* 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 20.1.8
-- The CXX compiler identification is Clang 20.1.8
-- 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) (2025-07-22 r88445) -- "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 (32.8s)
-- 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
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make -f CMakeFiles/Makefile2 all
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make -f CMakeFiles/utils.dir/build.make CMakeFiles/utils.dir/depend
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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="
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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="
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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="
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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'
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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%] 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
[ 17%] 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
/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");
| ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/cmake -E touch /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-mkdir
2 warnings generated.
make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build'
[ 23%] Performing download step (download, verify and extract) for 'hwloc'
[ 23%] Built target detect_blas
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'
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-- verifying file...
file='/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.12.1.tar.gz'
-- Downloading... done
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/verify-hwloc.cmake
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/extract-hwloc.cmake
-- extracting...
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
[ 29%] 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
[ 35%] 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
[ 41%] 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
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checking for sys/stat.h... yes
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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
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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
[ 47%] 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
make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/build'
[ 47%] Built target utils
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 distances.lo
CC traversal.lo
CC cpukinds.lo
CC components.lo
CC memattrs.lo
CC bind.lo
CC bitmap.lo
CC pci-common.lo
CC diff.lo
CC shmem.lo
CC misc.lo
CC base64.lo
CC topology-synthetic.lo
CC topology-noos.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
../../hwloc/hwloc/topology-synthetic.c:1443:20: warning: variable 'warned' set but not used [-Wunused-but-set-variable]
1443 | static int warned = 0;
| ^
../../hwloc/hwloc/components.c:883:9: warning: variable 'first' set but not used [-Wunused-but-set-variable]
883 | int first = 1;
| ^
CC topology-xml.lo
CC topology-xml-nolibxml.lo
CC topology-linux.lo
CC topology-hardwired.lo
1 warning generated.
CC topology-x86.lo
1 warning generated.
../../hwloc/hwloc/memattrs.c:799:9: warning: unused variable 'err' [-Wunused-variable]
799 | int err = from_internal_location(&imi->initiator, &initiators[i]);
| ^~~
../../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");
| ^~~~~~~~~~~~
7 warnings generated.
../../hwloc/hwloc/topology-linux.c:7779:26: warning: unused variable 'topology' [-Wunused-variable]
7779 | struct hwloc_topology *topology = backend->topology;
| ^~~~~~~~
1 warning generated.
4 warnings generated.
1 warning generated.
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'
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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
[ 52%] 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
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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'
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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
[ 58%] 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'
[ 58%] Built target hwloc
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="
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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
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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="
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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/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
[ 76%] 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
[ 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 -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o -MF CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o.d -o CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o -c /data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nnls/nnls_lib.cpp
[ 88%] Building CXX object nmf/CMakeFiles/nmflib.dir/__/common/data.cpp.o
[ 94%] Building CXX object nmf/CMakeFiles/nmflib.dir/__/common/parseutils.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/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
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
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<eT>::has_infinity) ? -(std::numeric_limits<eT>::infinity()) : std::numeric_limits<eT>::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<double>' requested here
751 | T max_val = (N != 1) ? priv::most_neg<T>() : 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<arma::Col<double>>' 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<arma::SpMat<double>>' 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<arma::SpMat<double>>::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<arma::SpMat<double>>::NMF' requested here
44 | HALSNMF(const T&A, const arma::mat&llf, const arma::mat&rlf, const int&ncores = 0) : NMF<T>(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<arma::SpMat<double>>::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<eT>::has_infinity) ? std::numeric_limits<eT>::infinity() : std::numeric_limits<eT>::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<double>' requested here
816 | T min_val = (N != 1) ? priv::most_pos<T>() : 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<arma::Col<double>>' 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<arma::SpMat<double>>' 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<arma::SpMat<double>>::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<arma::SpMat<double>>::NMF' requested here
44 | HALSNMF(const T&A, const arma::mat&llf, const arma::mat&rlf, const int&ncores = 0) : NMF<T>(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<arma::SpMat<double>>::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/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<arma::Mat<double>>::parseParams' hides overloaded virtual function [-Woverloaded-virtual]
73 | void parseParams(const internalSymmParams<T>&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<arma::Mat<double>>' 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<arma::Mat<double>, 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<double> planc::nmflib<T, double>::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<double>&Hinit);
| ^
/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/EmbeddedNMFDriver.hpp:16:22: note: hidden overloaded virtual function 'planc::EmbeddedNMFDriver<arma::Mat<double>>::parseParams' declared here: type mismatch at 1st parameter ('const internalParams<Mat<double>> &' vs 'const internalSymmParams<Mat<double>> &')
16 | virtual void parseParams(const internalParams<T>&pc) {
| ^
/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/EmbeddedNMFDriver.hpp:73:14: warning: 'planc::symmEmbeddedNMFDriver<arma::SpMat<double>>::parseParams' hides overloaded virtual function [-Woverloaded-virtual]
73 | void parseParams(const internalSymmParams<T>&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<arma::SpMat<double>>' 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<arma::SpMat<double>, 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<double> planc::nmflib<T, double>::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<double>&Hinit);
| ^
/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/EmbeddedNMFDriver.hpp:16:22: note: hidden overloaded virtual function 'planc::EmbeddedNMFDriver<arma::SpMat<double>>::parseParams' declared here: type mismatch at 1st parameter ('const internalParams<SpMat<double>> &' vs 'const internalSymmParams<SpMat<double>> &')
16 | virtual void parseParams(const internalParams<T>&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<arma::Mat<double>, 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<double> planc::nmflib<T, double>::uinmf(const std::vector<std::shared_ptr<T>> &matPtrVec, const std::vector<std::shared_ptr<T>> &unsharedPtrVec, std::vector<int> 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<arma::SpMat<double>, 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<double> planc::nmflib<T, double>::uinmf(const std::vector<std::shared_ptr<T>> &matPtrVec, const std::vector<std::shared_ptr<T>> &unsharedPtrVec, std::vector<int> 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<planc::H5Mat, double>::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<double> planc::nmflib<T, double>::uinmf(const std::vector<std::shared_ptr<T>> &matPtrVec, const std::vector<std::shared_ptr<T>> &unsharedPtrVec, std::vector<int> 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<planc::H5SpMat, double>::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<double> planc::nmflib<T, double>::uinmf(const std::vector<std::shared_ptr<T>> &matPtrVec, const std::vector<std::shared_ptr<T>> &unsharedPtrVec, std::vector<int> whichUnshared, const arma::uword &k, const int& nCores, const arma::vec &lambda, const arma::uword &niter, const bool &verbose);
| ^
2 warnings generated.
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<eT>::has_infinity) ? -(std::numeric_limits<eT>::infinity()) : std::numeric_limits<eT>::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<double>' requested here
635 | eT max_val = priv::most_neg<eT>();
| ^
/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<double>' 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<arma::subview_col<double>>' 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<arma::subview_col<double>>' 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<double>' 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<arma::Mat<double>>' 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<double>::operator=<arma::Mat<double>, 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<arma::Mat<double>>::CallNMF<planc::MUNMF<arma::Mat<double>>>' requested here
311 | CallNMF<MUNMF<T>>();
| ^
/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:245:15: note: in instantiation of member function 'planc::NMFDriver<arma::Mat<double>>::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<eT>::has_infinity) ? std::numeric_limits<eT>::infinity() : std::numeric_limits<eT>::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<double>' requested here
816 | T min_val = (N != 1) ? priv::most_pos<T>() : 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<arma::Mat<double>>' 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<arma::Mat<double>>' 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<arma::Mat<double>>::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<arma::Mat<double>>::NMF' requested here
43 | MUNMF(const T&A, const arma::mat&llf, const arma::mat&rlf, const int&ncores = 0) : NMF<T>(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<arma::Mat<double>>::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<arma::Mat<double>>::CallNMF<planc::MUNMF<arma::Mat<double>>>' requested here
311 | CallNMF<MUNMF<T>>();
| ^
/data/gannet/ripley/R/packages/tests-clang/RcppPlanc/src/planc/nmf/nmf_lib.inl:245:15: note: in instantiation of member function 'planc::NMFDriver<arma::Mat<double>>::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<eT>::has_infinity) ? eT(std::numeric_limits<eT>::infinity()) : eT(std::numeric_limits<eT>::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<double>' requested here
177 | template<typename eT> const eT Datum<eT>::inf = priv::Datum_helper::inf<eT>();
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/diskio_meat.hpp:465:73: note: in instantiation of static data member 'arma::Datum<double>::inf' requested here
465 | val = neg ? cond_rel< is_signed<eT>::value >::make_neg(Datum<eT>::inf) : Datum<eT>::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<double>' 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<double>' 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<double>' 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<double>' 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<double>::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<arma::Mat<double>>::loadMat' requested here
244 | NMFDriver<T> myNMF(opts);
| ^
9 warnings generated.
[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 20.1.8’
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)