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Mi 29. Apr 10:25:58 CEST 2020
currently architecture is x86_64
systype: x86_64-ubuntu-18.04.4
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
libncurses5-dev
system has libncurses5-dev
libglu1-mesa-dev
system has libglu1-mesa-dev
libjpeg-dev
system has libjpeg-dev
mesa-common-dev
system has mesa-common-dev
libgtk2.0-dev
system has libgtk2.0-dev
libgnomecanvas2-dev
system has libgnomecanvas2-dev
ATSAS=/home/mauricetam/Documents/software/atsas/ATSAS-2.8.4-1
AUTOBUILD_BUILD=/home/mauricetam/Documents/software/coot-0.9/autobuild
AUTOBUILD_INSTALLED=/home/mauricetam/Documents/software/coot-0.9/autobuild/coot
AUTOBUILD_SOURCES=/home/mauricetam/Documents/software/coot-0.9/autobuild/sources
BALBES_ROOT=/home/mauricetam/Documents/software/ccp4-7.0/BALBES
BASH=/bin/bash
BASHOPTS=cmdhist:complete_fullquote:extquote:force_fignore:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="0")
BASH_SOURCE=([0]="build-coot")
BASH_VERSINFO=([0]="4" [1]="4" [2]="20" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='4.4.20(1)-release'
BDG_home=/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319
BINARY_INSTALL_CMD=www-placement
CBIN=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/bin
CCP4=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0
CCP4I_TCLTK=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/bin
CCP4I_TOP=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i
CCP4_HELPDIR=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/help/
CCP4_MASTER=/home/mauricetam/Documents/software/ccp4-7.0
CCP4_OPEN=UNKNOWN
CCP4_SCR=/tmp/mauricetam
CETC=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/etc
CEXAM=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/examples
CHTML=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/html
CINCL=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/include
CLIB=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/lib
CLIBD=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/lib/data
CLIBD_MON=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/lib/data/monomers/
CLUTTER_IM_MODULE=xim
COLORTERM=truecolor
CRANK=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/share/ccp4i/crank
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus
DESKTOP_AUTOSTART_ID=102621d40379030a5215881465943334300000019370007
DESKTOP_MODE=1
DESKTOP_SESSION=ubuntu
DIRSTACK=()
DISPLAY=:0
ENABLE_GUILE_COOT=yes
ENABLE_PYTHON_COOT=yes
EUID=1001
GDMSESSION=ubuntu
GFORTRAN_UNBUFFERED_PRECONNECTED=Y
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_SHELL_SESSION_MODE=ubuntu
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/5de109fa_ddfe_426e_afe1_500b0df78442
GNOME_TERMINAL_SERVICE=:1.80
GPG_AGENT_INFO=/run/user/1001/gnupg/S.gpg-agent:0:1
GROUPS=()
GTK_IM_MODULE=ibus
GTK_MODULES=gail:atk-bridge
HOME=/home/mauricetam
HOST=mauricetam-XPS-13-9380
HOSTNAME=mauricetam-XPS-13-9380
HOSTTYPE=x86_64
IFS=$' \t\n'
IM_CONFIG_PHASE=2
KMP_STACKSIZE=8m
LANG=en_US.UTF-8
LC_ADDRESS=de_DE.UTF-8
LC_IDENTIFICATION=de_DE.UTF-8
LC_MEASUREMENT=de_DE.UTF-8
LC_MONETARY=de_DE.UTF-8
LC_NAME=de_DE.UTF-8
LC_NUMERIC=de_DE.UTF-8
LC_PAPER=de_DE.UTF-8
LC_TELEPHONE=de_DE.UTF-8
LC_TIME=de_DE.UTF-8
LD_LIBRARY_PATH=/home/mauricetam/Documents/software/atsas/ATSAS-2.8.4-1/lib/x86_64-linux-gnu/atsas:
LESSCLOSE='/usr/bin/lesspipe %s %s'
LESSOPEN='| /usr/bin/lesspipe %s'
LIBTBX_BUILD=
LIBTBX_OPATH=
LIBTBX_TMPVAL=
LOGNAME=mauricetam
LOGS=/home/mauricetam/Documents/software/coot-0.9/autobuild/logs
LS_COLORS='rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35
:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:'
MACHTYPE=x86_64-pc-linux-gnu
MMCIFDIC=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/lib/ccp4/cif_mmdic.lib
MakeTNT_home=/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319
NIGHTLY_DEST_DIR=/home/mauricetam/Documents/software/coot-0.9/autobuild
OLDPWD=/home/mauricetam
OPTERR=1
OPTIND=1
OS=Linux
OSTYPE=linux-gnu
PATH=/home/mauricetam/Documents/software/coot-0.9/autobuild/coot-pre-release-gtk2/bin:/home/mauricetam/Documents/software/vina/bin:/home/mauricetam/Documents/software/atsas/ATSAS-2.8.4-1/bin:/home/mauricetam/Documents/software/phenix-1.17.1-3660/phenix-1.17.1-3660/build/bin:/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319/MakeTNT/bin:/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319/autoBUSTER/bin/linux64:/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319/scripts:/home/mauricetam/Documents/software/pymol-open-source-master/bin:/home/mauricetam/Documents/software/chimera/bin:/home/mauricetam/Documents/software/coot/bin:/home/mauricetam/Documents/software/ccp4-7.0/arp_warp_8.0/bin/bin-x86_64-Linux:/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/etc:/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/bin:/home/mauricetam/Documents/software/XDS-INTEL64_Linux_x86_64:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/ga
mes:/usr/local/games:/snap/bin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
PHENIX=/home/mauricetam/Documents/software/phenix-1.17.1-3660/phenix-1.17.1-3660
PHENIX_VERSION=1.17.1-3660
PIPESTATUS=([0]="1")
PPID=2966
PS4='+ '
PWD=/home/mauricetam/Documents/software
QT4_IM_MODULE=xim
QT_ACCESSIBILITY=1
QT_IM_MODULE=ibus
SESSION_MANAGER=local/mauricetam-XPS-13-9380:@/tmp/.ICE-unix/1937,unix/mauricetam-XPS-13-9380:/tmp/.ICE-unix/1937
SHELL=/bin/bash
SHELLOPTS=braceexpand:hashall:interactive-comments
SHLVL=2
SSH_AGENT_PID=2014
SSH_AUTH_SOCK=/run/user/1001/keyring/ssh
SSL_CERT_FILE=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.0/etc/ssl/cacert.pem
STABLE_DEST_DIR=/home/mauricetam/Documents/software/coot-0.9/autobuild
TERM=xterm-256color
TEXTDOMAIN=im-config
TEXTDOMAINDIR=/usr/share/locale/
UBUNTU_MENUPROXY=0
UID=1001
USER=mauricetam
USERNAME=mauricetam
VTE_VERSION=5202
WINDOWPATH=2
XAUTHORITY=/run/user/1001/gdm/Xauthority
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
XDG_CURRENT_DESKTOP=ubuntu:GNOME
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
XDG_MENU_PREFIX=gnome-
XDG_RUNTIME_DIR=/run/user/1001
XDG_SEAT=seat0
XDG_SESSION_DESKTOP=ubuntu
XDG_SESSION_ID=6
XDG_SESSION_TYPE=x11
XDG_VTNR=2
XMODIFIERS=@im=ibus
_=']'
arch=x86_64
architecture=x86_64
build_coot_prerelease=1
build_type=gtk2-python
dep=libgnomecanvas2-dev
dep_list=$'\n patch\n m4\n g++\n libxext-dev\n libxmu-dev\n libxt-dev\n libc6-dev\n libncurses5-dev\n libglu1-mesa-dev \n libjpeg-dev\n mesa-common-dev\n libgtk2.0-dev\n libgnomecanvas2-dev'
dist_name=ubuntu
dist_ver=18.04.4
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=:
publish_logs=:
run_second_test=true
run_tests=false
script_version=5.35
shared_lib_ext=so
shared_static_flag=--disable-shared
specs=/home/mauricetam/autobuild/build-scripts/mauricetam-XPS-13-9380-specials
systype=x86_64-ubuntu-18.04.4
update_config_guess_sub=1
update_libtool=1
use_proxy=
warpbin=/home/mauricetam/Documents/software/ccp4-7.0/arp_warp_8.0/bin/bin-x86_64-Linux
warpdoc=/home/mauricetam/Documents/software/ccp4-7.0/arp_warp_8.0/manual
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-status;
if [ -e $LOGS/$test-status ]; then
rm $LOGS/$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 libexec/findwaters-bin libexec/findligand-bin libexec/mini-rsr-bin libexec/density-score-by-residue-bin bin/coot bin/findwaters bin/findligand bin/guile bin/coot-density-score-by-residue bin/coot-available-comp-id bin/coot-compare-dictionaries bin/coot-dictionary-bond-distributions bin/coot-make-shelx-restraints bin/lidia 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-18.04.4
g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 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 4.1
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
using 8 processors in compilation
MAKE set to make -j8
testing for patch
testing awk type (prefer GNU awk)
GNU Awk 4.1.4, API: 1.1 (GNU MPFR 4.0.1, GNU MP 6.1.2)
Copyright (C) 1989, 1991-2016 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: 2020-04-29__T08_25_59
checking wget
which wget
/usr/bin/wget
doing the awk
pre_release_files_html /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/index-pre-release.html
coot_version_tmp : :
clever coot_version extraction failed, using default.
debug:: wget -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources -O /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/index.html -o /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/wget-e.s.p.log http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/
INFO:: building pre-release and coot_version_pre is
trying to build pre-release coot, but failed to find pre-release version
make a stable release then
examining release server files /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/index.html
coot_version
INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is /home/mauricetam/Documents/software/coot-0.9/autobuild
coot_version_pre is
build_coot_prerelease:
release_server_dir http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases
coot_version
testing for install_top_dir: /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python
INFO:: /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python exists already.
done testing for /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python
ccp4_system_type linux
fftw should be built
curl should be built
installation does not have libidn, libcurl should be built also
pkg-config is /usr/bin/pkg-config
pkg-config is new enough 0.29.1
COOT_CCP4_PACKAGES
PKG_CONFIG_PATH is now /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-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 2.24.32
gtk is new enough for guile-gtk
freeglut should be built
libtool should be built
system has libgnomecanvas
gmp should be built
readline needs to be built
atempting to run installed guile-config (this may fail, that's OK).
guile-config failed. guile should be built
guile-gui needs to be installed
guile-lib needs to be installed
testing for greg using /home/mauricetam/Documents/software/coot/bin/guile
guile greg status 127
greg should be built
python should be built
gsl should be built
gtkglext should be built
installation does not have guile-gtk
guile-gtk.h not found, guile-gtk should be built
2.30.3
goocanvas: recent enough gtk+ version
goocanvas: recent enough cairo version
goocanvas: goocanvas_args set to --with-goocanvas-prefix=/home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python
installation has no mmdb, build mmdb.
SSM not found - needs to be built
mmdb needs to be built, so clipper needs building.
BUILDING: libccp4
ccp4/ccp4_program.c: In function 'ccp4_vers_no':
ccp4/ccp4_program.c:68:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(ccp4version,MAXLEN_PROGVERSION,cfile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ccp4/library_err.c: In function 'CFile_Perror':
ccp4/library_err.c:247:26: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (msg == NULL || msg == '\0') colon = "";
^~
ccp4/library_err.c:247:22: note: did you mean to dereference the pointer?
if (msg == NULL || msg == '\0') colon = "";
^
BUILDING mmdb:
wget -N -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/mmdb2-2.0.19.tar.gz
BUILDING SSM:
BUILDING fftw:
BUILDING clipper:
BUILDING freeglut:
BUILDING gtkglext:
status from gtkglext build was 0
BUILDING goocanvas
BUILDING Python 2.7.15:
wget -N -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources http://www.python.org/ftp/python/2.7.15/Python-2.7.15.tgz
got Python-2.7.15.tgz
post linking python to python2.7
removing old python
linking new...
done python linking.
BUILDING pygobject:
INFO:: pkg-config is new enough to build pygobject
path 1 wget -N -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.8/pygobject-2.8.0.tar.gz
OK got pygobject-2.8.0.tar.gz
BUILDING pygtk:
BUILDING gmp:
BUILDING libtool:
BUILDING readline:
BUILDING guile:
building greg:
BUILDING guile-gtk:
GTK minor version is good enough, 24
BUILDING guile-gui:
BUILDING guile-lib:
BUILDING libidn:
BUILDING curl:
BUILDING gsl:
BUILDING coot: version , guile=yes, python=yes
using coot version
4 -rw-r--r-- 1 mauricetam mauricetam 629 Apr 29 10:45 /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz
good /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz exists
Mi 29. Apr 10:45:18 CEST 2020
/home/mauricetam/Documents/software/coot-0.9/autobuild/mauricetam-XPS-13-9380_2020-04-29__T08_25_59
BUILDING coot: version , python=yes
coot build failed, exiting.
aving to: \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/gsl-1.16.tar.gz\u2019 gsl-1.16.tar.gz 100%[=====================================================================================>] 3,37M 228KB/s in 16s 2020-04-29 10:43:10 (219 KB/s) - \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/gsl-1.16.tar.gz\u2019 saved [3534080/3534080] ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') --2020-04-29 10:44:31-- http://skuld.bmsc.washington.edu/raster3d/Raster3D_3.0-3.tar.gz Resolving skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)... 128.95.235.53 Connecting to skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)|128.95.235.53|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1729356 (1,6M) [application/x-gzip] Saving to: \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/Raster3D_3.0-3.tar.gz\u2019 Raster3D_3.0-3.tar.gz 100%[=====================================================================================>] 1,65M 86,4KB/s in 24s 2020-04-29 10:44:56 (69,0 KB/s) - \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/Raster3D_3.0-3.tar.gz\u2019 saved [1729356/1729356] WARNING: timestamping does nothing in combination with -O. See the manual for details. --2020-04-29 10:44:57-- https://github.com/libgd/libgd/releases/download/gd-2.1.1/libgd-2.1.1.tar.gz Resolving github.com (github.com)... 140.82.118.4 Connecting to github.com (github.com)|140.82.118.4|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/29669711/e01ded48-7394-11e5-9c9b-285ad9d5d5ad?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20200429%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20200429T084457Z&X-Amz-Expires=300&X-Amz-Signature=c7a81a70efe47184ec87c00e8d5209bfa568f8a415eb66e1fc23f331cf2c46d9&X-Amz-SignedHeaders=host&actor_id=0&repo_id=29669711&response-content-disposition=attachment%3B%20filename%3Dlibgd-2.1.1.tar.gz&response-content-type=application%2Foctet-stream [following] --2020-04-29 10:44:57-- https://github-production-release-asset-2e65be.s3.amazonaws.com/29669711/e01ded48-7394-11e5-9c9b-285ad9d5d5ad?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20200429%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20200429T084457Z&X-Amz-Expires=300&X-Amz-Signature=c7a81a70efe47184ec87c00e8d5209bfa568f8a415eb66e1fc23f331cf2c46d9&X-Amz-SignedHeaders=host&actor_id=0&repo_id=29669711&response-content-disposition=attachment%3B%20filename%3Dlibgd-2.1.1.tar.gz&response-content-type=application%2Foctet-stream Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.217.41.180 Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.217.41.180|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 2390586 (2,3M) [application/octet-stream] Saving to: \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/libgd-2.1.1.tar.gz\u2019 libgd-2.1.1.tar.gz 100%[=====================================================================================>] 2,28M 562KB/s in 4,2s 2020-04-29 10:45:02 (562 KB/s) - \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/libgd-2.1.1.tar.gz\u2019 saved [2390586/2390586] ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') make: gfortran: Command not found make: *** [render.o] Error 127 make: *** Waiting for unfinished jobs.... local.c: In function \u2018addlabel_\u2019: local.c:689:9: warning: variable \u2018out_size\u2019 set but not used [-Wunused-but-set-variable] size_t out_size; /* out_size is just a dummy variable */ ^~~~~~~~ local.c:688:40: warning: variable \u2018justify\u2019 set but not used [-Wunused-but-set-variable] char *err, font[128], instring[128], *justify; ^~~~~~~ local.c:683:44: warning: variable \u2018last_z\u2019 set but not used [-Wunused-but-set-variable] static double last_x = 0.0, last_y = 0.0, last_z = 0.0; ^~~~~~ URL transformed to HTTPS due to an HSTS policy --2020-04-29 10:45:17-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 300 Multiple Choices Length: 629 [text/html] Saving to: \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz\u2019 .tar.gz 100%[=====================================================================================>] 629 --.-KB/s in 0s Last-modified header missing -- time-stamps turned off. 2020-04-29 10:45:18 (17,8 MB/s) - \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz\u2019 saved [629/629] gzip: /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz: not in gzip format tar: This does not look like a tar archive tar: Exiting with failure status due to previous errors
Wed 29 Apr 10:35:21 CEST 2020
currently architecture is x86_64
systype: x86_64-ubuntu-18.04.4
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
libncurses5-dev
system has libncurses5-dev
libglu1-mesa-dev
system has libglu1-mesa-dev
libjpeg-dev
system has libjpeg-dev
mesa-common-dev
system has mesa-common-dev
libgtk2.0-dev
system has libgtk2.0-dev
libgnomecanvas2-dev
system has libgnomecanvas2-dev
ATSAS=/home/mauricetam/Documents/software/atsas/ATSAS-2.8.4-1
AUTOBUILD_BUILD=/home/mauricetam/Documents/software/coot-0.9/autobuild
AUTOBUILD_INSTALLED=/home/mauricetam/Documents/software/coot-0.9/autobuild/coot
AUTOBUILD_SOURCES=/home/mauricetam/Documents/software/coot-0.9/autobuild/sources
BALBES_ROOT=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/BALBES
BASH=/bin/bash
BASHOPTS=cmdhist:complete_fullquote:extquote:force_fignore:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="0")
BASH_SOURCE=([0]="build-coot")
BASH_VERSINFO=([0]="4" [1]="4" [2]="20" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='4.4.20(1)-release'
BDG_home=/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319
BINARY_INSTALL_CMD=www-placement
CBIN=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/bin
CCP4=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1
CCP4I_TCLTK=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/bin
CCP4I_TOP=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/share/ccp4i
CCP4_HELPDIR=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/help/
CCP4_MASTER=/home/mauricetam/Documents/software/ccp4-7.0
CCP4_OPEN=UNKNOWN
CCP4_SCR=/tmp/mauricetam
CETC=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/etc
CEXAM=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/examples
CHTML=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/html
CINCL=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/include
CLIB=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/lib
CLIBD=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/lib/data
CLIBD_MON=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/lib/data/monomers/
CLUTTER_IM_MODULE=xim
COLORTERM=truecolor
CRANK=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/share/ccp4i/crank
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
DESKTOP_AUTOSTART_ID=104d00b092e23c67a3158814128630351100000017830007
DESKTOP_SESSION=ubuntu
DIRSTACK=()
DISPLAY=:0
ENABLE_GUILE_COOT=yes
ENABLE_PYTHON_COOT=yes
EUID=1000
GDMSESSION=ubuntu
GFORTRAN_UNBUFFERED_PRECONNECTED=Y
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_SHELL_SESSION_MODE=ubuntu
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/58a5e71f_bf30_469f_b81b_54b73011de87
GNOME_TERMINAL_SERVICE=:1.174
GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1
GROUPS=()
GTK2_MODULES=overlay-scrollbar
GTK_IM_MODULE=ibus
GTK_MODULES=gail:atk-bridge
HOME=/home/mauricetam
HOST=mauricetam-XPS-8900
HOSTNAME=mauricetam-XPS-8900
HOSTTYPE=x86_64
IFS=$' \t\n'
IM_CONFIG_PHASE=2
KMP_STACKSIZE=8m
LANG=en_US.UTF-8
LC_ADDRESS=en_GB.UTF-8
LC_IDENTIFICATION=en_GB.UTF-8
LC_MEASUREMENT=en_GB.UTF-8
LC_MONETARY=en_GB.UTF-8
LC_NAME=en_GB.UTF-8
LC_NUMERIC=en_GB.UTF-8
LC_PAPER=en_GB.UTF-8
LC_TELEPHONE=en_GB.UTF-8
LC_TIME=en_GB.UTF-8
LD_LIBRARY_PATH=/home/mauricetam/Documents/software/atsas/ATSAS-2.8.4-1/lib/x86_64-linux-gnu/atsas:
LESSCLOSE='/usr/bin/lesspipe %s %s'
LESSOPEN='| /usr/bin/lesspipe %s'
LIBTBX_BUILD=
LIBTBX_OPATH=
LIBTBX_TMPVAL=
LOGNAME=mauricetam
LOGS=/home/mauricetam/Documents/software/coot-0.9/autobuild/logs
LS_COLORS='rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35
:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:'
MACHTYPE=x86_64-pc-linux-gnu
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
MMCIFDIC=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/lib/ccp4/cif_mmdic.lib
MakeTNT_home=/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319
NIGHTLY_DEST_DIR=/home/mauricetam/Documents/software/coot-0.9/autobuild
OLDPWD=/home/mauricetam
OPTERR=1
OPTIND=1
OS=Linux
OSTYPE=linux-gnu
PAPERSIZE=a4
PATH=/home/mauricetam/Documents/software/coot-0.9/autobuild/coot-pre-release-gtk2/bin:/home/mauricetam/Documents/software/MGLTools-1.5.6/bin:/home/mauricetam/Documents/software/atsas/ATSAS-2.8.4-1/bin:/home/mauricetam/Documents/software/XDS-INTEL64_Linux_x86_64/:/home/mauricetam/Documents/software/ccp4-7.0/arp_warp_8.0/bin/bin-x86_64-Linux:/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/etc:/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/bin:/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319/MakeTNT/bin:/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319/autoBUSTER/bin/linux64:/home/mauricetam/Documents/software/GPhL/BUSTER_snapshot_20200319/scripts:/home/mauricetam/Documents/software/GPhL/sharp-2.8/scripts:/home/mauricetam/Documents/software/pymol-2.3.0/bin:/home/mauricetam/Documents/software/anisotropyserver/bin:/home/mauricetam/Documents/software/phenix-1.17.1-3660/phenix-1.17.1-3660/build/bin:/home/mauricetam/Documents/software/chimera/bin
/:/home/mauricetam/Documents/software/vina/bin/:/home/mauricetam/Documents/software/shelx/:/home/mauricetam/Documents/software/ccp4-7.0/arp_warp_8.0/bin/bin-x86_64-Linux:/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/etc:/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/bin:/home/mauricetam/Documents/software/coot/bin/:/home/mauricetam/Documents/software/XDS-INTEL64_Linux_x86_64/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
PHENIX=/home/mauricetam/Documents/software/phenix-1.17.1-3660/phenix-1.17.1-3660
PHENIX_VERSION=1.17.1-3660
PIPESTATUS=([0]="1")
PPID=9030
PS4='+ '
PWD=/home/mauricetam/Documents/software
QT4_IM_MODULE=xim
QT_ACCESSIBILITY=1
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
SESSION_MANAGER=local/mauricetam-XPS-8900:@/tmp/.ICE-unix/1783,unix/mauricetam-XPS-8900:/tmp/.ICE-unix/1783
SHARP_home=/home/mauricetam/Documents/software/GPhL/sharp-2.8
SHELL=/bin/bash
SHELLOPTS=braceexpand:hashall:interactive-comments
SHLVL=2
SSH_AGENT_PID=1870
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SSL_CERT_FILE=/home/mauricetam/Documents/software/ccp4-7.0/ccp4-7.1/etc/ssl/cacert.pem
STABLE_DEST_DIR=/home/mauricetam/Documents/software/coot-0.9/autobuild
TERM=xterm-256color
TEXTDOMAIN=im-config
TEXTDOMAINDIR=/usr/share/locale/
UBUNTU_MENUPROXY=0
UID=1000
USER=mauricetam
USERNAME=mauricetam
VTE_VERSION=5202
WINDOWPATH=2
XAUTHORITY=/run/user/1000/gdm/Xauthority
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
XDG_CURRENT_DESKTOP=ubuntu:GNOME
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop:/var/lib/snapd/desktop
XDG_MENU_PREFIX=gnome-
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
XDG_SESSION_DESKTOP=ubuntu
XDG_SESSION_ID=2
XDG_SESSION_TYPE=x11
XDG_VTNR=2
XMODIFIERS=@im=ibus
_=']'
arch=x86_64
architecture=x86_64
build_coot_prerelease=1
build_type=gtk2-python
dep=libgnomecanvas2-dev
dep_list=$'\n patch\n m4\n g++\n libxext-dev\n libxmu-dev\n libxt-dev\n libc6-dev\n libncurses5-dev\n libglu1-mesa-dev \n libjpeg-dev\n mesa-common-dev\n libgtk2.0-dev\n libgnomecanvas2-dev'
dist_name=ubuntu
dist_ver=18.04.4
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=:
publish_logs=:
run_second_test=true
run_tests=false
script_version=5.35
shared_lib_ext=so
shared_static_flag=--disable-shared
specs=/home/mauricetam/autobuild/build-scripts/mauricetam-XPS-8900-specials
systype=x86_64-ubuntu-18.04.4
update_config_guess_sub=1
update_libtool=1
use_proxy=
warpbin=/home/mauricetam/Documents/software/ccp4-7.0/arp_warp_8.0/bin/bin-x86_64-Linux
warpdoc=/home/mauricetam/Documents/software/ccp4-7.0/arp_warp_8.0/manual
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-status;
if [ -e $LOGS/$test-status ]; then
rm $LOGS/$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 libexec/findwaters-bin libexec/findligand-bin libexec/mini-rsr-bin libexec/density-score-by-residue-bin bin/coot bin/findwaters bin/findligand bin/guile bin/coot-density-score-by-residue bin/coot-available-comp-id bin/coot-compare-dictionaries bin/coot-dictionary-bond-distributions bin/coot-make-shelx-restraints bin/lidia 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-18.04.4
g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 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 4.1
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
using 8 processors in compilation
MAKE set to make -j8
testing for patch
testing awk type (prefer GNU awk)
GNU Awk 4.1.4, API: 1.1 (GNU MPFR 4.0.1, GNU MP 6.1.2)
Copyright (C) 1989, 1991-2016 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: 2020-04-29__T08_35_22
checking wget
which wget
/usr/bin/wget
doing the awk
pre_release_files_html /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/index-pre-release.html
coot_version_tmp : :
clever coot_version extraction failed, using default.
debug:: wget -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources -O /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/index.html -o /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/wget-e.s.p.log http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/
INFO:: building pre-release and coot_version_pre is
trying to build pre-release coot, but failed to find pre-release version
make a stable release then
examining release server files /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/index.html
coot_version
INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is /home/mauricetam/Documents/software/coot-0.9/autobuild
coot_version_pre is
build_coot_prerelease:
release_server_dir http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases
coot_version
testing for install_top_dir: /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python
/home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python does not exist
making directory /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python
done testing for /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python
making /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python/lib
ccp4_system_type linux
fftw should be built
curl should be built
installation does not have libidn, libcurl should be built also
pkg-config is /usr/bin/pkg-config
pkg-config is new enough 0.29.1
COOT_CCP4_PACKAGES
PKG_CONFIG_PATH is now /home/mauricetam/Documents/software/coot-0.9/autobuild/coot-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 2.24.32
gtk is new enough for guile-gtk
freeglut should be built
libtool should be built
system has libgnomecanvas
gmp should be built
readline needs to be built
atempting to run installed guile-config (this may fail, that's OK).
guile-config failed. guile should be built
guile-gui needs to be installed
guile-lib needs to be installed
testing for greg using /home/mauricetam/Documents/software/coot/bin//guile
guile greg status 127
greg should be built
python should be built
gsl should be built
gtkglext should be built
installation does not have guile-gtk
guile-gtk.h not found, guile-gtk should be built
2.30.3
goocanvas: recent enough gtk+ version
goocanvas: recent enough cairo version
goocanvas: goocanvas_args set to --with-goocanvas-prefix=/home/mauricetam/Documents/software/coot-0.9/autobuild/coot-gtk2-python
installation has no mmdb, build mmdb.
SSM not found - needs to be built
mmdb needs to be built, so clipper needs building.
BUILDING: libccp4
ccp4/ccp4_program.c: In function 'ccp4_vers_no':
ccp4/ccp4_program.c:68:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(ccp4version,MAXLEN_PROGVERSION,cfile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ccp4/library_err.c: In function 'CFile_Perror':
ccp4/library_err.c:247:26: warning: comparison between pointer and zero character constant [-Wpointer-compare]
if (msg == NULL || msg == '\0') colon = "";
^~
ccp4/library_err.c:247:22: note: did you mean to dereference the pointer?
if (msg == NULL || msg == '\0') colon = "";
^
BUILDING mmdb:
wget -N -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/mmdb2-2.0.19.tar.gz
BUILDING SSM:
BUILDING fftw:
BUILDING clipper:
BUILDING freeglut:
BUILDING gtkglext:
status from gtkglext build was 0
BUILDING goocanvas
BUILDING Python 2.7.15:
wget -N -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources http://www.python.org/ftp/python/2.7.15/Python-2.7.15.tgz
got Python-2.7.15.tgz
post linking python to python2.7
removing old python
linking new...
done python linking.
BUILDING pygobject:
INFO:: pkg-config is new enough to build pygobject
path 1 wget -N -P /home/mauricetam/Documents/software/coot-0.9/autobuild/sources http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.8/pygobject-2.8.0.tar.gz
OK got pygobject-2.8.0.tar.gz
BUILDING pygtk:
BUILDING gmp:
BUILDING libtool:
BUILDING readline:
BUILDING guile:
building greg:
BUILDING guile-gtk:
GTK minor version is good enough, 24
BUILDING guile-gui:
BUILDING guile-lib:
BUILDING libidn:
BUILDING curl:
BUILDING gsl:
BUILDING coot: version , guile=yes, python=yes
using coot version
4 -rw-r--r-- 1 mauricetam mauricetam 629 Apr 29 10:42 /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz
good /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz exists
Wed 29 Apr 10:42:47 CEST 2020
/home/mauricetam/Documents/software/coot-0.9/autobuild/mauricetam-XPS-8900_2020-04-29__T08_35_22
BUILDING coot: version , python=yes
coot build failed, exiting.
Saving to: \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/gsl-1.16.tar.gz\u2019 gsl-1.16.tar.gz 100%[==================================================================================>] 3.37M 2.40MB/s in 1.4s 2020-04-29 10:31:16 (2.40 MB/s) - \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/gsl-1.16.tar.gz\u2019 saved [3534080/3534080] ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') --2020-04-29 10:32:00-- http://skuld.bmsc.washington.edu/raster3d/Raster3D_3.0-3.tar.gz Resolving skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)... 128.95.235.53 Connecting to skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)|128.95.235.53|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1729356 (1.6M) [application/x-gzip] Saving to: \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/Raster3D_3.0-3.tar.gz\u2019 Raster3D_3.0-3.tar.gz 100%[==================================================================================>] 1.65M 431KB/s in 4.6s 2020-04-29 10:32:05 (370 KB/s) - \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/Raster3D_3.0-3.tar.gz\u2019 saved [1729356/1729356] f951: Warning: Nonconforming tab character in column 1 of line 50 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 54 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 55 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 56 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 57 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 58 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 60 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 61 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 62 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 63 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 64 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 66 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 176 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 180 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 181 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 182 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 183 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 184 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 185 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 186 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 187 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 188 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 189 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 190 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 191 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 192 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 196 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 197 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 198 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 199 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 200 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 201 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 202 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 204 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 209 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 210 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 211 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 213 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 214 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 215 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 216 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 217 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 218 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 219 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 220 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 221 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 222 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 224 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 225 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 228 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 229 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 230 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 231 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 233 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 234 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 235 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 236 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 237 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 238 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 239 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 243 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 248 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 249 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 250 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 251 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 252 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 253 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 254 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 255 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 256 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 257 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 258 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 259 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 260 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 261 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 262 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 263 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 264 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 265 [-Wtabs] f951: Warning: Nonconforming tab character in column 4 of line 266 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 272 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 273 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 274 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 279 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 280 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 281 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 284 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 285 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs] f951: Warning: Nonconforming tab character in column 3 of line 292 [-Wtabs] f951: Warning: Nonconforming tab character in column 3 of line 293 [-Wtabs] f951: Warning: Nonconforming tab character in column 3 of line 295 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 300 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 301 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 302 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 303 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 304 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 305 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 308 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 318 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 322 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 323 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 324 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 325 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 326 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 327 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 330 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 331 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 332 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 333 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 334 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 335 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 336 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 337 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 338 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 339 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 340 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 341 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 342 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 343 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 344 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 345 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 347 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 348 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 349 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 350 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 351 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 352 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 353 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 354 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 355 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 356 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 357 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 358 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 360 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 364 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 365 [-Wtabs] qinp.f:52:11: USE LISTS 1 Fatal Error: Can't open module file \u2018lists.mod\u2019 for reading at (1): No such file or directory compilation terminated. make: *** [qinp.o] Error 1 make: *** Waiting for unfinished jobs.... local.c: In function \u2018addlabel_\u2019: local.c:689:9: warning: variable \u2018out_size\u2019 set but not used [-Wunused-but-set-variable] size_t out_size; /* out_size is just a dummy variable */ ^~~~~~~~ local.c:688:40: warning: variable \u2018justify\u2019 set but not used [-Wunused-but-set-variable] char *err, font[128], instring[128], *justify; ^~~~~~~ local.c:683:44: warning: variable \u2018last_z\u2019 set but not used [-Wunused-but-set-variable] static double last_x = 0.0, last_y = 0.0, last_z = 0.0; ^~~~~~ URL transformed to HTTPS due to an HSTS policy --2020-04-29 10:32:10-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/.tar.gz Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100 Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected. HTTP request sent, awaiting response... 300 Multiple Choices Length: 629 [text/html] Saving to: \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz\u2019 .tar.gz 100%[==================================================================================>] 629 --.-KB/s in 0s Last-modified header missing -- time-stamps turned off. 2020-04-29 10:32:11 (23.7 MB/s) - \u2018/home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz\u2019 saved [629/629] gzip: /home/mauricetam/Documents/software/coot-0.9/autobuild/sources/.tar.gz: not in gzip format tar: This does not look like a tar archive tar: Exiting with failure status due to previous errors
