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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 /sci-libs/ccp4-libs/files
parentadd co-maintainer Coacher to metadata (diff)
downloadgentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.gz
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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>
Diffstat (limited to 'sci-libs/ccp4-libs/files')
-rw-r--r--sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch11
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-cbf.patch16
-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
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-noinstall.patch142
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-overflows.patch35
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch367
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch395
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch203
-rw-r--r--sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch16
-rw-r--r--sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch16
17 files changed, 0 insertions, 2421 deletions
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 a77d9494a05c..000000000000
--- 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 6930fcad766a..000000000000
--- 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 ca18d75bc840..000000000000
--- 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 b3147ad81bbf..000000000000
--- 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 583697cea0a1..000000000000
--- 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 6e3997647955..000000000000
--- 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 8bfa7db8cbff..000000000000
--- 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 0463b3719525..000000000000
--- 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 24a0a2d8e4a2..000000000000
--- 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 6a0cb5be7c3d..000000000000
--- 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 c1479f2b1155..000000000000
--- 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 0e3c941d1cc2..000000000000
--- 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 4271d5b76aec..000000000000
--- 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 c787df903dfc..000000000000
--- 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 96978320163b..000000000000
--- 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 367d53e3e4f6..000000000000
--- 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 caf62bb652e2..000000000000
--- 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);
- }
- }
-