Log of Meson test suite run on 2021-08-04T17:28:08.982255 Inherited environment: SHELL=/usr/bin/zsh LSCOLORS=Gxfxcxdxbxegedabagacad LESS=-R HISTCONTROL=ignoredups CONDA_EXE=/usr/bin/conda _CE_M='' HISTSIZE=50000 HOSTNAME=toxin.cs.vt.edu JAVA_HOME=/usr/lib/jvm/java-1.11.0-openjdk-amd64 SSH_AUTH_SOCK=/tmp/ssh-XXXXXXEacblF/agent.24291 SSH_AGENT_PID=24292 EDITOR='/opt/emacs/bin/emacsclient -t' PWD=/home/jsmith/build-dirs/rxdock/builddir LOGNAME=jsmith XDG_SESSION_TYPE=tty CONDA_PREFIX=/home/jsmith/.conda/envs/toxcastdata-tools _=/usr/bin/meson MOTD_SHOWN=pam HOME=/home/jsmith LANG=en_US.UTF-8 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;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:*.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:*.webp=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=01;36:*.au=01;36:*.flac=01;36:*.m4a=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:*.oga=01;36:*.opus=01;36:*.spx=01;36:*.xspf=01;36:' CONDA_PROMPT_MODIFIER='(toxcastdata-tools) ' SSH_CONNECTION='206.217.205.28 59272 192.168.2.99 2222' XDG_SESSION_CLASS=user TERM=xterm-256color ZSH=/home/jsmith/.oh-my-zsh _CE_CONDA='' LESSOPEN='||/usr/bin/lesspipe.sh %s' USER=jsmith CONDA_SHLVL=1 VISUAL='/opt/emacs/bin/emacsclient -c -a /opt/emacs/bin/emacs' SHLVL=1 PAGER=less XDG_SESSION_ID=31 CONDA_PYTHON_EXE=/usr/bin/python3 XDG_RUNTIME_DIR=/run/user/1001 SSH_CLIENT='206.217.205.28 59272 2222' CONDA_DEFAULT_ENV=toxcastdata-tools which_declare='typeset -f' KDEDIRS=/usr PATH=/home/jsmith/.conda/envs/toxcastdata-tools/bin:/opt/anaconda3/bin:/usr/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/jsmith/bin:/home/jsmith/bin:/home/jsmith/local/bin:/home/jsmith/bin:/home/jsmith/local/bin:/home/jsmith/bin:/home/jsmith/local/bin:/home/jsmith/bin:/home/jsmith/local/bin DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus MAIL=/var/spool/mail/jsmith SSH_TTY=/dev/pts/2 OLDPWD=/home/jsmith/build-dirs 1/5 cavity-search-1koc FAIL 0.05s exit status 1 21:28:08 MALLOC_PERTURB_=58 RBT_HOME=/home/jsmith/build-dirs/rxdock/tests/data RBT_ROOT=/home/jsmith/build-dirs/rxdock /home/jsmith/build-dirs/rxdock/builddir/rxcmd cavity-search -r /home/jsmith/build-dirs/rxdock/tests/data/1koc.json -W ----------------------------------- output ----------------------------------- Current log verbosity is -1. Supported log verbosities are: -2 (ERROR), -1 (adds WARNING), 0 (adds INFO), 1 (adds DEBUG), and 2 (adds TRACE) Log verbosity can be set using parameter -v and the desired value before the command name, e.g. rxcmd -v 1 dock -i input.sd -o output.sd -n 100 ... WARNING: THE INTERFACE AND THE OUTPUT OF THIS COMMAND IS NOT YET STABLE. Found an issue? Please report it here: https://gitlab.com/rxdock/rxdock/issues ((RxDock version 0.1.0 The RxDock molecular docking program is licensed under GNU LGPL version 3. RxDock is maintained by Vedran Miletić, Patrik Nikolić, and Luka Vretenar. Visit https://www.rxdock.org/ for more information. RxDock command-line interface -- rxcmd -- version 0.1.0 Executable: /home/jsmith/build-dirs/rxdock/builddir/rxcmd Data prefix: /home/jsmith/build-dirs/rxdock Working dir: /home/jsmith/build-dirs/rxdock/builddir Command line: /home/jsmith/build-dirs/rxdock/builddir/rxcmd cavity-search -r /home/jsmith/build-dirs/rxdock/tests/data/1koc.json -W RBT_FILE_PARSE_ERROR at ../lib/CrdFileSource.cxx, line 57 Missing title record terminator (*) in /home/jsmith/build-dirs/rxdock/tests/data/1koc.crd RxDock cavity-search command failed, please look at the error messages above. ------------------------------------------------------------------------------ 2/5 cavity-search-1yet FAIL 0.03s exit status 1 21:28:08 RBT_HOME=/home/jsmith/build-dirs/rxdock/tests/data MALLOC_PERTURB_=232 RBT_ROOT=/home/jsmith/build-dirs/rxdock /home/jsmith/build-dirs/rxdock/builddir/rxcmd cavity-search -r /home/jsmith/build-dirs/rxdock/tests/data/1YET.json -W ----------------------------------- output ----------------------------------- Current log verbosity is -1. Supported log verbosities are: -2 (ERROR), -1 (adds WARNING), 0 (adds INFO), 1 (adds DEBUG), and 2 (adds TRACE) Log verbosity can be set using parameter -v and the desired value before the command name, e.g. rxcmd -v 1 dock -i input.sd -o output.sd -n 100 ... WARNING: THE INTERFACE AND THE OUTPUT OF THIS COMMAND IS NOT YET STABLE. Found an issue? Please report it here: https://gitlab.com/rxdock/rxdock/issues ((RxDock version 0.1.0 The RxDock molecular docking program is licensed under GNU LGPL version 3. RxDock is maintained by Vedran Miletić, Patrik Nikolić, and Luka Vretenar. Visit https://www.rxdock.org/ for more information. RxDock command-line interface -- rxcmd -- version 0.1.0 Executable: /home/jsmith/build-dirs/rxdock/builddir/rxcmd Data prefix: /home/jsmith/build-dirs/rxdock Working dir: /home/jsmith/build-dirs/rxdock/builddir Command line: /home/jsmith/build-dirs/rxdock/builddir/rxcmd cavity-search -r /home/jsmith/build-dirs/rxdock/tests/data/1YET.json -W RBT_FILE_PARSE_ERROR at ../lib/MOL2FileSource.cxx, line 328 Corrupted MOL2 file: not enough fields in BOND RxDock cavity-search command failed, please look at the error messages above. ------------------------------------------------------------------------------ 3/5 cavity-search-1yet-test FAIL 0.02s exit status 1 21:28:09 RBT_HOME=/home/jsmith/build-dirs/rxdock/tests/data MALLOC_PERTURB_=241 RBT_ROOT=/home/jsmith/build-dirs/rxdock /home/jsmith/build-dirs/rxdock/builddir/rxcmd cavity-search -r /home/jsmith/build-dirs/rxdock/tests/data/1YET_test.json -W ----------------------------------- output ----------------------------------- Current log verbosity is -1. Supported log verbosities are: -2 (ERROR), -1 (adds WARNING), 0 (adds INFO), 1 (adds DEBUG), and 2 (adds TRACE) Log verbosity can be set using parameter -v and the desired value before the command name, e.g. rxcmd -v 1 dock -i input.sd -o output.sd -n 100 ... WARNING: THE INTERFACE AND THE OUTPUT OF THIS COMMAND IS NOT YET STABLE. Found an issue? Please report it here: https://gitlab.com/rxdock/rxdock/issues ((RxDock version 0.1.0 The RxDock molecular docking program is licensed under GNU LGPL version 3. RxDock is maintained by Vedran Miletić, Patrik Nikolić, and Luka Vretenar. Visit https://www.rxdock.org/ for more information. RxDock command-line interface -- rxcmd -- version 0.1.0 Executable: /home/jsmith/build-dirs/rxdock/builddir/rxcmd Data prefix: /home/jsmith/build-dirs/rxdock Working dir: /home/jsmith/build-dirs/rxdock/builddir Command line: /home/jsmith/build-dirs/rxdock/builddir/rxcmd cavity-search -r /home/jsmith/build-dirs/rxdock/tests/data/1YET_test.json -W RBT_FILE_PARSE_ERROR at ../lib/MOL2FileSource.cxx, line 328 Corrupted MOL2 file: not enough fields in BOND RxDock cavity-search command failed, please look at the error messages above. ------------------------------------------------------------------------------ 4/5 unit-test FAIL 0.01s exit status 1 21:28:09 MALLOC_PERTURB_=150 RBT_HOME=/home/jsmith/build-dirs/rxdock/tests/data RBT_ROOT=/home/jsmith/build-dirs/rxdock /home/jsmith/build-dirs/rxdock/builddir/unit-test ----------------------------------- output ----------------------------------- *********************************************** The RxDock molecular docking program is licensed under GNU LGPL version 3. RxDock is maintained by Vedran Miletić, Patrik Nikolić, and Luka Vretenar. Visit https://www.rxdock.org/ for more information. Executable: /home/jsmith/build-dirs/rxdock/builddir/unit-test ($Id$)/0.1.0 Library: librxdock.so/0.1.0 RBT_ROOT: /home/jsmith/build-dirs/rxdock RBT_HOME: /home/jsmith/build-dirs/rxdock/tests/data Current dir: /home/jsmith/build-dirs/rxdock/builddir Date: Wed Aug 4 17:28:09 2021 *********************************************** [==========] Running 55 tests from 3 test suites. [----------] Global test environment set-up. [----------] 7 tests from OccupancyTest [ RUN ] OccupancyTest.SolvationSF unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] OccupancyTest.SolvationSF (0 ms) [ RUN ] OccupancyTest.PolarSF unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] OccupancyTest.PolarSF (0 ms) [ RUN ] OccupancyTest.VdwSF unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] OccupancyTest.VdwSF (0 ms) [ RUN ] OccupancyTest.VdwSFSolventModes unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] OccupancyTest.VdwSFSolventModes (1 ms) [ RUN ] OccupancyTest.FlexAtomFactoryReceptor unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] OccupancyTest.FlexAtomFactoryReceptor (0 ms) [ RUN ] OccupancyTest.FlexAtomFactorySolvent unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] OccupancyTest.FlexAtomFactorySolvent (0 ms) [ RUN ] OccupancyTest.FlexAtomFactoryLigand unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] OccupancyTest.FlexAtomFactoryLigand (0 ms) [----------] 7 tests from OccupancyTest (1 ms total) [----------] 42 tests from ChromTest [ RUN ] ChromTest.ChromFactory unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ChromFactory (0 ms) [ RUN ] ChromTest.CloneDestructor unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CloneDestructor (0 ms) [ RUN ] ChromTest.CloneLengthEquals unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CloneLengthEquals (0 ms) [ RUN ] ChromTest.ChromOperatorEquals unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ChromOperatorEquals (0 ms) [ RUN ] ChromTest.ChromOperatorEqualsAfterMutate unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ChromOperatorEqualsAfterMutate (0 ms) [ RUN ] ChromTest.SyncToModel unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.SyncToModel (0 ms) [ RUN ] ChromTest.SyncToModelAfterMutate unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.SyncToModelAfterMutate (0 ms) [ RUN ] ChromTest.SyncToModelAfterReset unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.SyncToModelAfterReset (0 ms) [ RUN ] ChromTest.CloneReset unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CloneReset (0 ms) [ RUN ] ChromTest.MutatedCloneReset unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.MutatedCloneReset (0 ms) [ RUN ] ChromTest.ChromOperatorEqualsAfterRandomise unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ChromOperatorEqualsAfterRandomise (0 ms) [ RUN ] ChromTest.SyncToModelAfterRandomise unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.SyncToModelAfterRandomise (0 ms) [ RUN ] ChromTest.SyncToModelAfterRandomiseReset unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.SyncToModelAfterRandomiseReset (0 ms) [ RUN ] ChromTest.ChromOperatorEqualsAfterMutateReset unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ChromOperatorEqualsAfterMutateReset (0 ms) [ RUN ] ChromTest.ChromOperatorEqualsAfterRandomiseReset unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ChromOperatorEqualsAfterRandomiseReset (0 ms) [ RUN ] ChromTest.NullCrossover unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.NullCrossover (0 ms) [ RUN ] ChromTest.Euler unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.Euler (1 ms) [ RUN ] ChromTest.RepeatedSync unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.RepeatedSync (0 ms) [ RUN ] ChromTest.CompareWithNullChrom unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CompareWithNullChrom (0 ms) [ RUN ] ChromTest.CompareAfterMutate unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CompareAfterMutate (0 ms) [ RUN ] ChromTest.OperatorEqualsWithModifiedThreshold unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.OperatorEqualsWithModifiedThreshold (0 ms) [ RUN ] ChromTest.PopulationConstructor unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.PopulationConstructor (0 ms) [ RUN ] ChromTest.PopulationConstructorZeroSize unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.PopulationConstructorZeroSize (0 ms) [ RUN ] ChromTest.PopulationConstructorNullChromosome unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.PopulationConstructorNullChromosome (0 ms) [ RUN ] ChromTest.PopulationConstructorNullSF unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.PopulationConstructorNullSF (0 ms) [ RUN ] ChromTest.PopulationRWFitness unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.PopulationRWFitness (0 ms) [ RUN ] ChromTest.PopulationRWSelect unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.PopulationRWSelect (0 ms) [ RUN ] ChromTest.PopulationGAstep unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.PopulationGAstep (0 ms) [ RUN ] ChromTest.ModelGetChromUndefinedFlexData unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ModelGetChromUndefinedFlexData (0 ms) [ RUN ] ChromTest.ModelGetChromNullFlexData unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ModelGetChromNullFlexData (0 ms) [ RUN ] ChromTest.ModelGetChrom unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.ModelGetChrom (0 ms) [ RUN ] ChromTest.RandomiseTetheredOrientation unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.RandomiseTetheredOrientation (0 ms) [ RUN ] ChromTest.RandomiseTetheredCOM unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.RandomiseTetheredCOM (0 ms) [ RUN ] ChromTest.RandomiseTetheredDihedral unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.RandomiseTetheredDihedral (0 ms) [ RUN ] ChromTest.MutateTetheredOrientation unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.MutateTetheredOrientation (0 ms) [ RUN ] ChromTest.MutateTetheredCOM unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.MutateTetheredCOM (0 ms) [ RUN ] ChromTest.MutateTetheredDihedral unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.MutateTetheredDihedral (0 ms) [ RUN ] ChromTest.CrossoverTetheredOrientation unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CrossoverTetheredOrientation (1 ms) [ RUN ] ChromTest.CrossoverTetheredCOM unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CrossoverTetheredCOM (0 ms) [ RUN ] ChromTest.CrossoverTetheredDihedral unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.CrossoverTetheredDihedral (0 ms) [ RUN ] ChromTest.RandomiseOccupancy unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.RandomiseOccupancy (0 ms) [ RUN ] ChromTest.OccupancyThreshold unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] ChromTest.OccupancyThreshold (0 ms) [----------] 42 tests from ChromTest (2 ms total) [----------] 6 tests from SearchTest [ RUN ] SearchTest.PRMFactory unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] SearchTest.PRMFactory (0 ms) [ RUN ] SearchTest.HeavyAtomFactory unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] SearchTest.HeavyAtomFactory (0 ms) [ RUN ] SearchTest.GA unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] SearchTest.GA (0 ms) [ RUN ] SearchTest.Simplex unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] SearchTest.Simplex (0 ms) [ RUN ] SearchTest.SimAnn unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] SearchTest.SimAnn (0 ms) [ RUN ] SearchTest.Restart unknown file: Failure C++ exception with description "[json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal" thrown in SetUp(). [ FAILED ] SearchTest.Restart (0 ms) [----------] 6 tests from SearchTest (0 ms total) [----------] Global test environment tear-down [==========] 55 tests from 3 test suites ran. (3 ms total) [ PASSED ] 0 tests. [ FAILED ] 55 tests, listed below: [ FAILED ] OccupancyTest.SolvationSF [ FAILED ] OccupancyTest.PolarSF [ FAILED ] OccupancyTest.VdwSF [ FAILED ] OccupancyTest.VdwSFSolventModes [ FAILED ] OccupancyTest.FlexAtomFactoryReceptor [ FAILED ] OccupancyTest.FlexAtomFactorySolvent [ FAILED ] OccupancyTest.FlexAtomFactoryLigand [ FAILED ] ChromTest.ChromFactory [ FAILED ] ChromTest.CloneDestructor [ FAILED ] ChromTest.CloneLengthEquals [ FAILED ] ChromTest.ChromOperatorEquals [ FAILED ] ChromTest.ChromOperatorEqualsAfterMutate [ FAILED ] ChromTest.SyncToModel [ FAILED ] ChromTest.SyncToModelAfterMutate [ FAILED ] ChromTest.SyncToModelAfterReset [ FAILED ] ChromTest.CloneReset [ FAILED ] ChromTest.MutatedCloneReset [ FAILED ] ChromTest.ChromOperatorEqualsAfterRandomise [ FAILED ] ChromTest.SyncToModelAfterRandomise [ FAILED ] ChromTest.SyncToModelAfterRandomiseReset [ FAILED ] ChromTest.ChromOperatorEqualsAfterMutateReset [ FAILED ] ChromTest.ChromOperatorEqualsAfterRandomiseReset [ FAILED ] ChromTest.NullCrossover [ FAILED ] ChromTest.Euler [ FAILED ] ChromTest.RepeatedSync [ FAILED ] ChromTest.CompareWithNullChrom [ FAILED ] ChromTest.CompareAfterMutate [ FAILED ] ChromTest.OperatorEqualsWithModifiedThreshold [ FAILED ] ChromTest.PopulationConstructor [ FAILED ] ChromTest.PopulationConstructorZeroSize [ FAILED ] ChromTest.PopulationConstructorNullChromosome [ FAILED ] ChromTest.PopulationConstructorNullSF [ FAILED ] ChromTest.PopulationRWFitness [ FAILED ] ChromTest.PopulationRWSelect [ FAILED ] ChromTest.PopulationGAstep [ FAILED ] ChromTest.ModelGetChromUndefinedFlexData [ FAILED ] ChromTest.ModelGetChromNullFlexData [ FAILED ] ChromTest.ModelGetChrom [ FAILED ] ChromTest.RandomiseTetheredOrientation [ FAILED ] ChromTest.RandomiseTetheredCOM [ FAILED ] ChromTest.RandomiseTetheredDihedral [ FAILED ] ChromTest.MutateTetheredOrientation [ FAILED ] ChromTest.MutateTetheredCOM [ FAILED ] ChromTest.MutateTetheredDihedral [ FAILED ] ChromTest.CrossoverTetheredOrientation [ FAILED ] ChromTest.CrossoverTetheredCOM [ FAILED ] ChromTest.CrossoverTetheredDihedral [ FAILED ] ChromTest.RandomiseOccupancy [ FAILED ] ChromTest.OccupancyThreshold [ FAILED ] SearchTest.PRMFactory [ FAILED ] SearchTest.HeavyAtomFactory [ FAILED ] SearchTest.GA [ FAILED ] SearchTest.Simplex [ FAILED ] SearchTest.SimAnn [ FAILED ] SearchTest.Restart 55 FAILED TESTS ------------------------------------------------------------------------------ 5/5 dock-1yet-test FAIL 0.08s killed by signal 6 SIGABRT 21:28:09 MALLOC_PERTURB_=36 RBT_HOME=/home/jsmith/build-dirs/rxdock/tests/data RBT_ROOT=/home/jsmith/build-dirs/rxdock /home/jsmith/build-dirs/rxdock/builddir/rxcmd dock -r /home/jsmith/build-dirs/rxdock/tests/data/1YET_test.json -i /home/jsmith/build-dirs/rxdock/tests/data/1YET_c.sd -p dock.json -n 1 -s 48151623 -o /home/jsmith/build-dirs/rxdock/tests/data/1YET_test_out.sd ----------------------------------- output ----------------------------------- stderr: terminate called after throwing an instance of 'nlohmann::detail::parse_error' what(): [json.exception.parse_error.101] parse error at line 1, column 1: syntax error while parsing value - unexpected end of input; expected '[', '{', or a literal  Loguru caught a signal: SIGABRT Stack trace: 15 0x4102fe /home/jsmith/build-dirs/rxdock/builddir/rxcmd() [0x4102fe] 14 0x7fc961740b75 __libc_start_main + 213 13 0x40fc81 /home/jsmith/build-dirs/rxdock/builddir/rxcmd() [0x40fc81] 12 0x43a2ba /home/jsmith/build-dirs/rxdock/builddir/rxcmd() [0x43a2ba] 11 0x7fc961c91bd8 rxdock::operation::dock(std::string, std::string, bool, std::string, bool, std::string, std::string, std::string, bool, std::string, bool, unsigned long, bool, bool, bool, bool, double, bool, bool, unsigned long) + 4296 10 0x7fc961c8f3f8 nlohmann::detail::parser >::parse(bool, nlohmann::basic_json&) + 888 9 0x7fc961c8d6cd bool nlohmann::detail::parser >::sax_parse_internal > >(nlohmann::detail::json_sax_dom_parser >*) + 253 8 0x7fc961c80d99 nlohmann::detail::json_sax_dom_parser >::parse_error(unsigned long, std::string const&, nlohmann::detail::exception const&) + 377 7 0x7fc961c172b4 /home/jsmith/build-dirs/rxdock/builddir/librxdock.so.0(+0x8b2b4) [0x7fc961c172b4] 6 0x7fc9619b25a9 /lib64/libstdc++.so.6(+0xad5a9) [0x7fc9619b25a9] 5 0x7fc9619b2307 /lib64/libstdc++.so.6(+0xad307) [0x7fc9619b2307] 4 0x7fc9619b229c /lib64/libstdc++.so.6(+0xad29c) [0x7fc9619b229c] 3 0x7fc9619a6a46 /lib64/libstdc++.so.6(+0xa1a46) [0x7fc9619a6a46] 2 0x7fc96173f8a4 abort + 278 1 0x7fc9617562a2 gsignal + 322 0 0x7fc961756320 /lib64/libc.so.6(+0x3d320) [0x7fc961756320] 2021-08-04 17:28:09.058 ( 0.011s) [main thread ] :0 FATL| Signal: SIGABRT ------------------------------------------------------------------------------ Summary of Failures: 1/5 cavity-search-1koc FAIL 0.05s exit status 1 2/5 cavity-search-1yet FAIL 0.03s exit status 1 3/5 cavity-search-1yet-test FAIL 0.02s exit status 1 4/5 unit-test FAIL 0.01s exit status 1 5/5 dock-1yet-test FAIL 0.08s killed by signal 6 SIGABRT Ok: 0 Expected Fail: 0 Fail: 5 Unexpected Pass: 0 Skipped: 0 Timeout: 0