This is script version 5.26 for Gtk2
Mon Sep  7 11:36:03 BST 2015
currently architecture is x86_64
systype: x86_64-ubuntu-14.04
update_libtool: 1
update_config_guess_sub: 1
patch
system has patch
m4
system has m4
g++
system has g++
libxext-dev
system has libxext-dev
libxmu-dev
system has libxmu-dev
libxt-dev
system has libxt-dev
libc6-dev
system has libc6-dev
libglu1-mesa-dev
system has libglu1-mesa-dev
mesa-common-dev
system has mesa-common-dev
libgtk2.0-dev
system has libgtk2.0-dev
libgnomecanvas2-dev
system has libgnomecanvas2-dev
AUTOBUILD_BUILD=/home/paule/autobuild/building
AUTOBUILD_INSTALLED=/home/paule/autobuild/Linux-emsley-vm-ubuntu1404
AUTOBUILD_SOURCES=/home/paule/autobuild/building/sources
BALBES_ROOT=/home/paule/ccp4/ccp4-6.3.0/share/BALBES/Package
BASH=/bin/bash
BASHOPTS=cmdhist:complete_fullquote:extquote:force_fignore:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=([0]="1")
BASH_ARGV=([0]="build-it")
BASH_CMDS=()
BASH_LINENO=([0]="19" [1]="0")
BASH_SOURCE=([0]="build-it" [1]="autobuild")
BASH_VERSINFO=([0]="4" [1]="3" [2]="11" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='4.3.11(1)-release'
BINARY_INSTALL_CMD=www-placement
BINSORT_SCR=/tmp/
CBIN=/home/paule/ccp4/ccp4-6.3.0/bin
CCP4=/home/paule/ccp4/ccp4-6.3.0
CCP4I_HELP=/home/paule/ccp4/ccp4-6.3.0/share/ccp4i/help
CCP4I_TCLTK=/usr/bin
CCP4I_TOP=/home/paule/ccp4/ccp4-6.3.0/share/ccp4i
CCP4_BIN=/home/paule/ccp4/ccp4-6.3.0/bin
CCP4_BROWSER=firefox
CCP4_CRANK=1
CCP4_HELPDIR=/home/paule/ccp4/ccp4-6.3.0/help/
CCP4_LIB=/home/paule/ccp4/ccp4-6.3.0/lib
CCP4_MASTER=/home/paule/ccp4
CCP4_OPEN=UNKNOWN
CCP4_SCR=/tmp/
CDOC=/home/paule/ccp4/ccp4-6.3.0/doc
CETC=/home/paule/ccp4/ccp4-6.3.0/etc
CEXAM=/home/paule/ccp4/ccp4-6.3.0/examples
CHTML=/home/paule/ccp4/ccp4-6.3.0/html
CINCL=/home/paule/ccp4/ccp4-6.3.0/include
CLASSPATH=/home/paule/ccp4/ccp4-6.3.0/bin:
CLIB=/home/paule/ccp4/ccp4-6.3.0/lib
CLIBD=/home/paule/ccp4/ccp4-6.3.0/lib/data
CLIBD_MON=/home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/
CLIBS=/home/paule/ccp4/ccp4-6.3.0/lib/libccp4
CPROG=/home/paule/ccp4/ccp4-6.3.0/src
CRANK=/home/paule/ccp4/ccp4-6.3.0/share/ccp4i/crank
DBCCP4I_TOP=/home/paule/ccp4/ccp4-6.3.0/share/dbccp4i
DIRSTACK=()
DYLD_LIBRARY_PATH=/home/paule/ccp4/ccp4-6.3.0/lib
ENABLE_GUILE_COOT=yes
ENABLE_PYTHON_COOT=yes
EUID=1000
GFORTRAN_UNBUFFERED_ALL=1
GFORTRAN_UNBUFFERED_PRECONNECTED=Y
GROUPS=()
HARVESTHOME=/home/paule
HOME=/home/paule
HOST=emsley-vm-ubuntu1404
HOSTNAME=emsley-vm-ubuntu1404
HOSTTYPE=x86_64
IFS=$' \t\n'
LANG=en_US.UTF-8
LD_LIBRARY_PATH=/home/paule/ccp4/ccp4-6.3.0/lib
LOGNAME=paule
LOGS=/home/paule/public_html/build-logs/Linux-emsley-vm-ubuntu1404
MACHTYPE=x86_64-pc-linux-gnu
MANPATH=/home/paule/ccp4/ccp4-6.3.0/man:
MMCIFDIC=/home/paule/ccp4/ccp4-6.3.0/share/ccif/cif_mmdic.lib
MOLREPLIB=/home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/
MOSFLM_EXEC=/home/paule/ccp4/ccp4-6.3.0/bin/ipmosflm
MOSFLM_WISH=/usr/bin/wish
NIGHTLY_DEST_DIR=/home/paule/public_html/software/binaries/nightlies/pre-release
OPTERR=1
OPTIND=1
OS=Linux
OSTYPE=linux-gnu
PATH=/home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2/bin:/home/paule/bin:/home/paule/ccp4/ccp4-6.3.0/share/dbccp4i/bin:/home/paule/ccp4/ccp4-6.3.0/share/ccp4i/bin:/home/paule/ccp4/ccp4-6.3.0/bin:/home/paule/ccp4/ccp4-6.3.0/etc:/usr/bin:/bin:/home/paule/ccp4/ccp4-6.3.0/share/xia2/xia2core//Test:/home/paule/ccp4/ccp4-6.3.0/share/xia2/xia2//Applications:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
PIPESTATUS=([0]="1")
PISA_CONF_FILE=/home/paule/ccp4/ccp4-6.3.0/share/pisa/pisa.cfg
PLOT_COMMAND='lp -s'
PPID=17530
PRINT_COMMAND='lp -s'
PS4='+ '
PUBLIC_FONT84=/home/paule/ccp4/ccp4-6.3.0/lib/data/ccp4/font84.dat
PWD=/home/paule/autobuild
PYTHONPATH=/home/paule/ccp4/ccp4-6.3.0/share/python:
RASMOLPATH=/home/paule/ccp4/ccp4-6.3.0/x-windows/RasMol
SHELL=/bin/sh
SHELLOPTS=braceexpand:hashall:interactive-comments
SHLVL=1
STABLE_DEST_DIR=/home/paule/public_html/software/binaries/stable
TERM=dumb
UID=1000
VERSION=0.3.4.0
XIA2CORE_ROOT=/home/paule/ccp4/ccp4-6.3.0/share/xia2/xia2core/
XIA2_HOME=/home/paule/ccp4/ccp4-6.3.0/share/xia2
XIA2_ROOT=/home/paule/ccp4/ccp4-6.3.0/share/xia2/xia2/
XUSERFILESEARCHPATH=/home/paule/ccp4/ccp4-6.3.0/lib/X11/app-defaults/%N:/usr/lib/X11/app-defaults
_=']'
arch=x86_64
architecture=x86_64
build_coot_prerelease=1
build_type=gtk2-python
ccp4_first_in_path=1
ccp4pathlist='/home/paule/ccp4/ccp4-6.3.0/etc /home/paule/ccp4/ccp4-6.3.0/bin /home/paule/ccp4/ccp4-6.3.0/share/ccp4i/bin /home/paule/ccp4/ccp4-6.3.0/share/dbccp4i/bin'
dep=libgnomecanvas2-dev
dep_list=$'\n       patch\n       m4\n       g++\n       libxext-dev\n       libxmu-dev\n       libxt-dev\n       libc6-dev\n       libglu1-mesa-dev \n       mesa-common-dev\n       libgtk2.0-dev\n       libgnomecanvas2-dev'
dir=/home/paule/ccp4/ccp4-6.3.0/share/dbccp4i/bin
dist_name=ubuntu
dist_ver=14.04
do_nightlies=1
fallback_coot_version=coot-0.4
have_malloc=1
no_proxy=.corp.net.com
processor=GNU/Linux
proxy_host=myproxy.com
proxy_port=800
publish=transfer-to-web-server.sh
publish_logs=publish-logs.sh
run_tests=true
script_version=5.26
shared_lib_ext=so
shared_static_flag=--disable-shared
specs=/home/paule/autobuild/build-scripts/emsley-vm-ubuntu1404-specials
systype=x86_64-ubuntu-14.04
update_config_guess_sub=1
update_libtool=1
use_proxy=
fixup_libcurl () 
{ 
    sed s,-L/usr/lib,, curl-config > curl-config.tmp;
    mv curl-config.tmp curl-config;
    sed s,-L/usr/lib,, lib/libcurl.la > lib/libcurl.la.tmp;
    mv lib/libcurl.la.tmp lib/libcurl.la
}
make_tar () 
{ 
    echo in make_tar args: $1 $2;
    echo in make_tar: in dir: $PWD;
    tar_dir=$1;
    tar_file_name=$2;
    cd $install_top_dir/..;
    if [ -e $tar_dir ]; then
        echo taring nightly... from $tar_dir to $tar_file_name;
        tar czf $tar_file_name $tar_dir;
        status=$?;
        if [ "$status" != 0 ]; then
            echo ERROR:: tar czf $tar_file_name $tar_dir failed.;
            echo ERROR:: while in directory $(pwd);
            echo ERROR:: tar failed > $tar_file_name.md5sum;
            rm $tar_file_name;
        else
            md5sum $tar_file_name > $tar_file_name.md5sum;
            /bin/ls -l $tar_file_name >> $tar_file_name.md5sum;
            echo done tar successfully.;
        fi;
    else
        echo ERROR:: tar target directory $tar_dir does not exist.;
    fi
}
mkdir_maybe () 
{ 
    dir=$1;
    if [ ! -e "$dir" ]; then
        mkdir $dir;
    fi
}
my_exit () 
{ 
    exit_arg=$1;
    shift;
    extra_args=$*;
    echo fail-build $extra_args > $LOGS/$build_type-build-status;
    if [ -e $LOGS/$build_type-test-status ]; then
        rm $LOGS/$build_type-test-status;
    fi;
    exit $exit_arg
}
post_install_slim () 
{ 
    echo we are slimming directory $1;
    fat_dir="$1";
    cleaned_dir="$2";
    clear_type="$3";
    echo fat_dir is $fat_dir;
    echo clear_type is $clear_type;
    echo cleaned_dir is $cleaned_dir;
    mkdir_maybe $cleaned_dir;
    mkdir_maybe $cleaned_dir/bin;
    mkdir_maybe $cleaned_dir/lib;
    if [ "$ENABLE_PYTHON_COOT" = yes ]; then
        mkdir_maybe $cleaned_dir/include;
        mkdir_maybe $cleaned_dir/include/$python_version;
    fi;
    lib_sos=`cd $fat_dir && ls -1 lib/lib*.so*`;
    lib_as=`cd $fat_dir && ls -1 lib/lib*.a`;
    if [ "$clear_type" = "clear-dynamic" ]; then
        keep_lib_archs="$lib_as";
    fi;
    if [ "$clear_type" = "clear-static" ]; then
        keep_lib_archs="$lib_sos";
    fi;
    file_list="etc info man share libexec  	libexec/coot-bin                   	bin/coot                                   bin/findwaters                     	bin/findwaters-real                	bin/findligand bin/findligand-real 	bin/guile                          	bin/density-score-by-residue       	bin/density-score-by-residue-real  	bin/coot.available-comp-id         	bin/coot.compare-dictionaries      	bin/coot.dictionary-bond-distributions 	bin/coot.make-shelx-restraints         bin/curl 	$keep_lib_archs";
    if [ "$ENABLE_PYTHON_COOT" = yes ]; then
        file_list="$file_list html                     lib/$python_version include/$python_version";
    fi;
    echo rsyncing...;
    for file in $file_list;
    do
        dn=$(dirname $file);
        if [ -e $fat_dir/$file ]; then
            rsync -axr $fat_dir/$file $cleaned_dir/$dn;
        else
            echo $fat_dir/$file does not exist;
        fi;
    done;
    echo done rsyncing.
}
setup_ccp4 () 
{ 
    if test "$OS" = Linux; then
        setup_file=/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/include/ccp4.setup-sh;
        if test -e $setup_file; then
            . $setup_file;
        else
            if [ "$systype" = x86_64-centos-6 ]; then
                setup_file=/home/emsley/ccp4/setup-scripts/sh/ccp4.setup;
            else
                if [ "$systype" = x86_64-centos-5 ]; then
                    setup_file=/home/emsley/ccp4/ccp4-6.2.0/include/ccp4.setup-sh;
                else
                    setup_file=setup-ccp4;
                fi;
            fi;
            if test -e $setup_file; then
                echo evaluating $setup_file;
                . $setup_file;
            else
                echo WARNING:: ccp4 setup file $setup_file does not exist.;
            fi;
        fi;
    fi;
    if test "$OS" = Darwin; then
        . /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh;
    fi
}
ssh_copy () 
{ 
    if [ "$do_ssh_copy" = true ]; then
        dir=public_html/software/binaries/nightlies/pre-release/;
        echo ssh_copy copying over files using $HOME/bin/sput-with-dir $bin_tar_file $dir;
        $HOME/bin/sput-with-dir $bin_tar_file $dir;
        if [ -e $bin_tar_file.md5sum ]; then
            $HOME/bin/sput-with-dir $bin_tar_file.md5sum dir;
        fi;
    else
        echo Not ssh copying file to York, $domainname;
    fi
}
ssh_copy_logs_to_biop () 
{ 
    local_log_dir=$1;
    target_dir=$2;
    if [ "$do_ssh_biop_copy" = true ]; then
        echo copying over log files to Biop...;
        target_dir=$2;
        $HOME/bin/sput-with-dir $local_log_dir $target_dir;
    else
        echo Not ssh copying log files to biop;
    fi
}
ssh_copy_to_biop () 
{ 
    bin_tar_file=$1;
    if [ "$do_ssh_biop_copy" = true ]; then
        target_dir=public_html/coot/software/binaries/pre-releases/;
        echo copying over files to Biop: $HOME/bin/sput-with-dir $bin_tar_file $target_dir;
        $HOME/bin/sput-with-dir $bin_tar_file $target_dir;
        if [ -e $bin_tar_file.md5sum ]; then
            echo and also: $HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir;
            $HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir;
        fi;
    else
        echo Not ssh copying file to biop;
    fi
}
test_coot () 
{ 
    echo testing with greg;
    echo testing with greg 1>&2;
    echo currently we are here:;
    pwd;
    date;
    if [ "$1" != "" ]; then
        coot_binary=$1;
    else
        coot_binary=$install_top_dir/libexec/coot-bin;
    fi;
    if test "$run_tests" = true; then
        COOT_PYTHON_DIR=$install_top_dir/share/coot/python;
        PYTHONPATH=$COOT_PYTHON_DIR;
        PYTHONHOME=$install_top_dir;
        export COOT_PYTHON_DIR;
        export PYTHONPATH;
        export PYTHONHOME;
        if [ ! -d greg-tests ]; then
            echo greg-tests dir missing in this directory:;
            pwd;
            return 1;
        fi;
        setup_ccp4;
        cat  > command-line-greg.scm <<EOF
   (use-modules (ice-9 greg))
         (set! greg-tools (list "greg-tests"))
         (set! greg-debug #t)
         (set! greg-verbose 5)
         (let ((r (greg-test-run)))
            (if r
	        (coot-real-exit 0)
	        (coot-real-exit 1)))
EOF

        echo $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm;
        $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm;
        status=$?;
        if [ $status = 0 ]; then
            echo test_coot: coot test passed;
            return 0;
        else
            echo test_coot: coot test failed;
            return 1;
        fi;
    else
        echo run_tests is not true, not testing.;
        return 1;
    fi
}
test_coot_python () 
{ 
    echo testing with python unittest;
    echo testing with python unittest 1>&2;
    echo currently we are here:;
    pwd;
    if test "$run_tests" = true; then
        COOT_PYTHON_DIR=$install_top_dir/share/coot/python;
        PYTHONPATH=$COOT_PYTHON_DIR;
        PYTHONHOME=$install_top_dir;
        export COOT_PYTHON_DIR;
        export PYTHONPATH;
        export PYTHONHOME;
        echo $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py;
        $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py;
        status=$?;
        if [ $status = 0 ]; then
            echo test_coot_python: coot test passed;
            return 0;
        else
            echo test_coot_python: coot test failed;
            return 1;
        fi;
    else
        return 1;
    fi
}
INFO:: MACHTYPE is x86_64-pc-linux-gnu
INFO:: systype is x86_64-ubuntu-14.04
g++ (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

new version path
need_guile_unused_values_patch is true
Testing version of make
GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

This program built for x86_64-pc-linux-gnu
using 4 processors in compilation
MAKE set to make -j4
testing for patch
testing awk type (prefer GNU awk)
GNU Awk 4.0.1
Copyright (C) 1989, 1991-2012 Free Software Foundation.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/.
good, you have an awk from GNU.
Date: 2015-09-07__T10_36_05
checking wget
which wget
/usr/bin/wget
pre_release_files_html /home/paule/autobuild/building/sources/index-pre-release.html
coot_version_tmp : coot-0.8.3-pre-revision-5635 :
clever coot_version succeeded, setting coot_version to coot-0.8.3-pre-revision-5635 from extraction
INFO:: building pre-release and coot_version_pre is coot-0.8.3-pre-revision-5635
DEBUG:: set coot_source_tar_file to http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/coot-0.8.3-pre-revision-5635.tar.gz
INFO:: set the target destination for binary tar file (BINARY_TAR_DEST_DIR) to /home/paule/public_html/software/binaries/nightlies/pre-release
INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is /home/paule/public_html/software/binaries/nightlies/pre-release
coot_version_pre is coot-0.8.3-pre-revision-5635
build_coot_prerelease: 1
release_server_dir http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases
coot_version coot-0.8.3-pre-revision-5635
testing for install_top_dir: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python
INFO:: /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python exists already.
done testing for /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python
ccp4_system_type linux
installation has fftw
installation has curl/libcurl
installation has libidn devel
pkg-config is /usr/bin/pkg-config
pkg-config is new enough 0.26
COOT_CCP4_PACKAGES 
PKG_CONFIG_PATH is now /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/lib/pkgconfig
system/installation has freetype2
glib is not up to date, rebuild glib - maybe.
:::::::: gtk version is at least 2.10
:::::::: gtk version is 2.24.23
gtk is new enough for guile-gtk
installation has Freeglut
installation has libtool
installation has gmp
installation has readline
atempting to run installed guile-config (this may fail, that's OK).
installation has guile
installation has guile-gui
installation has guile-lib
testing for greg using /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/bin/guile
guile greg status 0
installation has greg
installation has python, Python 2.7.8
/home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/bin/python
installation has pygobject
pygtk demo exists, no build pygtk
/home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python
system/installation has the GSL version 1.16
build_gsl is 0
GSL is up to date
INFO:: found /home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/include/gtkglext-1.0/gdk/glext/glext.h
installation has gtkglext
installation has guile-gtk
guile-gtk should not be built
2.30.3
goocanvas: recent enough gtk+ version
goocanvas: recent enough cairo version
goocanvas: goocanvas_args set to --with-goocanvas-prefix=/home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python
SSM is found.
INFO:: shall we build clipper: mmdb not to be built
INFO:: shall we build clipper: fftw not to be built
/home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/include/clipper/ccp4/ccp4_mtz_io.h exist
/home/paule/autobuild/Linux-emsley-vm-ubuntu1404-pre-release-gtk2-python/include/clipper/contrib/sfscale.h exist
not building libccp4:
not building mmdb:
not building ssm:
not building fftw:
not building clipper:
not building freeglut:
not building gtkglext:
not building python:
not building pygobject:
not building pytgtk
not building gmp:
not building libtool:
not building readline:
not building guile:
not building greg:
not building guile-gtk:
not building guile-gui:
not building guile-lib
not building libidn:
not building curl:
not building gsl:
BUILDING coot: version coot-0.8.3-pre-revision-5635, guile=yes, python=yes
using coot version coot-0.8.3-pre-revision-5635
15324 -rw-rw-r-- 1 paule paule 15690159 Sep  7 03:54 /home/paule/autobuild/building/sources/coot-0.8.3-pre-revision-5635.tar.gz
good /home/paule/autobuild/building/sources/coot-0.8.3-pre-revision-5635.tar.gz exists
Mon Sep  7 11:36:09 BST 2015
/home/paule/autobuild/building/emsley-vm-ubuntu1404_2015-09-07__T10_36_05
BUILDING coot: version coot-0.8.3-pre-revision-5635, python=yes
coot build failed, exiting.