* installing *source* package ‘RcppPlanc’ ... ** this is package ‘RcppPlanc’ version ‘2.0.13’ ** package ‘RcppPlanc’ successfully unpacked and MD5 sums checked ** using staged installation -- The C compiler identification is Clang 20.1.7 -- The CXX compiler identification is Clang 20.1.7 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/bin/clang-20 - 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: /data/gannet/ripley/bin/clang++-20 - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done This is libplanc 1.0.2 containing component nmflib 1.0.1 -- Found R: /data/gannet/ripley/R/R-clang/bin/R (found version "R Under development (unstable) (2025-07-15 r88411) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/. ") -- MKL_ARCH: None, set to ` intel64` by default -- MKL_ROOT /data/gannet/ripley/intel/oneapi/mkl/2023.2.0 -- MKL_LINK: None, set to ` dynamic` by default -- MKL_INTERFACE_FULL: intel_lp64 -- MKL_THREADING: None, set to ` intel_thread` by default -- Found MKL: /data/gannet/ripley/intel/oneapi/mkl/2023.2.0 -- Found MKL: /data/gannet/ripley/intel/oneapi/mkl/2023.2.0/lib/intel64/libmkl_intel_lp64.so -- Found MKL: /data/gannet/ripley/intel/oneapi/mkl/2023.2.0/lib/intel64/libmkl_intel_thread.so -- Found MKL: /data/gannet/ripley/intel/oneapi/mkl/2023.2.0/lib/intel64/libmkl_core.so -- Found MKL: /usr/local/lib/libiomp5.so -- Performing Test MKL_LINKS -- Performing Test MKL_LINKS - Success -- Could NOT find OpenBLAS (missing: OpenBLAS_DIR) -- Found BLAS: /usr/lib64/libblas.so -- Found LAPACK: /usr/lib64/liblapack.so;/usr/lib64/libblas.so -- Found R_HighFive: /data/gannet/ripley/R/test-clang/HighFive -- Found HDF5: /usr/lib64/libhdf5.so (found version "1.14.6") found components: C -- Performing Test HDF5_LINKS -- Performing Test HDF5_LINKS - Success -- Found R_Rcpp: /data/gannet/ripley/R/test-clang/Rcpp -- Found R_RcppArmadillo: /data/gannet/ripley/R/test-clang/RcppArmadillo -- Found R_RcppProgress: /data/gannet/ripley/R/test-clang/RcppProgress -- Performing Test UNSAFE_MATH -- Performing Test UNSAFE_MATH - Success -- Performing Test FINITE_MATH -- Performing Test FINITE_MATH - Success -- Performing Test TRAPPING_MATH -- Performing Test TRAPPING_MATH - Success -- Performing Test ERRNO_MATH -- Performing Test ERRNO_MATH - Success -- Performing Test UNSIGNED_ZERO -- Performing Test UNSIGNED_ZERO - Success -- Performing Test RECIPROCAL_MATH -- Performing Test RECIPROCAL_MATH - Success -- Performing Test ARCH_AVX -- Performing Test ARCH_AVX - Success -- Performing Test HAS_POPCNT -- Performing Test HAS_POPCNT - Success -- Looking for cblas.h -- Looking for cblas.h - found -- A cache variable, namely HWLOC_DIR, has been set to specify the install directory of HWLOC -- Checking for one of the modules 'hwloc' -- Looking for HWLOC - not found using PkgConfig. Perhaps you should add the directory containing hwloc.pc to the PKG_CONFIG_PATH environment variable. -- Looking for HWLOC - PkgConfig not used -- Looking for hwloc -- hwloc.h not found -- Looking for hwloc -- lib hwloc not found -- Could NOT find HWLOC (missing: HWLOC_LIBRARIES HWLOC_WORKS) -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- NNLS_SOURCE_DIR = /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nnls -- NMF_SOURCE_DIR = /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf -- NMFLIB_COMMON = /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done (22.3s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: R_SHLIB_EXT -- Build files have been written to: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build ./configure: line 50: _deps/highfive-src/include/highfive/bits/H5Friends.hpp: No such file or directory make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' /usr/bin/cmake -S/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc -B/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' make -f CMakeFiles/utils.dir/build.make CMakeFiles/utils.dir/depend make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' make -f CMakeFiles/utils.dir/build.make CMakeFiles/utils.dir/build make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 5%] Building CXX object CMakeFiles/utils.dir/common/utils.cpp.o /data/gannet/ripley/bin/clang++-20 -DUSING_R -I/data/gannet/ripley/R/test-clang/HighFive/include -I/data/gannet/ripley/R/R-clang/include -I/data/gannet/ripley/R/test-clang/Rcpp/include -I/data/gannet/ripley/R/test-clang/RcppArmadillo/include -I/data/gannet/ripley/R/test-clang/RcppProgress/include -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -MD -MT CMakeFiles/utils.dir/common/utils.cpp.o -MF CMakeFiles/utils.dir/common/utils.cpp.o.d -o CMakeFiles/utils.dir/common/utils.cpp.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/utils.cpp make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 5%] Built target utils make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/depend make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles/hwloc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/build make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 11%] Creating directories for 'hwloc' /usr/bin/cmake -Dcfgdir= -P /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/tmp/hwloc-mkdirs.cmake /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-mkdir [ 17%] Performing download step (download, verify and extract) for 'hwloc' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src && /usr/bin/cmake -DCMAKE_MESSAGE_LOG_LEVEL=VERBOSE -P /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/download-hwloc.cmake -- Downloading... dst='/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.12.1.tar.gz' timeout='none' inactivity timeout='none' -- Using src='https://download.open-mpi.org/release/hwloc/v2.12/hwloc-2.12.1.tar.gz' -- [download 0% complete] -- [download 1% complete] -- [download 2% complete] -- [download 3% complete] -- [download 4% complete] -- [download 5% complete] -- [download 6% complete] -- [download 7% complete] -- [download 8% complete] -- [download 9% complete] -- [download 10% complete] -- [download 11% complete] -- [download 12% complete] -- [download 13% complete] -- [download 14% complete] -- [download 15% complete] -- [download 16% complete] -- 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src='/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.12.1.tar.gz' dst='/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src && /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-download [ 23%] No update step for 'hwloc' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-update [ 29%] Performing patch step for 'hwloc' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc && /usr/bin/cmake -E cat /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/../../tools/patches/00_remove_stdio.patch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/../../tools/patches/01_remove_sprintf.patch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/../../tools/patches/02_adjust_windows_types.patch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/../../tools/patches/03_remove_abort.patch | /usr/bin/patch -p1 -l patching file hwloc/components.c patching file hwloc/distances.c patching file hwloc/memattrs.c patching file hwloc/pci-common.c patching file hwloc/topology-aix.c patching file hwloc/topology-bgq.c patching file hwloc/topology-cuda.c patching file hwloc/topology-darwin.c patching file hwloc/topology-levelzero.c patching file hwloc/topology-linux.c patching file hwloc/topology-nvml.c patching file hwloc/topology-opencl.c patching file hwloc/topology-pci.c patching file hwloc/topology-rsmi.c patching file hwloc/topology-solaris.c patching file hwloc/topology-synthetic.c patching file hwloc/topology-windows.c patching file hwloc/topology-x86.c patching file hwloc/topology-xml-libxml.c patching file hwloc/topology-xml-nolibxml.c patching file hwloc/topology-xml.c patching file hwloc/topology.c patching file hwloc/cpukinds.c patching file hwloc/topology-freebsd.c patching file hwloc/topology-linux.c patching file hwloc/topology-rsmi.c patching file hwloc/topology-windows.c patching file hwloc/topology-xml.c patching file include/hwloc/cuda.h patching file include/hwloc/cudart.h patching file include/hwloc/levelzero.h patching file include/hwloc/nvml.h patching file include/hwloc/opencl.h patching file include/hwloc/openfabrics-verbs.h patching file include/hwloc/rsmi.h patching file hwloc/topology-x86.c patching file hwloc/topology-windows.c patching file hwloc/distances.c patching file hwloc/topology-linux.c patching file hwloc/memattrs.c cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc && /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-patch [ 35%] Performing configure step for 'hwloc' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E env LD= "CFLAGS=-DNDEBUG -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 " sh ../hwloc/configure --with-pic --prefix=/out/ --disable-picky --enable-shared=no --enable-static=yes --disable-cairo --disable-libxml2 --disable-io --disable-plugin-dlopen --disable-plugin-ltdl --enable-embedded-mode && /usr/bin/cmake -E touch_nocreate ../hwloc/aclocal.m4 && /usr/bin/cmake -E touch_nocreate ../hwloc/Makefile.in && /usr/bin/cmake -E touch_nocreate ../hwloc/configure && /usr/bin/cmake -E touch_nocreate config.status ### ### Configuring hwloc distribution tarball ### Startup tests ### checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether UID '1234' is supported by ustar format... yes checking whether GID '30010' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports the include directive... yes (GNU style) checking for gcc... clang-20 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether clang-20 accepts -g... yes checking for clang-20 option to enable C11 features... none needed checking whether clang-20 understands -c and -o together... yes checking dependency style of clang-20... gcc3 checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for ar... ar checking the archiver (ar) interface... ar checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by clang-20... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 4718592 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from clang-20 object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if clang-20 supports -fno-rtti -fno-exceptions... yes checking for clang-20 option to produce PIC... -fPIC -DPIC checking if clang-20 PIC flag -fPIC -DPIC works... yes checking if clang-20 static flag -static works... yes checking if clang-20 supports -c -o file.o... yes checking if clang-20 supports -c -o file.o... (cached) yes checking whether the clang-20 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking whether the compiler supports GNU C++... yes checking whether clang++-20 accepts -g... yes checking for clang++-20 option to enable C++11 features... none needed checking dependency style of clang++-20... gcc3 checking how to run the C++ preprocessor... clang++-20 -E checking for ld used by clang++-20... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the clang++-20 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for clang++-20 option to produce PIC... -fPIC -DPIC checking if clang++-20 PIC flag -fPIC -DPIC works... yes checking if clang++-20 static flag -static works... yes checking if clang++-20 supports -c -o file.o... yes checking if clang++-20 supports -c -o file.o... (cached) yes checking whether the clang++-20 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) clang-20 checking whether the compiler supports GNU C... (cached) yes checking whether clang-20 accepts -g... (cached) yes checking for clang-20 option to enable C11 features... (cached) none needed checking whether clang-20 understands -c and -o together... (cached) yes checking dependency style of clang-20... (cached) gcc3 checking for clang-20 options needed to detect all undeclared functions... none needed checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking how to run the C preprocessor... clang-20 -E checking for X... libraries , headers ### ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build configure: hwloc srcdir: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc configure: Detected VPATH build checking for hwloc version... 2.12.1 checking if want hwloc maintainer support... disabled (embedded mode) checking for hwloc directory prefix... (none) checking for hwloc symbol prefix... hwloc_ checking for the C compiler vendor... gnu checking size of void *... 8 checking which OS support to include... Linux checking which CPU support to include... x86_64 checking size of unsigned long... 8 checking size of unsigned int... 4 checking for __attribute__... yes checking for __attribute__(aligned)... yes checking for __attribute__(always_inline)... yes checking for __attribute__(cold)... yes checking for __attribute__(const)... yes checking for __attribute__(deprecated)... yes checking for __attribute__(constructor)... yes checking for __attribute__(format)... yes checking for __attribute__(hot)... yes checking for __attribute__(malloc)... yes checking for __attribute__(may_alias)... yes checking for __attribute__(no_instrument_function)... yes checking for __attribute__(nonnull)... yes checking for __attribute__(noreturn)... yes checking for __attribute__(packed)... yes checking for __attribute__(pure)... yes checking for __attribute__(sentinel)... yes checking for __attribute__(unused)... yes checking for __attribute__(warn_unused_result)... yes checking for __attribute__(weak_alias)... yes checking if clang-20 supports -fvisibility=hidden... yes checking whether to enable symbol visibility... yes (via -fvisibility=hidden) configure: WARNING: "-fvisibility=hidden" has been added to the hwloc CFLAGS checking whether the C compiler rejects function calls with too many arguments... yes checking whether the C compiler rejects function calls with too few arguments... yes checking for unistd.h... (cached) yes checking for dirent.h... yes checking for strings.h... (cached) yes checking for ctype.h... yes checking for strcasecmp... yes checking whether strcasecmp is declared... yes checking whether function strcasecmp has a complete prototype... yes checking for strncasecmp... yes checking whether strncasecmp is declared... yes checking whether function strncasecmp has a complete prototype... yes checking for strftime... yes checking for setlocale... yes checking for stdint.h... (cached) yes checking for sys/mman.h... yes **** Linux-specific checks checking whether sched_getcpu is declared... yes checking whether sched_setaffinity is declared... yes checking whether function sched_setaffinity has a complete prototype... yes checking for old prototype of sched_setaffinity... no checking for working CPU_SET... yes checking for working CPU_SET_S... yes checking for working syscall with 6 parameters... yes checking for libudev.h... yes checking for udev_device_new_from_subsystem_sysname in -ludev... yes **** end of Linux-specific checks checking whether pthread_setaffinity_np is declared... yes checking whether pthread_getaffinity_np is declared... yes checking whether fabsf is declared... yes checking for fabsf in -lm... yes checking whether modff is declared... yes checking for modff in -lm... yes checking whether _SC_NPROCESSORS_ONLN is declared... yes checking whether _SC_NPROCESSORS_CONF is declared... yes checking whether _SC_NPROC_ONLN is declared... no checking whether _SC_NPROC_CONF is declared... no checking whether _SC_PAGESIZE is declared... yes checking whether _SC_PAGE_SIZE is declared... yes checking whether _SC_LARGE_PAGESIZE is declared... no checking for mach/mach_init.h... no checking for mach_init.h... no checking for mach/mach_host.h... no checking whether strtoull is declared... yes checking for ssize_t... yes checking whether snprintf is declared... yes checking whether _strdup is declared... no checking whether _putenv is declared... no checking whether snprintf is correct... yes checking whether getprogname is declared... no checking whether getexecname is declared... no checking for program_invocation_name... yes checking for __progname... yes checking for pthread_t... yes checking for ffs... yes checking whether ffs is declared... yes checking whether function ffs has a complete prototype... yes checking for ffsl... yes checking whether ffsl is declared... yes checking whether function ffsl has a complete prototype... yes checking for fls... no checking for flsl... no checking for clz... no checking for clzl... no checking for openat... yes checking for malloc.h... yes checking for getpagesize... yes checking for memalign... yes checking for posix_memalign... yes checking for sys/utsname.h... yes checking for uname... yes checking for pthread_mutex_lock... yes **** x86 CPUID configuration checking for x86 cpuid... yes **** end of x86 CPUID configuration **** component and plugin-specific configuration checking if plugin support is enabled... no checking components to build statically... noos xml synthetic xml_nolibxml linux x86 checking components to build as plugins... **** end of component and plugin configuration checking for diff... /usr/bin/diff ### ### Performing final hwloc configuration ### checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating hwloc/Makefile config.status: creating include/private/autogen/config.h config.status: creating include/hwloc/autogen/config.h config.status: executing depfiles commands config.status: executing libtool commands ----------------------------------------------------------------------------- Hwloc optional build support status (more details can be found above): Probe / display I/O devices: no Graphical output: no (disabled in embedded mode) XML input / output: basic Plugin support: no ----------------------------------------------------------------------------- cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-configure [ 41%] Performing build step for 'hwloc' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && make make[4]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' /bin/sh ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating hwloc/Makefile config.status: creating include/private/autogen/config.h config.status: include/private/autogen/config.h is unchanged config.status: creating include/hwloc/autogen/config.h config.status: include/hwloc/autogen/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands Making all in include make[5]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' Making all in hwloc make[5]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' CC topology.lo CC traversal.lo CC distances.lo ../../hwloc/hwloc/distances.c:33:12: warning: unused variable 'nbobjs' [-Wunused-variable] 33 | unsigned nbobjs = dist->nbobjs; | ^~~~~~ ../../hwloc/hwloc/distances.c:34:16: warning: unused variable 'objs' [-Wunused-variable] 34 | hwloc_obj_t *objs = dist->objs; | ^~~~ ../../hwloc/hwloc/distances.c:35:19: warning: unused variable 'values' [-Wunused-variable] 35 | hwloc_uint64_t *values = dist->values; | ^~~~~~ ../../hwloc/hwloc/distances.c:36:7: warning: unused variable 'gp' [-Wunused-variable] 36 | int gp = !HWLOC_DIST_TYPE_USE_OS_INDEX(dist->unique_type); | ^~ ../../hwloc/hwloc/distances.c:37:12: warning: unused variable 'i' [-Wunused-variable] 37 | unsigned i, j; | ^ ../../hwloc/hwloc/distances.c:37:15: warning: unused variable 'j' [-Wunused-variable] 37 | unsigned i, j; | ^ ../../hwloc/hwloc/distances.c:793:16: warning: variable 'obj' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] 793 | else if (unique_type == HWLOC_OBJ_NUMANODE) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../hwloc/hwloc/distances.c:800:15: note: uninitialized use occurs here 800 | objs[i] = obj; | ^~~ ../../hwloc/hwloc/distances.c:793:12: note: remove the 'if' if its condition is always true 793 | else if (unique_type == HWLOC_OBJ_NUMANODE) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | obj = hwloc_get_numanode_obj_by_os_index(topology, (unsigned) indexes[i]); ../../hwloc/hwloc/distances.c:786:20: note: initialize the variable 'obj' to silence this warning 786 | hwloc_obj_t obj; | ^ | = NULL 7 warnings generated. CC memattrs.lo ../../hwloc/hwloc/memattrs.c:799:9: warning: unused variable 'err' [-Wunused-variable] 799 | int err = from_internal_location(&imi->initiator, &initiators[i]); | ^~~ 1 warning generated. CC cpukinds.lo CC components.lo ../../hwloc/hwloc/components.c:883:9: warning: variable 'first' set but not used [-Wunused-but-set-variable] 883 | int first = 1; | ^ 1 warning generated. CC bind.lo CC bitmap.lo CC pci-common.lo CC diff.lo CC shmem.lo CC misc.lo CC base64.lo CC topology-noos.lo CC topology-synthetic.lo ../../hwloc/hwloc/topology-synthetic.c:1443:20: warning: variable 'warned' set but not used [-Wunused-but-set-variable] 1443 | static int warned = 0; | ^ 1 warning generated. CC topology-xml.lo ../../hwloc/hwloc/topology-xml.c:276:13: warning: variable 'warned' set but not used [-Wunused-but-set-variable] 276 | static int warned = 0; | ^ ../../hwloc/hwloc/topology-xml.c:376:13: warning: variable 'warned' set but not used [-Wunused-but-set-variable] 376 | static int warned = 0; | ^ ../../hwloc/hwloc/topology-xml.c:805:15: warning: unused variable 'origversion' [-Wunused-variable] 805 | const char *origversion = hwloc_obj_get_info_by_name(topology->levels[0][0], "hwlocVersion"); | ^~~~~~~~~~~ ../../hwloc/hwloc/topology-xml.c:806:15: warning: unused variable 'origprogname' [-Wunused-variable] 806 | const char *origprogname = hwloc_obj_get_info_by_name(topology->levels[0][0], "ProcessName"); | ^~~~~~~~~~~~ 4 warnings generated. CC topology-xml-nolibxml.lo CC topology-linux.lo ../../hwloc/hwloc/topology-linux.c:7779:26: warning: unused variable 'topology' [-Wunused-variable] 7779 | struct hwloc_topology *topology = backend->topology; | ^~~~~~~~ 1 warning generated. CC topology-hardwired.lo CC topology-x86.lo CCLD libhwloc_embedded.la make[5]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[5]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[4]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-build [ 47%] Performing install step for 'hwloc' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && make install make[4]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' Making install in include make[5]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[6]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[5]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' Making install in hwloc make[5]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[6]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make install-exec-hook make[7]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[7]: Nothing to be done for 'install-exec-hook'. make[7]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[6]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[5]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[5]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[6]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[5]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[4]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-install [ 52%] Completed 'hwloc' /usr/bin/cmake -E make_directory /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles/hwloc-complete /usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-done /usr/bin/cmake -E remove_directory /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc/utils/lstopo make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 52%] Built target hwloc make -f CMakeFiles/detect_blas.dir/build.make CMakeFiles/detect_blas.dir/depend make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles/detect_blas.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' make -f CMakeFiles/detect_blas.dir/build.make CMakeFiles/detect_blas.dir/build make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 58%] Building C object CMakeFiles/detect_blas.dir/common/detect_blas.c.o /usr/local/bin/clang-20 -DUSING_R -I/data/gannet/ripley/R/R-clang/include -I/data/gannet/ripley/R/test-clang/Rcpp/include -I/data/gannet/ripley/R/test-clang/RcppArmadillo/include -I/data/gannet/ripley/R/test-clang/RcppProgress/include -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -std=gnu99 -fPIC -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT CMakeFiles/detect_blas.dir/common/detect_blas.c.o -MF CMakeFiles/detect_blas.dir/common/detect_blas.c.o.d -o CMakeFiles/detect_blas.dir/common/detect_blas.c.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/detect_blas.c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/detect_blas.c:16:27: warning: initializing 'const openblas_init_t' (aka 'int (*const)(void)') with an expression of type 'void *' converts between void pointer and function pointer [-Wpedantic] 16 | const openblas_init_t parallel_address = dlsym(libloc, "openblas_get_parallel"); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/detect_blas.c:21:26: warning: initializing 'const openblas_set_t' (aka 'void (*const)(int)') with an expression of type 'void *' converts between void pointer and function pointer [-Wpedantic] 21 | const openblas_set_t set_address = dlsym(libloc, "openblas_set_num_threads"); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 58%] Built target detect_blas make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/depend make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles/hw_detect.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/build make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 64%] Building C object CMakeFiles/hw_detect.dir/common/hw_detect.c.o /usr/local/bin/clang-20 -DUSING_R -I/data/gannet/ripley/R/R-clang/include -I/data/gannet/ripley/R/test-clang/Rcpp/include -I/data/gannet/ripley/R/test-clang/RcppArmadillo/include -I/data/gannet/ripley/R/test-clang/RcppProgress/include -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc/include -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -std=gnu99 -fPIC -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT CMakeFiles/hw_detect.dir/common/hw_detect.c.o -MF CMakeFiles/hw_detect.dir/common/hw_detect.c.o.d -o CMakeFiles/hw_detect.dir/common/hw_detect.c.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/hw_detect.c make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 64%] Built target hw_detect make -f nmf/CMakeFiles/nmflib.dir/build.make nmf/CMakeFiles/nmflib.dir/depend make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf/CMakeFiles/nmflib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' make -f nmf/CMakeFiles/nmflib.dir/build.make nmf/CMakeFiles/nmflib.dir/build make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [ 70%] Building CXX object nmf/CMakeFiles/nmflib.dir/nmf_lib.cpp.o cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf && /data/gannet/ripley/bin/clang++-20 -DUSING_R -I/data/gannet/ripley/R/R-clang/include -I/data/gannet/ripley/R/test-clang/Rcpp/include -I/data/gannet/ripley/R/test-clang/RcppArmadillo/include -I/data/gannet/ripley/R/test-clang/RcppProgress/include -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nnls -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf -I/data/gannet/ripley/R/test-clang/HighFive/include -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/nmf_lib.cpp.o -MF CMakeFiles/nmflib.dir/nmf_lib.cpp.o.d -o CMakeFiles/nmflib.dir/nmf_lib.cpp.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:4: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/EmbeddedNMFDriver.hpp:73:14: warning: 'planc::symmEmbeddedNMFDriver>::parseParams' hides overloaded virtual function [-Woverloaded-virtual] 73 | void parseParams(const internalSymmParams&pc) { | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:44:31: note: in instantiation of template class 'planc::symmEmbeddedNMFDriver>' requested here 44 | symmEmbeddedNMFDriver nmfRunner(options); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_types.inc:1:1: note: in instantiation of member function 'planc::nmflib, double>::symNMF' requested here 1 | X(arma::mat)\ | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:8:61: note: expanded from macro 'X' 8 | template planc::nmfOutput planc::nmflib::symNMF(const T&x, const arma::uword&k, const arma::uword&niter, const double& lambda, const std::string&algo, const int&nCores, const arma::Mat&Hinit); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/EmbeddedNMFDriver.hpp:16:22: note: hidden overloaded virtual function 'planc::EmbeddedNMFDriver>::parseParams' declared here: type mismatch at 1st parameter ('const internalParams> &' vs 'const internalSymmParams> &') 16 | virtual void parseParams(const internalParams&pc) { | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/EmbeddedNMFDriver.hpp:73:14: warning: 'planc::symmEmbeddedNMFDriver>::parseParams' hides overloaded virtual function [-Woverloaded-virtual] 73 | void parseParams(const internalSymmParams&pc) { | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:44:31: note: in instantiation of template class 'planc::symmEmbeddedNMFDriver>' requested here 44 | symmEmbeddedNMFDriver nmfRunner(options); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_types.inc:3:1: note: in instantiation of member function 'planc::nmflib, double>::symNMF' requested here 3 | X(arma::sp_mat)\ | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:8:61: note: expanded from macro 'X' 8 | template planc::nmfOutput planc::nmflib::symNMF(const T&x, const arma::uword&k, const arma::uword&niter, const double& lambda, const std::string&algo, const int&nCores, const arma::Mat&Hinit); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/EmbeddedNMFDriver.hpp:16:22: note: hidden overloaded virtual function 'planc::EmbeddedNMFDriver>::parseParams' declared here: type mismatch at 1st parameter ('const internalParams> &' vs 'const internalSymmParams> &') 16 | virtual void parseParams(const internalParams&pc) { | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:135:17: warning: suggest braces around initialization of subobject [-Wmissing-braces] 135 | return {solver.getW(), resolvedH, resolvedV, solver.objErr(), resolvedU}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | { } /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/inmf_types.inc:1:1: note: in instantiation of member function 'planc::nmflib, double>::uinmf' requested here 1 | X(arma::mat)\ | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:19:63: note: expanded from macro 'X' 19 | template planc::uinmfOutput planc::nmflib::uinmf(const std::vector> &matPtrVec, const std::vector> &unsharedPtrVec, std::vector whichUnshared, const arma::uword &k, const int& nCores, const arma::vec &lambda, const arma::uword &niter, const bool &verbose); | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:135:17: warning: suggest braces around initialization of subobject [-Wmissing-braces] 135 | return {solver.getW(), resolvedH, resolvedV, solver.objErr(), resolvedU}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | { } /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/inmf_types.inc:3:1: note: in instantiation of member function 'planc::nmflib, double>::uinmf' requested here 3 | X(arma::sp_mat)\ | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:19:63: note: expanded from macro 'X' 19 | template planc::uinmfOutput planc::nmflib::uinmf(const std::vector> &matPtrVec, const std::vector> &unsharedPtrVec, std::vector whichUnshared, const arma::uword &k, const int& nCores, const arma::vec &lambda, const arma::uword &niter, const bool &verbose); | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:135:17: warning: suggest braces around initialization of subobject [-Wmissing-braces] 135 | return {solver.getW(), resolvedH, resolvedV, solver.objErr(), resolvedU}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | { } /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/inmf_types.inc:5:1: note: in instantiation of member function 'planc::nmflib::uinmf' requested here 5 | X(planc::H5Mat)\ | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:19:63: note: expanded from macro 'X' 19 | template planc::uinmfOutput planc::nmflib::uinmf(const std::vector> &matPtrVec, const std::vector> &unsharedPtrVec, std::vector whichUnshared, const arma::uword &k, const int& nCores, const arma::vec &lambda, const arma::uword &niter, const bool &verbose); | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:135:17: warning: suggest braces around initialization of subobject [-Wmissing-braces] 135 | return {solver.getW(), resolvedH, resolvedV, solver.objErr(), resolvedU}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | { } /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/inmf_types.inc:7:1: note: in instantiation of member function 'planc::nmflib::uinmf' requested here 7 | X(planc::H5SpMat) | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:19:63: note: expanded from macro 'X' 19 | template planc::uinmfOutput planc::nmflib::uinmf(const std::vector> &matPtrVec, const std::vector> &unsharedPtrVec, std::vector whichUnshared, const arma::uword &k, const int& nCores, const arma::vec &lambda, const arma::uword &niter, const bool &verbose); | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:3: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.hpp:8: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/config.h:32: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:138: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/constants.hpp:226:56: warning: use of infinity is undefined behavior due to the currently enabled floating-point options [-Wnan-infinity-disabled] 226 | return (std::numeric_limits::has_infinity) ? -(std::numeric_limits::infinity()) : std::numeric_limits::lowest(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/op_norm_meat.hpp:635:22: note: in instantiation of function template specialization 'arma::priv::most_neg' requested here 635 | eT max_val = priv::most_neg(); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/op_norm_meat.hpp:410:21: note: in instantiation of function template specialization 'arma::op_norm::vec_norm_2_direct_robust' requested here 410 | return op_norm::vec_norm_2_direct_robust(tmp.M); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/fn_norm.hpp:49:42: note: in instantiation of function template specialization 'arma::op_norm::vec_norm_2>' requested here 49 | if(k == uword(2)) { return op_norm::vec_norm_2(P); } | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/op_normalise_meat.hpp:110:28: note: in instantiation of function template specialization 'arma::norm>' requested here 110 | const T norm_val_a = norm(A.col(i), p); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/op_normalise_meat.hpp:79:23: note: in instantiation of function template specialization 'arma::op_normalise_mat::apply' requested here 79 | op_normalise_mat::apply(out2, U.M, p, dim); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:5088:12: note: in instantiation of function template specialization 'arma::op_normalise_mat::apply>' requested here 5088 | op_type::apply(*this, X); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/NMFDriver.hpp:343:19: note: in instantiation of function template specialization 'arma::Mat::operator=, arma::op_normalise_mat>' requested here 343 | A = arma::normalise(A); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/NMFDriver.hpp:311:21: note: in instantiation of function template specialization 'planc::NMFDriver>::CallNMF>>' requested here 311 | CallNMF>(); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:245:15: note: in instantiation of member function 'planc::NMFDriver>::callNMF' requested here 245 | myNMF.callNMF(); | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:3: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.hpp:8: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/config.h:32: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:138: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/constants.hpp:246:54: warning: use of infinity is undefined behavior due to the currently enabled floating-point options [-Wnan-infinity-disabled] 246 | return (std::numeric_limits::has_infinity) ? std::numeric_limits::infinity() : std::numeric_limits::max(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/op_norm_meat.hpp:816:32: note: in instantiation of function template specialization 'arma::priv::most_pos' requested here 816 | T min_val = (N != 1) ? priv::most_pos() : std::abs(P[0]); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/fn_norm.hpp:96:75: note: in instantiation of function template specialization 'arma::op_norm::vec_norm_min>' requested here 96 | if( (sig == '-') ) { return op_norm::vec_norm_min(P); } | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/nmf.hpp:165:27: note: in instantiation of function template specialization 'arma::norm>' requested here 165 | this->normA = arma::norm(this->A, "fro"); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/nmf.hpp:232:13: note: in instantiation of member function 'planc::NMF>::otherInitializations' requested here 232 | this->otherInitializations(); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/mu.hpp:43:92: note: in instantiation of member function 'planc::NMF>::NMF' requested here 43 | MUNMF(const T&A, const arma::mat&llf, const arma::mat&rlf, const int&ncores = 0) : NMF(A, llf, rlf) { | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/NMFDriver.hpp:368:17: note: in instantiation of member function 'planc::MUNMF>::MUNMF' requested here 368 | NMFTYPE nmfAlgorithm(A, W, H, nCores); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/NMFDriver.hpp:311:21: note: in instantiation of function template specialization 'planc::NMFDriver>::CallNMF>>' requested here 311 | CallNMF>(); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:245:15: note: in instantiation of member function 'planc::NMFDriver>::callNMF' requested here 245 | myNMF.callNMF(); | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.cpp:4: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:3: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.hpp:8: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/config.h:32: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:138: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/constants.hpp:71:59: warning: use of infinity is undefined behavior due to the currently enabled floating-point options [-Wnan-infinity-disabled] 71 | return (std::numeric_limits::has_infinity) ? eT(std::numeric_limits::infinity()) : eT(std::numeric_limits::max()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/constants.hpp:177:77: note: in instantiation of function template specialization 'arma::priv::Datum_helper::inf' requested here 177 | template const eT Datum::inf = priv::Datum_helper::inf(); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/diskio_meat.hpp:465:73: note: in instantiation of static data member 'arma::Datum::inf' requested here 465 | val = neg ? cond_rel< is_signed::value >::make_neg(Datum::inf) : Datum::inf; | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/diskio_meat.hpp:1638:15: note: in instantiation of function template specialization 'arma::diskio::convert_token' requested here 1638 | diskio::convert_token( x.at(row,col), token ); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/diskio_meat.hpp:2835:12: note: in instantiation of function template specialization 'arma::diskio::load_arma_ascii' requested here 2835 | return load_arma_ascii(x, f, err_msg); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/diskio_meat.hpp:2796:25: note: in instantiation of function template specialization 'arma::diskio::load_auto_detect' requested here 2796 | load_okay = diskio::load_auto_detect(x, f, err_msg); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:8194:27: note: in instantiation of function template specialization 'arma::diskio::load_auto_detect' requested here 8194 | load_okay = diskio::load_auto_detect(*this, name, err_msg); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/NMFDriver.hpp:141:15: note: in instantiation of member function 'arma::Mat::load' requested here 141 | A.load(this->m_Afile_name, arma::coord_ascii); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:244:22: note: in instantiation of member function 'planc::NMFDriver>::loadMat' requested here 244 | NMFDriver myNMF(opts); | ^ [ 76%] Building CXX object nmf/CMakeFiles/nmflib.dir/bppnmf.cpp.o cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf && /data/gannet/ripley/bin/clang++-20 -DUSING_R -I/data/gannet/ripley/R/R-clang/include -I/data/gannet/ripley/R/test-clang/Rcpp/include -I/data/gannet/ripley/R/test-clang/RcppArmadillo/include -I/data/gannet/ripley/R/test-clang/RcppProgress/include -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nnls -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf -I/data/gannet/ripley/R/test-clang/HighFive/include -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/bppnmf.cpp.o -MF CMakeFiles/nmflib.dir/bppnmf.cpp.o.d -o CMakeFiles/nmflib.dir/bppnmf.cpp.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/bppnmf.cpp In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/bppnmf.cpp:4: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/bppnmf.hpp:7: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/config.h:32: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:138: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/constants.hpp:226:56: warning: use of infinity is undefined behavior due to the currently enabled floating-point options [-Wnan-infinity-disabled] 226 | return (std::numeric_limits::has_infinity) ? -(std::numeric_limits::infinity()) : std::numeric_limits::lowest(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/op_norm_meat.hpp:751:32: note: in instantiation of function template specialization 'arma::priv::most_neg' requested here 751 | T max_val = (N != 1) ? priv::most_neg() : std::abs(P[0]); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/fn_norm.hpp:261:23: note: in instantiation of function template specialization 'arma::op_norm::vec_norm_max>' requested here 261 | return op_norm::vec_norm_max(P_fake_vector); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/nmf.hpp:165:27: note: in instantiation of function template specialization 'arma::norm>' requested here 165 | this->normA = arma::norm(this->A, "fro"); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/nmf.hpp:232:13: note: in instantiation of member function 'planc::NMF>::otherInitializations' requested here 232 | this->otherInitializations(); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/hals.hpp:44:90: note: in instantiation of member function 'planc::NMF>::NMF' requested here 44 | HALSNMF(const T&A, const arma::mat&llf, const arma::mat&rlf, const int&ncores = 0) : NMF(A, llf, rlf) { | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/bppnmf.cpp:19:13: note: in instantiation of member function 'planc::HALSNMF>::HALSNMF' requested here 19 | HALSNMF tempHals(this->A, this->W, this->H); | ^ In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/bppnmf.cpp:4: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/bppnmf.hpp:7: In file included from /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/config.h:32: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:138: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/constants.hpp:246:54: warning: use of infinity is undefined behavior due to the currently enabled floating-point options [-Wnan-infinity-disabled] 246 | return (std::numeric_limits::has_infinity) ? std::numeric_limits::infinity() : std::numeric_limits::max(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/op_norm_meat.hpp:816:32: note: in instantiation of function template specialization 'arma::priv::most_pos' requested here 816 | T min_val = (N != 1) ? priv::most_pos() : std::abs(P[0]); | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/fn_norm.hpp:266:30: note: in instantiation of function template specialization 'arma::op_norm::vec_norm_min>' requested here 266 | const T val = op_norm::vec_norm_min(P_fake_vector); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/nmf.hpp:165:27: note: in instantiation of function template specialization 'arma::norm>' requested here 165 | this->normA = arma::norm(this->A, "fro"); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/nmf.hpp:232:13: note: in instantiation of member function 'planc::NMF>::otherInitializations' requested here 232 | this->otherInitializations(); | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/hals.hpp:44:90: note: in instantiation of member function 'planc::NMF>::NMF' requested here 44 | HALSNMF(const T&A, const arma::mat&llf, const arma::mat&rlf, const int&ncores = 0) : NMF(A, llf, rlf) { | ^ /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/bppnmf.cpp:19:13: note: in instantiation of member function 'planc::HALSNMF>::HALSNMF' requested here 19 | HALSNMF tempHals(this->A, this->W, this->H); | ^ 2 warnings generated. 9 warnings generated. [ 82%] Building CXX object nmf/CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf && /data/gannet/ripley/bin/clang++-20 -DUSING_R -I/data/gannet/ripley/R/R-clang/include -I/data/gannet/ripley/R/test-clang/Rcpp/include -I/data/gannet/ripley/R/test-clang/RcppArmadillo/include -I/data/gannet/ripley/R/test-clang/RcppProgress/include -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nnls -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf -I/data/gannet/ripley/R/test-clang/HighFive/include -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math 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-frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o -MF CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o.d -o CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/parseutils.cpp [ 94%] Building CXX object nmf/CMakeFiles/nmflib.dir/__/common/data.cpp.o cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf && /data/gannet/ripley/bin/clang++-20 -DUSING_R -I/data/gannet/ripley/R/R-clang/include -I/data/gannet/ripley/R/test-clang/Rcpp/include -I/data/gannet/ripley/R/test-clang/RcppArmadillo/include -I/data/gannet/ripley/R/test-clang/RcppProgress/include -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nnls -I/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf -I/data/gannet/ripley/R/test-clang/HighFive/include -isystem /usr/local/clang20/include -I/usr/local/clang/include -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/__/common/data.cpp.o -MF CMakeFiles/nmflib.dir/__/common/data.cpp.o.d -o CMakeFiles/nmflib.dir/__/common/data.cpp.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/common/data.cpp [100%] Linking CXX static library libnmflib.a cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf && /usr/bin/cmake -P CMakeFiles/nmflib.dir/cmake_clean_target.cmake cd /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/nmf && /usr/bin/cmake -E cmake_link_script CMakeFiles/nmflib.dir/link.txt --verbose=1 /usr/bin/llvm-ar-20 qc libnmflib.a CMakeFiles/nmflib.dir/nmf_lib.cpp.o CMakeFiles/nmflib.dir/bppnmf.cpp.o CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o CMakeFiles/nmflib.dir/__/common/data.cpp.o ../CMakeFiles/utils.dir/common/utils.cpp.o ../CMakeFiles/hw_detect.dir/common/hw_detect.c.o ../CMakeFiles/detect_blas.dir/common/detect_blas.c.o /usr/bin/llvm-ranlib-20 libnmflib.a make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' [100%] Built target nmflib make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' /usr/bin/cmake -E cmake_progress_start /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/CMakeFiles 0 make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build' -- Install configuration: "RelWithDebInfo" -- Installing: /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/libnmflib.a ** libs using C++ compiler: ‘clang version 20.1.7’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src' clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/HighFive/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/HighFive/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c rcppplanc_nmf.cpp -o rcppplanc_nmf.o clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/HighFive/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c rcppplanc_nnls.cpp -o rcppplanc_nnls.o clang++-20 -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang20/lib -L/usr/local/clang20/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang20/lib/clang/20/lib/x86_64-unknown-linux-gnu -o RcppPlanc.so RcppExports.o rcppplanc_nmf.o rcppplanc_nnls.o -L./ -lnmflib -fopenmp /usr/lib64/libblas.so /usr/lib64/liblapack.so /usr/lib64/libblas.so /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc/.libs/libhwloc_embedded.a /usr/lib64/libhdf5.so make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src' installing to /data/gannet/ripley/R/packages/tests-clang/RcppPlanc.Rcheck/00LOCK-RcppPlanc/00new/RcppPlanc/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RcppPlanc)