Update of /cvsroot/fink/dists/10.3/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12393
Added Files:
ccp4.patch
Log Message:
proper patch file for ccp4 (finally) 10.3 unstable sci
--- NEW FILE: ccp4.patch ---
diff -urN ccp4-5.0.1-orig/ccp4i/scripts/dhm_tool.script
ccp4-5.0.1/ccp4i/scripts/dhm_tool.script
--- ccp4-5.0.1-orig/ccp4i/scripts/dhm_tool.script 2004-07-02 08:56:14.000000000
-0700
+++ ccp4-5.0.1/ccp4i/scripts/dhm_tool.script 2004-07-12 16:12:40.000000000 -0700
@@ -10,7 +10,8 @@
if { $PDB_EXTRACT == 1 && $XML != 1 } {
- if { $EXTRACT_STEP == "scaling" && $SCALING != "" } {
+ if { $EXTRACT_STEP == "scaling" && $SCALING != "" &&
+ ($SCALING_LOGIN != "" || $SCALING1_LOGIN != "" || $SCALING_CIFIN != "")
} {
append cmd " -s " $SCALING
if { $SCALING_LOGIN != "" } {
append cmd " -iLOG " $SCALING_LOGIN
@@ -25,7 +26,9 @@
}
- if { $EXTRACT_STEP == "phasing" && $EXP_MENU != "" && $PHASING != ""} {
+ if { $EXTRACT_STEP == "phasing" && $EXP_MENU != "" && $PHASING != ""
+ && ($PHASING_LOGIN != "" || $PHASING1_LOGIN != "" ||
+ $PHASING_PDBIN != "" || $PHASING_CIFIN != "") } {
append cmd " -e " $EXP_MENU
append cmd " -p " $PHASING
if { $PHASING_LOGIN != "" } {
@@ -44,7 +47,9 @@
}
- if { $EXTRACT_STEP == "replacement" && $REPLACEMENT != "" } {
+ if { $EXTRACT_STEP == "replacement" && $REPLACEMENT != "" &&
+ ( $REPLACEMENT_LOGIN != "" || $REPLACEMENT1_LOGIN != "" ||
+ $REPLACEMENT_CIFIN != "") } {
append cmd " -m " $REPLACEMENT
if { $REPLACEMENT_LOGIN != "" } {
append cmd " -iLOG " $REPLACEMENT_LOGIN
@@ -59,7 +64,8 @@
}
- if { $EXTRACT_STEP == "den_mod" && $DEN_MOD != "" } {
+ if { $EXTRACT_STEP == "den_mod" && $DEN_MOD != "" &&
+ ( $DM_LOGIN != "" || $DM_CIFIN != "") } {
append cmd " -d " $DEN_MOD
if { $DM_LOGIN != "" } {
append cmd " -iLOG " $DM_LOGIN
@@ -71,7 +77,8 @@
}
- if { $EXTRACT_STEP == "refinement" && $REFINEMENT != "" } {
+ if { $EXTRACT_STEP == "refinement" && $REFINEMENT != "" &&
+ ($REFINE_CIFIN != "" || $REFINE_PDBIN != "" || $REFINE_LOGIN != "")} {
append cmd " -r " $REFINEMENT
if { $REFINE_CIFIN != "" } {
append cmd " -iCIF " $REFINE_CIFIN
@@ -97,7 +104,8 @@
if { $EXTRACT_STEP == "merge" } {
- if { $SCALING != "" } {
+ if { $SCALING != "" &&
+ ($SCALING_LOGIN != "" || $SCALING1_LOGIN != "" || $SCALING_CIFIN != "")}
{
append cmd " -s " $SCALING
if { $SCALING_LOGIN != "" } {
append cmd " -iLOG " $SCALING_LOGIN
@@ -111,7 +119,9 @@
}
- if { $EXP_MENU != "" && $PHASING != ""} {
+ if { $EXP_MENU != "" && $PHASING != "" &&
+ ($PHASING_LOGIN != "" || $PHASING1_LOGIN != "" ||
+ $PHASING_PDBIN != "" || $PHASING_CIFIN != "" )} {
append cmd " -e " $EXP_MENU
append cmd " -p " $PHASING
if { $PHASING_LOGIN != "" } {
@@ -129,7 +139,9 @@
}
- if { $REPLACEMENT != "" } {
+ if { $REPLACEMENT != "" &&
+ ($REPLACEMENT_LOGIN != "" || $REPLACEMENT1_LOGIN != ""||
+ $REPLACEMENT_CIFIN != "") } {
append cmd " -m " $REPLACEMENT
if { $REPLACEMENT_LOGIN != "" } {
append cmd " -iLOG " $REPLACEMENT_LOGIN
@@ -143,7 +155,8 @@
}
- if { $DEN_MOD != "" } {
+ if { $DEN_MOD != "" &&
+ ($DM_LOGIN != "" || $DM_CIFIN != "")} {
append cmd " -d " $DEN_MOD
if { $DM_LOGIN != "" } {
append cmd " -iLOG " $DM_LOGIN
@@ -154,7 +167,8 @@
}
- if { $REFINEMENT != "" } {
+ if { $REFINEMENT != "" &&
+ ($REFINE_CIFIN != "" || $REFINE_PDBIN != "" || $REFINE_LOGIN != "")} {
append cmd " -r " $REFINEMENT
if { $REFINE_CIFIN != "" } {
append cmd " -iCIF " $REFINE_CIFIN
diff -urN ccp4-5.0.1-orig/ccp4i/tasks/fffear.tcl ccp4-5.0.1/ccp4i/tasks/fffear.tcl
--- ccp4-5.0.1-orig/ccp4i/tasks/fffear.tcl 2004-01-26 03:24:01.000000000 -0800
+++ ccp4-5.0.1/ccp4i/tasks/fffear.tcl 2004-07-12 16:13:14.000000000 -0700
@@ -140,8 +140,8 @@
emp-turn_b-9 \
emp-helixend-9 \
theor-helix-10 \
- theor-strand-5 \
- theor-helix-10 \
+ theor-helix-5 \
+ theor-strand-10 \
theor-strand-5 ]
diff -urN ccp4-5.0.1-orig/etc/xloggraph ccp4-5.0.1/etc/xloggraph
--- ccp4-5.0.1-orig/etc/xloggraph 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-5.0.1/etc/xloggraph 2004-07-12 16:13:49.000000000 -0700
@@ -0,0 +1,6 @@
+#!/bin/zsh
+export XUSERFILESEARCHPATH=/sw/lib/app-defaults/XCCPJiffy
+xloggraph.exe "$@" &
+export XUSERFILESEARCHPATH=""
+print "Plot button sends pdf to Preview. Print or save pdf in Preview window."
+exit 0
diff -urN ccp4-5.0.1-orig/etc/xplot84 ccp4-5.0.1/etc/xplot84
--- ccp4-5.0.1-orig/etc/xplot84 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-5.0.1/etc/xplot84 2004-07-12 16:13:44.000000000 -0700
@@ -0,0 +1,6 @@
+#!/bin/zsh
+export XUSERFILESEARCHPATH=/sw/lib/app-defaults/XCCPJiffy
+xplot84driver.exe "$@" &
+export XUSERFILESEARCHPATH=""
+print "Plot button sends pdf to Preview. Print or save pdf in Preview window."
+exit 0
diff -urN ccp4-5.0.1-orig/etc/xplot84driver ccp4-5.0.1/etc/xplot84driver
--- ccp4-5.0.1-orig/etc/xplot84driver 1969-12-31 16:00:00.000000000 -0800
+++ ccp4-5.0.1/etc/xplot84driver 2004-07-12 16:13:44.000000000 -0700
@@ -0,0 +1,6 @@
+#!/bin/zsh
+export XUSERFILESEARCHPATH=/sw/lib/app-defaults/XCCPJiffy
+xplot84driver.exe "$@" &
+export XUSERFILESEARCHPATH=""
+print "Plot button sends pdf to Preview. Print or save pdf in Preview window."
+exit 0
diff -urN ccp4-5.0.1-orig/include/ccp4.setup-bash ccp4-5.0.1/include/ccp4.setup-bash
--- ccp4-5.0.1-orig/include/ccp4.setup-bash 2004-07-05 07:53:54.000000000 -0700
+++ ccp4-5.0.1/include/ccp4.setup-bash 1969-12-31 16:00:00.000000000 -0800
@@ -1,355 +0,0 @@
-#!/bin/bash
-# CCP4 setup file for bash or ksh (untested) users. -*- shell-script -*-
-# Actually, the aliases can't work asis in ksh. Should use builtins instead
-# and not worry about ease of keeping in step with the csh one.
-
-# $Id: ccp4.setup-bash,v 1.61 2004/07/05 14:53:54 pjx Exp $
-
-# This file is site specific and may also contain machine-specifics. The CCP4
-# administrator will have to edit this file and then have anyone who wants to
-# use CCP4 source it from their .login file. They will require the full path
-# name since no environment variables relevant to CCP4 are known until this is
-# executed.
-
-# For sites with more than one machine, it is recommended that the suite is
-# installed on a single machine and other machines access the source code, and
-# shareable files (such as this one) via shared file systems with NFS, RFS
-# etc. Non-shareable files reside in $CBIN and $CLIB (see below).
-
-# Copy this file to ccp4.setup and customise it for your needs. There are
-# three sections. You MUST check the first section. You may want to check
-# the second. You don't need to look at the third.
-
-################### THIS SECTION SHOULDN'T NEED EDITING #####################
-
-# first emulate csh setenv and alias so we can keep the bash and csh
-# versions as similar as possible
-setenv () { export $1="$2" ; }
-# Note that bash has a (different) alias command so we need to undo this
-# later. I wonder if it is robust :-)
-if [ "`basename $SHELL`" != "ksh" ]; then # can't redefine alias in ksh
-alias () { eval `echo $1; shift; echo '() { ' $*; echo '; }'` ; }
-fi
-
-################### THIS SECTION MUST BE EDITED #####################
-
-# CCP4_MASTER is the location of the top-level directory containing `ccp4-<version>'
-# This is usually the directory in which you ran the tar command to unpack the
-# code, and is assumed to be shared between machines at a multi-machine site.
-
-setenv CCP4_MASTER /xtal
-setenv CCP4 $CCP4_MASTER/ccp4-5.0.1
-
-# Check for existence of CCP4_MASTER
-if (! test -d $CCP4_MASTER) ; then
- echo "********************* WARNING **********************"
- echo "The directory $CCP4_MASTER"
- echo "(assigned to CCP4_MASTER) does not exist."
- echo "The CCP4 programs will not run correctly, and any"
- echo "installation attempt will have errors or will fail."
- echo "********************* WARNING **********************"
-fi
-
-# CCP4_SCR: a per-user directory for run-time-generated scratch
-# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
-# BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR
-
-setenv CCP4_SCR /tmp/$USER
-# check to see if this exists and if not try to make it
-test -d $CCP4_SCR || mkdir $CCP4_SCR
-test -d $CCP4_SCR || \
- echo "Unable to make CCP4_SCR. CCP4 progs will not run correctly."
-
-setenv BINSORT_SCR $CCP4_SCR
-
-### CCP4i setup - you may need to edit CCP4I_TCLTK ###
-# CCP4I_TOP - the top directory of the interface
-setenv CCP4I_TOP ${CCP4}/ccp4i
-# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
-# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
-# For 'standard' installations this is /usr/local/bin
-# but note the SGI distributed version of Tcl/Tk is not
-# appropriate version
-setenv CCP4I_TCLTK /usr/local/bin
-# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
-setenv CCP4I_HELP ${CCP4I_TOP}/help
-
-### Optional - setting http_proxy environment
-# The commented out 'setenv' line below may have to be declared to download
-# and edit protein sequences using the new "Import/Edit Protein Sequences"
-# (This may also be required for remote job submission in arp/warp.)
-# task. If so, uncomment this line and replace the example proxy URL with your
-# relevant URL
-
-#setenv HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah
-
-################### NOVICE USERS STOP HERE #####################
-
-################### OPTIONS TO CUSTOMISE CCP4 #####################
-
-# By default, CCP4 directories are appended to the end of paths (PATH,
-# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
-# to 1, then they will be prepended to the beginning of paths.
-ccp4_first_in_path=0
-
-# The commented-out switch statement below provides an example of how
-# to use this file for several machines/architectures sharing $CCP4_MASTER.
-# If necessary, uncomment and edit this. Otherwise, if you're only supporting
-# a single system alter the uncommented part as necessary.
-#
-# The significance of the environment variables is as follows:
-# CBIN: location of the executables -- must be on your path (see below);
-# CLIB: location of (binary) library files such as libccp4.a and libccp4.so;
-# MANPATH: set this if your system's `man' looks at such an environment
-# variable to determine where to look for man pages. By adding
-# $CCP4/man to the normal path you get the CCP4 man pages
-# with keyword searching as system ones.
-# MCTYPE: used for LAUE make -- see LAUE documentation
-# CCP4_BROWSER: set this if you intend to use the html documentation
-# (recommended). It should have the path and name of a html browser eg
-# /usr/bin/X11/netscape or /usr/local/bin/lynx. The browser will be
-# started with the alias ccp4help and will open the file
-# $CHTML/INDEX.html.
-
-# case `hostname` in # edit this case statement if used
-# # for multiple systems
-# foo)
- setenv CBIN $CCP4/bin
- setenv CLIB $CCP4/lib
-
- setenv CCP4_BROWSER netscape
-
- if test "$MANPATH"; then
- if [ $ccp4_first_in_path -eq 1 ]; then
- setenv MANPATH ${CCP4}/man:${MANPATH}
- else
- setenv MANPATH ${MANPATH}:${CCP4}/man
- fi
- else
- if [ $ccp4_first_in_path -eq 1 ]; then
- setenv MANPATH ${CCP4}/man:/usr/share/man
- else
- setenv MANPATH /usr/share/man:${CCP4}/man
- fi
- fi
- setenv MCTYPE unix # (only for Laue)
-# ;;
-# *)
-# echo "CCP4 not implemented on this system"
-# exit 1
-# ;;
-# esac
-
-case `uname` in
-*Darwin* )
- ulimit -s 65536
- ;;
-* )
- ;;
-esac
-
-# The following are for all systems
-setenv CCP4_LIB $CLIB
-setenv CCP4_BIN $CBIN
-
-# CLASSPATH for Java
-if test "$CLASSPATH"; then
- if [ $ccp4_first_in_path -eq 1 ]; then
- setenv CLASSPATH ${CBIN}:${CLASSPATH}
- else
- setenv CLASSPATH ${CLASSPATH}:${CBIN}
- fi
-else
- if [ $ccp4_first_in_path -eq 1 ]; then
- setenv CLASSPATH ${CBIN}:.
- else
- setenv CLASSPATH .:${CBIN}
- fi
-fi
-
-### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
-setenv PLOT_COMMAND 'lp -s -dmicrolaser'
-setenv PRINT_COMMAND 'lp -s -denscript'
-
-# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
-#setenv HARVESTHOME
-
-### CCP4_OPEN ###
-# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened
-# as NEW that already exist. Novices should use 'NEW' to avoid inadvertant
-# over-writing of existing files, which is then treated as a fatal error.
-
-setenv CCP4_OPEN UNKNOWN
-
-### BINSORT_MEM ###
-# BINSORT_MEM is workspace used by the binsort program. In principle this
-# value is machine-dependent. It may benefit from being enlarged, but values
-# higher than 2M have been reported to cause excessive paging on some systems.
-# You might like to experiment with a program such as fft with different
-# values -- 102400 (bytes) is the default. csh's `time' command can tell you
-# about paging.
-#
-# setenv BINSORT_MEM 8388608
-
-# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so)
-# at runtime
-if test "$LD_LIBRARY_PATH"; then
- if [ $ccp4_first_in_path -eq 1 ]; then
- setenv LD_LIBRARY_PATH ${CLIB}:${LD_LIBRARY_PATH}
- else
- setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${CLIB}
- fi
-else
- setenv LD_LIBRARY_PATH ${CLIB}
-fi
-
-# DYLD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.dylib)
-# at runtime (used on Mac OS X)
-if test "$DYLD_LIBRARY_PATH"; then
- if [ $ccp4_first_in_path -eq 1 ]; then
- setenv DYLD_LIBRARY_PATH ${CLIB}:${DYLD_LIBRARY_PATH}
- else
- setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${CLIB}
- fi
-else
- setenv DYLD_LIBRARY_PATH ${CLIB}
-fi
-
-### XAPPLRESDIR ###
-
-# If you want to use xloggraph/xplot84driver, you need to get the application
-# defaults picked up somehow. As distributed, the file can't just live in an
-# application defaults directory since it requires reading by xrdb to sort out
-# the differences for monochrome displays. At Daresbury a version of the file
-# assuming a monochrome display is kept in the directory
-# $CCP4_LIB/X11/app-defaults and this is picked up through the
-# XUSERFILESEARCHPATH environment variable. That means you only see black and
-# white on a colour display. Alternatively you might make sure that it is
-# read by xrdb on startup of the X Windows system or delegate the
-# responsibility to users to run it. There are disadvantages to putting an
-# invocation of xrdb in here, one being that the correct value of DISPLAY may
-# not be set at the time this file is read. Thus edit this part as
-# appropriate. (SunOS will normally want to use /usr/openwin or $OPENWINHOME
-# instead of /usr; others may want /usr/local/lib or somw such):
-if test "$XUSERFILESEARCHPATH"; then
- setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH
-else
- setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults
-fi
-
-### TRAPPFE ###
-# TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on floating
-# point exceptions under IRIX. It shouldn't cause harm on other systems, but
-# edit this to comment it out if necessary.
-setenv TRAP_FPE "OVERFL=ABORT; DIVZERO=ABORT; INVALID=ABORT"
-
-# The following can be used to put a message of the day to announce news about
-# CCP4 or whatever to CCP4 users. You might also want to edit this part to
-# have machine-specific messages dependent on `hostname`.
-test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
-
-################### EXPERIENCED USERS STOP HERE #####################
-
-################### THE REST SHOULDN'T NEED EDITING #####################
-
-### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
-# so on multiple installs it need to be unique and not in $CLIBD
-
-setenv MMCIFDIC $CLIB/cif_mmdic.lib
-
-### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource symlib.blc
-# They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or /
-
-setenv MOLREPLIB $CCP4/lib/data/monomers/
-
-### CLIBD_MON Point to the location of the dictionary files for REFMAC5
-# They are distributed with CCP4 in $CLIBD/monomers. This env must have
-# the trailing \ or /
-
-setenv CLIBD_MON $CCP4/lib/data/monomers/
-
-### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
-# (essential for the relevant programs)
-setenv PUBLIC_FONT84 $CLIB/font84.dat # plot84 fonts [used by plot84lib]
-
-# location of VMS-style help files required for mosflm [used by hlplib, chelp,
-# chlp, (ip)mosflm]:
-setenv CCP4_HELPDIR $CCP4/help/ # NB trailing /
-setenv HELPDIR $CCP4_HELPDIR # for chelp
-setenv MOSHELPFILE mosflm # required by (ip)mosflm
-
-# Rasmol path. Needed for prog. to find rasmol.hlp
-setenv RASMOLPATH $CCP4/x-windows/RasMol/src
-
-# CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
-# on the path in an appropriate order for scripts to be used as wrappers for
-# binaries of the same name. Put ccp4 stuff after the current path to avoid
-# confusion with `.' or whatever in the path:
-#
-# This construct prevents the path getting longer each time ccp4.setup is
-# executed (A. Perrakis)
-ccp4pathlist="${CCP4}/etc ${CBIN} ${CCP4I_TOP}/bin "
-#
-for dir in ${ccp4pathlist}; do
- if [ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]; then
- if [ $ccp4_first_in_path -eq 1 ]; then
- setenv PATH ${dir}:${PATH}
- else
- setenv PATH ${PATH}:${dir}
- fi
- fi
-done
-
-# Optional (useful) additional environment variables
- setenv CCP4 $CCP4
- setenv CDOC $CCP4/doc
- setenv CHTML $CCP4/html
- setenv CETC $CCP4/etc
- setenv CEXAM $CCP4/examples
- setenv CINCL $CCP4/include
- setenv CLIBD $CCP4/lib/data
- setenv CLIBS $CCP4/lib/src
- setenv CPROG $CCP4/src
-
-if [ "`basename $SHELL`" != "ksh" ]; then
-# useful aliases, at least for developers
- alias ccp4 'pushd $CCP4>/dev/null'
- alias xtal 'pushd $CCP4_MASTER>/dev/null'
- alias cbin 'pushd $CBIN>/dev/null'
- alias cetc 'pushd $CETC>/dev/null'
- alias cprog 'pushd $CPROG>/dev/null'
- alias cincl 'pushd $CINCL>/dev/null'
- alias clib 'pushd $CLIB>/dev/null'
- alias clibd 'pushd $CLIBD>/dev/null'
- alias clibs 'pushd $CLIBS>/dev/null'
- alias cbin 'pushd $CBIN>/dev/null'
- alias cexam 'pushd $CEXAM>/dev/null'
- alias cdoc 'pushd $CDOC>/dev/null'
- alias chtml 'pushd $CHTML>/dev/null'
- alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html \&'
-
-### laue, lget, linkimages ###
-# Essential aliases for the Laue software suite
- alias laue '$CCP4_MASTER/laue/cmd/laue.cmd'
- alias lget '$CCP4_MASTER/laue/cmd/lget.cmd'
- alias linkimages '$CCP4_MASTER/laue/cmd/linkimages.cmd'
-
-# additional useful aliases for Laue directories
- alias llaue 'pushd $CCP4_MASTER/laue'
- alias lsrc 'pushd $CCP4_MASTER/laue/src>/dev/null'
- alias llib 'pushd $CCP4_MASTER/laue/lib>/dev/null'
- alias llibs 'pushd $CCP4_MASTER/laue/lib/src>/dev/null'
- alias ldoc 'pushd $CCP4_MASTER/laue/doc>/dev/null'
- alias lmak 'pushd $CCP4_MASTER/laue/make>/dev/null'
- alias lutils 'pushd $CCP4_MASTER/laue/utils>/dev/null'
- alias lcmd 'pushd $CCP4_MASTER/laue/cmd>/dev/null'
- alias ldl 'pushd $CCP4_MASTER/laue/dl>/dev/null'
- alias ltestd 'pushd $CCP4_MASTER/laue/testdata>/dev/null'
- alias lxdl 'pushd $CCP4_MASTER/laue/xdl_view>/dev/null'
- alias lxdls 'pushd $CCP4_MASTER/laue/xdl_view/src>/dev/null'
- alias lgnom 'pushd $CCP4_MASTER/laue/gnom>/dev/null'
- alias lgnoms 'pushd $CCP4_MASTER/laue/gnom/src>/dev/null'
- alias lbin 'pushd $CBIN>/dev/null'
-
- unset alias # clean up
-fi # ksh test
diff -urN ccp4-5.0.1-orig/include/ccp4.setup-dist ccp4-5.0.1/include/ccp4.setup-dist
--- ccp4-5.0.1-orig/include/ccp4.setup-dist 2004-07-05 07:53:55.000000000 -0700
+++ ccp4-5.0.1/include/ccp4.setup-dist 2004-07-12 16:09:21.000000000 -0700
@@ -54,10 +54,10 @@
setenv CCP4I_TOP ${CCP4}/ccp4i
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
-# For 'standard' installations this is /usr/local/bin
+# For 'standard' installations this is /sw/bin
# but note the SGI distributed version of Tcl/Tk is not
# appropriate version
-setenv CCP4I_TCLTK /usr/local/bin
+setenv CCP4I_TCLTK /sw/bin
# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
setenv CCP4I_HELP ${CCP4I_TOP}/help
@@ -94,7 +94,7 @@
# MCTYPE: used for LAUE make -- see LAUE documentation
# CCP4_BROWSER: set this if you intend to use the html documentation
# (recommended). It should have the path and name of a html browser eg
-# /usr/bin/X11/netscape or /usr/local/bin/lynx. The browser will be
+# /usr/bin/X11/open or /sw/bin/lynx. The browser will be
# started with the alias ccp4help and will open the file
# $CHTML/INDEX.html.
@@ -104,7 +104,7 @@
setenv CBIN $CCP4/bin
setenv CLIB $CCP4/lib
- setenv CCP4_BROWSER netscape
+ setenv CCP4_BROWSER open
if (${?MANPATH}) then
if ($ccp4_first_in_path) then
@@ -155,8 +155,8 @@
endif
### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
-setenv PLOT_COMMAND 'lp -s -dmicrolaser'
-setenv PRINT_COMMAND 'lp -s -denscript'
+setenv PLOT_COMMAND 'lpr'
+setenv PRINT_COMMAND 'lpr'
# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
#setenv HARVESTHOME
@@ -178,51 +178,10 @@
#
# setenv BINSORT_MEM 8388608
-# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so)
-# at runtime
-if (${?LD_LIBRARY_PATH}) then
- if ($ccp4_first_in_path) then
- setenv LD_LIBRARY_PATH ${CLIB}:${LD_LIBRARY_PATH}
- else
- setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${CLIB}
- endif
-else
- setenv LD_LIBRARY_PATH ${CLIB}
-endif
-
-# DYLD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.dylib)
-# at runtime (used on Mac OS X)
-if (${?DYLD_LIBRARY_PATH}) then
- if ($ccp4_first_in_path) then
- setenv DYLD_LIBRARY_PATH ${CLIB}:${DYLD_LIBRARY_PATH}
- else
- setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${CLIB}
- endif
-else
- setenv DYLD_LIBRARY_PATH ${CLIB}
-endif
+# LD_LIBRARY_PATH and DYLD_LIBRARY_PATH unset per fink policy
-### XAPPLRESDIR ###
-# If you want to use xloggraph/xplot84driver, you need to get the application
-# defaults picked up somehow. As distributed, the file can't just live in an
-# application defaults directory since it requires reading by xrdb to sort out
-# the differences for monochrome displays. At Daresbury a version of the file
-# assuming a monochrome display is kept in the directory
-# $CCP4_LIB/X11/app-defaults and this is picked up through the
-# XUSERFILESEARCHPATH environment variable. That means you only see black and
-# white on a colour display. Alternatively you might make sure that it is
-# read by xrdb on startup of the X Windows system or delegate the
-# responsibility to users to run it. There are disadvantages to putting an
-# invocation of xrdb in here, one being that the correct value of DISPLAY may
-# not be set at the time this file is read. Thus edit this part as
-# appropriate. (SunOS will normally want to use /usr/openwin or $OPENWINHOME
-# instead of /usr; others may want /usr/local/lib or somw such):
-if ($?XUSERFILESEARCHPATH) then
- setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH
-else
- setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults
-endif
+# XUSERFILESEARCHPATH environment variable set in wrapper shell scripts.
### TRAPPFE ###
# TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on floating
@@ -274,8 +233,9 @@
# confusion with `.' or whatever in the path:
#
# This construct prevents the path getting longer each time ccp4.setup is
-# executed (A. Perrakis)
-set ccp4pathlist = "${CCP4}/etc ${CBIN} ${CCP4I_TOP}/bin "
+# executed (A. Perrakis). This was done wrong in the original file.
+#
+set ccp4pathlist = "${CCP4}/etc:${CBIN}:${CCP4I_TOP}/bin"
#
foreach dir ( ${ccp4pathlist} )
if ( ${?PATH} ) then
diff -urN ccp4-5.0.1-orig/include/ccp4.setup-sh ccp4-5.0.1/include/ccp4.setup-sh
--- ccp4-5.0.1-orig/include/ccp4.setup-sh 2003-11-12 07:23:49.000000000 -0800
+++ ccp4-5.0.1/include/ccp4.setup-sh 2004-07-12 16:05:09.000000000 -0700
@@ -1,9 +1,8 @@
#! /bin/sh
# [The above is just for emacs -- this file should not be executed.]
-# CCP4 setup file for bash or ksh (untested) users. Actually, the aliases
-# can't work asis in ksh. Should use builtins instead and not worry about
-# ease of keeping in step with the csh one.
+# CCP4 setup file for OS X bash or zsh users.
+
# $Id: ccp4.setup-sh,v 1.3 2003/11/12 15:23:49 ccb Exp $
@@ -13,22 +12,15 @@
# name since no environment variables relevant to CCP4 are known until this is
# executed.
-# For sites with more than one machine, it is recommended that the suite is
-# installed on a single machine and other machines access the source code, and
-# shareable files (such as this one) via shared file systems with NFS, RFS
-# etc. Non-shareable files reside in $CBIN and $CLIB (see below).
-
-# Copy this file to ccp4.setup and customise it for your needs. There are
-# three sections. You MUST check the first section. You may want to check
-# the second. You don't need to look at the third.
+# This should be set up correctly for fink users of CCP4.
-################### THIS SECTION MUST BE EDITED #####################
+################### THIS SECTION has already been EDITED #####################
# CCP4_MASTER is the location of the top-level directory containing `ccp4'.
-# This is assumed to be shared between machines at a multi-machine site.
+# This is usually /sw/share/xtal for a fink installation.
export CCP4_MASTER=/xtal
-export CCP4=$CCP4_MASTER/ccp4-5.0d
+export CCP4=$CCP4_MASTER/ccp4-5.0.1
# CCP4_SCR: a per-user directory for run-time-generated scratch
# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
@@ -46,7 +38,7 @@
export CCP4I_TOP=$CCP4/ccp4i
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
-# For 'standard' installations this is /usr/local/bin
+# For 'standard' installations this is /sw/bin
# but note the SGI distributed version of Tcl/Tk is not
# appropriate version
export CCP4I_TCLTK=/sw/bin
@@ -81,7 +73,7 @@
# MCTYPE: used for LAUE make -- see LAUE documentation
# CCP4_BROWSER: set this if you intend to use the html documentation
# (recommended). It should have the path and name of a html browser eg
-# /usr/bin/X11/netscape or /usr/local/bin/lynx. The browser will be
+# /usr/bin/X11/netscape or /sw/bin/lynx. The browser will be
# started with the alias ccp4help and will open the file
# $CHTML/INDEX.html.
@@ -91,7 +83,7 @@
export CBIN=$CCP4/bin
export CLIB=$CCP4/lib
- export CCP4_BROWSER=safari
+ export CCP4_BROWSER=open
export MANPATH=$CCP4/man:$MANPATH # edit this if necessary
export MCTYPE=unix # (only for Laue)
# ;;
@@ -110,8 +102,8 @@
export CLASSPATH=$CBIN:$CLASSPATH # edit this if necessary
### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
-export PLOT_COMMAND='lp -s'
-export PRINT_COMMAND='lp -s'
+export PLOT_COMMAND='lpr'
+export PRINT_COMMAND='lpr'
# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
export HARVESTHOME=$HOME
@@ -133,39 +125,11 @@
#
# export BINSORT_MEM=8388608
-# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so)
-# at runtime
-if test "LD_LIBRARY_PATH"; then
- export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CLIB
-else
- export LD_LIBRARY_PATH=$CLIB
-fi
-# DYLD_LIBRARY_PATH specifies where to find dynamic libraries
-# (e.g. libccp4.dylib) at runtime
-if test "DYLD_LIBRARY_PATH"; then
- export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$CLIB
-else
- export DYLD_LIBRARY_PATH=$CLIB
-fi
+# Fink does not allow LD_LIBRARY_PATH or DYLD_LIBRARY_PATH to be set
### XAPPLRESDIR ###
-
-# If you want to use xloggraph/xplot84driver, you need to get the application
-# defaults picked up somehow. As distributed, the file can't just live in an
-# application defaults directory since it requires reading by xrdb to sort out
-# the differences for monochrome displays. At Daresbury a version of the file
-# assuming a monochrome display is kept in the directory
-# $CCP4_LIB/X11/app-defaults and this is picked up through the
-# XUSERFILESEARCHPATH environment variable. That means you only see black and
-# white on a colour display. Alternatively you might make sure that it is
-# read by xrdb on startup of the X Windows system or delegate the
-# responsibility to users to run it. There are disadvantages to putting an
-# invocation of xrdb in here, one being that the correct value of DISPLAY may
-# not be set at the time this file is read. Thus edit this part as
-# appropriate. (SunOS will normally want to use /usr/openwin or $OPENWINHOME
-# instead of /usr; others may want /usr/local/lib or somw such):
-
-export XAPPLRESDIR=/sw/etc/app-defaults/
+# XUSERFILESEARCHPATH environment variable will be set in shell script wrapper.
+
### TRAPPFE ###
# TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on floating
@@ -217,8 +181,10 @@
# confusion with `.' or whatever in the path:
#
# This construct prevents the path getting longer each time ccp4.setup is
-# executed (A. Perrakis)
-ccp4pathlist="${CCP4}/etc ${CBIN} ${CCP4I_TOP}/bin "
+# executed (A. Perrakis) This was done wrong in the original file and is not
+# needed for zsh users.
+#
+ccp4pathlist="${CCP4}/etc:${CBIN}:${CCP4I_TOP}/bin"
#
for dir in ${ccp4pathlist}
do
diff -urN ccp4-5.0.1-orig/x-windows/XCCPJIFFY/plot84_file.h
ccp4-5.0.1/x-windows/XCCPJIFFY/plot84_file.h
--- ccp4-5.0.1-orig/x-windows/XCCPJIFFY/plot84_file.h 2004-06-03 08:27:20.000000000
-0700
+++ ccp4-5.0.1/x-windows/XCCPJIFFY/plot84_file.h 2004-07-12 16:11:20.000000000
-0700
@@ -28,7 +28,7 @@
float dvymin; /* device viewport Y min (mm) */
float dvymax; /* device viewport Y max (mm) */
int npics; /* number of pictures in this file */
- char paswrd [9]; /* password "PLOT%%84" */
+ char paswrd [8]; /* password "PLOT%%84" */
int spare [15]; /* spare bytes */
char titleh [80];/* plot title */
int lastspare [68]; /* filled to 512 bytes */
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