack])
-
-# Checks for programs.
-AC_PROG_FC
-AC_PROG_F77
-AC_OUTPUT([Makefile])
diff --git a/sci-chemistry/scala/metadata.xml b/sci-chemistry/scala/metadata.xml
deleted file mode 100644
index 2c9359ab351..00000000000
--- a/sci-chemistry/scala/metadata.xml
+++ /dev/null
@@ -1,13 +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>
-This program scales together multiple observations of reflections from
-Xray difraction experiments, and merges multiple observations into an
-average intensity.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/scala/scala-3.3.20.ebuild b/sci-chemistry/scala/scala-3.3.20.ebuild
deleted file mode 100644
index 3555cc29a9d..00000000000
--- a/sci-chemistry/scala/scala-3.3.20.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit autotools fortran-2
-
-DESCRIPTION="Scale together multiple observations of reflections"
-HOMEPAGE="http://www.ccp4.ac.uk/dist/html/scala.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- !<sci-chemistry/ccp4-6.1.2
- !dev-lang/scala-bin
- !dev-lang/scala
- sci-libs/ccp4-libs
- virtual/lapack"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-src_prepare() {
- cp "${FILESDIR}"/{configure.ac,Makefile.am} "${S}"
- eautoreconf
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin/
- doexe ${PN}
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
- dodoc ${PN}.doc
- dohtml ${PN}.html
-}
diff --git a/sci-chemistry/sfcheck/Manifest b/sci-chemistry/sfcheck/Manifest
deleted file mode 100644
index 77615cec106..00000000000
--- a/sci-chemistry/sfcheck/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sfcheck-7.03.18.tar.gz 535707 SHA256 def9ceec86fc50f35b9a729e6f84b45a83560e2c6c20a5105647182e10313148 SHA512 256aa1690e0f5ca6aca0483a7d00c1deeb7b77701d950771a134532a658f7c3189bc6abec620ea6da2af200fc879ac9ff07ef7f4ba8614b6cd4e8455a11bed93 WHIRLPOOL 7b9f99f1a8387c5bc63bdab2078d3fcfab4146046429c56503760ca12a1898e944b5aa3c42b358d303206487e5d493bdcb77fe1795490779e7bd79b8b66a2d7a
diff --git a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch b/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch
deleted file mode 100644
index 4163cb52ac1..00000000000
--- a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index ab43d7d..37e469f 100755
---- a/src/makefile
-+++ b/src/makefile
-@@ -60,6 +60,6 @@ main_sfcheck_ccp4.o: main_sfcheck_ccp4.f sfch_version.fh
- $(MR_FORT) -c main_sfcheck_ccp4.f
-
- sfcheck: $(OBJS)
-- $(MR_FORT) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY)
-+ $(MR_FORT) $(LDFLAGS) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY)
-
- # ----------------------------------------
diff --git a/sci-chemistry/sfcheck/metadata.xml b/sci-chemistry/sfcheck/metadata.xml
deleted file mode 100644
index 9ac9ffdb3a4..00000000000
--- a/sci-chemistry/sfcheck/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild b/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild
deleted file mode 100644
index e18673d0923..00000000000
--- a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild
+++ /dev/null
@@ -1,42 +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="Program for assessing the agreement between the atomic model and X-ray data or EM map"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/sfcheck.html"
-#SRC_URI="http://www.ysbl.york.ac.uk/~alexei/downloads/sfcheck.tar.gz"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="sci-libs/ccp4-libs"
-DEPEND="${RDEPEND}
- !<sci-chmistry/ccp4-apps-6.1.3"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
- epatch "${FILESDIR}"/7.03.17-ldflags.patch
-
- emake -C src clean
-}
-
-src_compile() {
- MR_FORT="$(tc-getFC) ${FFLAGS}" \
- MR_LIBRARY="-lccp4f" \
- emake -C src all
-}
-
-src_install() {
- exeinto /usr/libexec/ccp4/bin/
- doexe bin/${PN}
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
- dodoc readme ${PN}.com.gz doc/${PN}*
-}
diff --git a/sci-chemistry/solve-resolve-bin/Manifest b/sci-chemistry/solve-resolve-bin/Manifest
deleted file mode 100644
index 43fcf716e99..00000000000
--- a/sci-chemistry/solve-resolve-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST solve-2.13-linux-64.tar.gz 74444830 SHA256 e03250bb550686fc6e5f59d4e885b83b88cd342dfb4975eb31ddf95d9515650e SHA512 8f20715c3fb73940f03ba8a4bb3528f89ba01520cacead001796609bc15259ab7ab7f2d4960ea97efc43029863bc31e630c9e93f528a233652928220dafe0b4d WHIRLPOOL 125efe76024148656f3bb357ad1bc78d17f51eb8268c83241f4da9a94356170d0259fe48fadf6bf1ffe4b10b57bb27ed79199063dc95d0eef8d9e22de653c84a
-DIST solve-2.13-linux.tar.gz 71902534 SHA256 975466fe92d8f6256de20ea0b5101876f3e5a7e3093199946c9f4824236c79d3 SHA512 a3a779ada33bd189fc8c3e6fdc424ef9c032c5540138cce52e0c8dcf5a12847b1325402a2c1715ed4ab217f433169d3612c724f2d178ead576afc44ec4839c6a WHIRLPOOL 0fec411b795a107610e620586cba511a0cbf50400e0bdfef872b22ee05e3992fcc0a4b1cf1d84d450bbeb3838a7bc9633acd8f4cf97d5e4b7a01e6e7959ccd7c
diff --git a/sci-chemistry/solve-resolve-bin/metadata.xml b/sci-chemistry/solve-resolve-bin/metadata.xml
deleted file mode 100644
index ae9ec7c5f6a..00000000000
--- a/sci-chemistry/solve-resolve-bin/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild b/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild
deleted file mode 100644
index 6deae178afd..00000000000
--- a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Automated crystallographic structure solution for MIR, SAD, and MAD"
-HOMEPAGE="http://www.solve.lanl.gov/index.html"
-SRC_URI="
- x86? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux.tar.gz )
- amd64? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux-64.tar.gz )"
-
-SLOT="0"
-LICENSE="solve"
-KEYWORDS="-* x86 amd64"
-IUSE="examples"
-
-RDEPEND="sci-libs/ccp4-libs"
-DEPEND=""
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/solve-${PV}
-
-QA_PREBUILT="opt/solve-resolve/bin/*"
-
-src_install(){
- local IN_PATH="/opt/solve-resolve/"
-
- exeinto ${IN_PATH}bin/
- doexe bin/*
-
- insinto ${IN_PATH}lib/
- doins -r lib/{*sym,sym*,hist*,*dat,segments,patterns}
-
- docinto html
- dodoc -r lib/html/*
-
- sed \
- -e 's:/usr/local/lib/solve/:${EPREFIX}/opt/solve-resolve/lib/:' \
- -i lib/examples_solve/p9/solve* || die
- if use examples; then
- sed \
- -e 's:/usr/local/lib/resolve/:${EPREFIX}/opt/solve-resolve/lib/:' \
- -i lib/examples_resolve/{resolve.csh,prime_and_switch.csh} || die
- insinto /usr/share/${PF}/
- doins -r lib/examples_*solve
- fi
-
- cat >> "${T}"/20solve-resolve <<- EOF
- CCP4_OPEN="UNKNOWN"
- SYMOP="${EPREFIX}/usr/share/ccp4/data/symop.lib"
- SYMINFO="${EPREFIX}/usr/share/ccp4/data/syminfo.lib"
- SOLVEDIR="${EPREFIX}/${IN_PATH}lib/"
- PATH="${EPREFIX}/${IN_PATH}bin"
- EOF
-
- doenvd "${T}"/20solve-resolve
-}
-
-pkg_postinst(){
- einfo "Get a valid license key from"
- einfo "http://solve.lanl.gov/license.html"
- einfo "and place it in"
- einfo "${EPREFIX}${IN_PATH}lib/"
-}
diff --git a/sci-chemistry/xdsi/Manifest b/sci-chemistry/xdsi/Manifest
deleted file mode 100644
index e33598d7936..00000000000
--- a/sci-chemistry/xdsi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST xdsi_0.92.tar.gz 886028 SHA256 416403f167d26b56965283b407783ea80927ace533df76e330b51ca37c9bb9e4
diff --git a/sci-chemistry/xdsi/files/0.92-gentoo.patch b/sci-chemistry/xdsi/files/0.92-gentoo.patch
deleted file mode 100644
index f4a37ff1838..00000000000
--- a/sci-chemistry/xdsi/files/0.92-gentoo.patch
+++ /dev/null
@@ -1,27 +0,0 @@
- xdsi | 6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/xdsi b/xdsi
-index cbedee8..1037913 100755
---- a/xdsi
-+++ b/xdsi
-@@ -20,8 +20,8 @@
- ####################################################################
- # These are the only two things you should change#
-
--set Templates "/mydir/templates"
--set initial "/mydir/SLS-2009"
-+set Templates "GENTOOTEMPLATE"
-+set initial "./"
-
-
- ####################################################################
-@@ -121,7 +121,7 @@ your system administrator."
- }
-
-
--CheckExecutables "kpdf gnuplot xds_par xdsstat xds-viewer-0.6 convert pointless ipmosflm VIEW"
-+CheckExecutables "kpdf gnuplot xds_par xds-viewer convert pointless ipmosflm"
-
- #wm resizable . 0 0
-
diff --git a/sci-chemistry/xdsi/metadata.xml b/sci-chemistry/xdsi/metadata.xml
deleted file mode 100644
index 431fb2be13b..00000000000
--- a/sci-chemistry/xdsi/metadata.xml
+++ /dev/null
@@ -1,17 +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>
-XDSi offers you the possibility to process all your datasets in a given directory with minimum effort.
-* You just have to provide it with a resultdirectory and the directory where your frames are stored.
-* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
-* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
-* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
-* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
-* You can also generate plots for datasets that have been processed using XDS without XDSi
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild b/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild
deleted file mode 100644
index 6a6c9bb7ec8..00000000000
--- a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild
+++ /dev/null
@@ -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
-
-DESCRIPTION="A crude interface for running the XDS"
-HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsi"
-SRC_URI="ftp://turn5.biologie.uni-konstanz.de/pub/${PN}_${PV}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- app-text/mupdf
- dev-lang/tk
- || ( media-gfx/imagemagick media-gfx/graphicsmagick[imagemagick] )
- sci-chemistry/mosflm
- sci-chemistry/pointless
- sci-chemistry/xds-bin[smp]
- sci-visualization/gnuplot
- sci-visualization/xds-viewer"
-# Need to clarified for licensing
-# sci-chemistry/xdsstat-bin
-DEPEND=""
-
-RESTRICT="mirror bindist"
-
-S="${WORKDIR}"
-
-src_prepare() {
- epatch "${FILESDIR}"/${PV}-gentoo.patch
- sed \
- -e "s:GENTOOTEMPLATE:${EPREFIX}/usr/share/${PN}/templates:g" \
- -e "s:kpdf:mupdf:g" \
- -e "s:xds-viewer-0.6:xds-viewer:g" \
- -i ${PN} || die
-}
-
-src_install() {
- dobin ${PN}
- insinto /usr/share/${PN}/templates
- doins templates/{*.INP,bohr*,fortran,pauli,info.png,*.pck,tablesf_xdsi}
- dodoc templates/*.pdf
-}
-
-pkg_postinst() {
- elog "Documentation can be found here:"
- elog "ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/xdsi_doc_print.pdf"
-}
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest
deleted file mode 100644
index 52cb6c13f10..00000000000
--- a/sci-chemistry/xia2/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-DIST xia2-0.3.1.0.tar.bz2 3389906 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28 SHA512 cd595147164e4a281431a1d5a7298588001bb11662b517a5f95366e7b0ba4fdb33adf88dd2672c8c2ee84f48356fccb7cbd07667d5f04417a1564c7ea9f878c5 WHIRLPOOL e5493526d3075a5c61ce582a3bf42e2b4a2a73d7a28b1c8df786f0bdf5c8b1eaee986a60f379559ba556f256057794211a6c1e812b785aa9fe3179357b24b0da
-DIST xia2-0.3.1.6.tar.bz2 3464982 SHA256 fde814a763e6666a1618d01569c19d574f1bf71d754dc3960beeb13c35dd201f SHA512 d00ba2c42c88d01522859839cbee6a93662ed7f89fb146babffa1dd5d6af12ca72cc146157e0dc88bba1d6543f8509fc9027e1c42ed3ae15dd3e168ca18e1858 WHIRLPOOL ccedcbf910ec5bed637739f7519e14eb249b89ae6ccd83a632ab8571a3af62f1f168f8dfd88287fed9fe927b98230e083a0d2d4525f47bc49c4074375a46a796
-DIST xia2-0.3.1.7.tar.bz2 3650285 SHA256 54beb26396c4b6ecb343544c777c2505238385f2127482d035d2c47b24a7fcf1 SHA512 d25788e6564b0f8f4c8e6723347b7691277b01192ead8f37bc7e6d1cdfbee5b22a1329f4ff82d9287875df2de1358e738de08c6a4d19353ccb40c31343dce7bd WHIRLPOOL 1c7306a54a5262632e0319a289f57610badea3945b61653039c78772399557f895ea57e02bbff6804704df8a08f4aa35fce7746e9e03807143d0e395bcd93c75
-DIST xia2-0.3.3.1.tar.bz2 3074989 SHA256 f1bf94cd9305f768fea1b541ac53d66917126e92620263a96f9c23923ec829c4 SHA512 656abd51dc6764dee16423e2ea75f590e7a04046c5ac60ce013615c91b3fd41c0089351ceb948203643bff442753773aa639b036efc089ce26592b52b187f656 WHIRLPOOL f11a6bba359ce9f3095d2993fb331a8c70a44bc1ef31dc08663ee63372db995047d5e1b4693808a347eedeb487a1b799c4e080c05416786209f62e7b619ddec8
-DIST xia2-0.3.3.3.tar.bz2 2919316 SHA256 3cf09fcf9d2c0ea6d6cb8cf66a3c5af752b4345af6a882e2d398424cf3b4b0d3 SHA512 913b5a6e24c3c070cc36b404b987331d8de99756d0f598ef485ba5fef3b4bc42d17bf4b4e648d5c99f014872d554b94880a7542dfb9ab6969e272ec986127561 WHIRLPOOL 5f19e3b06df7d5a83d75296fe9c9956f5c0b995cd5d10f1adb66e519d9dbcdd73edcbec53acb90aede6f2955bbd88991d6283af9a3578ad26a686e8530bfdffa
-DIST xia2-0.3.4.0.tar.bz2 21404771 SHA256 20afe3d24c35446ef8c8944974d684229f053d3916e96e46766d8eefa4c5fabf SHA512 7d2444cb2acfcd2d7ca4c37d5714e7c249ffc419e9d7e1dbb33ccf18adc07f05a2b043af5aee721c64639b991dbbfd356181630229e91e0f871489870f9a8d51 WHIRLPOOL 14759e436d42e4b5ae558616d297f41eb9a345b19df4a4d02d2cb3c61937320d9161343b126b393049319ab6e37dc3890566b1bd3f2bff1a29cd108931640a90
diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
deleted file mode 100644
index 9d92af7e33c..00000000000
--- a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.0/Applications/xia2find.py
-+++ b/xia2-0.3.1.0/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
-
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
-- 'osc', 'cbf', 'mar2000']]
-+ 'osc', 'cbf', 'mar2000']
- known_sweeps = { }
-
- def is_image_name(file):
-diff --git a/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
- 'default':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'default':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
- 'depends-on':['xds', 'xscale']}
- }
-diff --git a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
- self.add_command_line(hklin)
-
- self.set_task('Rewriting reflections %s => %s' %
-- ` (os.path.split(hklin)[-1],
-- ` os.path.split(self.getHklout())[-1]))
-+ (os.path.split(hklin)[-1],
-+ os.path.split(self.getHklout())[-1]))
-
- self.start()
-
diff --git a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch
deleted file mode 100644
index 7770a53c445..00000000000
--- a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.6/Applications/xia2find.py
-+++ b/xia2-0.3.1.6/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
-
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
-- 'osc', 'cbf', 'mar2000']]
-+ 'osc', 'cbf', 'mar2000']
- known_sweeps = { }
-
- def is_image_name(file):
-diff --git a/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
- 'default':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'default':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
- 'depends-on':['xds', 'xscale']}
- }
-diff --git a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
- self.add_command_line(hklin)
-
- self.set_task('Rewriting reflections %s => %s' %
-- ` (os.path.split(hklin)[-1],
-- ` os.path.split(self.getHklout())[-1]))
-+ (os.path.split(hklin)[-1],
-+ os.path.split(self.getHklout())[-1]))
-
- self.start()
-
diff --git a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
deleted file mode 100644
index ec8ada48aad..00000000000
--- a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.7/Applications/xia2find.py b/xia2-0.3.1.7/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.7/Applications/xia2find.py
-+++ b/xia2-0.3.1.7/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
-
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
-- 'osc', 'cbf', 'mar2000']]
-+ 'osc', 'cbf', 'mar2000']
- known_sweeps = { }
-
- def is_image_name(file):
-diff --git a/xia2-0.3.1.7/Experts/DRStrategyExpert.py b/xia2-0.3.1.7/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.7/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.7/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
- 'default':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'default':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
- 'depends-on':['xds', 'xscale']}
- }
-diff --git a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
- self.add_command_line(hklin)
-
- self.set_task('Rewriting reflections %s => %s' %
-- ` (os.path.split(hklin)[-1],
-- ` os.path.split(self.getHklout())[-1]))
-+ (os.path.split(hklin)[-1],
-+ os.path.split(self.getHklout())[-1]))
-
- self.start()
-
diff --git a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
deleted file mode 100644
index 36cf6bb60d1..00000000000
--- a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.3.1/Applications/xia2find.py
-+++ b/xia2-0.3.3.1/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
-
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
-- 'osc', 'cbf', 'mar2000']]
-+ 'osc', 'cbf', 'mar2000']
- known_sweeps = { }
-
- def is_image_name(file):
-diff --git a/xia2-0.3.3.0/Experts/DRStrategyExpert.py b/xia2-0.3.3.0/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.3.1/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.3.1/Experts/DRStrategyExpert.py
-@@ -48,24 +48,24 @@ strategy_dict = {
- 'default':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'default':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':1,
- 'pipeline':{
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
- 'pointless-1.1.0.4']},
- 'mosaic':{
- 'score':2,
- 'pipeline':{
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
- 'depends-on':['xds', 'xscale']}
- }
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
- self.add_command_line(hklin)
-
- self.set_task('Rewriting reflections %s => %s' %
-- ` (os.path.split(hklin)[-1],
-- ` os.path.split(self.getHklout())[-1]))
-+ (os.path.split(hklin)[-1],
-+ os.path.split(self.getHklout())[-1]))
-
- self.start()
-
diff --git a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch
deleted file mode 100644
index 53cacbb5c68..00000000000
--- a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.3.3/Applications/xia2find.py
-+++ b/xia2-0.3.3.3/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
-
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
-- 'osc', 'cbf', 'mar2000']]
-+ 'osc', 'cbf', 'mar2000']
- known_sweeps = { }
-
- def is_image_name(file):
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
- self.add_command_line(hklin)
-
- self.set_task('Rewriting reflections %s => %s' %
-- ` (os.path.split(hklin)[-1],
-- ` os.path.split(self.getHklout())[-1]))
-+ (os.path.split(hklin)[-1],
-+ os.path.split(self.getHklout())[-1]))
-
- self.start()
-
diff --git a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
deleted file mode 100644
index 9ba4c94495e..00000000000
--- a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.4.0/Applications/xia2find.py
-+++ b/xia2-0.3.4.0/Applications/xia2find.py
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
- from Experts.FindImages import image2template_directory
-
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
-- 'osc', 'cbf', 'mar2000']]
-+ 'osc', 'cbf', 'mar2000']
- known_sweeps = { }
-
- def is_image_name(file):
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py
-@@ -49,8 +49,8 @@ def Cad(DriverType = None):
- self.add_command_line(hklin)
-
- self.set_task('Rewriting reflections %s => %s' %
-- ` (os.path.split(hklin)[-1],
-- ` os.path.split(self.getHklout())[-1]))
-+ (os.path.split(hklin)[-1],
-+ os.path.split(self.getHklout())[-1]))
-
- self.start()
-
diff --git a/sci-chemistry/xia2/metadata.xml b/sci-chemistry/xia2/metadata.xml
deleted file mode 100644
index 9ac9ffdb3a4..00000000000
--- a/sci-chemistry/xia2/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
deleted file mode 100644
index 33b3d841acf..00000000000
--- a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- >=sci-chemistry/ccp4-apps-6.1.2
- sci-chemistry/mosflm
- sci-chemistry/pointless
- >=sci-libs/ccp4-libs-6.1.2
- sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
- find . -name '*.bat' | xargs rm || die
-
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch
-}
-
-src_install() {
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
- insinto /usr/share/ccp4/XIAROOT/
- doins -r * || die
-
- # Set programs executable
-# fperms cannot handle wildcards
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
- cat >> "${T}"/23XIA <<- EOF
- XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
- XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
- XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
- PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
- EOF
-
- doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
- python_mod_optimize /usr/share/ccp4/XIAROOT
-}
-
-pkg_postrm() {
- python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild
deleted file mode 100644
index 537735e1351..00000000000
--- a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- >=sci-chemistry/ccp4-apps-6.1.2
- sci-chemistry/mosflm
- sci-chemistry/pointless
- >=sci-libs/ccp4-libs-6.1.2
- sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- find . -name '*.bat' -delete || die
-
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch
- python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
- insinto /usr/share/ccp4/XIAROOT/
- doins -r * || die
-
- # Set programs executable
-# fperms cannot handle wildcards
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
- cat >> "${T}"/23XIA <<- EOF
- XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
- XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
- XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
- PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
- EOF
-
- doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
- python_mod_optimize /usr/share/ccp4/XIAROOT
-}
-
-pkg_postrm() {
- python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
deleted file mode 100644
index 16fbf797d1b..00000000000
--- a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- >=sci-chemistry/ccp4-apps-6.1.2
- sci-chemistry/mosflm
- sci-chemistry/pointless
- >=sci-libs/ccp4-libs-6.1.2
- sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- find . -name '*.bat' -delete || die
-
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch
- python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
- insinto /usr/share/ccp4/XIAROOT/
- doins -r * || die
-
- # Set programs executable
-# fperms cannot handle wildcards
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
- cat >> "${T}"/23XIA <<- EOF
- XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
- XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
- XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
- PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
- EOF
-
- doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
- python_mod_optimize /usr/share/ccp4/XIAROOT
-}
-
-pkg_postrm() {
- python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild
deleted file mode 100644
index 26fb7d0d4c8..00000000000
--- a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- >=sci-chemistry/ccp4-apps-6.1.2
- sci-chemistry/mosflm
- sci-chemistry/pointless
- >=sci-libs/ccp4-libs-6.1.2
- sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- find . -name '*.bat' -delete || die
-
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch
- python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
- insinto /usr/share/ccp4/XIAROOT/
- doins -r * || die
-
- # Set programs executable
-# fperms cannot handle wildcards
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
- cat >> "${T}"/23XIA <<- EOF
- XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT"
- XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}"
- XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}"
- PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications"
- EOF
-
- doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
- python_mod_optimize /usr/share/ccp4/XIAROOT
- echo ""
- elog "In order to use the package, you need to"
- elog "\t source ${EPREFIX}/etc/profile"
- echo ""
-}
-
-pkg_postrm() {
- python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild
deleted file mode 100644
index 60778aa75fb..00000000000
--- a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- >=sci-chemistry/ccp4-apps-6.1.2
- sci-chemistry/mosflm
- sci-chemistry/pointless
- >=sci-libs/ccp4-libs-6.1.2
- sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- find . -name '*.bat' -delete || die
-
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch
- python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
- insinto /usr/share/ccp4/XIAROOT/
- doins -r * || die
-
- # Set programs executable
-# fperms cannot handle wildcards
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
- cat >> "${T}"/23XIA <<- EOF
- XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT"
- XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}"
- XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}"
- PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications"
- EOF
-
- doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
- python_mod_optimize /usr/share/ccp4/XIAROOT
- echo ""
- elog "In order to use the package, you need to"
- elog "\t source ${EPREFIX}/etc/profile"
- echo ""
-}
-
-pkg_postrm() {
- python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild
deleted file mode 100644
index 1d27abd355d..00000000000
--- a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit eutils python
-
-DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.ccp4.ac.uk/xia/"
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- >=sci-chemistry/ccp4-apps-6.1.2
- sci-chemistry/mosflm
- sci-chemistry/pointless
- >=sci-libs/ccp4-libs-6.1.2
- sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- find . -name '*.bat' -delete || die
-
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch
- python_convert_shebangs -r $(python_get_version) .
-}
-
-src_install() {
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
-
- insinto /usr/share/ccp4/XIAROOT/
- doins -r * || die
-
- # Set programs executable
-# fperms cannot handle wildcards
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
-
- cat >> "${T}"/23XIA <<- EOF
- XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT"
- XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}"
- XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}"
- PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications"
- EOF
-
- doenvd "${T}"/23XIA
-}
-
-pkg_postinst() {
- python_mod_optimize /usr/share/ccp4/XIAROOT
- echo ""
- elog "In order to use the package, you need to"
- elog "\t source ${EPREFIX}/etc/profile"
- echo ""
-}
-
-pkg_postrm() {
- python_mod_cleanup /usr/share/ccp4/XIAROOT
-}
diff --git a/sci-libs/balbes-db/Manifest b/sci-libs/balbes-db/Manifest
deleted file mode 100644
index 86fed7e6ab9..00000000000
--- a/sci-libs/balbes-db/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ccp4-6.1.3-balbesdb-10-11-08.tar.gz 600856059 SHA256 5606fc5e131138b56fa3a1afce014225a6c07826b99587f132f6c337585f4f0d SHA512 5b7f3b3465312da72ff4816c96244252a6f0bf039fde8ff772ea683e6317053d903cdc2b3b86b78e8edbb1c766d1b3676048ac4e7d4d0db29ed7bf62dfb00ab2 WHIRLPOOL 9a01610c9767aece4c9cc052a8aa2fd5dff9c9967f11688f5e6e206a82e2714751e086a7ddbe6a99da23b70163c7b096f57d281eebe53b8dd7cdb18faed23d63
diff --git a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild b/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild
deleted file mode 100644
index bd973c5120d..00000000000
--- a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-MY_P="ccp4-${PV}"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-VERSION="10-11-08"
-
-DESCRIPTION="The database for the BALBES automated crystallographic molecular replacement pipeline"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/"
-SRC_URI="${SRC}/${PV}/${MY_P}-${PN/-/}-${VERSION}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RDEPEND="
- >=dev-python/pyxml-0.8.4
- sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}/${MY_P}"
-
-src_install() {
- dodir /usr/share/balbes/BALBES_0.0.1
- rm -rf share/balbes/BALBES_0.0.1/dic || die
- # We don't want to wait around to copy all this, or suck up double
- # the disk space
- einfo "Installing files, which can take some time ..."
- mv "${S}"/share/balbes/BALBES_0.0.1/* "${ED}"/usr/share/balbes/BALBES_0.0.1/ || die
- # db files shouldn't be executable
- find "${ED}"/usr/share/balbes/BALBES_0.0.1/ \
- -type f \
- -exec chmod 664 '{}' \; || die
- dosym ../../ccp4/data/monomers /usr/share/balbes/BALBES_0.0.1/dic
-
- cat >> "${T}"/20balbes <<- EOF
- BALBES_ROOT="${EPREFIX}/usr/share/balbes/BALBES_0.0.1/"
- EOF
-
- doenvd "${T}"/20balbes
-}
diff --git a/sci-libs/balbes-db/metadata.xml b/sci-libs/balbes-db/metadata.xml
deleted file mode 100644
index 51fdedab1b3..00000000000
--- a/sci-libs/balbes-db/metadata.xml
+++ /dev/null
@@ -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>
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
deleted file mode 100644
index 9d3fe280636..00000000000
--- a/sci-libs/ccp4-libs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild
deleted file mode 100644
index dcd74163704..00000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild
+++ /dev/null
@@ -1,359 +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 gnuconfig multilib python-single-r1 toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# 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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="minimal"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
- ${PYTHON_DEPS}
- !<sci-chemistry/ccp4-6.1.3
- !<sci-chemistry/ccp4-apps-${PV}-r10
- app-shells/tcsh
- dev-lang/tcl:0
- >=sci-libs/cbflib-0.9.2.2
- sci-libs/fftw:2.1
- sci-libs/mmdb:0
- sci-libs/monomer-db
- sci-libs/ssm
- virtual/jpeg:0=
- virtual/lapack
- virtual/blas"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-pkg_setup() {
- fortran-2_pkg_setup
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- tc-export PKG_CONFIG RANLIB AR
-
- sed \
- -e "/^AR/s:ar:$(tc-getAR):g" \
- -i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
-
- 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 ..."
- # fix buffer overflows wrt bug 339706
- ccp_patch "${FILESDIR}"/${PV}-overflows.patch
-
- # it tries to create libdir, bindir etc on live system in configure
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- # make creation of libccif.so smooth
- ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
- # lets try to build libmmdb seperatly
- ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
- # unbundle libjpeg and cbflib
- ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
-
- # Fix missing DESTIDR
- # not installing during build
- ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
- sed \
- -e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
- -i configure || die
-
- # Fix upstreams code
- ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
- # use pkg-config to detect BLAS/LAPACK
- ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
- # proto type changing in version 0.9.2.2
- ccp_patch "${FILESDIR}"/${PV}-cbf.patch
-
- # proto type changing in version 0.9.2.2
- ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
-
- ccp_patch "${FILESDIR}"/${P}-force.patch
-
- ccp_patch "${FILESDIR}"/${P}-format-security.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- # not needed, we have it extra
- rm -rf src/rapper/{libxml2,gc7.0} || die
-
- 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' \
- -i configure || die
-
- gnuconfig_update
-
- for i in lib/DiffractionImage src/rapper src/pisa; do
- pushd ${i} > /dev/null
- sed 's:-g::g' -i configure* || die
- [[ -f configure.in ]] && mv configure.{in,ac}
- eautoreconf
- popd > /dev/null
- done
-
- ## unbundle libssm
- sed -e '/libdir/s:ssm::g' -i Makefile.in || die
- find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
-}
-
-src_configure() {
- rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
-
- # Build system is broken if we set LDFLAGS
- userldflags="${LDFLAGS}"
- export SHARED_LIB_FLAGS="${LDFLAGS}"
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "$(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 || die
-
- # 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 SHARE_LIB="\
- $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
- $(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw="${EPREFIX}/usr" \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --disable-ssm \
- --tmpdir="${TMPDIR}" \
- --bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
- --libdir="${EPREFIX}/usr/$(get_libdir)" \
- ${GENTOO_OSNAME} || die "configure failed"
-}
-
-src_compile() {
- emake DESTDIR="${D}" onlylib
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup-sh
-
- emake \
- DESTDIR="${D}" \
- includedir="${EPREFIX}/usr/include" \
- library_includedir="${EPREFIX}/usr/include" \
- install
-
- sed \
- -e "330,1000d" \
- -i "${S}"/include/ccp4.setup-sh || die
-
- sed \
- -e "378,1000d" \
- -i "${S}"/include/ccp4.setup-csh || die
-
- sed \
- -e "s:-${PV/-r*/}::g" \
- -e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
- -e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
- -e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
- -e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
- -e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
- -e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
- -e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
- -e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
- -e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
- -e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
- -e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
- -e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
- -e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
- -e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
- -e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
- -e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
- -e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
- -e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
- -e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
- -e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
- -e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
- -e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
- -e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
- -e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
- -e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
- -e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
- -e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
- -e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
- -e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
- -e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
- -e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
- -e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
- -e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
- -e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
- -e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
- -e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
- -e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
- -e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
- -e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \
- -e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \
- -e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
- -e '/CLIB=/d' \
- -e '/CLIB /d' \
- -e '/CLIBS=/d' \
- -e '/CLIBS /d' \
- -e "/alias/d" \
- -e "/CCP4_HELPDIR/d" \
- -e "/IMOSFLM_VERSION/d" \
- -i "${S}"/include/ccp4.setup* || die
-
- # Don't check for updates on every sourcing of /etc/profile
- sed -i \
- -e "s:\(eval python.*\):#\1:g" \
- "${S}"/include/ccp4.setup* || die
-
- # Libs
- for file in "${S}"/lib/*; do
- if [[ -d ${file} ]]; then
- continue
- elif [[ -x ${file} ]]; then
- dolib.so ${file}
- else
- insinto /usr/$(get_libdir)
- doins ${file}
- fi
- done
-
- prune_libtool_files
-
- sed \
- -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
- -i "${S}"/include/ccp4.setup-sh || die
-
- if ! use minimal; then
- # Setup scripts
- insinto /etc/profile.d
- newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
- newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
-
- # Data
- insinto /usr/share/ccp4/data/
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
-
- # Environment files, setup scripts, etc.
- rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
- insinto /usr/share/ccp4/
- doins -r "${S}"/include
- fi
-
- rm -f "${S}"/include/ccp4.setup* || die
-
- dodoc "${S}"/lib/data/*.doc
- newdoc "${S}"/lib/data/README DATA-README
-}
-
-pkg_postinst() {
- einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
- einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
deleted file mode 100644
index a77d9494a05..00000000000
--- a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
+++ /dev/null
@@ -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;
diff --git a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
deleted file mode 100644
index 6930fcad766..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- lib/DiffractionImage/DiffractionImageCBF.cpp | 2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..3ffee26 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -62,7 +62,7 @@ namespace DI
- int* tmpimg;
- tmpimg=new int[height*width];
- test= cbf_decompress_byte_offset ((void *)tmpimg,sizeof(int),sign,
-- nelements,&nread,0,32,sign,ccbbff,0,
-+ nelements,&nread,0,0,32,sign,ccbbff,0,
- byte_ord.c_str(),2,(size_t) width,
- (size_t) height,1,(size_t) padding);
- for(int i=0;i<height*width;i++)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
deleted file mode 100644
index ca18d75bc84..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- configure 2009-08-04 22:35:34.000000000 +0200
-+++ configure.new 2009-08-04 22:54:32.000000000 +0200
-@@ -3136,8 +3136,8 @@
- 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/$$.cache_file ) || \
-- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib
- rm -f /tmp/$$.cache_file
- if [ "X$LIBFOPTIM" != "X" ]; then
- FOPTIM=$FOPTIM_save
---- lib/ccif/configure 2009-08-04 22:35:37.000000000 +0200
-+++ lib/ccif/configure.new 2009-08-04 23:05:44.000000000 +0200
-@@ -5568,7 +5568,7 @@
- enable_shared_lib=no
- ;;
-
-- i?86-unknown-linux | i?86-pc-linux-gnu )
-+ i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu)
- if test $enable_shared_lib = yes ; then
-
- SO_LOC_VAR='LD_LIBRARY_PATH'
-@@ -5585,7 +5585,7 @@
- else
- SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
- fi
-- SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+ SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
- # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
- SHARED_LIB_EXPORTS_CMD=''
- fi
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
deleted file mode 100644
index b3147ad81bb..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
-index c23f488..b32dd1e 100755
---- a/lib/src/Makefile.in
-+++ b/lib/src/Makefile.in
-@@ -176,7 +176,7 @@ $(mmdbsrcdir)/mmdb_sbase0.h $(mmdbsrcdir)/hybrid_36.h
-
- ##### Makefile targets ######
-
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all: fsplit $(LC) $(LF) $(SCRIPT_MODULES)
- # maybe create shared library
- $(SHARE_LIB)
-
-@@ -717,10 +717,8 @@ uninstall-mmdbHEADERS:
- done
-
- install : all install-ccp4HEADERS install-mmdbHEADERS
-- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
-- $(RANLIB) $(libdir)/$(LMMDB)
- $(RANLIB) $(libdir)/$(LC)
- $(RANLIB) $(libdir)/$(LF)
- $(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea0a..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -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
-
diff --git a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
deleted file mode 100644
index 6e399764795..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- lib/ccif/configure.in 2009-06-10 13:52:59.000000000 +0200
-+++ lib/ccif/configure.in.new 2009-06-10 14:04:31.000000000 +0200
-@@ -363,7 +363,7 @@
- fi
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
- --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
-- $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+ $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
- fi
- ;;
---- lib/ccif/configure 2009-06-10 14:26:58.000000000 +0200
-+++ lib/ccif/configure.new 2009-06-10 14:43:31.000000000 +0200
-@@ -1807,7 +1807,7 @@
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
- $(SHARED_LIB_NAME) \\\
- --whole-archive $L \\\
-- -o $(SHARED_LIB_NAME)'
-+ -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD=''
- fi
- ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch b/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch
deleted file mode 100644
index 8bfa7db8cbf..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch
+++ /dev/null
@@ -1,140 +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/sci-libs/ccp4-libs/files/6.1.3-lapack.patch b/sci-libs/ccp4-libs/files/6.1.3-lapack.patch
deleted file mode 100644
index 0463b371952..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch
+++ /dev/null
@@ -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 lapack)
-+ 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}
diff --git a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
deleted file mode 100644
index 24a0a2d8e4a..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
+++ /dev/null
@@ -1,230 +0,0 @@
---- lib/src/Makefile.in 2009-03-02 17:53:15.000000000 +0100
-+++ lib/src/Makefile.in.new 2009-03-02 17:52:09.000000000 +0100
-@@ -172,9 +172,8 @@
-
- ##### Makefile targets ######
-
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all: fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
- # maybe create shared library
-- $(SHARE_LIB)
-
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
- $(AR) $(LC) $?
-@@ -186,6 +185,27 @@
- $(AR) $(LF) $(FINTERFACEOBJS)
- $(RANLIB) $@
-
-+LMMDB_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
-+ $(MMDBOBJS) && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so
-+
-+LC_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
-+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so
-+
-+LF_SO :
-+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
-+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so
-+
- # cmtz library only
-
- cmtz: $(LCMTZ)
-@@ -339,9 +356,7 @@
- fi
- cd parser.dir && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f parser.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- parser : parser.o
- $(RANLIB) $(LF)
-
-@@ -351,9 +366,7 @@
- echo ' END' >> ccplib.dir/ccplib.$F
- cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f ccplib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- ccplib : ccplib.o
- $(RANLIB) $(LF)
-
-@@ -364,9 +377,7 @@
- @$(SETFLAGS) ; \
- cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f lgglib.dir/*.o
-+ eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
- lgglib : lgglib.o
- $(RANLIB) $(LF)
-
-@@ -376,9 +387,7 @@
- echo ' END' >> plot84lib.dir/plot84lib.$F
- cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plot84lib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plot84lib : plot84lib.o
- $(RANLIB) $(LF)
-
-@@ -388,9 +397,7 @@
- echo ' END' >> libhtml.dir/libhtml.$F
- cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f libhtml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- libhtml : libhtml.o
- $(RANLIB) $(LF)
-
-@@ -400,9 +407,7 @@
- echo ' END' >> pxxml.dir/pxxml.$F
- cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f pxxml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- pxxml : pxxml.o
- $(RANLIB) $(LF)
-
-@@ -412,9 +417,7 @@
- echo ' END' >> rwbrook.dir/rwbrook.$F
- cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f rwbrook.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- rwbrook : rwbrook.o
- $(RANLIB) $(LF)
-
-@@ -424,9 +427,7 @@
- echo ' END' >> cciflib.dir/cciflib.$F
- cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f cciflib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
- cciflib : cciflib.o
- $(RANLIB) $(LF)
-
-@@ -440,9 +441,7 @@
- && $(AR) ../$(LF) *.o ; else \
- cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o ; fi
-- rm -f harvlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
- harvlib : harvlib.o
- $(RANLIB) $(LF)
-
-@@ -452,9 +451,7 @@
- echo ' END' >> keyparse.dir/keyparse.$F
- cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f keyparse.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- keyparse : keyparse.o
- $(RANLIB) $(LF)
-
-@@ -464,9 +461,7 @@
- echo ' END' >> dna_output.dir/dna_output.$F
- cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f dna_output.dir/*.o
-+ $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- dna_output : dna_output.o
- $(RANLIB) $(LF)
-
-@@ -474,10 +469,9 @@
- # for ipdisp. May be useful but could be moved.
- $(LF)(pack_c.o): $(srcdir)/pack_c.c $(srcdir)/pack_c.h
- $(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
-- $(AR) $(LF) pack_c.o && rm pack_c.o
-+ $(AR) $(LF) pack_c.o
- $(LF)(pack_f.o): $(srcdir)/pack_f.f
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
-- && rm pack_f.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
- pack: $(LF)(pack_c.o) $(LF)(pack_f.o)
- $(RANLIB) $(LF)
-
-@@ -488,9 +482,7 @@
- echo ' END' >> sorting_main.dir/sorting_main.$F
- cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f sorting_main.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- sorting_main : sorting_main.o
- $(RANLIB) $(LF)
-
-@@ -500,9 +492,7 @@
- echo ' END' >> plotsubs.dir/plotsubs.$F
- cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plotsubs.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plotsubs : plotsubs.o
- $(RANLIB) $(LF)
-
-@@ -512,9 +502,7 @@
- echo ' END' >> modlib.dir/modlib.$F
- cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f modlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- modlib : modlib.o
- $(RANLIB) $(LF)
-
-@@ -524,9 +512,7 @@
- echo ' END' >> fftlib.dir/fftlib.$F
- cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
-- && $(AR) ../$(LF) *.o
-- rm -f fftlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- fftlib : fftlib.o
- $(RANLIB) $(LF)
-
-@@ -541,9 +527,7 @@
- echo ' END' >> unix.dir/unix.f
- cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f unix.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- unix : unix.o
- $(RANLIB) $(LF)
-
diff --git a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch b/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch
deleted file mode 100644
index 6a0cb5be7c3..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch
+++ /dev/null
@@ -1,87 +0,0 @@
- include/ccp4.setup-bash | 8 --------
- include/ccp4.setup-csh | 11 -----------
- include/ccp4.setup-sh | 8 --------
- include/ccp4.setup-zsh | 10 ----------
- 4 files changed, 37 deletions(-)
-
-diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash
-index 3a67791..80aef23 100755
---- a/include/ccp4.setup-bash
-+++ b/include/ccp4.setup-bash
-@@ -185,14 +185,6 @@ else
- fi
- fi
-
--#Python path for the subprocess fixed module
--
--if [ $ccp4_first_in_path -eq 1 ]; then
-- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
--else
-- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
--fi
--
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
- setenv PLOT_COMMAND 'lp -s -dmicrolaser'
- setenv PRINT_COMMAND 'lp -s -denscript'
-diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh
-index 10d3ab8..72cc479 100755
---- a/include/ccp4.setup-csh
-+++ b/include/ccp4.setup-csh
-@@ -177,17 +177,6 @@ else
- endif
- endif
-
--#Python path for the subprocess fixed module
--if (${?PYTHONPATH}) then
-- if ($ccp4_first_in_path) then
-- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
-- else
-- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
-- endif
--else
-- setenv PYTHONPATH ${CCP4}/share/python
--endif
--
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
- setenv PLOT_COMMAND 'lp -s -dmicrolaser'
- setenv PRINT_COMMAND 'lp -s -denscript'
-diff --git a/include/ccp4.setup-sh b/include/ccp4.setup-sh
-index 2298bba..44643ab 100755
---- a/include/ccp4.setup-sh
-+++ b/include/ccp4.setup-sh
-@@ -225,14 +225,6 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
-
- ################### EXPERIENCED USERS STOP HERE #####################
-
--#Python path for the subprocess fixed module
--
--if test $ccp4_first_in_path -eq 1; then
-- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
--else
-- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
--fi
--
- ################### THE REST SHOULDN'T NEED EDITING #####################
-
- ### dbCCP4i database handler setup ###
-diff --git a/include/ccp4.setup-zsh b/include/ccp4.setup-zsh
-index 660b35b..e453db9 100755
---- a/include/ccp4.setup-zsh
-+++ b/include/ccp4.setup-zsh
-@@ -154,16 +154,6 @@ export CCP4_BIN=$CBIN
- CLASSPATH=$CBIN:$CLASSPATH # edit this if necessary
- export CLASSPATH
-
--#Python path for the subprocess fixed module
--
--if ($ccp4_first_in_path) then
-- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
-- export PYTHONPATH
--else
-- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
-- export PYTHONPATH
--fi
--
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
- export PLOT_COMMAND='lpr'
- export PRINT_COMMAND='lpr'
diff --git a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch
deleted file mode 100644
index c1479f2b115..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch
+++ /dev/null
@@ -1,142 +0,0 @@
-diff --git a/Makefile.in b/Makefile.in
-index ac552fe..fab1a87 100755
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -30,8 +30,7 @@ lapacklib : FORCE
-
- cciflib : FORCE
- if test -n "$(ccifdir)"; then cd $(ccifdir); \
-- $(MAKE) $(MFLAGS) $(MVARS); else true; fi; \
-- $(MAKE) install
-+ $(MAKE) $(MFLAGS) $(MVARS); else true; fi
-
- cctbx: FORCE
- if test -n "$(cctbxdir)"; then cd $(top_srcdir)/$(cctbxdir); \
-@@ -40,8 +39,7 @@ cctbx: FORCE
- libdir : FORCE lapacklib cciflib libccp4 clipper ssm diffractionImg
-
- libccp4: FORCE
-- cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) ; \
-- $(MAKE) install
-+ cd lib/src; $(MAKE) $(MFLAGS) $(MVARS)
-
- share : FORCE
- cd share; $(MAKE) $(MFLAGS) $(MVARS)
-@@ -51,18 +49,15 @@ ccp4i : FORCE
-
- clipper: FORCE fftw
- if test -n "$(clipperdir)"; then cd $(top_srcdir)/lib/clipper/clipper; \
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
-- $(MAKE) install
-+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
-
- diffractionImg:
- if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
-- $(MAKE) install
-+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
-
- ssm:
- if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
-- $(MAKE) install
-+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
-
- fftw: FORCE
- if test -n "$(fftwdir)"; then cd $(top_srcdir)/lib/fftw; \
-@@ -79,7 +74,7 @@ unsupported : FORCE libdir
- $(MAKE) $(MFLAGS) $(MVARS); else true; fi
-
- datadir : FORCE libdir
-- cd lib/data; $(MAKE) $(MFLAGS) $(MVARS)
-+ cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) font84.dat
-
- xwindir : FORCE libdir
- if test -f x-windows/Makefile; then cd x-windows; \
-diff --git a/lib/ccif/Makefile.in b/lib/ccif/Makefile.in
-index 975f1d9..75eda9f 100755
---- a/lib/ccif/Makefile.in
-+++ b/lib/ccif/Makefile.in
-@@ -371,11 +371,11 @@ condition.h condition_list.h: $(srcdir)/condition.list $(srcdir)/condition.awk
- #
-
- install : all
-- $(INSTALL_DATA) `pwd`/$L $(libdir)/$L
-- $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(libdir)/$(CIFMMLIB)
-- $(RANLIB) $(libdir)/$L
-+ $(RANLIB) $L
-+ $(INSTALL_DATA) `pwd`/$L $(DESTDIR)/$(libdir)/$L
-+ $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(DESTDIR)$(libdir)/$(CIFMMLIB)
- if (test -f $(SHARED_LIB_NAME)); then \
-- $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(libdir)/$(SHARED_LIB_NAME); \
-+ $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(DESTDIR)/$(libdir)/$(SHARED_LIB_NAME); \
- fi
-
- uninstall :
-diff --git a/lib/data/Makefile.in b/lib/data/Makefile.in
-index cc25c5c..017502d 100755
---- a/lib/data/Makefile.in
-+++ b/lib/data/Makefile.in
-@@ -30,9 +30,9 @@ font84.dat : fontpack $(srcdir)/font84.ascii
-
- install : all
- -rm -f font84.dat
-- test -f font84.ascii || $(LNS) $(srcdir)/font84.ascii .
-- ./fontpack
-- $(INSTALL) `pwd`/font84.dat $(libdir)/font84.dat
-+ test -f font84.ascii || $(LNS) $(DESTDIR)/$(srcdir)/font84.ascii .
-+ LD_LIBRARY_PATH="../src:../ccif" ./fontpack
-+ $(INSTALL) `pwd`/font84.dat $(DESTDIR)/$(libdir)/font84.dat
-
- uninstall :
- -rm -f $(libdir)/font84.dat
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
-index b32dd1e..6aa107d 100755
---- a/lib/src/Makefile.in
-+++ b/lib/src/Makefile.in
-@@ -685,7 +685,7 @@ testlib : $(srcdir)/testlib.f $(LF)
- #
-
- install-ccp4HEADERS: $(ccp4_HEADERS)
-- if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir $(DESTDIR)$(includedir)/ccp4; fi
-+ if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir -p $(DESTDIR)$(includedir)/ccp4; fi
- @list='$(ccp4_HEADERS)'; for p in $$list; do \
- if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
- f="`echo $$p | sed -e 's|^.*/||'`"; \
-@@ -716,11 +716,11 @@ uninstall-mmdbHEADERS:
- rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
- done
-
--install : all install-ccp4HEADERS install-mmdbHEADERS
-- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
-- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
-- $(RANLIB) $(libdir)/$(LC)
-- $(RANLIB) $(libdir)/$(LF)
-+install : all install-ccp4HEADERS
-+ $(RANLIB) $(LC)
-+ $(RANLIB) $(LF)
-+ $(INSTALL_DATA) `pwd`/$(LC) $(DESTDIR)/$(libdir)/$(LC)
-+ $(INSTALL_DATA) `pwd`/$(LF) $(DESTDIR)/$(libdir)/$(LF)
- $(SHARE_INST)
-
- uninstall : uninstall-ccp4HEADERS uninstall-mmdbHEADERS
-diff --git a/lib/ssm/Makefile.in b/lib/ssm/Makefile.in
-index 27d3aa2..0a14fe5 100755
---- a/lib/ssm/Makefile.in
-+++ b/lib/ssm/Makefile.in
-@@ -375,12 +375,12 @@ distclean-libtool:
- uninstall-info-am:
- install-library_includeHEADERS: $(library_include_HEADERS)
- @$(NORMAL_INSTALL)
-- test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)"
-+ test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)/ssm"
- @list='$(library_include_HEADERS)'; for p in $$list; do \
- if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
- f=$(am__strip_dir) \
-- echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/$$f'"; \
-- $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/$$f"; \
-+ echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/ssm/$$f'"; \
-+ $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/ssm/$$f"; \
- done
-
- uninstall-library_includeHEADERS:
diff --git a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch b/sci-libs/ccp4-libs/files/6.1.3-overflows.patch
deleted file mode 100644
index 0e3c941d1cc..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-Fix overflows and array subscript above array bounds
-
-http://bugs.gentoo.org/show_bug.cgi?id=339706
-
---- ccp4-6.1.3/lib/ccif/f_interface.c
-+++ ccp4-6.1.3/lib/ccif/f_interface.c
-@@ -926,7 +926,7 @@
- #endif
-
- {
-- char logname_c[81];
-+ char logname_c[MAXFLEN];
- size_t Length;
- int unit;
- CIF_FILE_LIST file_list_entry;
-@@ -4064,7 +4064,7 @@
- #endif
-
- {
-- char lognam_c[81], *blknam_c;
-+ char lognam_c[MAXFLEN], *blknam_c;
- size_t loglen, blklen;
- int i, j, new;
-
---- ccp4-6.1.3/lib/src/ccp4_diskio_f.c
-+++ ccp4-6.1.3/lib/src/ccp4_diskio_f.c
-@@ -705,7 +705,7 @@
- log_name = strdup("diskio.dft");
- if (!(file_name = getenv(log_name)))
- file_name = log_name;
-- for ( *istrm = 1; *istrm == MAXFILES; *istrm++)
-+ for ( *istrm = 1; *istrm < MAXFILES; *istrm++)
- if (!strcmp(file_name,_ioChannels[*istrm]->iobj->name)) break;
- }
- if (*istrm != MAXFILES) {
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch
deleted file mode 100644
index 4271d5b76ae..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch
+++ /dev/null
@@ -1,367 +0,0 @@
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..602e35f 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -6,10 +6,10 @@
- // images.
-
- #include "DiffractionImage.h"
--#include "cbf.h"
--#include "cbf_simple.h"
--#include "cbf_string.h"
--#include "cbf_byte_offset.h"
-+#include <cbflib/cbf.h>
-+#include <cbflib/cbf_simple.h>
-+#include <cbflib/cbf_string.h>
-+#include <cbflib/cbf_byte_offset.h>
-
-
- using namespace std;
-diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am
-index fedb7ac..89a048e 100755
---- a/lib/DiffractionImage/MAR/Makefile.am
-+++ b/lib/DiffractionImage/MAR/Makefile.am
-@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu
-
- noinst_LTLIBRARIES = libmar.la
-
--AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include
-+AM_CPPFLAGS =
-
- libmar_la_SOURCES = mar300_header.c \
- mar345_header.c \
-@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \
- utils.c \
- pck.c
-
--libmar_la_LDFLAGS = -static
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
-index d3f4212..2c37108 100755
---- a/lib/DiffractionImage/MAR/marcif.c
-+++ b/lib/DiffractionImage/MAR/marcif.c
-@@ -31,8 +31,7 @@
- #include "marcif_header.h"
- #include "mar345_header.h"
-
--#include <cbf.h>
--#include <img.h>
-+#include <cbflib/cbf.h>
-
- #define printe(x) printf("%s: %s: %s\n",prg,f,x)
- #undef cbf_failnez
-diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am
-index 189a1d7..6652576 100755
---- a/lib/DiffractionImage/Makefile.am
-+++ b/lib/DiffractionImage/Makefile.am
-@@ -1,7 +1,9 @@
- AUTOMAKE_OPTIONS = gnu
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg
-+SUBDIRS = Bruker MAR Rigaku
-
--AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
-+SYSLIBS = -ljpeg -lcbf
-+
-+AM_CPPFLAGS =-I./MAR
- lib_LTLIBRARIES = libDiffImage.la
-
- if WANT_PYTHONMOD
-@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
- Profile.cpp \
- Peak.cpp \
- dps_peaksearch_cn.c
--libDiffImage_la_LDFLAGS = -static
-+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libDiffImage_la_LIBADD = $(SYSLIBS) \
-+ ./MAR/libmar.la ./Bruker/libbruker.la \
-+ ./Rigaku/librigaku.la
-
--libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
- libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp
--libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-- --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \
-+ libDiffImage.la \
-+ ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
-
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
- lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp
--lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-- --no-whole-archive -rpath '$(libdir)'
-+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \
-+ ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
-
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
- libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp
--libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-- --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImaJ_la_LIBADD = libDiffImage.la \
-+ ./Bruker/libbruker.la $(SYSLIBS) \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
-
- bin_PROGRAMS = automask diffdump printpeaks diff2jpeg
--automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
- automask_SOURCES = automask.cpp
--diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
- diffdump_SOURCES = diffdump.cpp
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS)
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
- printpeaks_SOURCES = printpeaks.cpp
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
- diff2jpeg_SOURCES = diff2jpeg.cpp
-+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS)
-
- install-data-local:
- @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC}
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
-index 3fb5784..fdf9683 100755
---- a/lib/DiffractionImage/configure
-+++ b/lib/DiffractionImage/configure
-@@ -21768,7 +21768,7 @@ _ACEOF
- fi
-
-
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
-
-
- cat >confcache <<\_ACEOF
-@@ -22407,12 +22407,9 @@ do
- case $ac_config_target in
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
-- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
- "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
- "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
- "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
-- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
-
- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
-index 7f54b4b..16efc64 100755
---- a/lib/DiffractionImage/configure.in
-+++ b/lib/DiffractionImage/configure.in
-@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then
- HAVE_PYTHON=1
- CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}"
- ])
-+ PYLIB="-lpython${PYTHON_VER}"
-+ AC_SUBST(PYLIB)
- fi
- AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1])
-
-@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
- AC_CHECK_LIB([m], [sqrt])
-
- AC_CONFIG_FILES([Makefile
-- CBFlib/Makefile
-- CBFlib/src/Makefile
- MAR/Makefile
- Rigaku/Makefile
-- Bruker/Makefile
-- jpg/Makefile])
-+ Bruker/Makefile])
-
- AC_OUTPUT
-diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am
-index e9554e1..a3ba33d 100755
---- a/lib/ssm/Makefile.am
-+++ b/lib/ssm/Makefile.am
-@@ -1,7 +1,11 @@
-+ACLOCAL_AMFLAGS = -I macros
- #libtool
- lib_LTLIBRARIES = libssm.la
-+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libssm_la_CFLAGS = @MMDB_CFLAGS@
- libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \
- ssm_align.cpp ss_graph.cpp
-+libssm_la_LIBADD = @MMDB_LIBS@
-
- #non libtool
- #lib_LIBRARIES = libssm.a
-@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp
-
- bin_PROGRAMS = superpose
-
--INCLUDES = $(MMDB_CXXFLAGS)
--
--AM_LDFLAGS = $(MMDB_LIBS)
-+INCLUDES = @MMDB_CFLAGS@
-
- EXTRA_DIST = macros/mmdb.m4
-
--superpose_LDADD = libssm.la
-+superpose_LDADD = libssm.la @MMDB_LIBS@
-
- libssm_a_AR = $(AR) $(AR_FLAGS)
-diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac
-index 783cb46..d637d11 100755
---- a/lib/ssm/configure.ac
-+++ b/lib/ssm/configure.ac
-@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug,
- [ac_cv_enable_debug=no ] )
-
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
-- [ if test "x$mmdb_prefix" != x ; then
-- if test "x$ac_MMDB_CXXFLAGS" != x ; then
-- case "$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/lib/src/mmdb -I$mmdb_prefix/include/mmdb"
-- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb"
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
-- fi
-- else
-- AC_MSG_WARN([mmdb not found])
-- fi
-- ]
--)
-+
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
-
- # Checks for typedefs, structures, and compiler characteristics.
- #
-@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- # test for function in m
- AC_CHECK_LIB([m], [sqrt])
-
-+
- AC_SUBST(AR_FLAGS)
- AC_SUBST(superpose_LDFLAGS)
- AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes)
-diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am
-index 094fd6b..922a131 100755
---- a/src/pisa/Makefile.am
-+++ b/src/pisa/Makefile.am
-@@ -1,3 +1,4 @@
-+ACLOCAL_AMFLAGS = -I macros
- SUBDIRS = molref pisastore sbase
-
- pkgdatadir = $(datadir)/pisa
-@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp
-
- bin_PROGRAMS = pisa
-
--INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS)
-+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS)
-
--pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS)
-+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@
-
- EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
-index 81afdda..4f99df6 100755
---- a/src/pisa/configure.ac
-+++ b/src/pisa/configure.ac
-@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- AC_CHECK_LIB([m], [sqrt])
-
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
-- [ if test "x$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 $MMDB_CXXFLAGS])
-- fi
-- else
-- AC_MSG_ERROR([mmdb not found])
-- fi
-- ]
--)
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
-
- ac_saved_CXXFLAGS=$CXXFLAGS
- ac_saved_LIBS=$LIBS
--CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
-+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS"
- LIBS="$MMDB_LIBS $LIBS"
- AM_PATH_SSM(,
- [ if test "x$ssm_prefix" != x ; then
-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..11b63ec 100755
---- a/src/rapper/configure.ac
-+++ b/src/rapper/configure.ac
-@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
-
- AC_SUBST(rapper_LDFLAGS)
-
--AC_CONFIG_SUBDIRS([gc7.0 libxml2])
-+#AC_CONFIG_SUBDIRS([gc7.0 libxml2])
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch
deleted file mode 100644
index c787df903df..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch
+++ /dev/null
@@ -1,395 +0,0 @@
- lib/DiffractionImage/DiffractionImageCBF.cpp | 8 ++--
- lib/DiffractionImage/MAR/Makefile.am | 3 +-
- lib/DiffractionImage/MAR/marcif.c | 3 +-
- lib/DiffractionImage/Makefile.am | 68 +++++++++++++++-----------
- lib/DiffractionImage/configure | 5 +--
- lib/DiffractionImage/configure.in | 7 +--
- lib/src/Makefile.in | 2 +-
- lib/ssm/Makefile.am | 10 ++--
- lib/ssm/configure.ac | 30 ++---------
- src/pisa/Makefile.am | 5 +-
- src/pisa/configure.ac | 30 ++----------
- src/rapper/Makefile.am | 2 +-
- src/rapper/configure.ac | 2 +-
- 13 files changed, 70 insertions(+), 105 deletions(-)
-
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..602e35f 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -6,10 +6,10 @@
- // images.
-
- #include "DiffractionImage.h"
--#include "cbf.h"
--#include "cbf_simple.h"
--#include "cbf_string.h"
--#include "cbf_byte_offset.h"
-+#include <cbflib/cbf.h>
-+#include <cbflib/cbf_simple.h>
-+#include <cbflib/cbf_string.h>
-+#include <cbflib/cbf_byte_offset.h>
-
-
- using namespace std;
-diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am
-index fedb7ac..89a048e 100755
---- a/lib/DiffractionImage/MAR/Makefile.am
-+++ b/lib/DiffractionImage/MAR/Makefile.am
-@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu
-
- noinst_LTLIBRARIES = libmar.la
-
--AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include
-+AM_CPPFLAGS =
-
- libmar_la_SOURCES = mar300_header.c \
- mar345_header.c \
-@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \
- utils.c \
- pck.c
-
--libmar_la_LDFLAGS = -static
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
-index d3f4212..2c37108 100755
---- a/lib/DiffractionImage/MAR/marcif.c
-+++ b/lib/DiffractionImage/MAR/marcif.c
-@@ -31,8 +31,7 @@
- #include "marcif_header.h"
- #include "mar345_header.h"
-
--#include <cbf.h>
--#include <img.h>
-+#include <cbflib/cbf.h>
-
- #define printe(x) printf("%s: %s: %s\n",prg,f,x)
- #undef cbf_failnez
-diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am
-index 189a1d7..6652576 100755
---- a/lib/DiffractionImage/Makefile.am
-+++ b/lib/DiffractionImage/Makefile.am
-@@ -1,7 +1,9 @@
- AUTOMAKE_OPTIONS = gnu
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg
-+SUBDIRS = Bruker MAR Rigaku
-
--AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
-+SYSLIBS = -ljpeg -lcbf
-+
-+AM_CPPFLAGS =-I./MAR
- lib_LTLIBRARIES = libDiffImage.la
-
- if WANT_PYTHONMOD
-@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
- Profile.cpp \
- Peak.cpp \
- dps_peaksearch_cn.c
--libDiffImage_la_LDFLAGS = -static
-+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libDiffImage_la_LIBADD = $(SYSLIBS) \
-+ ./MAR/libmar.la ./Bruker/libbruker.la \
-+ ./Rigaku/librigaku.la
-
--libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
- libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp
--libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-- --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \
-+ libDiffImage.la \
-+ ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
-
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
- lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp
--lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-- --no-whole-archive -rpath '$(libdir)'
-+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \
-+ ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
-
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
- libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp
--libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-- --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImaJ_la_LIBADD = libDiffImage.la \
-+ ./Bruker/libbruker.la $(SYSLIBS) \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
-
- bin_PROGRAMS = automask diffdump printpeaks diff2jpeg
--automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
- automask_SOURCES = automask.cpp
--diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
- diffdump_SOURCES = diffdump.cpp
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS)
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
- printpeaks_SOURCES = printpeaks.cpp
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
- diff2jpeg_SOURCES = diff2jpeg.cpp
-+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS)
-
- install-data-local:
- @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC}
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
-index 3fb5784..fdf9683 100755
---- a/lib/DiffractionImage/configure
-+++ b/lib/DiffractionImage/configure
-@@ -21768,7 +21768,7 @@ _ACEOF
- fi
-
-
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
-
-
- cat >confcache <<\_ACEOF
-@@ -22407,12 +22407,9 @@ do
- case $ac_config_target in
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
-- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
- "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
- "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
- "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
-- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
-
- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
-index 7f54b4b..16efc64 100755
---- a/lib/DiffractionImage/configure.in
-+++ b/lib/DiffractionImage/configure.in
-@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then
- HAVE_PYTHON=1
- CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}"
- ])
-+ PYLIB="-lpython${PYTHON_VER}"
-+ AC_SUBST(PYLIB)
- fi
- AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1])
-
-@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
- AC_CHECK_LIB([m], [sqrt])
-
- AC_CONFIG_FILES([Makefile
-- CBFlib/Makefile
-- CBFlib/src/Makefile
- MAR/Makefile
- Rigaku/Makefile
-- Bruker/Makefile
-- jpg/Makefile])
-+ Bruker/Makefile])
-
- AC_OUTPUT
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
-index c23f488..9579b3b 100755
---- a/lib/src/Makefile.in
-+++ b/lib/src/Makefile.in
-@@ -659,7 +659,7 @@ csymlib.o: $(srcdir)/csymlib.c $(srcdir)/csymlib.h
- csymlib_f.o: $(srcdir)/csymlib_f.c $(srcdir)/csymlib.h
- ccp4_unitcell.o: $(srcdir)/ccp4_unitcell.c $(srcdir)/ccp4_unitcell.h
- ccp4_unitcell_f.o: $(srcdir)/ccp4_unitcell_f.c $(srcdir)/ccp4_unitcell.h
--hybrid_36_f.o: $(srcdir)/hybrid_36_f.c $(mmdbsrcdir)/hybrid_36.h
-+hybrid_36_f.o: $(srcdir)/hybrid_36_f.c
- cvecmat.o: $(srcdir)/cvecmat.c $(srcdir)/cvecmat.h
- cmtzlib_python_wrap.o: $(srcdir)/cmtzlib_python_wrap.c $(srcdir)/mtzdata.h
- cmaplib_python_wrap.o: $(srcdir)/cmaplib_python_wrap.c
-diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am
-index e9554e1..a3ba33d 100755
---- a/lib/ssm/Makefile.am
-+++ b/lib/ssm/Makefile.am
-@@ -1,7 +1,11 @@
-+ACLOCAL_AMFLAGS = -I macros
- #libtool
- lib_LTLIBRARIES = libssm.la
-+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libssm_la_CFLAGS = @MMDB_CFLAGS@
- libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \
- ssm_align.cpp ss_graph.cpp
-+libssm_la_LIBADD = @MMDB_LIBS@
-
- #non libtool
- #lib_LIBRARIES = libssm.a
-@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp
-
- bin_PROGRAMS = superpose
-
--INCLUDES = $(MMDB_CXXFLAGS)
--
--AM_LDFLAGS = $(MMDB_LIBS)
-+INCLUDES = @MMDB_CFLAGS@
-
- EXTRA_DIST = macros/mmdb.m4
-
--superpose_LDADD = libssm.la
-+superpose_LDADD = libssm.la @MMDB_LIBS@
-
- libssm_a_AR = $(AR) $(AR_FLAGS)
-diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac
-index 783cb46..d637d11 100755
---- a/lib/ssm/configure.ac
-+++ b/lib/ssm/configure.ac
-@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug,
- [ac_cv_enable_debug=no ] )
-
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
-- [ if test "x$mmdb_prefix" != x ; then
-- if test "x$ac_MMDB_CXXFLAGS" != x ; then
-- case "$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/lib/src/mmdb -I$mmdb_prefix/include/mmdb"
-- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb"
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
-- fi
-- else
-- AC_MSG_WARN([mmdb not found])
-- fi
-- ]
--)
-+
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
-
- # Checks for typedefs, structures, and compiler characteristics.
- #
-@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- # test for function in m
- AC_CHECK_LIB([m], [sqrt])
-
-+
- AC_SUBST(AR_FLAGS)
- AC_SUBST(superpose_LDFLAGS)
- AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes)
-diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am
-index 094fd6b..922a131 100755
---- a/src/pisa/Makefile.am
-+++ b/src/pisa/Makefile.am
-@@ -1,3 +1,4 @@
-+ACLOCAL_AMFLAGS = -I macros
- SUBDIRS = molref pisastore sbase
-
- pkgdatadir = $(datadir)/pisa
-@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp
-
- bin_PROGRAMS = pisa
-
--INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS)
-+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS)
-
--pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS)
-+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@
-
- EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
-index 81afdda..4f99df6 100755
---- a/src/pisa/configure.ac
-+++ b/src/pisa/configure.ac
-@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- AC_CHECK_LIB([m], [sqrt])
-
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
-- [ if test "x$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 $MMDB_CXXFLAGS])
-- fi
-- else
-- AC_MSG_ERROR([mmdb not found])
-- fi
-- ]
--)
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
-
- ac_saved_CXXFLAGS=$CXXFLAGS
- ac_saved_LIBS=$LIBS
--CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
-+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS"
- LIBS="$MMDB_LIBS $LIBS"
- AM_PATH_SSM(,
- [ if test "x$ssm_prefix" != x ; then
-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..11b63ec 100755
---- a/src/rapper/configure.ac
-+++ b/src/rapper/configure.ac
-@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
-
- AC_SUBST(rapper_LDFLAGS)
-
--AC_CONFIG_SUBDIRS([gc7.0 libxml2])
-+#AC_CONFIG_SUBDIRS([gc7.0 libxml2])
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch
deleted file mode 100644
index 96978320163..00000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch
+++ /dev/null
@@ -1,203 +0,0 @@
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..602e35f 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -6,10 +6,10 @@
- // images.
-
- #include "DiffractionImage.h"
--#include "cbf.h"
--#include "cbf_simple.h"
--#include "cbf_string.h"
--#include "cbf_byte_offset.h"
-+#include <cbflib/cbf.h>
-+#include <cbflib/cbf_simple.h>
-+#include <cbflib/cbf_string.h>
-+#include <cbflib/cbf_byte_offset.h>
-
-
- using namespace std;
-diff --git a/lib/DiffractionImage/MAR/Makefile.in b/lib/DiffractionImage/MAR/Makefile.in
-index 4264696..00c4d8d 100755
---- a/lib/DiffractionImage/MAR/Makefile.in
-+++ b/lib/DiffractionImage/MAR/Makefile.in
-@@ -174,7 +174,7 @@ top_builddir = @top_builddir@
- top_srcdir = @top_srcdir@
- AUTOMAKE_OPTIONS = gnu
- noinst_LTLIBRARIES = libmar.la
--AM_CPPFLAGS = -I../CBFlib/src -I../CBFlib/include
-+AM_CPPFLAGS =
- libmar_la_SOURCES = mar300_header.c \
- mar345_header.c \
- marcif.c \
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
-index d3f4212..2c37108 100755
---- a/lib/DiffractionImage/MAR/marcif.c
-+++ b/lib/DiffractionImage/MAR/marcif.c
-@@ -31,8 +31,7 @@
- #include "marcif_header.h"
- #include "mar345_header.h"
-
--#include <cbf.h>
--#include <img.h>
-+#include <cbflib/cbf.h>
-
- #define printe(x) printf("%s: %s: %s\n",prg,f,x)
- #undef cbf_failnez
-diff --git a/lib/DiffractionImage/Makefile.in b/lib/DiffractionImage/Makefile.in
-index 8197956..807cf25 100755
---- a/lib/DiffractionImage/Makefile.in
-+++ b/lib/DiffractionImage/Makefile.in
-@@ -106,23 +106,19 @@ PROGRAMS = $(bin_PROGRAMS)
- am_automask_OBJECTS = automask.$(OBJEXT)
- automask_OBJECTS = $(am_automask_OBJECTS)
- automask_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
-- ./jpg/libjpeg.la
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
- am_diff2jpeg_OBJECTS = diff2jpeg.$(OBJEXT)
- diff2jpeg_OBJECTS = $(am_diff2jpeg_OBJECTS)
- diff2jpeg_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
-- ./jpg/libjpeg.la
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
- am_diffdump_OBJECTS = diffdump.$(OBJEXT)
- diffdump_OBJECTS = $(am_diffdump_OBJECTS)
- diffdump_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
-- ./jpg/libjpeg.la
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
- am_printpeaks_OBJECTS = printpeaks.$(OBJEXT)
- printpeaks_OBJECTS = $(am_printpeaks_OBJECTS)
- printpeaks_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
-- ./jpg/libjpeg.la
-+ ./MAR/libmar.la ./Rigaku/librigaku.la
- DEFAULT_INCLUDES = -I.@am__isrc@
- depcomp = $(SHELL) $(top_srcdir)/depcomp
- am__depfiles_maybe = depfiles
-@@ -284,8 +280,8 @@ target_alias = @target_alias@
- top_builddir = @top_builddir@
- top_srcdir = @top_srcdir@
- AUTOMAKE_OPTIONS = gnu
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg
--AM_CPPFLAGS = -I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
-+SUBDIRS = Bruker MAR Rigaku
-+AM_CPPFLAGS = -I./MAR
- lib_LTLIBRARIES = libDiffImage.la $(am__append_1) $(am__append_2) \
- $(am__append_3)
- libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
-@@ -311,50 +307,50 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
- dps_peaksearch_cn.c
-
- libDiffImage_la_LDFLAGS = -static
--libDiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImage_la_DEPENDENCIES = libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
-
- libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp
- libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-+ -lcbf ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
- --no-whole-archive -rpath '$(libdir)'
-
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
-
- lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp
- lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-+ -lcbf ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
- --no-whole-archive -rpath '$(libdir)'
-
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \
- ./Bruker/libbruker.la ./MAR/libmar.la \
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+ ./Rigaku/librigaku.la
-
- libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp
- libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-+ -lcbf ./Bruker/libbruker.la \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
- --no-whole-archive -rpath '$(libdir)'
-
--automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
-
- automask_SOURCES = automask.cpp
--diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
-
- diffdump_SOURCES = diffdump.cpp
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
-
- printpeaks_SOURCES = printpeaks.cpp
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
-
- diff2jpeg_SOURCES = diff2jpeg.cpp
- all: all-recursive
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
-index 3fb5784..fdf9683 100755
---- a/lib/DiffractionImage/configure
-+++ b/lib/DiffractionImage/configure
-@@ -21768,7 +21768,7 @@ _ACEOF
- fi
-
-
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
-
-
- cat >confcache <<\_ACEOF
-@@ -22407,12 +22407,9 @@ do
- case $ac_config_target in
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
-- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
- "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
- "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
- "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
-- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
-
- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
-index 7f54b4b..69b10e1 100755
---- a/lib/DiffractionImage/configure.in
-+++ b/lib/DiffractionImage/configure.in
-@@ -65,11 +65,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
- AC_CHECK_LIB([m], [sqrt])
-
- AC_CONFIG_FILES([Makefile
-- CBFlib/Makefile
-- CBFlib/src/Makefile
- MAR/Makefile
- Rigaku/Makefile
-- Bruker/Makefile
-- jpg/Makefile])
-+ Bruker/Makefile])
-
- AC_OUTPUT
diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch
deleted file mode 100644
index 367d53e3e4f..00000000000
--- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- Makefile.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/Makefile.in b/Makefile.in
-index 60033eb..13ddbd0 100755
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -53,7 +53,7 @@ clipper: FORCE fftw
-
- diffractionImg:
- if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
-+ $(MAKE) $(MFLAGS) $(MVARS); fi
-
- ssm:
- if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \
diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch
deleted file mode 100644
index caf62bb652e..00000000000
--- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- lib/DiffractionImage/DiffractionImagePythonInterface.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp
-index f729fc5..4c24e82 100755
---- a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp
-+++ b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp
-@@ -867,7 +867,7 @@ SWIG_Python_AddErrorMsg(const char* mesg)
- Py_DECREF(old_str);
- Py_DECREF(value);
- } else {
-- PyErr_Format(PyExc_RuntimeError, mesg);
-+ PyErr_Format(PyExc_RuntimeError, "%s", mesg);
- }
- }
-
diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml
deleted file mode 100644
index c0432fefe85..00000000000
--- a/sci-libs/ccp4-libs/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- <name>Justin Lecher (jlec)</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild b/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild
deleted file mode 100644
index 1757c6960b8..00000000000
--- a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils eutils flag-o-matic
-
-MY_PV=${PV/_p/-}
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Object-oriented libraries for crystallographic data and crystallographic computation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html"
-SRC_URI="http://www.ysbl.york.ac.uk/~cowtan/clipper/${MY_P}-ac.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="debug static-libs"
-
-RDEPEND="
- sci-libs/ccp4-libs
- sci-libs/fftw
- sci-libs/mmdb"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${PN}-2.1
-
-PATCHES=(
- "${FILESDIR}"/20091215-missing-var.patch
- "${FILESDIR}"/${PV}-makefile.patch
- "${FILESDIR}"/${P}-outofsourcebuild.patch
- )
-
-src_configure() {
- # Recommended on ccp4bb/coot ML to fix crashes when calculating maps
- # on 64-bit systems
- append-flags -fno-strict-aliasing
-
- local myeconfargs=(
- --enable-ccp4
- --enable-cif
- --enable-cns
- --enable-contrib
- --enable-minimol
- --enable-mmdb
- --enable-phs
- --with-mmdb="${EPREFIX}/usr"
- $(use_enable debug)
- )
- autotools-utils_src_configure
-}
-
-src_test() {
- emake -C "${AUTOTOOLS_BUILD_DIR}"/examples check
-}
diff --git a/sci-libs/coot-data/coot-data-2-r1.ebuild b/sci-libs/coot-data/coot-data-2-r1.ebuild
deleted file mode 100644
index 1640d461d01..00000000000
--- a/sci-libs/coot-data/coot-data-2-r1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-#SRC_URI="http://lmb.bioch.ox.ac.uk/coot/software/dependencies/reference-structures.tar.gz"
-SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"
-
-src_install() {
- insinto /usr/share/coot
- doins -r reference-structures
-
- # Coot looks in the wrong spot for the monomer library
- # Listens to ccp4's CCP4_LIB rather than CLIBD_MON
- cat >> "${T}"/coot <<- EOF
- COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/"
- COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/"
- EOF
-
- newenvd "${T}"/coot 20coot
-}
diff --git a/sci-libs/coot-data/coot-data-2.ebuild b/sci-libs/coot-data/coot-data-2.ebuild
deleted file mode 100644
index 2b7d33178ad..00000000000
--- a/sci-libs/coot-data/coot-data-2.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-#SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz"
-SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"
-
-src_install() {
- insinto /usr/share/coot
- doins -r reference-structures || die
-
- # Coot looks in the wrong spot for the monomer library
- # Listens to ccp4's CCP4_LIB rather than CLIBD_MON
- cat >> "${T}"/coot <<- EOF
- COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/"
- COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/"
- EOF
-
- newenvd "${T}"/coot 20coot || die
-}
diff --git a/sci-libs/mmdb/mmdb-1.24.ebuild b/sci-libs/mmdb/mmdb-1.24.ebuild
deleted file mode 100644
index f44a3ae67ee..00000000000
--- a/sci-libs/mmdb/mmdb-1.24.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit autotools-utils
-
-DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="
- http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz
- https://launchpad.net/mmdb/1.23/${PV}/+download/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-DEPEND="!<sci-libs/ccp4-libs-6.1.3"
-RDEPEND=""
-
-src_install() {
- autotools-utils_src_install
-
- # create missing mmdb.pc
- cat >> "${T}"/mmdb.pc <<- EOF
- prefix=${EPREFIX}/usr
- exec_prefix=${EPREFIX}/usr
- libdir=${EPREFIX}/usr/$(get_libdir)
- includedir=${EPREFIX}/usr/include/mmdb
-
- Name: ${PN}
- Description: Macromolecular coordinate library
- Version: ${PV}
- Requires:
- Conflicts:
- Libs: -L"${EPREFIX}/usr/$(get_libdir)" -lmmdb
- Cflags: -I"${EPREFIX}/usr/include/mmdb"
-
- EOF
-
- insinto /usr/$(get_libdir)/pkgconfig
- doins "${T}"/mmdb.pc
-}
diff --git a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
index 8cae49d97a8..6389827c63e 100644
--- a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
+++ b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
@@ -15,7 +15,4 @@ SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
IUSE="static-libs"
-DEPEND="!<sci-libs/ccp4-libs-6.1.3"
-RDEPEND=""
-
PATCHES=( "${FILESDIR}"/${P}-include-path.patch )
diff --git a/sci-libs/mmdb/mmdb-1.25.5.ebuild b/sci-libs/mmdb/mmdb-1.25.5.ebuild
deleted file mode 100644
index 9be8cec5a89..00000000000
--- a/sci-libs/mmdb/mmdb-1.25.5.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-DEPEND="!<sci-libs/ccp4-libs-6.1.3"
-RDEPEND=""
diff --git a/sci-libs/monomer-db/monomer-db-0.090729.ebuild b/sci-libs/monomer-db/monomer-db-0.090729.ebuild
deleted file mode 100644
index 6513cbc0404..00000000000
--- a/sci-libs/monomer-db/monomer-db-0.090729.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="Monomer library used for macromolecular structure building and refinement"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-# SRC_URI="http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_dictionary.tar.gz"
-SRC_URI="https://dev.gentoo.org/~jlec/science-dist/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<sci-chemistry/ccp4-6.1.3"
-DEPEND="${RDEPEND}"
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"/dic
-
-src_install() {
- insinto /usr/share/ccp4/data/monomers/
- for i in {a..z} {1..9} *list *.cif *.txt; do
- doins -r ${i}
- done
- docinto html
- dodoc *.html
-}
diff --git a/sci-libs/ssm/ssm-1.1.ebuild b/sci-libs/ssm/ssm-1.1.ebuild
deleted file mode 100644
index d247077313d..00000000000
--- a/sci-libs/ssm/ssm-1.1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="A macromolecular coordinate superposition library"
-HOMEPAGE="https://launchpad.net/ssm"
-SRC_URI="https://launchpad.net/${PN}/trunk/${PV}/+download/${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-DEPEND=">=sci-libs/mmdb-1.23:0"
-RDEPEND="${DEPEND}
- !<sci-libs/ccp4-libs-6.1.3-r10"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-mmdb.patch \
- "${FILESDIR}"/${P}-pc.patch
- eautoreconf
-}
-
-src_configure() {
- econf $(use_enable static-libs static)
-}
diff --git a/sys-apps/coreutils/coreutils-8.20.ebuild b/sys-apps/coreutils/coreutils-8.20.ebuild
index 48946b21875..96434764771 100644
--- a/sys-apps/coreutils/coreutils-8.20.ebuild
+++ b/sys-apps/coreutils/coreutils-8.20.ebuild
@@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} )
!sys-apps/mktemp
!<app-forensics/tct-1.18-r1
!<net-fs/netatalk-2.0.3-r4
- !<sci-chemistry/ccp4-6.1.1"
+"
DEPEND="${RDEPEND}
static? ( ${LIB_DEPEND} )
app-arch/xz-utils"
diff --git a/sys-apps/coreutils/coreutils-8.21.ebuild b/sys-apps/coreutils/coreutils-8.21.ebuild
index 92fccdf5c8a..fdaa4c2de1c 100644
--- a/sys-apps/coreutils/coreutils-8.21.ebuild
+++ b/sys-apps/coreutils/coreutils-8.21.ebuild
@@ -36,7 +36,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} )
!sys-apps/mktemp
!<app-forensics/tct-1.18-r1
!<net-fs/netatalk-2.0.3-r4
- !<sci-chemistry/ccp4-6.1.1"
+"
DEPEND="${RDEPEND}
static? ( ${LIB_DEPEND} )
app-arch/xz-utils"
diff --git a/sys-apps/coreutils/coreutils-8.22-r1.ebuild b/sys-apps/coreutils/coreutils-8.22-r1.ebuild
index 940d49ea1f3..78fcad4daac 100644
--- a/sys-apps/coreutils/coreutils-8.22-r1.ebuild
+++ b/sys-apps/coreutils/coreutils-8.22-r1.ebuild
@@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} )
!sys-apps/mktemp
!<app-forensics/tct-1.18-r1
!<net-fs/netatalk-2.0.3-r4
- !<sci-chemistry/ccp4-6.1.1"
+"
DEPEND="${RDEPEND}
static? ( ${LIB_DEPEND} )
app-arch/xz-utils"
diff --git a/sys-apps/coreutils/coreutils-8.22.ebuild b/sys-apps/coreutils/coreutils-8.22.ebuild
index 5f3370ca2ed..d570dee30b4 100644
--- a/sys-apps/coreutils/coreutils-8.22.ebuild
+++ b/sys-apps/coreutils/coreutils-8.22.ebuild
@@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} )
!sys-apps/mktemp
!<app-forensics/tct-1.18-r1
!<net-fs/netatalk-2.0.3-r4
- !<sci-chemistry/ccp4-6.1.1"
+"
DEPEND="${RDEPEND}
static? ( ${LIB_DEPEND} )
app-arch/xz-utils"
diff --git a/sys-apps/coreutils/coreutils-8.23.ebuild b/sys-apps/coreutils/coreutils-8.23.ebuild
index 9d7ebab1a06..bfb0c9bc167 100644
--- a/sys-apps/coreutils/coreutils-8.23.ebuild
+++ b/sys-apps/coreutils/coreutils-8.23.ebuild
@@ -40,7 +40,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} )
!sys-apps/mktemp
!<app-forensics/tct-1.18-r1
!<net-fs/netatalk-2.0.3-r4
- !<sci-chemistry/ccp4-6.1.1"
+"
DEPEND="${RDEPEND}
static? ( ${LIB_DEPEND} )
app-arch/xz-utils"
diff --git a/sys-apps/coreutils/coreutils-8.24.ebuild b/sys-apps/coreutils/coreutils-8.24.ebuild
index f5f6bd0d946..5b88e1c96f5 100644
--- a/sys-apps/coreutils/coreutils-8.24.ebuild
+++ b/sys-apps/coreutils/coreutils-8.24.ebuild
@@ -40,7 +40,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} )
!sys-apps/mktemp
!<app-forensics/tct-1.18-r1
!<net-fs/netatalk-2.0.3-r4
- !<sci-chemistry/ccp4-6.1.1"
+"
DEPEND="${RDEPEND}
static? ( ${LIB_DEPEND} )
app-arch/xz-utils"
diff --git a/x11-libs/libxdl_view/Manifest b/x11-libs/libxdl_view/Manifest
deleted file mode 100644
index 8f5dc9db9b3..00000000000
--- a/x11-libs/libxdl_view/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libxdl_view-4.2.tar.gz 857566 SHA256 826adc9c6d6706ffc6f9b52e6f7871e3ebf397837010a75daa971812f162d0b3 SHA512 1ea461cc27e53e94b89cdeef9fc435342d66f618f52a6bb936ff2c7ee63fbc89ecbbecfb4da0209ec8969f09b422af3690408dc61470299ce23e3cf84b202266 WHIRLPOOL 212c7e9f09c804bf58445a116ad75d343f6cd8e393e88ed2b2fcd4f311bd59f8a803c7fbf2d3c3a799cc7e88a9ba55f6e148c07a4956b8c6f22a0398f4b8e91f
diff --git a/x11-libs/libxdl_view/files/4.2-as-needed.patch b/x11-libs/libxdl_view/files/4.2-as-needed.patch
deleted file mode 100644
index a59d1997c2e..00000000000
--- a/x11-libs/libxdl_view/files/4.2-as-needed.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 347bb21..cbb04db 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -19,7 +19,11 @@ lib_LTLIBRARIES = libxdl_view.la libxdl_viewextra.la
- ## The initial value of this was a mistake!
- ## See the libtool doc.
- libxdl_view_la_LDFLAGS = -version-info 2:0:0
-+libxdl_view_la_LIBADD = -lX11 -lXt -lm
-+
- libxdl_viewextra_la_LDFLAGS = -version-info 0:0:0
-+libxdl_viewextra_la_DEPENDENCIES = libxdl_view.la
-+libxdl_viewextra_la_LIBADD = -lm -lxdl_view -ljwc_c
-
- EXTRA_DIST = doc/xdl_view_icon.gif doc/xdl_view_top.gif \
- doc/xdl_view_top.html doc/xdl_view_updates.html \
diff --git a/x11-libs/libxdl_view/files/4.2-impl-dec.patch b/x11-libs/libxdl_view/files/4.2-impl-dec.patch
deleted file mode 100644
index 41814377733..00000000000
--- a/x11-libs/libxdl_view/files/4.2-impl-dec.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 347bb21..aa41ba3 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -3,6 +3,8 @@
-
- ## Process this file with automake.
-
-+CFLAGS += -std=c99 -L.libs
-+
- libxdl_view_la_SOURCES = xdl_base_fr.c xdl_blank_obj.c xdl_image.c \
- xdl_bg.c xdl_img_rd.c xdl_film_img.c xdl_io_window.c \
- xdl_menu_area.c xdl_text_tab.c xdl_panel_itm.c \
diff --git a/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild b/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild
deleted file mode 100644
index 6a9900710a5..00000000000
--- a/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild
+++ /dev/null
@@ -1,32 +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
-
-DESCRIPTION="An X-Windows Based Toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/dist/x-windows/xdl_view/doc/xdl_view_top.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-RDEPEND="
- dev-libs/libjwc_c
- x11-libs/libXt"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
- "${FILESDIR}"/${PV}-impl-dec.patch
- "${FILESDIR}"/${PV}-as-needed.patch )
-
-src_prepare() {
- rm missing || die
- autotools-utils_src_prepare
-}
diff --git a/x11-libs/libxdl_view/metadata.xml b/x11-libs/libxdl_view/metadata.xml
deleted file mode 100644
index d747d72a25b..00000000000
--- a/x11-libs/libxdl_view/metadata.xml
+++ /dev/null
@@ -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>