gorpipe / gor Goto Github PK

(base) [sguo2@comet-ln3 gor]$ /share/apps/compute/gor/tools/build/install/tools/bin/gorshell
GOR shell - 2.5-SNAPSHOT (git SHA e86b3af)
> gor /home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10
>
(query running)> #
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 32744 bytes for ChunkPool::allocate
# An error report file with more information is saved as:
# /tmp/hs_err_pid14054.log
(base) [sguo2@comet-ln3 gor]$

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/Users/gummi/source/gor/gortools/build/install/gor-scripts/lib/guice-4.2.2.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Chrom	gene_start	gene_end	Gene_Symbol
chr1	131024	134836	RP11-34P13.10

(base) [sguo2@comet-ln2 gor]$ gor
GOR Command Line

Usage:

gor [-v] [COMMAND]

Description:

Command line interface for gor query language and processes.

Options:

  -v, --version   Print version information and exits.

Commands:

  query, q    Execute a gor query, script or template
  help, h     Gives help on gor commands and functions.
  manager, m  Gor table manager operations.
  index, i    Index gor data files
  cache, c    Cache management
  render, r   Render reports and scripts
  info        List general gor information

(c) WuxiNextcode 2019

(base) [sguo2@comet-ln2 gor]$ make build
./gradlew installDist
Downloading https://services.gradle.org/distributions/gradle-6.2.2-all.zip
....................................................................................................................................

Welcome to Gradle 6.2.2!

Here are the highlights of this release:
 - Dependency checksum and signature verification
 - Shareable read-only dependency cache
 - Documentation links in deprecation messages

For more details see https://docs.gradle.org/6.2.2/release-notes.html

Starting a Gradle Daemon (subsequent builds will be faster)
The message received from the daemon indicates that the daemon has disappeared.
Build request sent: Build{id=cc88c77f-e91f-410f-801a-56e37ae6eb7d, currentDir=/projects/ps-janssen4/oasis/bin/gor}
Attempting to read last messages from the daemon log...
Daemon pid: 19520
  log file: /home/sguo2/.sdkman/candidates/gradle/6.4/daemon/6.2.2/daemon-19520.out.log
----- Last  20 lines from daemon log file - daemon-19520.out.log -----
2020-05-06T18:36:10.734-0700 [DEBUG] [org.gradle.launcher.daemon.server.DefaultDaemonConnection] thread 25: Received non-IO message from client: Build{id=cc88c77f-e91f-410f-801a-56e37ae6eb7d, currentDir=/projects/ps-janssen4/oasis/bin/gor}
2020-05-06T18:36:10.735-0700 [INFO] [org.gradle.launcher.daemon.server.DefaultIncomingConnectionHandler] Received command: Build{id=cc88c77f-e91f-410f-801a-56e37ae6eb7d, currentDir=/projects/ps-janssen4/oasis/bin/gor}.
2020-05-06T18:36:10.735-0700 [DEBUG] [org.gradle.launcher.daemon.server.DefaultIncomingConnectionHandler] Starting executing command: Build{id=cc88c77f-e91f-410f-801a-56e37ae6eb7d, currentDir=/projects/ps-janssen4/oasis/bin/gor} with connection: socket connection from /127.0.0.1:46327 to /127.0.0.1:40750.
2020-05-06T18:36:10.737-0700 [ERROR] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] Command execution: started DaemonCommandExecution[command = Build{id=cc88c77f-e91f-410f-801a-56e37ae6eb7d, currentDir=/projects/ps-janssen4/oasis/bin/gor}, connection = DefaultDaemonConnection: socket connection from /127.0.0.1:46327 to /127.0.0.1:40750] after 0.0 minutes of idle
2020-05-06T18:36:10.737-0700 [INFO] [org.gradle.launcher.daemon.server.DaemonRegistryUpdater] Marking the daemon as busy, address: [65d71a9e-06a2-4de5-b556-c93e09edc48c port:46327, addresses:[localhost/127.0.0.1]]
2020-05-06T18:36:10.737-0700 [DEBUG] [org.gradle.launcher.daemon.registry.PersistentDaemonRegistry] Marking busy by address: [65d71a9e-06a2-4de5-b556-c93e09edc48c port:46327, addresses:[localhost/127.0.0.1]]
2020-05-06T18:36:10.738-0700 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Waiting to acquire exclusive lock on daemon addresses registry.
2020-05-06T18:36:10.877-0700 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Lock acquired on daemon addresses registry.
2020-05-06T18:36:11.098-0700 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Releasing lock on daemon addresses registry.
2020-05-06T18:36:11.202-0700 [DEBUG] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] resetting idle timer
2020-05-06T18:36:11.202-0700 [DEBUG] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] daemon is running. Sleeping until state changes.
2020-05-06T18:36:11.203-0700 [INFO] [org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy] Daemon is about to start building Build{id=cc88c77f-e91f-410f-801a-56e37ae6eb7d, currentDir=/projects/ps-janssen4/oasis/bin/gor}. Dispatching build started information...
2020-05-06T18:36:11.203-0700 [DEBUG] [org.gradle.launcher.daemon.server.SynchronizedDispatchConnection] thread 27: dispatching org.gradle.launcher.daemon.protocol.BuildStarted@25f8912c
2020-05-06T18:36:11.205-0700 [DEBUG] [org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment] Configuring env variables: {PATH=/home/sguo2/perl5/bin:/home/sguo2/janssen4/oasis/bin/jdk1.8.0_251/bin:/home/sguo2/.sdkman/candidates/gradle/6.4/bin:/home/sguo2/janssen4/oasis/bin/executable:/home/sguo2/janssen4/oasis/bin/cmake-3.17.2/bin:/home/sguo2/janssen4/oasis/bin/ncbi-blast-2.10.0+/bin:/home/sguo2/bin/gatk-4.1.7.0:/home/sguo2/bin/minimap2:/home/sguo2/bin/bedtools2/bin:/home/sguo2/bin/EMBOSS-6.6.0/emboss:/home/sguo2/bin/mafft-7.464-with-extensions:/home/sguo2/bin/mafft-7.464-without-extensions/core:/home/sguo2/bin/mafft-7.464-with-extensions/binaries:/home/sguo2/bin/bin:/home/sguo2/bin/jvarkit:/home/sguo2/bin/clustalw-2.1/src:/home/sguo2/janssen4/oasis/bin/annovar:/home/sguo2/janssen4/oasis/ensembl-vep-release-99/htslib:/home/sguo2/bin/executable:/home/sguo2/bin/gatk-4.1.6.0:/home/sguo2/bin/gcta_1.93.1beta:/home/sguo2/bin/miniconda3/bin:/home/sguo2/bin/dx-toolkit/bin:/home/sguo2/bin/R-alpha/bin:/home/sguo2/bin/annovar:/home/sguo2/bin/samtools-1.10:/home/sguo2/bin/htslib-1.10.2:/home/sguo2/bin/bcftools-1.10.2:/home/sguo2/bin:/home/sguo2/perl5/bin:/home/sguo2/janssen4/oasis/bin/jdk1.8.0_251/bin:/home/sguo2/janssen4/oasis/bin/executable:/home/sguo2/janssen4/oasis/bin/cmake-3.17.2/bin:/home/sguo2/janssen4/oasis/bin/ncbi-blast-2.10.0+/bin:/home/sguo2/bin/gatk-4.1.7.0:/home/sguo2/bin/minimap2:/home/sguo2/bin/bedtools2/bin:/home/sguo2/bin/EMBOSS-6.6.0/emboss:/home/sguo2/bin/mafft-7.464-with-extensions:/home/sguo2/bin/mafft-7.464-without-extensions/core:/home/sguo2/bin/mafft-7.464-with-extensions/binaries:/home/sguo2/bin/bin:/home/sguo2/bin/jvarkit:/home/sguo2/bin/clustalw-2.1/src:/home/sguo2/janssen4/oasis/bin/annovar:/home/sguo2/janssen4/oasis/ensembl-vep-release-99/htslib:/home/sguo2/bin/executable:/home/sguo2/bin/gatk-4.1.6.0:/home/sguo2/bin/gcta_1.93.1beta:/home/sguo2/bin/miniconda3/bin:/home/sguo2/bin/dx-toolkit/bin:/home/sguo2/bin/R-alpha/bin:/home/sguo2/bin/annovar:/home/sguo2/bin/samtools-1.10:/home/sguo2/bin/htslib-1.10.2:/home/sguo2/bin/bcftools-1.10.2:/home/sguo2/bin:/home/sguo2/.sdkman/candidates/gradle/current/bin:/home/sguo2/perl5/bin:/home/sguo2/bin/miniconda3/bin:/home/sguo2/bin/miniconda3/condabin:/home/sguo2/janssen4/oasis/bin/jdk1.8.0_251/bin:/home/sguo2/janssen4/oasis/bin/executable:/home/sguo2/janssen4/oasis/bin/cmake-3.17.2/bin:/home/sguo2/janssen4/oasis/bin/ncbi-blast-2.10.0+/bin:/home/sguo2/bin/gatk-4.1.7.0:/home/sguo2/bin/minimap2:/home/sguo2/bin/bedtools2/bin:/home/sguo2/bin/EMBOSS-6.6.0/emboss:/home/sguo2/bin/mafft-7.464-with-extensions:/home/sguo2/bin/mafft-7.464-without-extensions/core:/home/sguo2/bin/mafft-7.464-with-extensions/binaries:/home/sguo2/bin/bin:/home/sguo2/bin/jvarkit:/home/sguo2/bin/clustalw-2.1/src:/home/sguo2/janssen4/oasis/bin/annovar:/home/sguo2/janssen4/oasis/ensembl-vep-release-99/htslib:/home/sguo2/bin/executable:/home/sguo2/bin/gatk-4.1.6.0:/home/sguo2/bin/gcta_1.93.1beta:/home/sguo2/bin/miniconda3/bin:/home/sguo2/bin/dx-toolkit/bin:/home/sguo2/bin/R-alpha/bin:/home/sguo2/bin/annovar:/home/sguo2/bin/samtools-1.10:/home/sguo2/bin/htslib-1.10.2:/home/sguo2/bin/bcftools-1.10.2:/home/sguo2/bin:/opt/mvapich2/intel/ib/bin:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/bin/intel64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/sdsc/bin:/opt/sdsc/sbin:/opt/ibutils/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/home/sguo2/bin, PERL_MM_OPT=INSTALL_BASE=/home/sguo2/perl5, HISTCONTROL=ignoredups, SDKMAN_VERSION=5.8.1+484, XDG_DATA_DIRS=/home/sguo2/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share, TBBROOT=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/tbb, CONDA_DEFAULT_ENV=base, MODULEPATH=/opt/modulefiles/mpi/.intel:/opt/modulefiles/mpi:/opt/modulefiles/compilers:/opt/modulefiles/applications:/usr/share/Modules/modulefiles:/etc/modulefiles, CONDA_PYTHON_EXE=/home/sguo2/bin/miniconda3/bin/python, MIC_LD_LIBRARY_PATH=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/compiler/lib/mic:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl/lib/mic:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/tbb/lib/mic, MPIHOME=/opt/mvapich2/intel/ib, INTEL_LICENSE_FILE=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/licenses:/opt/intel/licenses:/root/intel/licenses, _LMFILES_=/opt/modulefiles/compilers/intel/2018.1.163:/opt/modulefiles/mpi/mvapich2_ib/2.3.2, CONDA_PREFIX=/home/sguo2/bin/miniconda3, MPM_LAUNCHER=/opt/intel/2018.1.163/debugger_YEAR/mpm/intel64_igfx/bin/start_mpm.sh, PERL_MB_OPT=--install_base "/home/sguo2/perl5", MV2_ALLTOALL_TUNING=2, MAIL=/var/spool/mail/sguo2, FPATH=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl/include, LD_LIBRARY_PATH=/opt/mvapich2/intel/ib/lib:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/compiler/lib/intel64_lin:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/ipp/../compiler/lib/intel64:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/ipp/lib/intel64:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64/gcc4.4, SDKMAN_DIR=/home/sguo2/.sdkman, LOGNAME=sguo2, INCLUDE=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl/include, PWD=/home/sguo2/janssen4/oasis/bin/gor, INFOPATH=/opt/intel/2018.1.163/documentation_YEAR/en/debugger/gdb-ia/info/:/opt/intel/2018.1.163/documentation_YEAR/en/debugger/gdb-mic/info, PYTHONPATH=/opt/sdsc/lib, LESSOPEN=||/usr/bin/lesspipe.sh %s, SHELL=/bin/bash, QT_GRAPHICSSYSTEM_CHECKED=1, INTEL_PYTHONHOME=/opt/intel/2018.1.163/debugger_YEAR/gdb/intel64/share/gdb/python, QTINC=/usr/lib64/qt-3.3/include, SDKMAN_CANDIDATES_API=https://api.sdkman.io/2, LM_LICENSE_FILE=/opt/flexlm/license/license.dat, OLDPWD=/home/sguo2/janssen4/oasis/bin/gor, MKL_ROOT=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl, ROCKSROOT=/opt/rocks/share/devel, INTELHOME=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux, LIBRARY_PATH=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/compiler/lib/intel64_lin:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/ipp/../compiler/lib/intel64:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/ipp/lib/intel64:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64/gcc4.4, CONDA_PROMPT_MODIFIER=(base) , 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:, CPATH=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/ipp/include:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl/include:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/tbb/include, SHLVL=1, MKLROOT=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/mkl, LOADEDMODULES=intel/2018.1.163:mvapich2_ib/2.3.2, SDSCDEVEL=/opt/sdsc/devel, MANPATH=/opt/intel/2018.1.163/documentation_2018/en/man/common:/usr/share/man:/usr/local/share/man, CONDA_EXE=/home/sguo2/bin/miniconda3/bin/conda, HISTSIZE=1000, JAVA_HOME=/home/sguo2/janssen4/oasis/bin/jdk1.8.0_251, MAKEFLAGS=, zip_output=/home/sguo2/.sdkman/tmp/gradle-6.4.zip, TERM=xterm, LANG=en_US.UTF-8, XDG_SESSION_ID=1494100, GRADLE_HOME=/home/sguo2/.sdkman/candidates/gradle/current, ANT_HOME=/opt/rocks, IPPROOT=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/ipp, GRADLE_USER_HOME=/home/sguo2/.sdkman/candidates/gradle/6.4, GDBSERVER_MIC=/opt/intel/2018.1.163/debugger_YEAR/gdb/targets/mic/bin/gdbserver, _CE_M=, MFLAGS=, SDSCHOME=/opt/sdsc, PERL5LIB=/home/sguo2/perl5/lib/perl5:/home/sguo2/janssen4/oasis/ensembl-vep-release-99:/home/sguo2/perl5/lib/perl5:/home/sguo2/janssen4/oasis/ensembl-vep-release-99:/home/sguo2/perl5/lib/perl5:/home/sguo2/janssen4/oasis/ensembl-vep-release-99:, CONDA_SHLVL=1, SDKMAN_CANDIDATES_DIR=/home/sguo2/.sdkman/candidates, CVS_RSH=ssh, SSH_TTY=/dev/pts/55, SSH_CLIENT=96.245.69.138 51110 22, L_MKL_TEMP=M_VERS, SDKMAN_PLATFORM=Linux64, USER=sguo2, PDSHROOT=/opt/pdsh, ROLLSROOT=/opt/rocks/share/devel/src/roll, _CE_CONDA=, SSH_CONNECTION=96.245.69.138 51110 198.202.113.253 22, MIC_LIBRARY_PATH=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/compiler/lib/mic:/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/tbb/lib/mic, HOSTNAME=comet-ln2.sdsc.edu, MAKELEVEL=1, MODULESHOME=/usr/share/Modules, QTDIR=/usr/lib64/qt-3.3, NLSPATH=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/compiler/lib/intel64_lin/locale/%l_%t/%N:/opt/intel/2018.1.163/debugger_YEAR/gdb/intel64/share/locale/%l_%t/%N, binary_input=/home/sguo2/.sdkman/tmp/gradle-6.4.bin, BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
}, ROCKS_ROOT=/opt/rocks, XDG_RUNTIME_DIR=/run/user/526189, QTLIB=/usr/lib64/qt-3.3/lib, PERL_LOCAL_LIB_ROOT=/home/sguo2/perl5:/home/sguo2/perl5:/home/sguo2/perl5, HOME=/home/sguo2, GDB_CROSS=/opt/intel/2018.1.163/compilers_and_libraries_2018.1.163/linux/bin/intel64/gdb-mic}
2020-05-06T18:36:11.209-0700 [DEBUG] [org.gradle.launcher.daemon.server.exec.LogToClient] About to start relaying all logs to the client via the connection.
2020-05-06T18:36:11.210-0700 [INFO] [org.gradle.launcher.daemon.server.exec.LogToClient] The client will now receive all logging from the daemon (pid: 19520). The daemon log file: /home/sguo2/.sdkman/candidates/gradle/6.4/daemon/6.2.2/daemon-19520.out.log
2020-05-06T18:36:11.211-0700 [INFO] [org.gradle.launcher.daemon.server.exec.LogAndCheckHealth] Starting build in new daemon [memory: 954.7 MB]
2020-05-06T18:36:11.216-0700 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] The daemon has started executing the build.
2020-05-06T18:36:11.216-0700 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] Executing build with daemon context: DefaultDaemonContext[uid=039a43f4-507d-45b8-92d4-e0dc54d24e86,javaHome=/projects/ps-janssen4/oasis/bin/jdk1.8.0_251,daemonRegistryDir=/home/sguo2/.sdkman/candidates/gradle/6.4/daemon,pid=19520,idleTimeout=10800000,priority=NORMAL,daemonOpts=-Xms256m,-Xmx1024m,-Dfile.encoding=UTF-8,-Duser.country=US,-Duser.language=en,-Duser.variant]
----- End of the daemon log -----


FAILURE: Build failed with an exception.

* What went wrong:
Gradle build daemon disappeared unexpectedly (it may have been killed or may have crashed)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org
make: *** [build] Error 1

(base) [sguo2@comet-ln2 gor]$ git submodule update --init --recursive
(base) [sguo2@comet-ln2 gor]$ make build
./gradlew installDist

FAILURE: Build failed with an exception.

* What went wrong:
Could not create service of type FileAccessTimeJournal using GradleUserHomeScopeServices.createFileAccessTimeJournal().
> Timeout waiting to lock journal cache (/home/sguo2/.gradle/caches/journal-1). It is currently in use by another Gradle instance.
  Owner PID: 6958
  Our PID: 14757
  Owner Operation:
  Our operation:
  Lock file: /home/sguo2/.gradle/caches/journal-1/journal-1.lock

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 1m 1s
make: *** [build] Error 1
(base) [sguo2@comet-ln2 gor]$

make build
./gradlew installDist

ERROR: JAVA_HOME is set to an invalid directory: /usr/java/latest

Please set the JAVA_HOME variable in your environment to match the
location of your Java installation.

make: *** [build] Error 1