ld: symbol(s) not found for architecture x86_64 x86_64-apple-darwin13.4: error: linker command failed with exit code 1

[royfrancis]

Installation error:

install.packages('RcppPlanc', repos = c('https://welch-lab.r-universe.dev', 'https://cloud.r-project.org'))

Installation error

``` ... HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o "_H5free_memory", referenced from: int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o ... "_H5open", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType::isReference() const in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in conversion.cpp.o ... ld: symbol(s) not found for architecture x86_64 x86_64-apple-darwin13.4: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [CMakeFiles/RcppPlanc.dir/build.make:160: RcppPlanc.so] Error 1 make[2]: Leaving directory '/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpWJPPHF/R.INSTALL1a00690d3207/RcppPlanc/src' make[1]: *** [CMakeFiles/Makefile2:107: CMakeFiles/RcppPlanc.dir/all] Error 2 make[1]: Leaving directory '/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpWJPPHF/R.INSTALL1a00690d3207/RcppPlanc/src' make: *** [Makefile:139: all] Error 2 ERROR: compilation failed for package ‘RcppPlanc’ * removing ‘/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppPlanc’ The downloaded source packages are in ‘/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpMkKMsG/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("RcppPlanc", repos = c("https://welch-lab.r-universe.dev", : installation of package ‘RcppPlanc’ had non-zero exit status ```

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin13.4.0
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/liblapack-netlib.3.9.0.dylib

locale:
[1] sv_SE.UTF-8/sv_SE.UTF-8/sv_SE.UTF-8/C/sv_SE.UTF-8/sv_SE.UTF-8

time zone: Europe/Stockholm
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.4.1 tools_4.4.1

I am working in a conda environment, so here are the conda packages which includes cmake, clang etc..

Conda environment

``` # Name Version Build Channel _r-mutex 1.0.0 anacondar_1 appnope 0.1.4 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge binutils 1.0.1 1 conda-forge blas 2.123 accelerate conda-forge blas-devel 3.9.0 23_osx64_accelerate conda-forge bwidget 1.9.16 h6066b31_0 bzip2 1.0.8 h6c40b1e_6 c-ares 1.28.1 h10d778d_0 conda-forge ca-certificates 2024.8.30 h8857fd0_0 conda-forge cairo 1.18.0 h9f650ed_2 conda-forge cctools 986 hd3558d4_0 conda-forge cctools_osx-64 986 h58a35ae_0 conda-forge clang 18.1.8 default_h179603d_0 conda-forge clang-18 18.1.8 default_h0c94c6a_0 conda-forge clang_impl_osx-64 18.1.8 h6a44ed1_16 conda-forge clang_osx-64 18.1.8 hb91bd55_16 conda-forge clangxx 18.1.8 default_h179603d_0 conda-forge clangxx_impl_osx-64 18.1.8 h4b7810f_16 conda-forge clangxx_osx-64 18.1.8 hb91bd55_16 conda-forge cmake 3.30.3 h7243fc2_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge compiler-rt 18.1.8 h734a56e_0 conda-forge compiler-rt_osx-64 18.1.8 h7312ed1_0 conda-forge curl 8.9.1 hcd6fca1_0 conda-forge debugpy 1.8.5 py39h09c4c31_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 hcec6c5f_0 font-ttf-dejavu-sans-mono 2.37 hd3eb1b0_0 font-ttf-inconsolata 2.001 hcb22688_0 font-ttf-source-code-pro 2.030 hd3eb1b0_0 font-ttf-ubuntu 0.83 h8b1ccd4_0 fontconfig 2.14.2 h5bb23bf_0 conda-forge fonts-anaconda 1 h8fa9717_0 fonts-conda-ecosystem 1 hd3eb1b0_0 freetype 2.12.1 h60636b9_2 conda-forge fribidi 1.0.10 haf1e3a3_0 gfortran_impl_osx-64 12.3.0 h54fd467_1 conda-forge gfortran_osx-64 12.3.0 h18f7dce_1 conda-forge gmp 6.2.1 he9d5cce_3 graphite2 1.3.14 he9d5cce_1 gsl 2.7.1 hdbe807d_1 harfbuzz 8.5.0 h053f038_0 conda-forge hdf5 1.14.3 nompi_h687a608_105 conda-forge icu 73.2 hf5e326d_0 conda-forge importlib-metadata 8.2.0 pyha770c72_0 conda-forge importlib_metadata 8.2.0 hd8ed1ab_0 conda-forge ipykernel 6.29.5 pyh57ce528_0 conda-forge ipython 8.18.1 pyh707e725_3 conda-forge isl 0.25 hb486fe8_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.1 py39h6e9494a_0 conda-forge krb5 1.21.3 h37d8d59_0 conda-forge ld64 711 h4e51db5_0 conda-forge ld64_osx-64 711 had5d0d3_0 conda-forge lerc 4.0.0 hb486fe8_0 conda-forge libaec 1.1.3 h73e2aa4_0 conda-forge libasprintf 0.22.5 h5ff76d1_2 conda-forge libblas 3.9.0 23_osx64_accelerate conda-forge libcblas 3.9.0 23_osx64_accelerate conda-forge libclang-cpp18.1 18.1.8 default_h0c94c6a_0 conda-forge libcurl 8.9.1 hfcf2730_0 conda-forge libcxx 17.0.6 h8d2f0da_1 conda-forge libdeflate 1.20 h49d49c5_0 conda-forge libedit 3.1.20230828 h6c40b1e_0 libev 4.33 h9ed2024_1 libexpat 2.6.2 h73e2aa4_0 conda-forge libffi 3.4.4 hecd8cb5_1 libgettextpo 0.22.5 h5ff76d1_2 conda-forge libgfortran 5.0.0 13_2_0_h97931a8_3 conda-forge libgfortran-devel_osx-64 12.3.0 h0b6f5ec_3 conda-forge libgfortran5 13.2.0 h2873a65_3 conda-forge libgit2 1.8.1 h59467ec_1 conda-forge libglib 2.80.2 h736d271_1 conda-forge libiconv 1.17 hd75f5a5_2 conda-forge libintl 0.22.5 h5ff76d1_2 conda-forge libjpeg-turbo 3.0.0 h0dc2134_1 conda-forge liblapack 3.9.0 23_osx64_accelerate conda-forge liblapacke 3.9.0 23_osx64_accelerate conda-forge libllvm18 18.1.8 h9ce406d_0 conda-forge libnghttp2 1.58.0 h64cf6d3_1 conda-forge libopenblas 0.3.28 openmp_h8869122_0 conda-forge libpng 1.6.43 h92b6c6a_0 conda-forge libsodium 1.0.18 hbcb3906_1 conda-forge libsqlite 3.46.0 h1b8f9f3_0 conda-forge libssh2 1.11.0 hd019ec5_0 conda-forge libtiff 4.6.0 h129831d_3 conda-forge libuv 1.48.0 h67532ce_0 conda-forge libv8 8.9.83 h8241635_4 conda-forge libwebp-base 1.3.2 h6c40b1e_0 libxml2 2.12.7 h3e169fe_1 conda-forge libzlib 1.3.1 h87427d6_1 conda-forge llvm-openmp 18.1.8 h15ab845_0 conda-forge llvm-tools 18.1.8 h9ce406d_0 conda-forge make 4.2.1 h3efe00b_1 matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mpc 1.3.1 h81bd1dd_0 conda-forge mpfr 4.2.1 h0c69b56_0 conda-forge ncurses 6.5 hf036a51_1 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge openblas 0.3.28 openmp_hba01982_0 conda-forge openssl 3.3.1 hd23fc13_3 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandoc 3.2.1 h694c41f_0 conda-forge pango 1.54.0 h880b76c_0 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge pcre2 10.44 h7634a1b_0 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pip 24.2 pyhd8ed1ab_0 conda-forge pixman 0.43.4 h73e2aa4_0 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.47 pyha770c72_0 conda-forge psutil 6.0.0 py39hded5825_0 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge python 3.9.18 h7a9c478_1_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python_abi 3.9 4_cp39 conda-forge pyzmq 26.1.0 py39hf975025_0 conda-forge r-assertthat 0.2.1 r44hc72bb7e_5 conda-forge r-base 4.4.1 h50cb0cb_2 conda-forge r-cli 3.6.3 r44h25d921d_1 conda-forge r-codetools 0.2_20 r44hc72bb7e_1 conda-forge r-colorspace 2.1_1 r44h6b9d099_0 conda-forge r-cowplot 1.1.3 r44hc72bb7e_1 conda-forge r-cpp11 0.5.0 r44hc72bb7e_0 conda-forge r-crayon 1.5.3 r44hc72bb7e_1 conda-forge r-dplyr 1.1.4 r44h25d921d_1 conda-forge r-ellipsis 0.3.2 r44h6b9d099_3 conda-forge r-fansi 1.0.6 r44h6b9d099_1 conda-forge r-farver 2.1.2 r44h25d921d_1 conda-forge r-generics 0.1.3 r44hc72bb7e_3 conda-forge r-ggplot2 3.5.1 r44hc72bb7e_1 conda-forge r-glue 1.7.0 r44h6b9d099_1 conda-forge r-gtable 0.3.5 r44hc72bb7e_1 conda-forge r-harmony 1.2.1 r44haa2a3db_0 conda-forge r-isoband 0.2.7 r44h25d921d_3 conda-forge r-labeling 0.4.3 r44hc72bb7e_1 conda-forge r-lattice 0.22_6 r44h6b9d099_1 conda-forge r-lifecycle 1.0.4 r44hc72bb7e_1 conda-forge r-lobstr 1.1.2 r44h25d921d_4 conda-forge r-magrittr 2.0.3 r44h6b9d099_3 conda-forge r-mass 7.3_60.0.1 r44h6b9d099_1 conda-forge r-matrix 1.6_5 r44h9cf22e7_1 conda-forge r-mgcv 1.9_1 r44h374a70c_1 conda-forge r-munsell 0.5.1 r44hc72bb7e_1 conda-forge r-nlme 3.1_165 r44h9612530_1 conda-forge r-pillar 1.9.0 r44hc72bb7e_2 conda-forge r-pkgconfig 2.0.3 r44hc72bb7e_4 conda-forge r-prettyunits 1.2.0 r44hc72bb7e_1 conda-forge r-pryr 0.1.6 r44h25d921d_2 conda-forge r-r6 2.5.1 r44hc72bb7e_3 conda-forge r-rcolorbrewer 1.1_3 r44h785f33e_3 conda-forge r-rcpp 1.0.13 r44h25d921d_0 conda-forge r-rcpparmadillo 14.0.0_1 r44h6a638e2_2 conda-forge r-rcppprogress 0.4.2 r44hc72bb7e_4 conda-forge r-rhpcblasctl 0.23_42 r44hc5191ce_2 conda-forge r-rlang 1.1.4 r44h25d921d_1 conda-forge r-scales 1.3.0 r44hc72bb7e_1 conda-forge r-stringi 1.8.4 r44ha6447fb_2 conda-forge r-stringr 1.5.1 r44h785f33e_1 conda-forge r-tibble 3.2.1 r44h6b9d099_3 conda-forge r-tidyselect 1.2.1 r44hc72bb7e_1 conda-forge r-utf8 1.2.4 r44h6b9d099_1 conda-forge r-vctrs 0.6.5 r44h25d921d_1 conda-forge r-viridislite 0.4.2 r44hc72bb7e_2 conda-forge r-withr 3.0.1 r44hc72bb7e_0 conda-forge readline 8.2 hca72f7f_0 rhash 1.4.4 h0dc2134_0 conda-forge setuptools 72.1.0 pyhd8ed1ab_0 conda-forge sigtool 0.1.3 h88f4db0_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge tapi 1100.0.11 h1527ee5_1 tk 8.6.13 h1abcd95_1 conda-forge tktable 2.10 h032784e_1 tornado 6.4.1 py39hded5825_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge wheel 0.44.0 pyhd8ed1ab_0 conda-forge xz 5.4.6 h6c40b1e_1 zeromq 4.3.5 hde137ed_4 conda-forge zipp 3.19.2 pyhd8ed1ab_0 conda-forge zlib 1.3.1 h87427d6_1 conda-forge zstd 1.5.6 h915ae27_0 conda-forge ```

[theAeon]

Could you please get me the full install log?

[royfrancis]

Full log

``` trying URL 'https://welch-lab.r-universe.dev/src/contrib/RcppPlanc_1.0.0.tar.gz' Content type 'application/x-gzip' length 1426513 bytes (1.4 MB) ================================================== downloaded 1.4 MB * installing *source* package ‘RcppPlanc’ ... ** using staged installation -- The C compiler identification is Clang 18.1.8 -- The CXX compiler identification is Clang 18.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found R: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/R (found version "3.4.0") -- MKL_THREADING = OMP -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib;-lm;-ldl -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- Found R_Rcpp: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/Rcpp -- Found R_RcppArmadillo: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo -- Found R_RcppProgress: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppProgress -- 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) CMake Warning (dev) at /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/share/cmake-3.30/Modules/ExternalProject/shared_internal_commands.cmake:1282 (message): The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is not set. The policy's OLD behavior will be used. When using a URL download, the timestamps of extracted files should preferably be that of the time of extraction, otherwise code that depends on the extracted contents might not be rebuilt if the URL changes. The OLD behavior preserves the timestamps from the archive instead, but this is usually not what you want. Update your project to the NEW behavior or specify the DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this robustness issue. Call Stack (most recent call first): /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/share/cmake-3.30/Modules/ExternalProject.cmake:3035 (_ep_add_download_command) CMakeLists.txt:135 (ExternalProject_Add) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/share/cmake-3.30/Modules/FetchContent.cmake:1373 (message): The DOWNLOAD_EXTRACT_TIMESTAMP option was not given and policy CMP0135 is not set. The policy's OLD behavior will be used. When using a URL download, the timestamps of extracted files should preferably be that of the time of extraction, otherwise code that depends on the extracted contents might not be rebuilt if the URL changes. The OLD behavior preserves the timestamps from the archive instead, but this is usually not what you want. Update your project to the NEW behavior or specify the DOWNLOAD_EXTRACT_TIMESTAMP option with a value of true to avoid this robustness issue. Call Stack (most recent call first): CMakeLists.txt:162 (FetchContent_Declare) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/_deps/highfive-src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Found HDF5: hdf5-static (found version "1.14.3") -- Performing Test FINITE_MATH -- Performing Test FINITE_MATH - Success -- Performing Test SIGNALING_NANS -- Performing Test SIGNALING_NANS - Failed -- Performing Test ROUNDING_MATH -- Performing Test ROUNDING_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 -- Looking for openblas/cblas.h -- Looking for openblas/cblas.h - not found -- Configuring done (15.1s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_INSTALL_NAME_TOOL CMAKE_LIBTOOL -- Build files have been written to: /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src ** libs /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -S/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools -B/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src --check-build-system CMakeFiles/Makefile.cmake 0 /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E cmake_progress_start /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/CMakeFiles /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/depend cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E cmake_depends "Unix Makefiles" /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/CMakeFiles/hwloc.dir/DependInfo.cmake "--color=" make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/build [ 7%] Creating directories for 'hwloc' /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -Dcfgdir= -P /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/tmp/hwloc-mkdirs.cmake /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-mkdir [ 14%] Performing download step (download, verify and extract) for 'hwloc' cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -DCMAKE_MESSAGE_LOG_LEVEL=VERBOSE -P /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/download-hwloc.cmake -- Downloading... dst='/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-2.9.3.tar.gz' timeout='none' inactivity timeout='none' -- Using src='https://download.open-mpi.org/release/hwloc/v2.9/hwloc-2.9.3.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] -- [download 17% complete] -- [download 18% complete] -- [download 19% complete] -- [download 20% complete] -- [download 21% complete] -- [download 22% complete] -- [download 23% complete] -- [download 24% complete] -- [download 25% complete] -- [download 26% complete] -- [download 27% complete] -- [download 28% complete] -- [download 29% complete] -- [download 30% complete] -- [download 31% complete] -- [download 32% complete] -- [download 33% complete] -- [download 34% complete] -- [download 35% complete] -- [download 36% complete] -- [download 37% complete] -- [download 38% complete] -- [download 39% complete] -- [download 40% complete] -- [download 41% complete] -- [download 42% complete] -- [download 43% complete] -- [download 44% complete] -- [download 45% complete] -- [download 46% complete] -- [download 47% complete] -- [download 48% complete] -- [download 49% complete] -- [download 50% complete] -- [download 51% complete] -- [download 52% complete] -- [download 53% complete] -- [download 54% complete] -- [download 55% complete] -- [download 56% complete] -- [download 57% complete] -- [download 58% complete] -- [download 59% complete] -- [download 60% complete] -- [download 61% complete] -- [download 62% complete] -- [download 63% complete] -- [download 64% complete] -- [download 65% complete] -- [download 66% complete] -- [download 67% complete] -- [download 68% complete] -- [download 69% complete] -- [download 70% complete] -- [download 71% complete] -- [download 72% complete] -- [download 73% complete] -- [download 74% complete] -- [download 75% complete] -- [download 76% complete] -- [download 77% complete] -- [download 78% complete] -- [download 79% complete] -- [download 80% complete] -- [download 81% complete] -- [download 82% complete] -- [download 83% complete] -- [download 84% complete] -- [download 85% complete] -- [download 86% complete] -- [download 87% complete] -- [download 88% complete] -- [download 89% complete] -- [download 90% complete] -- [download 91% complete] -- [download 92% complete] -- [download 93% complete] -- [download 94% complete] -- [download 95% complete] -- [download 96% complete] -- [download 97% complete] -- [download 98% complete] -- [download 99% complete] -- [download 100% complete] -- verifying file... file='/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-2.9.3.tar.gz' -- Downloading... done cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -DCMAKE_MESSAGE_LOG_LEVEL=VERBOSE -P /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/verify-hwloc.cmake cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -DCMAKE_MESSAGE_LOG_LEVEL=VERBOSE -P /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/extract-hwloc.cmake -- extracting... src='/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-2.9.3.tar.gz' dst='/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-download [ 21%] No update step for 'hwloc' /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E echo_append /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-update [ 28%] Performing patch step for 'hwloc' cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E cat /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/patches/00_remove_stdio.patch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/patches/01_remove_sprintf.patch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/patches/02_adjust_windows_types.patch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/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-windows.c' patching file 'hwloc/distances.c' patching file 'hwloc/topology-linux.c' cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-patch [ 35%] Performing configure step for 'hwloc' cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E env "CFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1719423301177/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4=/usr/local/src/conda-prefix -mmacosx-version-min=11" 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 ### ### Configuring hwloc distribution tarball ### Startup tests ### checking build system type... x86_64-apple-darwin13.4.0 checking host system type... x86_64-apple-darwin13.4.0 checking target system type... x86_64-apple-darwin13.4.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /opt/homebrew/bin/gmkdir -p checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '501' is supported by ustar format... yes checking whether GID '20' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports nested variables... (cached) yes checking whether make supports the include directive... yes (GNU style) checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang 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 x86_64-apple-darwin13.4.0-clang accepts -g... yes checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes checking dependency style of x86_64-apple-darwin13.4.0-clang... 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 x86_64-apple-darwin13.4.0-ar... x86_64-apple-darwin13.4.0-ar checking the archiver (x86_64-apple-darwin13.4.0-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 x86_64-apple-darwin13.4.0-clang... x86_64-apple-darwin13.4.0-ld checking if the linker (x86_64-apple-darwin13.4.0-ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... x86_64-apple-darwin13.4.0-nm checking the name lister (x86_64-apple-darwin13.4.0-nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop checking for x86_64-apple-darwin13.4.0-ld option to reload object files... -r checking for x86_64-apple-darwin13.4.0-file... no checking for file... file checking for x86_64-apple-darwin13.4.0-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for x86_64-apple-darwin13.4.0-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-apple-darwin13.4.0-ar... (cached) x86_64-apple-darwin13.4.0-ar checking for archiver @FILE support... no checking for x86_64-apple-darwin13.4.0-strip... x86_64-apple-darwin13.4.0-strip checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib checking command to parse x86_64-apple-darwin13.4.0-nm output from x86_64-apple-darwin13.4.0-clang object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-apple-darwin13.4.0-mt... no checking for mt... no checking if : is a manifest tool... no checking for x86_64-apple-darwin13.4.0-dsymutil... no checking for dsymutil... dsymutil checking for x86_64-apple-darwin13.4.0-nmedit... x86_64-apple-darwin13.4.0-nmedit checking for x86_64-apple-darwin13.4.0-lipo... x86_64-apple-darwin13.4.0-lipo checking for x86_64-apple-darwin13.4.0-otool... x86_64-apple-darwin13.4.0-otool checking for x86_64-apple-darwin13.4.0-otool64... no checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-apple-darwin13.4.0-clang supports -fno-rtti -fno-exceptions... yes checking for x86_64-apple-darwin13.4.0-clang option to produce PIC... -fno-common -DPIC checking if x86_64-apple-darwin13.4.0-clang PIC flag -fno-common -DPIC works... yes checking if x86_64-apple-darwin13.4.0-clang static flag -static works... no checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... yes checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes checking whether the x86_64-apple-darwin13.4.0-clang linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.4.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes 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 x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 accepts -g... yes checking for x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 option to enable C++11 features... none needed checking dependency style of x86_64-apple-darwin13.4.0-clang++ -std=gnu++17... gcc3 checking how to run the C++ preprocessor... x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 -E checking for ld used by x86_64-apple-darwin13.4.0-clang++ -std=gnu++17... x86_64-apple-darwin13.4.0-ld checking if the linker (x86_64-apple-darwin13.4.0-ld) is GNU ld... no checking whether the x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes checking for x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 option to produce PIC... -fno-common -DPIC checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 PIC flag -fno-common -DPIC works... yes checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 static flag -static works... no checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 supports -c -o file.o... yes checking if x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 supports -c -o file.o... (cached) yes checking whether the x86_64-apple-darwin13.4.0-clang++ -std=gnu++17 linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.4.0 dyld checking how to hardcode library paths into programs... immediate checking for x86_64-apple-darwin13.4.0-gcc... (cached) x86_64-apple-darwin13.4.0-clang checking whether the compiler supports GNU C... (cached) yes checking whether x86_64-apple-darwin13.4.0-clang accepts -g... (cached) yes checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... (cached) none needed checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... (cached) yes checking dependency style of x86_64-apple-darwin13.4.0-clang... (cached) gcc3 checking for x86_64-apple-darwin13.4.0-clang options needed to detect all undeclared functions... none needed checking for x86_64-apple-darwin13.4.0-pkg-config... no checking for pkg-config... /opt/homebrew/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E checking for X... libraries /usr/X11/lib, headers ### ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build configure: hwloc srcdir: /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc configure: Detected VPATH build checking for hwloc version... 2.9.3 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... Darwin 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)... no checking if x86_64-apple-darwin13.4.0-clang 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 **** Darwin-specific checks checking for the Foundation framework... yes checking for the IOKit framework... yes **** end of Darwin-specific checks checking for sys/param.h... yes checking for sys/sysctl.h... yes checking whether CTL_HW is declared... yes checking whether HW_NCPU is declared... yes checking whether HW_REALMEM64 is declared... no checking whether HW_MEMSIZE64 is declared... no checking whether HW_PHYSMEM64 is declared... no checking whether HW_USERMEM64 is declared... no checking whether HW_REALMEM is declared... no checking whether HW_MEMSIZE is declared... yes checking whether HW_PHYSMEM is declared... yes checking whether HW_USERMEM is declared... yes checking for sysctl... yes checking for sysctlbyname... yes checking whether pthread_setaffinity_np is declared... no checking whether pthread_getaffinity_np is declared... no 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... yes checking for mach_init.h... no checking for mach/mach_host.h... yes checking for host_info... yes 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... yes checking whether getexecname is declared... no checking for program_invocation_name... no checking for __progname... yes checking for pthread_t... yes checking for bash... /bin/sh 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... yes checking whether fls is declared... yes checking whether function fls has a complete prototype... yes checking for flsl... yes checking whether flsl is declared... yes checking whether function flsl has a complete prototype... yes checking for clz... no checking for clzl... no checking for openat... yes checking for malloc.h... no checking for getpagesize... yes checking for memalign... no 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 darwin 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 Netloc functionality: no Plugin support: no ----------------------------------------------------------------------------- cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-configure [ 42%] Performing build step for 'hwloc' cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build && make Making all in include make[4]: Nothing to be done for `all'. Making all in hwloc CC topology.lo CC traversal.lo CC distances.lo CC memattrs.lo CC cpukinds.lo CC components.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-noos.lo CC topology-synthetic.lo CC topology-xml.lo CC topology-xml-nolibxml.lo CC topology-darwin.lo CC topology-x86.lo CCLD libhwloc_embedded.la make[4]: Nothing to be done for `all-am'. cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-build [ 50%] Performing install step for 'hwloc' cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build && make install Making install in include make[5]: Nothing to be done for `install-exec-am'. Making install in hwloc make install-exec-hook make[6]: Nothing to be done for `install-exec-hook'. make[5]: Nothing to be done for `install-exec-am'. cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-install [ 57%] Completed 'hwloc' /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E make_directory /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/CMakeFiles /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/CMakeFiles/hwloc-complete /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E touch /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-stamp/hwloc-done /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E remove_directory /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc/utils/lstopo [ 57%] Built target hwloc make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/depend cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E cmake_depends "Unix Makefiles" /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/CMakeFiles/hw_detect.dir/DependInfo.cmake "--color=" make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/build [ 64%] Building C object CMakeFiles/hw_detect.dir/common/hw_detect.c.o /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc-build/include -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/hwloc-prefix/src/hwloc/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1719423301177/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu99 -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-version-min=11 -fPIC -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 /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/common/hw_detect.c [ 64%] Built target hw_detect make -f CMakeFiles/RcppPlanc.dir/build.make CMakeFiles/RcppPlanc.dir/depend cd /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src && /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E cmake_depends "Unix Makefiles" /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/CMakeFiles/RcppPlanc.dir/DependInfo.cmake "--color=" make -f CMakeFiles/RcppPlanc.dir/build.make CMakeFiles/RcppPlanc.dir/build [ 71%] Building CXX object CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang++ -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nnls -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/Rcpp/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppProgress/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib/Frameworks/vecLib.framework/Headers -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/_deps/highfive-src/include -isystem /opt/homebrew/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1719423301177/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4=/usr/local/src/conda-prefix -O3 -DNDEBUG -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-version-min=11 -fPIC -fopenmp=libomp -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -MD -MT CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o -MF CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o.d -o CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o -c /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/rcppplanc_nmf.cpp In file included from /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/rcppplanc_nmf.cpp:5: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/armadillo:137: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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(); | ^ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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; | ^ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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 ); | ^ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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); | ^ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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); | ^ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:8117:27: note: in instantiation of function template specialization 'arma::diskio::load_auto_detect' requested here 8117 | load_okay = diskio::load_auto_detect(*this, name, err_msg); | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common/utils.hpp:298:5: note: in instantiation of member function 'arma::Mat::load' requested here 298 | A.load(std::move(fname)); | ^ In file included from /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/rcppplanc_nmf.cpp:5: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/armadillo:137: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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]); | ^ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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); | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common/nmf.hpp:171:25: note: in instantiation of function template specialization 'arma::norm>' requested here 171 | this->normA = arma::norm(this->A, "fro"); | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common/nmf.hpp:240:11: note: in instantiation of member function 'planc::NMF>::otherInitializations' requested here 240 | this->otherInitializations(); | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf/hals.hpp:43:92: note: in instantiation of member function 'planc::NMF>::NMF' requested here 43 | HALSNMF(const T &A, const arma::mat &llf, const arma::mat &rlf, const int& ncores = 0) : NMF(A, llf, rlf) { | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf/bppnmf.hpp:295:25: note: in instantiation of member function 'planc::HALSNMF>::HALSNMF' requested here 295 | HALSNMF tempHals(this->A, this->W, this->H); | ^ In file included from /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/rcppplanc_nmf.cpp:5: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include/armadillo:137: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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]); | ^ /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/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); | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common/nmf.hpp:171:25: note: in instantiation of function template specialization 'arma::norm>' requested here 171 | this->normA = arma::norm(this->A, "fro"); | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common/nmf.hpp:240:11: note: in instantiation of member function 'planc::NMF>::otherInitializations' requested here 240 | this->otherInitializations(); | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf/hals.hpp:43:92: note: in instantiation of member function 'planc::NMF>::NMF' requested here 43 | HALSNMF(const T &A, const arma::mat &llf, const arma::mat &rlf, const int& ncores = 0) : NMF(A, llf, rlf) { | ^ /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf/bppnmf.hpp:295:25: note: in instantiation of member function 'planc::HALSNMF>::HALSNMF' requested here 295 | HALSNMF tempHals(this->A, this->W, this->H); | ^ 3 warnings generated. [ 78%] Building CXX object CMakeFiles/RcppPlanc.dir/RcppExports.cpp.o /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang++ -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nnls -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/Rcpp/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppProgress/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib/Frameworks/vecLib.framework/Headers -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/_deps/highfive-src/include -isystem /opt/homebrew/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1719423301177/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4=/usr/local/src/conda-prefix -O3 -DNDEBUG -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-version-min=11 -fPIC -fopenmp=libomp -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -MD -MT CMakeFiles/RcppPlanc.dir/RcppExports.cpp.o -MF CMakeFiles/RcppPlanc.dir/RcppExports.cpp.o.d -o CMakeFiles/RcppPlanc.dir/RcppExports.cpp.o -c /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/RcppExports.cpp [ 85%] Building CXX object CMakeFiles/RcppPlanc.dir/conversion.cpp.o /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang++ -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nnls -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/Rcpp/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppProgress/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib/Frameworks/vecLib.framework/Headers -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/_deps/highfive-src/include -isystem /opt/homebrew/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1719423301177/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4=/usr/local/src/conda-prefix -O3 -DNDEBUG -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-version-min=11 -fPIC -fopenmp=libomp -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -MD -MT CMakeFiles/RcppPlanc.dir/conversion.cpp.o -MF CMakeFiles/RcppPlanc.dir/conversion.cpp.o.d -o CMakeFiles/RcppPlanc.dir/conversion.cpp.o -c /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/conversion.cpp [ 92%] Building C object CMakeFiles/RcppPlanc.dir/common/detect_blas.c.o /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/common -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nnls -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/tools/../src/nmf -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/Rcpp/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppArmadillo/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppProgress/include -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib/Frameworks/vecLib.framework/Headers -I/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/_deps/highfive-src/include -isystem /opt/homebrew/include -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1719423301177/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu99 -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-version-min=11 -fPIC -fopenmp=libomp -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -MD -MT CMakeFiles/RcppPlanc.dir/common/detect_blas.c.o -MF CMakeFiles/RcppPlanc.dir/common/detect_blas.c.o.d -o CMakeFiles/RcppPlanc.dir/common/detect_blas.c.o -c /private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/RtmpaqOhTr/R.INSTALLb88a5f9777d3/RcppPlanc/src/common/detect_blas.c [100%] Linking CXX shared library RcppPlanc.so /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/cmake -E cmake_link_script CMakeFiles/RcppPlanc.dir/link.txt --verbose=1 /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/x86_64-apple-darwin13.4.0-clang++ -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1719423301177/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4=/usr/local/src/conda-prefix -O3 -DNDEBUG -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-version-min=11 -dynamiclib -Wl,-headerpad_max_install_names -shared -L/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/lib -fopenmp=libomp -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib -L/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib -o RcppPlanc.so -install_name @rpath/RcppPlanc.so CMakeFiles/RcppPlanc.dir/rcppplanc_nmf.cpp.o CMakeFiles/RcppPlanc.dir/RcppExports.cpp.o CMakeFiles/RcppPlanc.dir/conversion.cpp.o CMakeFiles/RcppPlanc.dir/common/detect_blas.c.o CMakeFiles/hw_detect.dir/common/hw_detect.c.o -lR /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libopenblas.dylib -lm -ldl /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libsz.dylib /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libz.dylib /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libdl.tbd /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd /opt/homebrew/lib/libhdf5.a -lm -ldl /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd /opt/homebrew/lib/libsz.dylib hwloc-prefix/src/hwloc-build/hwloc/.libs/libhwloc_embedded.a -framework Foundation -framework IOKit -framework OpenCL ld: warning: text-based stub file /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libdl.tbd and library file /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libdl.tbd are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd and library file /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd are out of sync. Falling back to library file for linking. ld: warning: text-based stub file /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd and library file /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd are out of sync. Falling back to library file for linking. ld: warning: ignoring file /opt/homebrew/lib/libhdf5.a, building for macOS-x86_64 but attempting to link with file built for macOS-arm64 ld: warning: ignoring file /opt/homebrew/lib/libsz.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64 ld: warning: dylib (/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libc++.dylib) was built for newer macOS version (12.0) than being linked (11.0) Undefined symbols for architecture x86_64: "_H5Dcreate2", referenced from: HighFive::detail::h5d_create2(long long, char const*, long long, long long, long long, long long, long long) in rcppplanc_nmf.cpp.o HighFive::detail::h5d_create2(long long, char const*, long long, long long, long long, long long, long long) in conversion.cpp.o "_H5Dget_create_plist", referenced from: planc::H5Mat::H5Mat(std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o planc::H5SpMat::H5SpMat(std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&, unsigned long long, unsigned long long) in rcppplanc_nmf.cpp.o "_H5Dget_space", referenced from: HighFive::SliceTraits::select(HighFive::HyperSlab const&, HighFive::DataSpace const&) const in rcppplanc_nmf.cpp.o planc::H5Mat::H5Mat(std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o planc::H5SpMat::H5SpMat(std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&, unsigned long long, unsigned long long) in rcppplanc_nmf.cpp.o HighFive::SliceTraits::select(std::__1::vector> const&) const in rcppplanc_nmf.cpp.o HighFive::SliceTraits::select(HighFive::HyperSlab const&, HighFive::DataSpace const&) const in conversion.cpp.o "_H5Dopen2", referenced from: HighFive::detail::h5d_open2(long long, char const*, long long) in rcppplanc_nmf.cpp.o "_H5Dread", referenced from: void HighFive::SliceTraits::read(double*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) const in rcppplanc_nmf.cpp.o void HighFive::SliceTraits::read(unsigned long long*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) const in rcppplanc_nmf.cpp.o "_H5Dwrite", referenced from: void HighFive::SliceTraits::write_raw(double const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in rcppplanc_nmf.cpp.o void HighFive::SliceTraits::write_raw(unsigned long long const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in rcppplanc_nmf.cpp.o void HighFive::SliceTraits::write_raw(double const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in conversion.cpp.o void HighFive::SliceTraits::write_raw(int const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in conversion.cpp.o "_H5Eclear2", referenced from: void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in conversion.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in conversion.cpp.o ... "_H5Eget_auto2", referenced from: HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o "_H5Eget_current_stack", referenced from: void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in conversion.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in conversion.cpp.o ... "_H5Eget_major", referenced from: int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o ... "_H5Eget_minor", referenced from: int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o ... "_H5Eset_auto2", referenced from: HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o std::__1::unique_ptr>::~unique_ptr[abi:ue170006]() in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o std::__1::unique_ptr>::~unique_ptr[abi:ue170006]() in conversion.cpp.o "_H5Ewalk2", referenced from: void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in conversion.cpp.o void HighFive::HDF5ErrMapper::ToException(std::__1::basic_string, std::__1::allocator> const&) in conversion.cpp.o ... "_H5Fcreate", referenced from: HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o "_H5Fflush", referenced from: planc::H5Mat::~H5Mat() in rcppplanc_nmf.cpp.o planc::H5Mat::t() in rcppplanc_nmf.cpp.o planc::H5SpMat::~H5SpMat() in rcppplanc_nmf.cpp.o planc::H5SpMat::t() in rcppplanc_nmf.cpp.o "_H5Fopen", referenced from: HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o "_H5Idec_ref", referenced from: HighFive::Object::~Object() in rcppplanc_nmf.cpp.o HighFive::Object::~Object() in conversion.cpp.o "_H5Iget_file_id", referenced from: HighFive::PathTraits::PathTraits() in rcppplanc_nmf.cpp.o HighFive::PathTraits::PathTraits() in conversion.cpp.o "_H5Iinc_ref", referenced from: HighFive::Object::Object(HighFive::Object const&) in rcppplanc_nmf.cpp.o HighFive::Object::Object(HighFive::Object const&) in conversion.cpp.o "_H5Iis_valid", referenced from: HighFive::PathTraits::PathTraits() in rcppplanc_nmf.cpp.o HighFive::Object::~Object() in rcppplanc_nmf.cpp.o HighFive::Object::Object(HighFive::Object const&) in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o HighFive::Object::~Object() in conversion.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o HighFive::PathTraits::PathTraits() in conversion.cpp.o ... "_H5P_CLS_DATASET_CREATE_ID_g", referenced from: void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in conversion.cpp.o "_H5P_CLS_LINK_CREATE_ID_g", referenced from: void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in conversion.cpp.o "_H5Pcreate", referenced from: void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in conversion.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in conversion.cpp.o "_H5Pget_chunk", referenced from: HighFive::Chunking::Chunking(HighFive::PropertyList<(HighFive::PropertyType)3>&, unsigned long) in rcppplanc_nmf.cpp.o "_H5Pset_chunk", referenced from: void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in conversion.cpp.o "_H5Pset_create_intermediate_group", referenced from: void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in conversion.cpp.o "_H5Scopy", referenced from: HighFive::DataSpace::clone() const in rcppplanc_nmf.cpp.o HighFive::DataSpace::clone() const in conversion.cpp.o "_H5Screate_simple", referenced from: HighFive::DataSpace::DataSpace, std::__1::__wrap_iter>(std::__1::__wrap_iter, std::__1::__wrap_iter) in rcppplanc_nmf.cpp.o HighFive::DataSpace::DataSpace(unsigned long const*, unsigned long const*) in rcppplanc_nmf.cpp.o HighFive::DataSpace::DataSpace(unsigned long const*, unsigned long const*) in conversion.cpp.o HighFive::DataSpace::DataSpace, std::__1::__wrap_iter>(std::__1::__wrap_iter, std::__1::__wrap_iter) in conversion.cpp.o "_H5Sget_simple_extent_dims", referenced from: HighFive::DataSpace::getDimensions() const in rcppplanc_nmf.cpp.o "_H5Sget_simple_extent_ndims", referenced from: planc::H5Mat::H5Mat(std::__1::basic_string, std::__1::allocator> const&, std::__1::basic_string, std::__1::allocator> const&) in rcppplanc_nmf.cpp.o HighFive::DataSpace::getDimensions() const in rcppplanc_nmf.cpp.o "_H5Sselect_hyperslab", referenced from: HighFive::HyperSlab::apply(HighFive::DataSpace const&) const in rcppplanc_nmf.cpp.o HighFive::HyperSlab::apply(HighFive::DataSpace const&) const in conversion.cpp.o "_H5Sselect_none", referenced from: HighFive::HyperSlab::apply(HighFive::DataSpace const&) const in rcppplanc_nmf.cpp.o HighFive::HyperSlab::apply(HighFive::DataSpace const&) const in conversion.cpp.o "_H5T_NATIVE_DOUBLE_g", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o "_H5T_NATIVE_INT_g", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o "_H5T_NATIVE_ULLONG_g", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o "_H5T_STD_REF_OBJ_g", referenced from: HighFive::DataType::isReference() const in rcppplanc_nmf.cpp.o HighFive::DataType::isReference() const in conversion.cpp.o "_H5Tcopy", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o "_H5Tequal", referenced from: HighFive::DataType::isReference() const in rcppplanc_nmf.cpp.o HighFive::DataType::isReference() const in conversion.cpp.o "_H5Tget_class", referenced from: HighFive::DataType::getClass() const in rcppplanc_nmf.cpp.o HighFive::DataType::getClass() const in conversion.cpp.o "_H5Tget_size", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType::getSize() const in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o HighFive::DataType::getSize() const in conversion.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o "_H5Tis_variable_str", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in conversion.cpp.o "_H5check_version", referenced from: HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o "_H5free_memory", referenced from: int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o int HighFive::HDF5ErrMapper::stackWalk(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o ... "_H5open", referenced from: HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::DataType::isReference() const in rcppplanc_nmf.cpp.o HighFive::DataType HighFive::create_and_check_datatype() in rcppplanc_nmf.cpp.o HighFive::File::File(std::__1::basic_string, std::__1::allocator> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)13>::add(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o void HighFive::PropertyList<(HighFive::PropertyType)3>::add(HighFive::Chunking const&) in conversion.cpp.o ... ld: symbol(s) not found for architecture x86_64 x86_64-apple-darwin13.4: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [RcppPlanc.so] Error 1 make[1]: *** [CMakeFiles/RcppPlanc.dir/all] Error 2 make: *** [all] Error 2 ERROR: compilation failed for package ‘RcppPlanc’ * removing ‘/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library/RcppPlanc’ The downloaded source packages are in ‘/private/var/folders/2x/8klyghhd06x61bvf368z7d140000gn/T/Rtmph8YBrY/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("RcppPlanc", repos = c("https://welch-lab.r-universe.dev", : installation of package ‘RcppPlanc’ had non-zero exit status ```

[theAeon]

ld: warning: ignoring file /opt/homebrew/lib/libhdf5.a, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/lib/libsz.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: dylib (/opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/libc++.dylib) was built for newer macOS version (12.0) than being linked (11.0)
Undefined symbols for architecture x86_64:

Found your problem. If I may ask, why are you using x86_64 conda on an arm mac?

[royfrancis]

Not all R packages are available for arm64, and I frequently get stuck when installing. So, to be on the safe side, I just use x86 conda environment. And it almost always works. This package has been an exception.

[theAeon]

I don't know that cross-compiling like this is something I'm willing/able to support.

On the flip side, I do have a conda-forge feedstock that's been languishing in staged-recipes for months which would solve this problem in a different way if it were to be merged.

https://github.com/conda-forge/staged-recipes/pull/25904

if you want to help me pester them

[theAeon]

https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=1015299&view=artifacts&pathAsName=false&type=publishedArtifacts

alternatively, you can just grab the build from here