* installing *source* package ‘rlibkriging’ ... ** package ‘rlibkriging’ successfully unpacked and MD5 sums checked ** using staged installation set CMAKE_BIN=/usr/bin/cmake3 set CC=/usr/local/clang-trunk/bin/clang set FC=/usr/local/clang-trunk/bin/flang-new set CFLAGS=-isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 set CXX=/usr/local/clang-trunk/bin/clang++ set CXXFLAGS=-std=gnu++17 -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 set LDFLAGS=-L/usr/local/clang/lib64 -L/usr/local/clang-trunk/lib -L/usr/local/lib64 travis-ci ---------------------------------------------------------------- Look for HDF5 installation ---------------------------------------------------------------- -- Color mode enabled fatal: not a git repository (or any parent up to mount point /data) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). -- The C compiler identification is Clang 17.0.0 -- The CXX compiler identification is Clang 17.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/clang-trunk/bin/clang - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/clang-trunk/bin/clang++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- *** set cmake policy CMP0025 to NEW -- CMAKE_CXX_STANDARD = 11 -- Configuring Armadillo 11.4.2 -- -- *** WARNING: variable 'CMAKE_CXX_FLAGS' is not empty; this may cause problems! -- -- Detected Clang 6.0 or later -- ARMA_USE_EXTERN_RNG = true -- CMAKE_SYSTEM_NAME = Linux -- CMAKE_CXX_COMPILER_ID = Clang -- CMAKE_CXX_COMPILER_VERSION = 17.0.0 -- CMAKE_COMPILER_IS_GNUCXX = -- -- *** Options: -- BUILD_SHARED_LIBS = off -- DETECT_HDF5 = true -- OPENBLAS_PROVIDES_LAPACK = OFF -- ALLOW_FLEXIBLAS_LINUX = ON -- ALLOW_OPENBLAS_MACOS = OFF -- ALLOW_BLAS_LAPACK_MACOS = OFF -- BUILD_SMOKE_TEST = OFF -- -- *** Looking for external libraries -- Found FlexiBLAS: /usr/lib64/libflexiblas.so -- Found ATLAS: /usr/lib64/atlas/libtatlas.so -- Found BLAS: /usr/lib64/libblas.so -- Found LAPACK: /usr/lib64/liblapack.so -- FlexiBLAS_FOUND = YES -- MKL_FOUND = NO -- OpenBLAS_FOUND = NO -- ATLAS_FOUND = YES -- BLAS_FOUND = YES -- LAPACK_FOUND = YES -- -- *** Using FlexiBLAS to access BLAS and LAPACK functions. -- *** https://www.mpi-magdeburg.mpg.de/projects/flexiblas -- *** WARNING: SuperLU and ARPACK must also link with FlexiBLAS. -- -- *** If using FlexiBLAS causes problems, -- *** rerun cmake with FlexiBLAS detection disabled: -- *** cmake -D ALLOW_FLEXIBLAS_LINUX=false . -- -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.0") -- HDF5_FOUND = TRUE -- ARMA_HDF5_INCLUDE_DIR = /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/inst/hdf5/include -- -- *** If use of HDF5 is causing problems, -- *** rerun cmake with HDF5 detection disabled: -- *** cmake -D DETECT_HDF5=false . -- -- Found ARPACK: /usr/lib64/libarpack.so -- ARPACK_FOUND = YES -- Looking for SuperLU version 5 -- Found SuperLU: /usr/lib64/libsuperlu.so -- SuperLU_FOUND = YES -- SuperLU_INCLUDE_DIR = /usr/include/SuperLU -- -- *** Result of configuration: -- *** ARMA_USE_WRAPPER = true -- *** ARMA_USE_LAPACK = true -- *** ARMA_USE_BLAS = true -- *** ARMA_USE_ATLAS = false -- *** ARMA_USE_HDF5_CMAKE = true -- *** ARMA_USE_ARPACK = true -- *** ARMA_USE_EXTERN_RNG = true -- *** ARMA_USE_SUPERLU = true -- -- *** Armadillo wrapper library will use the following libraries: -- *** ARMA_LIBS = /usr/lib64/libflexiblas.so;/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/inst/hdf5/lib/libhdf5.a;/usr/lib64/libsz.so;/usr/lib64/libaec.so;/usr/lib64/libz.so;/usr/lib64/libarpack.so;/usr/lib64/libsuperlu.so -- -- Copying /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/armadillo/include/ to /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/tmp/include/ -- Generating /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/tmp/include/config.hpp -- CMAKE_CXX_FLAGS = -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -O2 -- CMAKE_SHARED_LINKER_FLAGS = -L/usr/local/clang/lib64 -L/usr/local/clang-trunk/lib -L/usr/local/lib64 -Wl,--no-as-needed -- CMAKE_REQUIRED_INCLUDES = /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/inst/hdf5/include;/usr/include/SuperLU -- -- CMAKE_INSTALL_PREFIX = /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/installed -- CMAKE_INSTALL_LIBDIR = lib -- CMAKE_INSTALL_INCLUDEDIR = include -- CMAKE_INSTALL_DATADIR = share -- CMAKE_INSTALL_BINDIR = bin -- Generating '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/ArmadilloConfig.cmake' -- Generating '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/ArmadilloConfigVersion.cmake' -- Generating '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/InstallFiles/ArmadilloConfig.cmake' -- Generating '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/InstallFiles/ArmadilloConfigVersion.cmake' -- Copying /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/armadillo/misc/ to /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/tmp/misc/ -- Generating '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/armadillo/tmp/misc/armadillo.pc' -- Compiling lbfgsb_cpp as an external library gmake[1]: Entering directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- [ 12%] Creating directories for 'lbfgsb-build' -- [ 25%] No download step for 'lbfgsb-build' -- [ 37%] No update step for 'lbfgsb-build' -- [ 50%] No patch step for 'lbfgsb-build' -- [ 62%] Performing configure step for 'lbfgsb-build' -- -- Using Fortran compiler: /usr/local/clang-trunk/bin/flang-new -- -- Using Fortran library flags: -lFortran_main -lFortranRuntime -lFortranDecimal -lm -- -- Using CMake generator: Unix Makefiles -- -- The Fortran compiler identification is LLVMFlang 17.0.0 -- -- Detecting Fortran compiler ABI info -- -- Detecting Fortran compiler ABI info - done -- -- Check for working Fortran compiler: /usr/local/clang-trunk/bin/flang-new - skipped -- CMake Warning at CMakeLists.txt:37 (message): -- lbfgsb will use local implementation of blas functions -- -- -- -- Processing external lib option: -lFortran_main -- -- Library Fortran_main found at location LIB_Fortran_main-NOTFOUND -- -- Processing external lib option: -lFortranRuntime -- -- Library FortranRuntime found at location LIB_FortranRuntime-NOTFOUND -- -- Processing external lib option: -lFortranDecimal -- -- Library FortranDecimal found at location LIB_FortranDecimal-NOTFOUND -- -- Processing external lib option: -lm -- -- Library m found at location /usr/lib64/libm.so -- -- Configuring done (25.8s) -- CMake Error: The following variables are used in this project, but they are set to NOTFOUND. -- Please set them or make sure they are set and tested correctly in the CMake files: -- LIB_FortranDecimal -- linked by target "lbfgsb" in directory /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/lbfgsb_cpp/Lbfgsb.3.0 -- LIB_FortranRuntime -- linked by target "lbfgsb" in directory /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/lbfgsb_cpp/Lbfgsb.3.0 -- LIB_Fortran_main -- linked by target "lbfgsb" in directory /data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/lbfgsb_cpp/Lbfgsb.3.0 -- -- -- Generating done (0.0s) -- CMake Generate step failed. Build files cannot be regenerated correctly. -- make[3]: *** [CMakeFiles/lbfgsb-build.dir/build.make:92: lbfgsb-build-prefix/src/lbfgsb-build-stamp/lbfgsb-build-configure] Error 1 -- make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- make[2]: *** [CMakeFiles/Makefile2:83: CMakeFiles/lbfgsb-build.dir/all] Error 2 -- make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- gmake[1]: *** [Makefile:91: all] Error 2 -- gmake[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-flang2/rlibkriging/src/libK/build/lbfgsb_cpp/lbfgsb-virtual-project' -- CMake Error at lbfgsb_cpp/CMakeLists.txt:64 (message): Build step for lbfgsb-build failed: 2 -- Configuring incomplete, errors occurred! ERROR: configuration failed for package ‘rlibkriging’ * removing ‘/data/gannet/ripley/R/packages/tests-flang2/rlibkriging.Rcheck/rlibkriging’