Compile error: Could NOT find Java


#1

I get an error compiling SciDB 15.7 saying Java is not installed, even though I have installed oracle java using sudo apt-get install oracle-java8-installer.

$ java -version
java version "1.8.0_74"
Java(TM) SE Runtime Environment (build 1.8.0_74-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.74-b02, mixed mode)

Any suggestions?
I am running linux mint 17.


$ JAVA_HOME=/usr/lib/jvm/java-8-oracle/ Java_JAVA_EXECUTABLE=/usr/lib/jvm/java-1.8.0-openjdk/bin/java Java_JAR_EXECUTABLE=/usr/lib/jvm/java-1.8.0-openjdk/bin/jar Java_JAVAC_EXECUTABLE=/usr/lib/jvm/java-1.8.0-openjdk/bin/javac Java_JAVAH_EXECUTABLE=/usr/lib/jvm/java-1.8.0-openjdk/bin/javah Java_JAVADOC_EXECUTABLE=/usr/lib/jvm/java-1.8.0-openjdk/bin/javadoc BOOST_INCLUDEDIR=/usr/include ./run.py setuprun.py: WARNING: Deleting old CMakeCache file:/tmp/scidb-15.7.0.9267/stage/build/CMakeCache.txt
WARNING: about to delete *all* contents of /tmp/scidb-15.7.0.9267/stage/build/* [y]|n: y
-- ****************** BEGIN CMakeLists.txt ******************
-- The C compiler identification is GNU 4.9.3
-- The CXX compiler identification is GNU 4.9.3
-- The Fortran compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc-4.9
-- Check for working C compiler: /usr/bin/gcc-4.9 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++-4.9
-- Check for working CXX compiler: /usr/bin/g++-4.9 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran-4.9
-- Check for working Fortran compiler: /usr/bin/gfortran-4.9  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran-4.9 supports Fortran 90
-- Checking whether /usr/bin/gfortran-4.9 supports Fortran 90 -- yes
-- CMAKE_INSTALL_PREFIX not Initialized to default keeping: /tmp/scidb-15.7.0.9267/stage/install
-- Found Subversion: /usr/bin/svn (found version "1.8.8") 
-- Found Git: /usr/bin/git (found version "1.9.1") 
-- Reading revision from file: 9267
-- Build type (use -DCMAKE_BUILD_TYPE=[RelWithDebInfo]/Debug/Release/Profile/CC/Valgrind): Debug
-- DISTRO_NAME_VER is Linux-
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") 
-- Found LibRT: /usr/lib/x86_64-linux-gnu/librt.so  
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   system
--   program_options
--   serialization
--   regex
--   filesystem
--   thread
--   date_time
-- Found Protobuf: /usr/include/google/protobuf  
-- GPB - /usr/lib/x86_64-linux-gnu/libprotobuf.so
-- Found Log4CXX: /usr/lib/liblog4cxx.so  
-- LOG4CXX - /usr/lib/liblog4cxx.so
-- Could NOT find Doxygen (missing:  DOXYGEN_EXECUTABLE) 
-- Found LibPQXX: /usr/lib  
-- Found LibPQ: /usr/bin/pg_config  
-- Found LibPQ: /usr/lib  
-- checking for module 'cppunit'
--   package 'cppunit' not found
-- Found FLEX: /usr/bin/flex  
-- Found BISON: /usr/bin/bison  
-- Found SED: /bin/sed  
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") 
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") 
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Found LibReadline: /usr/lib/x86_64-linux-gnu/libreadline.so  
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found PythonInterp: /usr/bin/python (found version "2.7.6") 
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Could NOT find XSLTPROC (missing:  XSLTPROC_EXECUTABLE) 
-- Could NOT find FOP (missing:  FOP_EXECUTABLE) 
-- Could NOT find docbook.xsl (missing:  DOCBOOK_XSL_FILE) 
-- Looking for malloc_stats
-- Looking for malloc_stats - found
-- ****************** BEGIN src/CMakeLists.txt ******************
-- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libssl.so;/usr/lib/x86_64-linux-gnu/libcrypto.so (found version "1.0.1f") 
-- Configuring /tmp/scidb-15.7.0.9267/src/system/Constants.cpp.in as /tmp/scidb-15.7.0.9267/stage/build/src/system/Constants.cpp
-- Configuring /tmp/scidb-15.7.0.9267/src/system/System.h.in as /tmp/scidb-15.7.0.9267/stage/build/src/system/System.h
-- Configuring /tmp/scidb-15.7.0.9267/src/util/scidb-sample.conf.in as /tmp/scidb-15.7.0.9267/stage/build/bin/packaging_only/scidb-sample.conf
-- **BEGIN util/dmalloc/CMakeLists.txt --------------------------------
-- Debug: CMAKE_C_FLAGS is  -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
-- Debug: CMAKE_CXX_FLAGS is  -std=c++14 -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -fPIC -D__STDC_FORMAT_MACROS -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_LIMIT_MACROS -DPROJECT_ROOT=\"/tmp/scidb-15.7.0.9267/\"
-- Debug: GENERAL_OUTPUT_DIRECTORY is /tmp/scidb-15.7.0.9267/stage/build/bin
-- **END util/dmalloc/CMakeLists.txt --------------------------------
-- ****************** BEGIN src/mpi/CMakeLists.txt ******************
-- WARNING-- using locally installed MPICH2
-- Local MPICH2 path: UNDEFINED_FOR_THIS_PLATFORM
-- WARNING-- using locally installed ScaLAPACK for MPICH2
-- Debug: To refresh/rebuild the local copy of scalapack, remove /tmp/scidb-15.7.0.9267/stage/build/src/mpi/local_scalapack/container.
-- ****************** BEGIN mpi/local_scalapack/CMakeLists.txt ******************
-- DEBUG BLAS_FOUND=TRUE LAPACK_FOUND=TRUE MPICH_FOUND=
-- Debug: SCALAPACK_LIBRARIES is /tmp/scidb-15.7.0.9267/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/libscalapack.a
-- Debug: SCALAPACK_INC_DIR is /tmp/scidb-15.7.0.9267/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/include
CMake Warning at src/mpi/CMakeLists.txt:107 (message):
  MPI not present.  ScaLAPACK-based functionality will NOT be built


CMake Warning at src/mpi/CMakeLists.txt:108 (message):
  Debug: MPI_C_FOUND is , MPI_CXX_FOUND is , MPI_Fortran_FOUND is


CMake Warning at src/mpi/CMakeLists.txt:109 (message):
  Ubuntu Hint: $ sudo apt-get install libopenmpi-dev


-- Debug: FINAL PACKAGE SETTINGS src/mpi ================================>
-- Debug: SCALAPACK_LIBRARIES is /tmp/scidb-15.7.0.9267/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/libscalapack.a
-- Debug: LAPACK_LIBRARIES is /usr/lib/liblapack.so.3gf;/usr/lib/libblas.so.3gf
-- Debug: BLAS_LIBRARIES is /usr/lib/libblas.so.3gf
-- Debug: MPI_LIBRARIES is 
-- Debug: MPI_INCLUDE is 
-- Debug: MPI_Fortran_COMPILER is 
-- Debug: CMAKE_C_FLAGS is  -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
-- Debug: CMAKE_CXX_FLAGS is  -std=c++14 -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -fPIC -D__STDC_FORMAT_MACROS -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_LIMIT_MACROS -DPROJECT_ROOT=\"/tmp/scidb-15.7.0.9267/\" -DOMPI_IGNORE_CXX_SEEK
-- Debug: CMAKE_Fortran_FLAGS is  -fno-f2c -Wline-truncation -I/opt/scidb/15.7/3rdparty/boost/include/boost 
-- Debug: CMAKE_Fortran_COMPLIER is /usr/bin/gfortran-4.9
-- Debug: CMAKE_CXX_COMPILER is /usr/bin/g++-4.9
-- Debug: FINAL PACKAGE SETTINGS <================================
CMake Warning at src/mpi/CMakeLists.txt:171 (message):
  Can't build MPI/ScaLAPACK functionality


CMake Warning at src/mpi/CMakeLists.txt:172 (message):
  because one of the following is missing:


CMake Warning at src/mpi/CMakeLists.txt:173 (message):
  BLAS_FOUND is TRUE


CMake Warning at src/mpi/CMakeLists.txt:174 (message):
  LAPACK_FOUND is TRUE


CMake Warning at src/mpi/CMakeLists.txt:175 (message):
  SCALAPACK_FOUND is 1


CMake Warning at src/mpi/CMakeLists.txt:176 (message):
  MPI_CXX_FOUND is


CMake Warning at src/mpi/CMakeLists.txt:177 (message):
  MPI_Fortran_FOUND is


CMake Warning at src/mpi/CMakeLists.txt:178 (message):


CMake Warning at src/mpi/CMakeLists.txt:184 (message):
  Can't build ScaLAPACK extensions


CMake Warning at src/mpi/CMakeLists.txt:185 (message):
  without ScaLAPACK, MPI, LAPACK, and BLAS


CMake Warning at src/mpi/CMakeLists.txt:186 (message):
  This is only a warning, SciDB will build but without


CMake Warning at src/mpi/CMakeLists.txt:187 (message):
  the libdense_linear_algebra.so plugin.


CMake Warning at src/mpi/CMakeLists.txt:188 (message):
  If that is not desired, please make sure the following are correctly
  resolved:


CMake Warning at src/mpi/CMakeLists.txt:189 (message):
  ----------------------------------------------------


CMake Warning at src/mpi/CMakeLists.txt:190 (message):
  Debug: MPI_Fortran_COMPLIER is


CMake Warning at src/mpi/CMakeLists.txt:191 (message):
  Debug: CMAKE_Fortran_COMPLIER is /usr/bin/gfortran-4.9


CMake Warning at src/mpi/CMakeLists.txt:192 (message):
  Debug: CMAKE_CXX_COMPILER is /usr/bin/g++-4.9


CMake Warning at src/mpi/CMakeLists.txt:193 (message):
  Debug: SCALAPACK_FOUND is 1


CMake Warning at src/mpi/CMakeLists.txt:194 (message):
  Debug: LAPACK_FOUND is TRUE


CMake Warning at src/mpi/CMakeLists.txt:195 (message):
  Debug: BLAS_FOUND is TRUE


CMake Warning at src/mpi/CMakeLists.txt:196 (message):
  Debug: MPI_CXX_FOUND is


CMake Warning at src/mpi/CMakeLists.txt:197 (message):
  Debug: MPI_Fortran_FOUND is


CMake Warning at src/mpi/CMakeLists.txt:198 (message):
  ----------------------------------------------------


-- ****************** END src/mpi/CMakeLists.txt ******************
-- *****BEGIN dense_linear_algebra/CMakeLists.txt ***********************
-- Found MPI_C: /usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so  
-- Found MPI_CXX: /usr/lib/libmpi_cxx.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so  
-- Found MPI_Fortran: /usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so  
-- MPI_Fortran_COMPILER=/usr/bin/mpif77
-- Debug: BLAS_LIBRARIES is /usr/lib/libblas.so.3gf
-- Debug: LAPACK_LIBRARIES is /usr/lib/liblapack.so.3gf;/usr/lib/libblas.so.3gf
-- Debug: SCALAPACK_LIBRARIES is 
-- Debug: MPI_LIBRARIES is /usr/lib/libmpi_cxx.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so
-- Debug: CMAKE_C_FLAGS is  -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
-- Debug: CMAKE_CXX_FLAGS is  -std=c++14 -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -fPIC -D__STDC_FORMAT_MACROS -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_LIMIT_MACROS -DPROJECT_ROOT=\"/tmp/scidb-15.7.0.9267/\"
-- Debug: CMAKE_Fortran_FLAGS is  -fno-f2c -Wline-truncation -I/opt/scidb/15.7/3rdparty/boost/include/boost 
-- Debug: MPI_Fortran_COMPILER is /usr/bin/mpif77
-- *****END linear_algebra/CMakeLists.txt ***********************
-- **BEGIN linear_algebra/CMakeLists.txt --------------------------------
-- Debug: CMAKE_C_FLAGS is  -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
-- Debug: CMAKE_CXX_FLAGS is  -std=c++14 -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -fPIC -D__STDC_FORMAT_MACROS -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_LIMIT_MACROS -DPROJECT_ROOT=\"/tmp/scidb-15.7.0.9267/\"
-- **END linear_algebra/CMakeLists.txt --------------------------------
-- Could NOT find Java (missing:  Java_JAVA_EXECUTABLE Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE Java_JAVAH_EXECUTABLE Java_JAVADOC_EXECUTABLE) 
CMake Error at src/jdbc/CMakeLists.txt:4 (message):
  Java 1.8 is currently the only supported version for building JDBC!


-- Configuring incomplete, errors occurred!
See also "/tmp/scidb-15.7.0.9267/stage/build/CMakeFiles/CMakeOutput.log".
See also "/tmp/scidb-15.7.0.9267/stage/build/CMakeFiles/CMakeError.log".
run.py: ERROR: Command setup failed: Abnormal return code: 1 on command ['cmake', '-DCMAKE_BUILD_TYPE=Debug', '-DCMAKE_INSTALL_PREFIX=/tmp/scidb-15.7.0.9267/stage/install', '/tmp/scidb-15.7.0.9267']
run.py: ERROR: Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests

#2

Looks like SciDB does not support oracle jdk. I installed openjdk-8-jdk and java was found correctly.