build-it-3-3 failed

[sunchang1990]

I checked out the gtk3 branch, commit aea798e
I then tried the autobuild using bash build-it-3-3, but the autobuild failed (log file attached below).

FYI, my OS is centos 7, I have installed cmake 3.23.1, and the centos equivalent packages (libxext-devel,libXt-devel,glibc-devel,mesa-libGLU-devel,gtk2-devel,libgnomecanvas-devel) specified in the INSTALL document.

Thanks!

================================================================
Fri Apr 22 13:35:39 PDT 2022
currently architecture is x86_64
dist is package fedora-release is not installed
dist is package redhat-release is not installed
dist is package redhat-release-workstation is not installed
dist is centos-release
systype: x86_64-centos-7
update_libtool: 1
update_config_guess_sub: 1
AUTOBUILD_BUILD=/home/sunch/autobuild/building
AUTOBUILD_INSTALLED=/home/sunch/autobuild/Linux-Pangu
AUTOBUILD_SOURCES=/home/sunch/autobuild/building/sources
BASH=/usr/bin/bash
BASHOPTS=cmdhist: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-it-3-3")
BASH_VERSINFO=([0]="4" [1]="2" [2]="46" [3]="2" [4]="release" [5]="x86_64-redhat-linux-gnu")
BASH_VERSION='4.2.46(2)-release'
BINARY_INSTALL_CMD=www-placement
CBIN=/home/sunch/Programs/ccp4-7.0/bin
CCP4=/home/sunch/Programs/ccp4-7.0
CCP4I_TCLTK=/home/sunch/Programs/ccp4-7.0/bin
CCP4I_TOP=/home/sunch/Programs/ccp4-7.0/share/ccp4i
CCP4_HELPDIR=/home/sunch/Programs/ccp4-7.0/help/
CCP4_MASTER=/home/sunch/Programs
CCP4_OPEN=UNKNOWN
CCP4_SCR=/tmp/sunch
CCPEM=/home/sunch/Programs/ccpem-1.4.1
CETC=/home/sunch/Programs/ccp4-7.0/etc
CEXAM=/home/sunch/Programs/ccp4-7.0/examples
CHTML=/home/sunch/Programs/ccp4-7.0/html
CINCL=/home/sunch/Programs/ccp4-7.0/include
CLIB=/home/sunch/Programs/ccp4-7.0/lib
CLIBD=/home/sunch/Programs/ccp4-7.0/lib/data
CLIBD_MON=/home/sunch/Programs/ccp4-7.0/lib/data/monomers/
COLORTERM=truecolor
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/sunch/miniconda3/bin/conda
CONDA_PREFIX=/home/sunch/miniconda3
CONDA_PROMPT_MODIFIER='(base) '
CONDA_PYTHON_EXE=/home/sunch/miniconda3/bin/python
CONDA_SHLVL=1
CRANK=/home/sunch/Programs/ccp4-7.0/share/ccp4i/crank
CUDA_ROOT=/usr/local/cuda
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-wf6Nqb0Esc,guid=8fdbc6a58b156cb3d48d725f6247703a
DBUS_STARTER_ADDRESS=unix:abstract=/tmp/dbus-wf6Nqb0Esc,guid=8fdbc6a58b156cb3d48d725f6247703a
DBUS_STARTER_BUS_TYPE=session
DESKTOP_SESSION=gnome-classic
DIRSTACK=()
DISPLAY=:0
EUID=1000
FOR_DISABLE_STACK_TRACE=1
GDMSESSION=gnome-classic
GDM_LANG=en_US.UTF-8
GFORTRAN_UNBUFFERED_PRECONNECTED=Y
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_SHELL_SESSION_MODE=classic
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/2a2420aa_2a12_45fc_9eb8_3a679d3ee0ca
GNOME_TERMINAL_SERVICE=:1.116
GOPATH=/home/sunch/go
GROUPS=()
GSETTINGS_SCHEMA_DIR=/home/sunch/miniconda3/share/glib-2.0/schemas
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
HISTCONTROL=ignoredups
HISTSIZE=1000
HOME=/home/sunch
HOST=Pangu
HOSTNAME=Pangu
HOSTTYPE=x86_64
IFS=$' \t\n'
IMOD_CALIB_DIR=/usr/local/ImodCalib
IMOD_DIR=/usr/local/IMOD
IMOD_JAVADIR=/usr/local/java
IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug
IMOD_QTLIBDIR=/usr/local/IMOD/qtlib
IMSETTINGS_INTEGRATE_DESKTOP=yes
IMSETTINGS_MODULE=none
KDEDIRS=/usr
LANG=en_US.UTF-8
LESSOPEN='||/usr/bin/lesspipe.sh %s'
LIBTBX_BUILD=
LIBTBX_OPATH=
LIBTBX_TMPVAL=
LOADEDMODULES=
LOGNAME=sunch
LOGS=/home/sunch/public_html/build-logs/Linux-Pangu
LS_COLORS='rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:.tar=38;5;9:.tgz=38;5;9:.arc=38;5;9:.arj=38;5;9:.taz=38;5;9:.lha=38;5;9:.lz4=38;5;9:.lzh=38;5;9:.lzma=38;5;9:.tlz=38;5;9:.txz=38;5;9:.tzo=38;5;9:.t7z=38;5;9:.zip=38;5;9:.z=38;5;9:.Z=38;5;9:.dz=38;5;9:.gz=38;5;9:.lrz=38;5;9:.lz=38;5;9:.lzo=38;5;9:.xz=38;5;9:.bz2=38;5;9:.bz=38;5;9:.tbz=38;5;9:.tbz2=38;5;9:.tz=38;5;9:.deb=38;5;9:.rpm=38;5;9:.jar=38;5;9:.war=38;5;9:.ear=38;5;9:.sar=38;5;9:.rar=38;5;9:.alz=38;5;9:.ace=38;5;9:.zoo=38;5;9:.cpio=38;5;9:.7z=38;5;9:.rz=38;5;9:.cab=38;5;9:.jpg=38;5;13:.jpeg=38;5;13:.gif=38;5;13:.bmp=38;5;13:.pbm=38;5;13:.pgm=38;5;13:.ppm=38;5;13:.tga=38;5;13:.xbm=38;5;13:.xpm=38;5;13:.tif=38;5;13:.tiff=38;5;13:.png=38;5;13:.svg=38;5;13:.svgz=38;5;13:.mng=38;5;13:.pcx=38;5;13:.mov=38;5;13:.mpg=38;5;13:.mpeg=38;5;13:.m2v=38;5;13:.mkv=38;5;13:.webm=38;5;13:.ogm=38;5;13:.mp4=38;5;13:.m4v=38;5;13:.mp4v=38;5;13:.vob=38;5;13:.qt=38;5;13:.nuv=38;5;13:.wmv=38;5;13:.asf=38;5;13:.rm=38;5;13:.rmvb=38;5;13:.flc=38;5;13:.avi=38;5;13:.fli=38;5;13:.flv=38;5;13:.gl=38;5;13:.dl=38;5;13:.xcf=38;5;13:.xwd=38;5;13:.yuv=38;5;13:.cgm=38;5;13:.emf=38;5;13:.axv=38;5;13:.anx=38;5;13:.ogv=38;5;13:.ogx=38;5;13:.aac=38;5;45:.au=38;5;45:.flac=38;5;45:.mid=38;5;45:.midi=38;5;45:.mka=38;5;45:.mp3=38;5;45:.mpc=38;5;45:.ogg=38;5;45:.ra=38;5;45:.wav=38;5;45:.axa=38;5;45:.oga=38;5;45:.spx=38;5;45:.xspf=38;5;45:'
MACHTYPE=x86_64-redhat-linux-gnu
MAIL=/var/spool/mail/sunch
MMCIFDIC=/home/sunch/Programs/ccp4-7.0/lib/ccp4/cif_mmdic.lib
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
MODULESHOME=/usr/share/Modules
NIGHTLY_DEST_DIR=/home/sunch/public_html/software/binaries/nightlies/pre-release
OPTERR=1
OPTIND=1
OS=Linux
OSTYPE=linux-gnu
PATH=/home/sunch/autobuild/Linux-Pangu-pre-release-gtk3/bin:/usr/local/phenix-1.20.1-4487/build/bin:/home/sunch/bin:/home/sunch/Programs/cistem-1.0.0-beta:/home/sunch/Documents/git-projects/relion/build/bin:/home/sunch/Programs/ccpem-1.4.1/bin:/home/sunch/Programs/ccp4-7.0/etc:/home/sunch/Programs/ccp4-7.0/bin:/home/sunch/miniconda3/bin:/home/sunch/miniconda3/condabin:/usr/local/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/cuda/bin:/home/sunch/.local/UCSF-Chimera64-1.14/bin:/home/sunch/.local/bin:/home/sunch/Programs/frealign_v9.11/bin:/home/sunch/Programs/julia-1.6.1/bin:/home/sunch/Downloads/Situs_3.1/bin:/home/sunch/Downloads/MAINMAST:/home/sunch/Programs/cryoEF_v1.1.0/bin:/home/sunch/Programs/hole2/hole2/exe:/usr/local/go/bin:/home/sunch/Programs/frealign_v9.11/bin:/home/sunch/Programs/julia-1.6.1/bin:/home/sunch/Downloads/Situs_3.1/bin:/home/sunch/Downloads/MAINMAST:/home/sunch/Programs/cryoEF_v1.1.0/bin:/home/sunch/Programs/hole2/hole2/exe:/usr/local/go/bin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
PHENIX=/usr/local/phenix-1.20.1-4487
PHENIX_VERSION=1.20.1-4487
PIPESTATUS=([0]="1")
PPID=9554
PS4='+ '
PWD=/home/sunch/Documents/git-projects/coot
QT_GRAPHICSSYSTEM_CHECKED=1
QT_IM_MODULE=ibus
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
ROSETTA3=/home/sunch/Programs/rosetta_bin_linux_2020.08.61146_bundle/main/source
ROSETTA3_DB=/home/sunch/Programs/rosetta_bin_linux_2020.08.61146_bundle/main/database
ROSETTA3_TOOLS=/home/sunch/Programs/rosetta_bin_linux_2020.08.61146_bundle/main/tools
SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/4646,unix/unix:/tmp/.ICE-unix/4646
SHELL=/bin/bash
SHELLOPTS=braceexpand:hashall:interactive-comments
SHLVL=3
SSH_AGENT_PID=4784
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SSL_CERT_FILE=/home/sunch/Programs/ccp4-7.0/etc/ssl/cacert.pem
STABLE_DEST_DIR=/home/sunch/public_html/software/binaries/stable
TERM=xterm-256color
UID=1000
USER=sunch
USERNAME=sunch
VTE_VERSION=5202
WINDOWPATH=1
XAUTHORITY=/run/gdm/auth-for-sunch-seRIMY/database
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
XDG_DATA_DIRS=/home/sunch/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/
XDG_MENU_PREFIX=gnome-
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
XDG_SESSION_DESKTOP=gnome-classic
XDG_SESSION_ID=3
XDG_SESSION_TYPE=x11
XDG_VTNR=1
XMODIFIERS=@im=ibus
_=']'
_CE_CONDA=
_CE_M=
arch=x86_64
architecture=x86_64
build_coot_prerelease=1
build_type=gtk3
dist=centos-release
dist_name=centos
dist_ver=7
do_nightlies=1
fallback_coot_version=coot-0.4
gtk_version=3
have_malloc=1
i=centos-release
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=6.02
shared_lib_ext=so
shared_static_flag=--disable-static
specs=/home/sunch/autobuild/build-scripts/Pangu-specials
systype=x86_64-centos-7
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
}
module ()
{
eval /usr/bin/modulecmd bash $*
}
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-make-shelx-restraints bin/coot-dictionary-bond-distributions 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-redhat-linux-gnu
INFO:: systype is x86_64-centos-7
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright (C) 2015 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 3.82
Built for x86_64-redhat-linux-gnu
Copyright (C) 2010 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 4.0.2
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.
cmake version 3.23.1 CMake suite maintained and supported by Kitware (kitware.com/cmake).
found recent cmake
cmake_is_good: true
cmake passes
start_dir /home/sunch/Documents/git-projects/coot
Date: 2022-04-22__T20_35_39
pkg-config is /usr/bin/pkg-config
pkg-config is new enough 0.27.1
checking wget
which wget
/usr/bin/wget
pre_release_files_html /home/sunch/autobuild/building/sources/index-pre-release.html
coot_version_tmp : :
clever coot_version extraction failed, using default.
debug:: wget -P /home/sunch/autobuild/building/sources -O /home/sunch/autobuild/building/sources/index.html -o /home/sunch/autobuild/building/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/sunch/autobuild/building/sources/index.html
coot_version
INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is /home/sunch/public_html/software/binaries/stable
INFO:: coot_version_pre is
INFO:: build_coot_prerelease is
INFO:: release_server_dir is http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases
INFO:: coot_version is
INFO:: build_type is gtk3
python_libs is LIBS=-L/home/sunch/autobuild/Linux-Pangu-gtk3/lib64
install_top_dir /home/sunch/autobuild/Linux-Pangu-gtk3
COOT_CCP4_PACKAGES
PKG_CONFIG_PATH is now /home/sunch/autobuild/Linux-Pangu-gtk3/lib64/pkgconfig:/home/sunch/autobuild/Linux-Pangu-gtk3/lib/pkgconfig:/home/sunch/autobuild/Linux-Pangu-gtk3/lib/x86_64-linux-gnu/pkgconfig:/lib/pkgconfig
system/installation has freetype2
glib is not up to date, rebuild glib - maybe.
testing for install_top_dir: /home/sunch/autobuild/Linux-Pangu-gtk3
INFO:: /home/sunch/autobuild/Linux-Pangu-gtk3 exists already.
done testing for /home/sunch/autobuild/Linux-Pangu-gtk3
ccp4_system_type linux
installation has fftw
installation has curl/libcurl
installation does not have libidn2, libcurl should be built also
libtool test: looking for /home/sunch/autobuild/Linux-Pangu-gtk3/include/ltdl.h
/home/sunch/autobuild/Linux-Pangu-gtk3/include/ltdl.h
installation has libtool
/home/sunch/autobuild/Linux-Pangu-gtk3
system/installation has the GSL version 1.16
build_gsl is 0
GSL is up to date
SSM is found.
INFO:: shall we build clipper: mmdb not to be built
INFO:: shall we build clipper: fftw not to be built
Python 3.9.12
we have python3
not building libccp4:
not building mmdb:
not building ssm:
not building fftw:
not building clipper:
BUILDING readline:
ffi build - testing existance /home/sunch/autobuild/Linux-Pangu-gtk3/lib/libffi-3.2.1/include/fffi.h
/home/sunch/autobuild/Linux-Pangu-gtk3/lib/libffi-3.2.1/include does not exist
BUILDING libffi 3.2.1:
not building python:
0.61.2
we have meson
not building meson
not building glib:
BUILDING gobject-introspection:
installation has pycairo
BUILDING pygobject:
Fri Apr 22 13:35:56 PDT 2022
/home/sunch/autobuild/building/Pangu_2022-04-22__T20_35_39
BUILDING pygobject 3.36.1:
not building gmp:
not building libtool:
BUILDING libidn:
BUILDING curl:
not building gsl:
not building boost
not building Raster3D render
not building glm
installing pygobject with pip3
pip3 install --upgrade pip
Requirement already satisfied: pip in /home/sunch/autobuild/Linux-Pangu-gtk3/lib/python3.9/site-packages (22.0.4)
pip3 install cython
Requirement already satisfied: cython in /home/sunch/autobuild/Linux-Pangu-gtk3/lib/python3.9/site-packages (0.29.28)
-rw-r--r--. 1 sunch sunch 4855 Apr 21 16:09 /home/sunch/autobuild/Linux-Pangu-gtk3/lib/python3.9/site-packages/numpy-1.19.4-py3.9-linux-x86_64.egg/numpy/lib/_version.py
numpy is found, skip
not building rdkit:
building QED
libunistring skip_this true
not building libunistring
not building gc
not building gmp
BUILDING guile:
BUILDING g-wrap:
BUILDING guile-cairo
guile-lib needs to be installed
some test here
guile-config found
guile-gnome-platform skip_this false
222222222222222 Now Coot.....
Fri Apr 22 13:36:46 PDT 2022
/home/sunch/Documents/git-projects/coot
BUILDING coot
coot build failed, exiting.

[pemsley]

Sorry I didn't deal with this in a timely fashion.