Hi,
I tried to update our crystallographic packages including ccp4 under OS X
10.4.11 using "fink update-all" (after fink selfupdate etc). So far I never had
problems but this time, I get an error message at the end of some verbose
output I cannot make sense of (attached below).
Has anyone encountered similar issues and/or am I doing something wrong?!
Any suggestion is highly appreciated! Many thanks in advance
Christian
-------------------------------------------------------
admin% fink update-all
Information about 9273 packages read in 0 seconds.
The following 43 packages will be installed or updated:
apbs avahi avahi-dev ccp4 ccp4-shlibs clipper clipper-dev clipper-shlibs dbus
dbus-dev dbus-shlibs gnuplot gpp4 gpp4-dev gpp4-shlibs gst-plugins-base-0.10
gst-plugins-base-0.10-dev gst-plugins-base-0.10-shlibs gstreamer-0.10
gstreamer-0.10-dev gstreamer-0.10-shlibs gtk+2 gtk+2-dev gtk+2-shlibs
guile18-gtk
guile18-gtk-dev guile18-gtk-shlibs guile18-gui guile18-www
libavahi-client3-shlibs libavahi-common3-shlibs libavahi-glib1-dev
libavahi-glib1-shlibs
libgnomecanvas2-dev libgnomecanvas2-shlibs libgnomeprintui2.2-dev
libgnomeprintui2.2-shlibs libmng2-shlibs liboil-0.3 liboil-0.3-shlibs nedit
pycairo-py26
pycairo-py26-dev
The following 4 additional packages will be installed:
automake1.10 intltool libavahi-core6-shlibs libtool2
The following 10 packages might be temporarily removed:
clipper clipper-dev fort77 gpp4 gpp4-dev mmdb mmdb-dev python ssm ssm-dev
Do you want to continue? [Y/n]
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i
/sw/fink/dists/unstable/main/binary-darwin-i386/devel/automake1.10_1.10.2-2_darwin-i386.deb
Selecting previously deselected package automake1.10.
dpkg: considering removing automake1.11 in favour of automake1.10 ...
dpkg: yes, will remove automake1.11 in favour of automake1.10.
(Reading database ... 75745 files and directories currently installed.)
Unpacking automake1.10 (from .../automake1.10_1.10.2-2_darwin-i386.deb) ...
install-info(automake.info): deleting entry `* Automake: (automake) ...'
Setting up automake1.10 (1.10.2-2) ...
* Automake: (automake). Making GNU standards-compliant Makefiles.
Temporarily removing BuildConflicts:
clipper clipper-dev gpp4 gpp4-dev mmdb mmdb-dev python ssm ssm-dev
Reading buildlock packages...
/sw/bin/dpkg-lockwait --remove clipper clipper-dev gpp4 gpp4-dev mmdb mmdb-dev
python ssm ssm-dev
(Reading database ... 75736 files and directories currently installed.)
Removing clipper ...
Removing clipper-dev ...
Removing gpp4 ...
Removing gpp4-dev ...
Removing mmdb-dev ...
Removing python ...
Removing ssm ...
Removing ssm-dev ...
Removing mmdb ...
Setting runtime build-lock...
dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-ccp4-6.1.2-4
/sw/src/fink.build
dpkg-deb: building package `fink-buildlock-ccp4-6.1.2-4' in
`/sw/src/fink.build/fink-buildlock-ccp4-6.1.2-4_2009.09.16-15.55.13_darwin-i386.deb'.
Installing build-lock package...
/sw/bin/dpkg-lockwait -i
/sw/src/fink.build/fink-buildlock-ccp4-6.1.2-4_2009.09.16-15.55.13_darwin-i386.deb
Selecting previously deselected package fink-buildlock-ccp4-6.1.2-4.
(Reading database ... 75512 files and directories currently installed.)
Unpacking fink-buildlock-ccp4-6.1.2-4 (from
.../fink-buildlock-ccp4-6.1.2-4_2009.09.16-15.55.13_darwin-i386.deb) ...
Setting up fink-buildlock-ccp4-6.1.2-4 (2009.09.16-15.55.13) ...
gzip -dc /sw/src/ccp4-6.1.2-core-src.tar.gz | /sw/bin/tar -xf -
--no-same-owner --no-same-permissions
cp /sw/src/XCCPJiffy-custom.gz .
gzip -dc /sw/src/phaser-2.1.4-cctbx-src.tar.gz | /sw/bin/tar -xf -
--no-same-owner --no-same-permissions
[ -r /sw/fink/dists/unstable/main/finkinfo/sci/ccp4.patch ]
/var/tmp/tmp.1.sOokce
#!/bin/zsh -efv
#
umask 0022
# Now apply the primary patch
sed 's|@PREFIX@|/sw|g'
</sw/fink/dists/unstable/main/finkinfo/sci/ccp4.patch | patch -p1
patching file ccp4i/etc/configure.def.dist
patching file ccp4i/etc/osx_ccp4_mail
patching file ccp4i/src/local.tcl
patching file configure
patching file etc/xloggraph
patching file etc/xplot84
patching file etc/xplot84driver
patching file include/ccp4.setup-bash
patching file include/ccp4.setup-dist
patching file include/ccp4.setup-zsh
patching file lib/ccif/configure
patching file src/rapper/gc7.0/Makefile.in
patching file x-windows/Mosflm/src/dps/util/filec/wrmad.c
patching file x-windows/Mosflm/src/dps/util/filec/wrfile.c
patching file x-windows/Mosflm/src/dps/util/filec/rdbinary.c
patching file x-windows/Mosflm/src/dps/util/filec/namfil.c
patching file x-windows/XCCPJIFFY/log_file.c
patching file src/rapper/libxml2/threads.c
patching file x-windows/XCCPJIFFY/plot84_file.c
patching file x-windows/Mosflm/src/dps/util/filec/wrfile.c
patching file x-windows/XCCPJIFFY/log_file.c
patching file x-windows/XCCPJIFFY/ZDr2d.c
patching file x-windows/XCCPJIFFY/EditString.c
# setup script for tcsh, zsh and bash users
export TEMPXTAL=$PWD:h
#
perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup-csh #
build prefix (changed in install)
perl -pi.bak -e 's|/prefix|/sw|g' include/ccp4.setup* #
location of tcktk, blt
perl -pi.bak -e 's|/usr/local/bin|/sw/bin|g' include/ccp4.setup* # same
perl -pi.bak -e 's|limit stacksize 65536|limit stacksize unlimited|g'
include/ccp4.setup* # same
perl -pi.bak -e 's|ccp4_first_in_path=1|ccp4_first_in_path=0|g'
include/ccp4.setup*
perl -pi.bak -e 's|ccp4_first_in_path\ =\ 1|ccp4_first_in_path\ =\ 0|g'
include/ccp4.setup*
perl -pi.bak -e 's|setenv GFORTRAN_UNBUFFERED_ALL Y|# setenv
GFORTRAN_UNBUFFERED_ALL Y|g' include/ccp4.setup*
perl -pi.bak -e 's|export GFORTRAN_UNBUFFERED_ALL|# export
GFORTRAN_UNBUFFERED_ALL|g' include/ccp4.setup*
if [[ $(sw_vers -productVersion) < 10.6 ]]; then
true
else
/usr/bin/grep -v "char \*strcat( char \*, const char \*);"
x-windows/Mosflm/src/dps/index/ind_gen_direct.c >|
x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp
/bin/cp x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp
x-windows/Mosflm/src/dps/index/ind_gen_direct.c
/bin/rm -f x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp
fi
#
/bin/cp include/ccp4.setup-dist include/ccp4.setup
rm -f include/ccp4.setup-sh include/ccp4.setup*.bak
#
# Set up XCCPJiffy wrapper scripts in $CCP4/etc
# These are small wrapper scripts for xplot84driver and xloggraph generated
by the patch
chmod a+x etc/x*
# Fix the dylib install path in configure
perl -pi.bak -e 's|\$rpath|/sw/lib/ccp4-6.1.2|g' **/configure
#
#
/var/tmp/tmp.2.Amg1le
#!/bin/bash -efv
umask 0022
# These are required for the build environment
TEMPXTAL=$(dirname $PWD)
dirname $PWD
export TEMPXTAL
export CCP4_VERSION=""
export CCP4_MASTER=""
export BLTWISHPREFIX=""
export CCP4=""
#
source $PWD/include/ccp4.setup-bash
#!/bin/bash
# [The above is just for emacs -- this file should not be executed.]
# CCP4 setup file for bash users. -*- shell-script -*-
# $Id: ccp4.setup-bash,v 1.91.2.3 2008/06/09 08:51:17 ccb Exp $
###############################################################################
# Edit this for the current version of ccp4:
# if [[ -z $CCP4_VERSION ]];then
CCP4_VERSION="ccp4-6.1.2"
# fi
###############################################################################
# NOTE: You should not need to edit the rest of this file unless you want to
over-ride the
# following assignments of $CCP4_MASTER and $BLTWISHPREFIX
# NOTE: If you have installed ccp4 on OS X with fink, you should not need to
# change this file or to source it (fink takes care of sourcing it for you).
# CCP4_MASTER is the location of the top-level directory containing `ccp4'.
# Set it manually by uncommenting and editing the following line:
# export CCP4_MASTER="/sw/share/xtal"
# or discover it from the source command if we have a current version of
the bash shell
# if [[ -z "$CCP4_MASTER" ]];then
if [[ ${BASH_VERSION} > 3 ]];then
CCP4_MASTER="$(dirname $(dirname $(dirname ${BASH_SOURCE} )))"
else
# Attempt to this the hard way for older versions of bash
if [[ -d "/sw/share/xtal/${CCP4_VERSION}" ]]; then
CCP4_MASTER="/sw/share/xtal"
elif [[ -d "/sw/share/xtal/${CCP4_VERSION}" ]]; then
CCP4_MASTER="/sw/share/xtal"
elif [[ -d "/usr/local/${CCP4_VERSION}" ]]; then
CCP4_MASTER="/usr/local"
elif [[ -d "/usr/local/ccp4/${CCP4_VERSION}" ]]; then
CCP4_MASTER="/usr/local/ccp4"
elif [[ -d "/sw/share/xtal/ccp4/${CCP4_VERSION}" ]]; then
CCP4_MASTER="/sw/share/xtal/ccp4"
else
CCP4_MASTER="/sw/share/xtal"
fi
fi
# fi
export CCP4_MASTER
# Discover where bltwish executable is located
if [[ -z $BLTWISHPREFIX && -x $(which bltwish) ]];then
BLTWISHPREFIX=$( dirname $( which bltwish ) )
fi
which bltwish
dirname $( which bltwish )
which bltwish
###############################################################################
# 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 $CLIB (see below).
# Copy this file to ccp4.setup and customise it for your needs. There are
# three sections. You MUST check the first section. You may want to check
# the second. You don't need to look at the third.
################### THIS SECTION MUST BE EDITED #####################
# CCP4_MASTER is the location of the top-level directory containing
`ccp4-<version>'
# This is usually the directory in which you ran the tar command to unpack the
# code, and is assumed to be shared between machines at a multi-machine site.
# CCP4_MASTER="/sw/share/xtal"; export CCP4_MASTER
# CCP4="$CCP4_MASTER/ccp4-6.1.2" ; export CCP4
# Check for existence of CCP4_MASTER
if [[ ! -d $CCP4_MASTER ]] ; then
echo "********************* WARNING **********************"
echo "The directory $CCP4_MASTER"
echo "(assigned to CCP4_MASTER) does not exist."
echo "The CCP4 programs will not run correctly, and any"
echo "installation attempt will have errors or will fail."
echo "********************* WARNING **********************"
else
if [[ -d "$CCP4_MASTER/$CCP4_VERSION" ]];then
CCP4="$CCP4_MASTER/$CCP4_VERSION" ; export CCP4
else
echo "The directory "$CCP4_MASTER/$CCP4_VERSION" cannot be found."
echo " Please check that "$CCP4_VERSION" is the right ccp4 version. "
fi
fi
The directory /sw/share/xtal/ccp4-6.1.2 cannot be found.
Please check that ccp4-6.1.2 is the right ccp4 version.
# 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
export 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 $CCP4_SCR || \
echo "Unable to make CCP4_SCR. CCP4 progs will not run correctly."
export BINSORT_SCR="$CCP4_SCR"
### CCP4i setup - you may need to edit CCP4I_TCLTK ###
# CCP4I_TOP - the top directory of the interface
export CCP4I_TOP="${CCP4}/ccp4i"
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
# For 'standard' installations this is /sw/bin
# but note the SGI distributed version of Tcl/Tk is not
# appropriate version
# export CCP4I_TCLTK="/sw/bin"
if [[ -d "$BLTWISHPREFIX" && -x "$BLTWISHPREFIX/bltwish" ]]; then
export CCP4I_TCLTK="$BLTWISHPREFIX"
else
echo " Cannot find bltwish executable. Please make sure it is in your
\$PATH "
fi
# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
export CCP4I_HELP="${CCP4I_TOP}/help"
### Optional - setting http_proxy environment
# The commented out 'export' 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
#export HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah
################### NOVICE USERS STOP HERE #####################
################### OPTIONS TO CUSTOMISE CCP4 #####################
# By default, CCP4 directories are prepended to the beginning of paths (PATH,
# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
# to 0, then they will be appended to the end of paths.
# When deciding local policy, bear in mind the possible existence of
# other CCP4 installations, and the possibility of non-CCP4 programs
# with conflicting names.
ccp4_first_in_path=0
# The following checks the CCP4 server for available updates, and reports back.
# Comment this line out if you find it annoying.
# eval python -V >& /dev/null && python $CCP4/etc/ccp4_updates.py -l
# Set GFORTRAN_UNBUFFERED_ALL to either 1 or Y to ensure that the logfile
# output from programs compiled with Gfortran is in the correct order.
# Note that there will be some performance penalty for this.
# # # export GFORTRAN_UNBUFFERED_ALL="Y"
# 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/mozilla or /sw/bin/lynx. The browser will be
# started with the alias ccp4help and will open the file
# $CHTML/INDEX.html.
export CBIN="$CCP4/bin"
export CLIB="$CCP4/lib"
CCP4_BROWSER=""; export CCP4_BROWSER="Safari"
if test "$MANPATH"; then
if [[ $ccp4_first_in_path -eq 1 ]]; then
export MANPATH="${CCP4}/man:${MANPATH}"
else
export MANPATH="${MANPATH}:${CCP4}/man"
fi
else
if [ $ccp4_first_in_path -eq 1 ]; then
export MANPATH="${CCP4}/man:/usr/share/man"
else
export MANPATH="/usr/share/man:${CCP4}/man"
fi
fi
export MCTYPE="unix" # (only for Laue)
if [[ $(uname) == Darwin && $(sw_vers -productVersion) < 10.5 ]];then
ulimit -s 65536
fi
uname
sw_vers -productVersion
# The following are for all systems
export CCP4_LIB="$CLIB"
export CCP4_BIN="$CBIN"
# CLASSPATH for Java
if test "$CLASSPATH"; then
if [[ $ccp4_first_in_path -eq 1 ]]; then
export CLASSPATH="${CBIN}:${CLASSPATH}"
else
export CLASSPATH="${CLASSPATH}:${CBIN}"
fi
else
if [ $ccp4_first_in_path -eq 1 ]; then
export CLASSPATH="${CBIN}:."
else
export CLASSPATH=".:${CBIN}"
fi
fi
### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
export PLOT_COMMAND='lp -s -dmicrolaser'
export PRINT_COMMAND='lp -s -denscript'
# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
#export HARVESTHOME
### CCP4_OPEN ###
# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened
# as NEW that already exist. Novices should use 'NEW' to avoid inadvertant
# over-writing of existing files, which is then treated as a fatal error.
export CCP4_OPEN="UNKNOWN"
### BINSORT_MEM ###
# BINSORT_MEM is workspace used by the binsort program. In principle this
# value is machine-dependent. It may benefit from being enlarged, but values
# higher than 2M have been reported to cause excessive paging on some systems.
# You might like to experiment with a program such as fft with different
# values -- 102400 (bytes) is the default. csh's `time' command can tell you
# about paging.
#
# export BINSORT_MEM="8388608"
# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so)
# at runtime
##### if test "$LD_LIBRARY_PATH"; then
##### if [[ $ccp4_first_in_path -eq 1 ]]; then
##### export LD_LIBRARY_PATH="${CLIB}:${LD_LIBRARY_PATH}"
##### else
##### export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${CLIB}"
##### fi
##### else
##### export LD_LIBRARY_PATH="${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 [[ $ccp4_first_in_path -eq 1 ]]; then
##### export DYLD_LIBRARY_PATH="${CLIB}:${DYLD_LIBRARY_PATH}"
##### else
##### export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}:${CLIB}"
##### fi
##### else
##### export DYLD_LIBRARY_PATH="${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
$OPENWINHOME
##### # instead of /usr; others may want /usr/local/lib or some such):
##### if test "$XUSERFILESEARCHPATH"; then
##### export
XUSERFILESEARCHPATH="$CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH"
##### else
##### export
XUSERFILESEARCHPATH="$CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults"
##### fi
#####
##### ### TRAPPFE ###
##### # TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on
floating
##### # point exceptions under IRIX. It shouldn't cause harm on other
systems, but
##### # edit this to comment it out if necessary.
##### export TRAP_FPE="OVERFL=ABORT" ; export DIVZERO="ABORT" ; export
INVALID="ABORT"
#####
##### # The following can be used to put a message of the day to announce
news about
##### # CCP4 or whatever to CCP4 users. You might also want to edit this
part to
##### # have machine-specific messages dependent on `hostname`.
##### [[ -f "$CCP4/include/ccp4.msg" ]] && cat "$CCP4/include/ccp4.msg"
################### EXPERIENCED USERS STOP HERE #####################
################### THE REST SHOULDN'T NEED EDITING #####################
### dbCCP4i database handler setup ###
export DBCCP4I_TOP="${CCP4}/share/dbccp4i"
### IMOSFLM environment is now defined here
export MOSFLM_EXEC="${CBIN}/ipmosflm"
export MOSFLM_WISH="${CCP4I_TCLTK}/wish"
export IMOSFLM_VERSION="0.6.1"
### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
# so on multiple installs it need to be unique and not in $CLIBD
export MMCIFDIC="$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 $CLIBD. This env must have the trailing \
or /
export MOLREPLIB="$CCP4/lib/data/monomers/"
### CRANK points to location of Crank automation suite within ccp4i
export CRANK="$CCP4/ccp4i/crank"
export CCP4_CRANK="1"
# ### XIA2 setup
# # XIAROOT directory (default is under the share folder)
#
# if [[ -f "$CCP4/share/XIAROOT/setup.sh" ]]; then
# source "$CCP4/share/XIAROOT/setup.sh"
# fi
#
# Note: The PATH is updated with the xia2 Applications directory in the
# construct below.
### PISA_CONF_FILE is the config file needed to run the stand-alone PISA,
# though this can be set on the command line too.
export PISA_CONF_FILE="$CCP4/share/pisa/pisa.cfg"
### CLIBD_MON Point to the location of the dictionary files for REFMAC5
# They are distributed with CCP4 in $CLIBD/monomers. This env must have
# the trailing \ or /
export CLIBD_MON="$CCP4/lib/data/monomers/"
### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
# (essential for the relevant programs)
export PUBLIC_FONT84="$CLIB/font84.dat" # plot84 fonts [used by plot84lib]
# location of VMS-style help files required for mosflm [used by hlplib, chelp,
# chlp, (ip)mosflm]:
export CCP4_HELPDIR="$CCP4/help/" # NB trailing /
# Rasmol path. Needed for prog. to find rasmol.hlp
export RASMOLPATH="$CCP4/x-windows/RasMol/src"
if [[ $ZSH_NAME != "zsh" ]];then
# This is specific to bash, so protect it from zsh users
# 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 ${DBCCP4I_TOP}/bin
${CCP4}/share/XIAROOT/xia2/Applications"
#
for dir in ${ccp4pathlist}; do
if [[ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]]; then
if [[ $ccp4_first_in_path -eq 1 ]]; then
export PATH="${dir}:${PATH}"
else
export PATH="${PATH}:${dir}"
fi
fi
done
fi
expr ":${PATH}:" : ".*:${dir}:"
expr ":${PATH}:" : ".*:${dir}:"
expr ":${PATH}:" : ".*:${dir}:"
expr ":${PATH}:" : ".*:${dir}:"
expr ":${PATH}:" : ".*:${dir}:"
# Optional (useful) additional environment variables
#export CCP4="$CCP4"
export CDOC="$CCP4/doc"
export CHTML="$CCP4/html"
export CETC="$CCP4/etc"
export CEXAM="$CCP4/examples"
export CINCL="$CCP4/include"
export CLIBD="$CCP4/lib/data"
export CLIBS="$CCP4/lib/src"
export CPROG="$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'
fi # ksh test
basename $SHELL
#### # Set-up cctbx environment
#### [[ -f "$CCP4/lib/cctbx/cctbx_build/setpaths.sh" ]] && source
"$CCP4/lib/cctbx/cctbx_build/setpaths.sh"
####
#### # Set-up phaser environment
#### if [[ -d $CCP4/src/phaser ]] ; then
#### export phaser_mtype=`$CCP4/src/phaser/bin/machine_type`
#### export phaser_version=`grep PHASER_VERSION
$CCP4/src/phaser/conf/version | awk '{print $3}'`
#### export
phaser_setup_file="${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.sh"
#### [[ -f "$phaser_setup_file" ]] && source "$phaser_setup_file"
#### fi
####
#BALBES root configuration
export BALBES_ROOT="$CCP4/share/balbes/BALBES_0.0.1"
#
echo $PWD should be the same as $CCP4
/sw/src/fink.build/ccp4-6.1.2-4/ccp4-6.1.2 should be the same as
[[ $CCP4 == $PWD ]] || exit 1
### execution of /var/tmp/tmp.2.Amg1le failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-ccp4-6.1.2-4
(Reading database ... 75513 files and directories currently installed.)
Removing fink-buildlock-ccp4-6.1.2-4 ...
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i /sw/fink/debs/gpp4-dev_1.0.4-10_darwin-i386.deb
/sw/fink/debs/gpp4_1.0.4-10_darwin-i386.deb
/sw/fink/dists/unstable/main/binary-darwin-i386/sci/ssm_0.1-12_darwin-i386.deb
/sw/fink/dists/unstable/main/binary-darwin-i386/sci/ssm-dev_0.1-12_darwin-i386.deb
/sw/fink/dists/unstable/main/binary-darwin-i386/sci/mmdb_1.21-12_darwin-i386.deb
/sw/fink/dists/unstable/main/binary-darwin-i386/sci/mmdb-dev_1.21-12_darwin-i386.deb
/sw/fink/debs/clipper_2.1-11_darwin-i386.deb
/sw/fink/debs/clipper-dev_2.1-11_darwin-i386.deb
/sw/fink/dists/unstable/main/binary-darwin-i386/languages/python_2.6.2-2_darwin-i386.deb
Selecting previously deselected package gpp4-dev.
(Reading database ... 75512 files and directories currently installed.)
Unpacking gpp4-dev (from .../gpp4-dev_1.0.4-10_darwin-i386.deb) ...
Selecting previously deselected package gpp4.
Unpacking gpp4 (from .../gpp4_1.0.4-10_darwin-i386.deb) ...
Selecting previously deselected package ssm.
Unpacking ssm (from .../sci/ssm_0.1-12_darwin-i386.deb) ...
Selecting previously deselected package ssm-dev.
Unpacking ssm-dev (from .../ssm-dev_0.1-12_darwin-i386.deb) ...
Selecting previously deselected package mmdb.
Unpacking mmdb (from .../mmdb_1.21-12_darwin-i386.deb) ...
Selecting previously deselected package mmdb-dev.
Unpacking mmdb-dev (from .../mmdb-dev_1.21-12_darwin-i386.deb) ...
Selecting previously deselected package clipper.
Unpacking clipper (from .../clipper_2.1-11_darwin-i386.deb) ...
Selecting previously deselected package clipper-dev.
Unpacking clipper-dev (from .../clipper-dev_2.1-11_darwin-i386.deb) ...
Selecting previously deselected package python.
Unpacking python (from .../python_2.6.2-2_darwin-i386.deb) ...
Setting up gpp4-dev (1.0.4-10) ...
Setting up gpp4 (1.0.4-10) ...
Setting up ssm (0.1-12) ...
Setting up ssm-dev (0.1-12) ...
Setting up mmdb (1.21-12) ...
Setting up mmdb-dev (1.21-12) ...
Setting up clipper (2.1-11) ...
Setting up clipper-dev (2.1-11) ...
Setting up python (2.6.2-2) ...
Failed: phase compiling: ccp4-6.1.2-4 failed
Before reporting any errors, please run "fink selfupdate" and
try again. If you continue to have issues, please check to see if the
FAQ on fink's website solves the problem. If not, ask on the fink-users
or fink-beginners mailing lists, with a carbon copy to the maintainer:
W. G. Scott <[email protected]>
Note that this is preferable to emailing the maintainer directly, since
most fink package maintainers do not have access to all possible
hardware and software configurations.
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