Wed 2 Aug 00:30:02 BST 2017 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-7.3 update_libtool: 1 update_config_guess_sub: 1 AMPSBINDIR=/usr/local/bin/ AUTOBUILD_BUILD=/lmb/home/pemsley/autobuild/building AUTOBUILD_INSTALLED=/lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8 AUTOBUILD_SOURCES=/lmb/home/pemsley/autobuild/building/sources BABEL_DIR=/public/xtal/lmb/src/babel BALBES_ROOT=/public/xtal/balbes/Package BASH=/bin/bash BASHOPTS=cmdhist:extquote:force_fignore:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=([0]="1") BASH_ARGV=([0]="./build-it") BASH_CMDS=() BASH_LINENO=([0]="40" [1]="0") BASH_SOURCE=([0]="./build-it" [1]="autobuild-gcc-4.8.sh") BASH_VERSINFO=([0]="4" [1]="2" [2]="46" [3]="1" [4]="release" [5]="x86_64-redhat-linux-gnu") BASH_VERSION='4.2.46(1)-release' BDG_home=/lmb/home/sharp/buster_snapshot_090517 BINARY_INSTALL_CMD=www-placement CBIN=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/bin CCP4=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5 CCP4I_TCLTK=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/bin CCP4I_TOP=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/share/ccp4i CCP4_HELPDIR=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/help/ CCP4_MASTER=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2 CCP4_OLD=/public/xtal/ccp4_old/bin CCP4_OPEN=UNKNOWN CCP4_SCR=/tmp/pemsley CETC=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/etc CEXAM=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/examples CHOOCHDAT=/public/xtal/Chooch-3.01/data CHTML=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/html CINCL=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/include CLIB=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib CLIBD=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data CLIBD_MON=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/data/monomers/ CNS_ARCH=intel-x86_64bit-linux CNS_CONFDB=/public/xtal/cns/cns_solve_1.3_mp/libraries/confdb CNS_HELPLIB=/public/xtal/cns/cns_solve_1.3_mp/helplib CNS_INST=/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux CNS_LIB=/public/xtal/cns/cns_solve_1.3_mp/libraries CNS_MODULE=/public/xtal/cns/cns_solve_1.3_mp/modules CNS_NMRLIB=/public/xtal/cns/cns_solve_1.3_mp/libraries/nmr CNS_NMRMODULE=/public/xtal/cns/cns_solve_1.3_mp/modules/nmr CNS_SOLVE=/public/xtal/cns/cns_solve_1.3_mp CNS_SOURCE=/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/source CNS_TOPPAR=/public/xtal/cns/cns_solve_1.3_mp/libraries/toppar CNS_XRAYLIB=/public/xtal/cns/cns_solve_1.3_mp/libraries/xray CNS_XTALLIB=/public/xtal/cns/cns_solve_1.3_mp/libraries/xtal CNS_XTALMODULE=/public/xtal/cns/cns_solve_1.3_mp/modules/xtal CRANK=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/share/ccp4i/crank CSDHOME=/lmb/home/public/CSD DIALS=/public/xtal/dials/dials-v1-6-2 DIALS_VERSION=v1-6-2 DIRSTACK=() DISPLAY=localhost:10.0 EDENHOME=/public/xtal/Eden/EDEN EDITOR=vim ENABLE_GUILE_COOT=yes ENABLE_PYTHON_COOT=yes EUID=25202 FITING_NR=500000 GCC=/public/gcc/4_8_3 GFORTRAN_UNBUFFERED_PRECONNECTED=Y GKLIB=/public/xtal/Uppsala/xutil_etc GROUP=pemsley GROUPS=() GR_HOME=/usr/local/src/xmgr-3.01 HKLDIR=/lmb/home/public/xtal/HKL/hklint HKLPATH=/lmb/home/public/xtal/HKL HOME=/lmb/home/pemsley HOST=lg19.lmb.internal HOSTNAME=lg19.lmb.internal HOSTTYPE=x86_64-linux IFS=$' \t\n' KDEDIRS=/usr KMP_STACKSIZE=64m LANG=en_GB.UTF-8 LD_LIBRARY_PATH=/public/gcc/4_8_3/lib64:/public/gcc/4_8_3/lib::/public/ImageMagick/latest/lib LD_RUN_PATH=/public/gcc/4_8_3/lib64:/public/gcc/4_8_3/lib: LESS=semiR LESSOPEN='||/usr/bin/lesspipe.sh %s' LMB_CBIN=/public/xtal/lmb/bin LMB_CDOC=/public/xtal/lmb/doc LMB_CPROG=/public/xtal/lmb/src LMB_LOGGED_IN=Yes LMB_MASTER=/public/xtal LMB_XTAL=/public/xtal/lmb LOGNAME=pemsley LOGS=/lmb/home/pemsley/public_html/build-logs/Linux-lg19.lmb.internal 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=01;05;37;41: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:*.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:*.jpg=01;35:*.jpeg=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:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:' MACHTYPE=x86_64 MAFFT_BINARIES=/public/xtal/mafft/mafft-6.240/binaries MAGICK_HOME=/public/ImageMagick/latest MAIL=/usr/spool/mail/pemsley MAIN=/lmb/home/public/xtal/main2015/ MAIN_CMDS=/lmb/home/public/xtal/main2015/cmds/ MAIN_CMDS_NEW=/lmb/home/public/xtal/main2015/cmds_new/ MAIN_COM=/lmb/home/public/xtal/main2015/doc/com/ MAIN_CONF=/lmb/home/public/xtal/main2015/config/ MAIN_DOC=/lmb/home/public/xtal/main2015/doc/ MAIN_MENU=/lmb/home/public/xtal/main2015/doc/menu/ MAIN_SYMM=/lmb/home/public/xtal/main2015/symm/ MAIN_UTILS=/lmb/home/public/xtal/main2015/utils/ MANPATH=/public/gcc/4_8_3/share/man/man1:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/share/man:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/share/man:/public/ImageMagick/latest/share/man:/gridware/sge/man:/usr/share/man:/usr/X11R6/man:/usr/local/man MMCIFDIC=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/lib/ccp4/cif_mmdic.lib MOSFLM_EXEC=/public/xtal/linux-bin/ipmosflm MRCLMB_CPUTYPE=Z80 MakeTNT_home=/lmb/home/sharp/buster_snapshot_090517 NIGHTLY_DEST_DIR=/lmb/home/pemsley/public_html/software/binaries/nightlies/pre-release OLD_CBIN=/public/xtal/ccp4_old/bin OMP_NUM_THREADS=8 OPTERR=1 OPTIND=1 OS=Linux OSTYPE=linux PATH=/lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2/bin:/lmb/home/pemsley/bin:/public/gcc/4_8_3/bin:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/arp_warp_7.5/bin/bin-x86_64-Linux:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/etc:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/bin:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/ccp4-6.5/share/xia2/Applications:/lmb/home/sharp/buster_snapshot_090517/scripts:/lmb/home/sharp/buster_snapshot_090517/MakeTNT/bin:/lmb/home/sharp/buster_snapshot_090517/autoBUSTER/bin/linux64:/lmb/home/sharp/buster_snapshot_090517/scripts:/lmb/home/sharp/sharp-2.8/scripts:/public/xtal/CCP4/ccp4-64/Prerelease/bin:/public/xtal/linux-bin:/public/xtal/bin:/net/nfs1/public/xtal/dials/dials-v1-6-2/build/bin:/public/xtal/Coot:/lmb/home/public/xtal/autoPROC-1.0/autoPROC/bin/linux64:/net/nfs1/public/xtal/Phenix/Phenix64/phenix-1.12-2829/build/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/utils:.:/lmb/home/public/xtal/main2015/:/lmb/home/public/xtal/main2015//prog:/lmb/home/public/xtal/main2015//config:/lmb/home/public/xtal/CCP4/ccp4-64/arp_warp_7.6/bin/bin-x86_64-Linux:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/etc:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/bin:/public/ImageMagick/latest/bin:/gridware/sge/bin/lx24-amd64:/bin:/usr/bin:/usr/local/bin:/public/com:/public/bin/noarch:/public/bin/i686:/lmb/home/pemsley/bzr:/lmb/home/pemsley/git/bin:/lmb/home/pemsley/scsh/bin:/lmb/home/pemsley/bin:/lmb/home/flong/workplace/LIBG/bin:/lmb/home/pemsley/glade/bin:/lmb/home/pemsley/vim/bin:/lmb/home/pemsley/gqview/bin:/lmb/home/pemsley/bin.Linux:/lmb/home/pemsley/x86_64-linux/bin:/lmb/home/pemsley/build/bin:/lmb/home/pemsley/build/Linux/bin:/usr/sbin:/usr/X11R6/bin:/usr/bin/X11:/lmb/home/public/CSD/bin:/public/xtal/vmd:/public/xtal/Raster3D/Raster3D_2.5f/bin:/public/xtal/situs/Situs_2.6.3/bin:/public/xtal/mafft/mafft-6.240/scripts:/public/xtal/mafft/mafft-6.240/binaries:/public/xtal/script:/public/xtal/imosflm/src:/lmb/home/public/xtal/CCP4/clustalw-2.0.9/bin:/lmb/home/public/xtal/CCP4/fasta-35.4.1/bin:/lmb/home/public/xtal/CCP4/graphviz-2.20.2/bin:/public/xtal/HKL:/public/xtal/XDS-versions/current:/public/xtal/XDS-versions/share:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc PGPLOT_DIR=/public/xtal/pgplot PHENIX=/public/xtal/Phenix/Phenix64/phenix-1.12-2829 PHENIX_ROSETTA_PATH=/public/xtal/rosetta PHENIX_VERSION=1.12-2829 PIPESTATUS=([0]="1") POVINI=/public/xtal/povray3.6_linux/povray.ini PPID=16144 PRINTER=lj2420s6 PS4='+ ' PUBLIC_FONT84=/public/plot84/font84.dat PVM_ARCH=ALPHA PVM_ROOT=/local/src/pvm/pvm3 PWD=/lmb/home/pemsley/autobuild/b-e-l-lg19 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 RASMOLPATH=/public/xtal/Rasmol RASMOLPDBPATH=/nfs/al/pdb REMOTEHOST=hal.lmb.internal ROTING_MC=2900000 ROTING_MI=600000 SGE_CELL=default SGE_CLUSTER_NAME=lmbgrid SGE_ROOT=/gridware/sge SHARP_home=/lmb/home/sharp/sharp-2.8 SHELL=/bin/tcsh SHELLOPTS=braceexpand:hashall:interactive-comments SHLVL=2 SOLVEDIR=/public/xtal/lib/solve/ SSH_CLIENT='10.1.1.24 48082 22' SSH_CONNECTION='10.1.1.24 48082 10.91.192.131 22' SSH_TTY=/dev/pts/6 STABLE_DEST_DIR=/lmb/home/pemsley/public_html/software/binaries/stable STEREO=ON TABLING_MI=1500000 TABLING_MR=5400000 TERM=xterm TOPPAR=/public/xplor/xplor3.8/toppar TRAING_NR=500000 UID=25202 USER=pemsley VENDOR=unknown WWWCPE=http://www.mrc-cpe.cam.ac.uk/cpe-home-page.html WWW_HOME=http://www.mrc-lmb.cam.ac.uk/ XAPPLRESDIR=/lmb/home/pemsley/app-defaults XDG_RUNTIME_DIR=/run/user/25202 XDG_SESSION_ID=3373 XDOC=/public/xtal/doc XPLOR=/public/xplor/xplor3.8 XUSERFILESEARCHPATH=/lmb/home/pemsley/app-defaults/%N _=']' __GL_FSAA_MODE=5 arch=x86_64 architecture=x86_64 arpwarphome=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/arp_warp_7.5 autoPROC_home=/lmb/home/public/xtal/autoPROC-1.0 build_coot_prerelease=1 build_type=gtk2-python dist=sl-release dist_name=sl dist_ver=7.3 do_nightlies=1 fallback_coot_version=coot-0.4 have_malloc=1 i=sl-release identifier=x86_64-Linux motifdir=/public/xtal/UCL/Promotif n_proc=12 nameprocessor=x86_64 namesystem=Linux no_proxy=.corp.net.com node=lg19.lmb.internal processor=GNU/Linux proxy_host=myproxy.com proxy_port=800 publish=: publish_logs=publish-logs.sh run_second_test=true run_tests=true script_version=5.26 shared_lib_ext=so shared_static_flag=--disable-shared specs=/lmb/home/pemsley/autobuild/build-scripts/lg19.lmb.internal-specials systype=x86_64-scientific-linux-7.3 testccp=0 update_config_guess_sub=1 update_libtool=1 use_proxy= warpbin=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/arp_warp_7.5/bin/bin-x86_64-Linux warpdoc=/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-6.5-i2/arp_warp_7.5/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 <&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 INFO:: systype is x86_64-scientific-linux-7.3 g++ (GCC) 4.8.3 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. new version path need_guile_unused_values_patch is true Testing version of make GNU Make 3.82 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: 2017-08-01__T23_30_02 checking wget which wget /bin/wget pre_release_files_html /lmb/home/pemsley/autobuild/building/sources/index-pre-release.html coot_version_tmp : coot-0.8.9-pre-revision-6870 : clever coot_version succeeded, setting coot_version to coot-0.8.9-pre-revision-6870 from extraction debug:: wget -P /lmb/home/pemsley/autobuild/building/sources -O /lmb/home/pemsley/autobuild/building/sources/index.html -o /lmb/home/pemsley/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-pre-revision-6870 DEBUG:: set coot_source_tar_file to http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/coot-0.8.9-pre-revision-6870.tar.gz INFO:: set the target destination for binary tar file (BINARY_TAR_DEST_DIR) to /lmb/home/pemsley/public_html/software/binaries/nightlies/pre-release INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is /lmb/home/pemsley/public_html/software/binaries/nightlies/pre-release coot_version_pre is coot-0.8.9-pre-revision-6870 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-pre-revision-6870 testing for install_top_dir: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python INFO:: /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python exists already. done testing for /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python ccp4_system_type linux fftw should be built curl should be built system does not have libidn installation does not have libidn, libcurl should be built also pkg-config is /bin/pkg-config pkg-config is new enough 0.27.1 COOT_CCP4_PACKAGES PKG_CONFIG_PATH is now /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-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 2.24.28 gtk is new enough for guile-gtk freeglut should be built libtool should be built 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 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=/lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python SSM is found. INFO:: shall we build clipper: mmdb not to be built not building libccp4: not building mmdb: not building ssm: BUILDING fftw: BUILDING clipper: BUILDING freeglut: BUILDING gtkglext: status from gtkglext build was 0 BUILDING goocanvas BUILDING Python 2.7.12: wget -N -P /lmb/home/pemsley/autobuild/building/sources http://www.python.org/ftp/python/2.7.12/Python-2.7.12.tgz got Python-2.7.12.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 /lmb/home/pemsley/autobuild/building/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 coot-0.8.9-pre-revision-6870, guile=yes, python=yes using coot version coot-0.8.9-pre-revision-6870 1 -rw-r--r-- 1 pemsley pemsley 19021660 Jul 19 00:18 /lmb/home/pemsley/autobuild/building/sources/coot-0.8.9-pre-revision-6870.tar.gz good /lmb/home/pemsley/autobuild/building/sources/coot-0.8.9-pre-revision-6870.tar.gz exists Wed 2 Aug 00:39:46 BST 2017 /lmb/home/pemsley/autobuild/building/lg19.lmb.internal_2017-08-01__T23_30_02 BUILDING coot: version coot-0.8.9-pre-revision-6870, python=yes coot build was good. done coot build. INSTALLING refmac monomer library... GETTING reference structures tar... INSTALLING reference structures... we are slimming directory /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python fat_dir is /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python clear_type is clear-static cleaned_dir is /lmb/home/pemsley/autobuild/coot-Linux-x86_64-scientific-linux-7.3-pre-release-gtk2-python rsyncing... /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/etc does not exist /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/libexec/density-score-by-residue-bin does not exist /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/bin/coot-dictionary-bond-distributions does not exist /lmb/home/pemsley/autobuild/Linux-scientific-7.3-el-experimental-gcc-4.8-pre-release-gtk2-python/html does not exist done rsyncing. running tests: ======================== first coot test failed ======================== greg test status: 1 python test status: 0 debug:: input: coot/build-logs/Linux-lg19.lmb.internal debug:: ftp_name: coot/build-logs/Linux-lg19.lmb.internal file is /lmb/home/pemsley/public_html/build-logs/Linux-lg19.lmb.internal/build.log dest_dir is coot/build-logs/Linux-lg19.lmb.internal no server check calling ftp_it /lmb/home/pemsley/public_html/build-logs/Linux-lg19.lmb.internal/build.log coot/build-logs/Linux-lg19.lmb.internal will cd to coot/build-logs/Linux-lg19.lmb.internal will put /lmb/home/pemsley/public_html/build-logs/Linux-lg19.lmb.internal/build.log build.log