Thu 2 Jan 17:04:58 GMT 2020 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 package centos-release is not installed dist is sl-release systype: x86_64-scientific-linux-7.6 update_libtool: 1 update_config_guess_sub: 1 AUTOBUILD_BUILD=/d/emsley/autobuild/building AUTOBUILD_INSTALLED=/d/emsley/autobuild/install AUTOBUILD_SOURCES=/d/emsley/autobuild/building/sources BASH=/usr/bin/bash BASHOPTS=cmdhist:extquote:force_fignore:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=([0]="1") BASH_ARGV=([0]="/home/emsley/Projects/coot/git/coot/build-it") BASH_CMDS=() BASH_ENV=/usr/share/lmod/lmod/init/bash BASH_LINENO=([0]="20" [1]="0") BASH_SOURCE=([0]="/home/emsley/Projects/coot/git/coot/build-it" [1]="autobuild") 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/emsley/ccp4/ccp4-7.0/bin CCP4=/home/emsley/ccp4/ccp4-7.0 CCP4I_TCLTK=/home/emsley/ccp4/ccp4-7.0/bin CCP4I_TOP=/home/emsley/ccp4/ccp4-7.0/share/ccp4i CCP4_HELPDIR=/home/emsley/ccp4/ccp4-7.0/help/ CCP4_MASTER=/home/emsley/ccp4 CCP4_OPEN=UNKNOWN CCP4_SCR=/d/emsley/scratch CETC=/home/emsley/ccp4/ccp4-7.0/etc CEXAM=/home/emsley/ccp4/ccp4-7.0/examples CHTML=/home/emsley/ccp4/ccp4-7.0/html CINCL=/home/emsley/ccp4/ccp4-7.0/include CLIB=/home/emsley/ccp4/ccp4-7.0/lib CLIBD=/home/emsley/ccp4/ccp4-7.0/lib/data CLIBD_MON=/home/emsley/ccp4/ccp4-7.0/lib/data/monomers/ CRANK=/home/emsley/ccp4/ccp4-7.0/share/ccp4i/crank CVS_RSH=ssh DIRSTACK=() DISPLAY=localhost:10.0 EDITOR=vim ENABLE_GUILE_COOT=yes ENABLE_PYTHON_COOT=yes EUID=1000 GFORTRAN_UNBUFFERED_PRECONNECTED=Y GIT_PAGER=less GROUP=emsley GROUPS=() HOME=/home/emsley HOST=charybdis HOSTNAME=charybdis HOSTTYPE=x86_64-linux IFS=$' \t\n' KDEDIRS=/usr LANG=en_GB.UTF-8 LESS=semiR LESSOPEN='||/usr/bin/lesspipe.sh %s' LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod LMOD_DIR=/usr/share/lmod/lmod/libexec LMOD_PKG=/usr/share/lmod/lmod LMOD_SETTARG_CMD=: LMOD_SETTARG_FULL_SUPPORT=no LMOD_VERSION=7.8.16 LMOD_sys=Linux LOADEDMODULES= LOGNAME=emsley LOGS=/home/emsley/public_html/build-logs/Linux-charybdis 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 MAIL=/var/spool/mail/emsley MANPATH=/home/emsley/ccp4/ccp4-7.0/share/man:/d/emsley/ccp4/ccp4-7.0/share/man:/usr/share/lmod/lmod/share/man: MMCIFDIC=/home/emsley/ccp4/ccp4-7.0/lib/ccp4/cif_mmdic.lib MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core MODULEPATH_ROOT=/usr/share/modulefiles MODULESHOME=/usr/share/lmod/lmod NIGHTLY_DEST_DIR=/home/emsley/public_html/software/binaries/nightlies/pre-release OPTERR=1 OPTIND=1 OS=Linux OSTYPE=linux PATH=/d/emsley/autobuild/install-pre-release-gtk2/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/d/emsley/ccp4/ccp4-7.0/etc:/d/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/ninja/bin:/home/emsley/vim/bin:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/usr/lib/cups/filter:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc PIPESTATUS=([0]="1") PPID=9662 PS4='+ ' PWD=/home/emsley/autobuild QTDIR=/usr/lib64/qt-3.3 QTINC=/usr/lib64/qt-3.3/include QTLIB=/usr/lib64/qt-3.3/lib QT_GRAPHICSSYSTEM_CHECKED=1 QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins REMOTEHOST=atg.lmb.internal SHELL=/bin/tcsh SHELLOPTS=braceexpand:hashall:interactive-comments SHLVL=2 SSH_CLIENT='10.1.1.220 36250 22' SSH_CONNECTION='10.1.1.220 36250 10.91.193.8 22' SSH_TTY=/dev/pts/2 SSL_CERT_FILE=/d/emsley/ccp4/ccp4-7.0/etc/ssl/cacert.pem STABLE_DEST_DIR=/home/emsley/public_html/software/binaries/stable TARG_TITLE_BAR_PAREN=' ' TERM=xterm UID=1000 USER=emsley VENDOR=unknown VK_SDK_PATH=/home/emsley/Projects/nvidia-graphics-samples/vulkansdk/1.1.106.0/x86_64 XAPPLRESDIR=/home/emsley/app-defaults XDG_RUNTIME_DIR=/run/user/1000 XDG_SESSION_ID=58993 XUSERFILESEARCHPATH=/home/emsley/app-defaults/%N _=']' arch=x86_64 architecture=x86_64 build_coot_prerelease=1 build_type=gtk2-python dist=sl-release dist_name=sl dist_ver=7.6 do_nightlies=1 fallback_coot_version=coot-0.4 have_malloc=1 i=sl-release 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_second_test=true run_tests=true script_version=5.35 shared_lib_ext=so shared_static_flag=--disable-shared specs=/home/emsley/autobuild/build-scripts/charybdis-specials systype=x86_64-scientific-linux-7.6 update_config_guess_sub=1 update_libtool=1 use_proxy= clearMT () { eval $($LMOD_DIR/clearMT_cmd bash) } 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 } ml () { eval $($LMOD_DIR/ml_cmd "$@") } module () { eval $($LMOD_CMD bash "$@") && eval $(${LMOD_SETTARG_CMD:-:} -s sh) } 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 <&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 } xSetTitleLmod () { builtin echo -n -e "\033]2;$1\007" } INFO:: MACHTYPE is x86_64 INFO:: systype is x86_64-scientific-linux-7.6 g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36) 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 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. Date: 2020-01-02__T17_04_58 checking wget which wget /usr/bin/wget doing the awk coot-0.8.9.3-pre-revision-7957 coot-0.8.9.3-pre-revision-7969 coot-0.8.9.3-pre-revision-8011 coot-0.8.9.3-pre-revision-8031 coot-0.8.9.3-pre-revision-8032 coot-0.8.9.3-pre-revision-8033 coot-0.8.9.3-pre-revision-8034 pre_release_files_html /d/emsley/autobuild/building/sources/index-pre-release.html coot_version_tmp : coot-0.8.9.3-pre-revision-8034 : clever coot_version succeeded, setting coot_version to coot-0.8.9.3-pre-revision-8034 from extraction debug:: wget -P /d/emsley/autobuild/building/sources -O /d/emsley/autobuild/building/sources/index.html -o /d/emsley/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 coot-0.8.9.3-pre-revision-8034 DEBUG:: set coot_source_tar_file to http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/coot-0.8.9.3-pre-revision-8034.tar.gz INFO:: set the target destination for binary tar file (BINARY_TAR_DEST_DIR) to /home/emsley/public_html/software/binaries/nightlies/pre-release INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is /home/emsley/public_html/software/binaries/nightlies/pre-release coot_version_pre is coot-0.8.9.3-pre-revision-8034 build_coot_prerelease: 1 release_server_dir http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases coot_version coot-0.8.9.3-pre-revision-8034 testing for install_top_dir: /d/emsley/autobuild/install-pre-release-gtk2-python INFO:: /d/emsley/autobuild/install-pre-release-gtk2-python exists already. done testing for /d/emsley/autobuild/install-pre-release-gtk2-python ccp4_system_type linux installation has fftw installation has curl/libcurl installation has libidn pkg-config is /usr/bin/pkg-config pkg-config is new enough 0.27.1 COOT_CCP4_PACKAGES PKG_CONFIG_PATH is now /d/emsley/autobuild/install-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 2.24.31 gtk is new enough for guile-gtk installation has Freeglut installation has libtool system has libgnomecanvas 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 /d/emsley/autobuild/install-pre-release-gtk2-python/bin/guile guile greg status 0 installation has greg installation has python, Python 2.7.15 /d/emsley/autobuild/install-pre-release-gtk2-python/bin/python installation has pygobject pygtk demo exists, no build pygtk /d/emsley/autobuild/install-pre-release-gtk2-python system/installation has the GSL version 1.16 build_gsl is 0 GSL is up to date INFO:: found /d/emsley/autobuild/install-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=/d/emsley/autobuild/install-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 /d/emsley/autobuild/install-pre-release-gtk2-python/include/clipper/ccp4/ccp4_mtz_io.h exist /d/emsley/autobuild/install-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 libidn2: not building curl: not building gsl: not building Raster3D render BUILDING coot: version coot-0.8.9.3-pre-revision-8034, guile=yes, python=yes using coot version coot-0.8.9.3-pre-revision-8034 19276 -rw-r--r-- 1 emsley emsley 19735022 Jan 2 17:01 /d/emsley/autobuild/building/sources/coot-0.8.9.3-pre-revision-8034.tar.gz good /d/emsley/autobuild/building/sources/coot-0.8.9.3-pre-revision-8034.tar.gz exists Thu 2 Jan 17:04:59 GMT 2020 /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58 BUILDING coot: version coot-0.8.9.3-pre-revision-8034, python=yes coot build was good. done coot build. INFO:: installation has refmac monomer library INFO:: installation has reference structures we are slimming directory /d/emsley/autobuild/install-pre-release-gtk2-python fat_dir is /d/emsley/autobuild/install-pre-release-gtk2-python clear_type is clear-static cleaned_dir is /d/emsley/autobuild/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python rsyncing... /d/emsley/autobuild/install-pre-release-gtk2-python/etc does not exist /d/emsley/autobuild/install-pre-release-gtk2-python/libexec/density-score-by-residue-bin does not exist /d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot-dictionary-bond-distributions does not exist /d/emsley/autobuild/install-pre-release-gtk2-python/html does not exist done rsyncing. running tests: ======================== first coot test passed ========----============ in make_tar args: coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python /home/emsley/public_html/software/binaries/nightlies/pre-release/holding/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz in make_tar: in dir: /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre taring nightly... from coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python to /home/emsley/public_html/software/binaries/nightlies/pre-release/holding/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz done tar successfully. cding into coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python from /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/test-tar ln -s ../../coot-0.8.9.3-pre/greg-tests . second coot test... ======================== second coot test passed ======================== INFO:: in /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre and about to copy over README and RELEASE-NOTES to /home/emsley/public_html/software/binaries/nightlies/pre-release about to publish files: transfer-to-web-server.sh /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz /home/emsley/public_html/software/binaries/nightlies/pre-release debug:: input: /home/emsley/public_html/software/binaries/nightlies/pre-release debug:: ftp_name: coot/binaries/pre-releases file is /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz dest_dir is coot/binaries/pre-releases no server check calling ftp_it /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz coot/binaries/pre-releases will cd to coot/binaries/pre-releases will put /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz transfer-to-web-server.sh /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz.md5sum /home/emsley/public_html/software/binaries/nightlies/pre-release debug:: input: /home/emsley/public_html/software/binaries/nightlies/pre-release debug:: ftp_name: coot/binaries/pre-releases file is /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz.md5sum dest_dir is coot/binaries/pre-releases no server check calling ftp_it /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz.md5sum coot/binaries/pre-releases will cd to coot/binaries/pre-releases will put /home/emsley/public_html/software/binaries/nightlies/pre-release/coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz.md5sum coot-0.8.9.3-pre-revision-8034-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz.md5sum transfer-to-web-server.sh --no-server-check ChangeLog file is ChangeLog dest_dir is coot/binaries/pre-releases no server check calling ftp_it ChangeLog coot/binaries/pre-releases will cd to coot/binaries/pre-releases will put ChangeLog ChangeLog transfer-to-web-server.sh --no-server-check coot-README file is coot-README dest_dir is coot/binaries/pre-releases no server check calling ftp_it coot-README coot/binaries/pre-releases will cd to coot/binaries/pre-releases will put coot-README coot-README transfer-to-web-server.sh --no-server-check /home/emsley/public_html/software/binaries/nightlies/pre-release/PRE-RELEASE-NOTES file is /home/emsley/public_html/software/binaries/nightlies/pre-release/PRE-RELEASE-NOTES dest_dir is coot/binaries/pre-releases no server check calling ftp_it /home/emsley/public_html/software/binaries/nightlies/pre-release/PRE-RELEASE-NOTES coot/binaries/pre-releases will cd to coot/binaries/pre-releases will put /home/emsley/public_html/software/binaries/nightlies/pre-release/PRE-RELEASE-NOTES PRE-RELEASE-NOTES done copy of README and RELEASE-NOTES debug:: input: coot/build-logs/Linux-charybdis debug:: ftp_name: coot/build-logs/Linux-charybdis file is /home/emsley/public_html/build-logs/Linux-charybdis/build.log dest_dir is coot/build-logs/Linux-charybdis no server check calling ftp_it /home/emsley/public_html/build-logs/Linux-charybdis/build.log coot/build-logs/Linux-charybdis will cd to coot/build-logs/Linux-charybdis will put /home/emsley/public_html/build-logs/Linux-charybdis/build.log build.log