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ld: symbol(s) not found for architecture x86_64 x86_64-apple-darwin13.4: error: linker command failed with exit code 1 #11

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royfrancis opened this issue Aug 31, 2024 · 6 comments
Open

ld: symbol(s) not found for architecture x86_64 x86_64-apple-darwin13.4: error: linker command failed with exit code 1 #11

royfrancis opened this issue Aug 31, 2024 · 6 comments

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@royfrancis
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royfrancis commented Aug 31, 2024 •
edited
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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<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<HighFive::DataSetException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataSpaceException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataTypeException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      ...
  "_H5open", referenced from:
      HighFive::DataType HighFive::create_and_check_datatype<double>() in rcppplanc_nmf.cpp.o
      HighFive::DataType::isReference() const in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<unsigned long long>() in rcppplanc_nmf.cpp.o
      HighFive::File::File(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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>(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)3>::add<HighFive::Chunking>(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
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theAeon commented Aug 31, 2024

Could you please get me the full install log?

@royfrancis
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royfrancis commented Sep 1, 2024 •
edited
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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 <min> value or use a ...<max> 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]
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-- 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
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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
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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
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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<eT>::has_infinity) ? eT(std::numeric_limits<eT>::infinity()) : eT(std::numeric_limits<eT>::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<double>' requested here
  177 | template<typename eT> const eT Datum<eT>::inf         = priv::Datum_helper::inf<eT>();
      |                                                                             ^
/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<double>::inf' requested here
  465 |       val = neg ? cond_rel< is_signed<eT>::value >::make_neg(Datum<eT>::inf) : Datum<eT>::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<double>' 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<double>' 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<double>' 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<double>' 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<double>::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<eT>::has_infinity) ? -(std::numeric_limits<eT>::infinity()) : std::numeric_limits<eT>::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<double>' requested here
  751 |   T max_val = (N != 1) ? priv::most_neg<T>() : 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<arma::Col<double>>' 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<arma::SpMat<double>>' 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<arma::SpMat<double>>::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<arma::SpMat<double>>::NMF' requested here
   43 |   HALSNMF(const T &A, const arma::mat &llf, const arma::mat &rlf, const int& ncores = 0) : NMF<T>(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<arma::SpMat<double>>::HALSNMF' requested here
  295 |   HALSNMF<arma::sp_mat> 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<eT>::has_infinity) ? std::numeric_limits<eT>::infinity() : std::numeric_limits<eT>::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<double>' requested here
  816 |   T min_val = (N != 1) ? priv::most_pos<T>() : 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<arma::Col<double>>' 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<arma::SpMat<double>>' 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<arma::SpMat<double>>::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<arma::SpMat<double>>::NMF' requested here
   43 |   HALSNMF(const T &A, const arma::mat &llf, const arma::mat &rlf, const int& ncores = 0) : NMF<T>(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<arma::SpMat<double>>::HALSNMF' requested here
  295 |   HALSNMF<arma::sp_mat> 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      planc::H5SpMat::H5SpMat(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long, unsigned long long) in rcppplanc_nmf.cpp.o
  "_H5Dget_space", referenced from:
      HighFive::SliceTraits<HighFive::DataSet>::select(HighFive::HyperSlab const&, HighFive::DataSpace const&) const in rcppplanc_nmf.cpp.o
      planc::H5Mat::H5Mat(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      planc::H5SpMat::H5SpMat(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long, unsigned long long) in rcppplanc_nmf.cpp.o
      HighFive::SliceTraits<HighFive::DataSet>::select(std::__1::vector<unsigned long, std::__1::allocator<unsigned long>> const&) const in rcppplanc_nmf.cpp.o
      HighFive::SliceTraits<HighFive::DataSet>::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<HighFive::Selection>::read<double>(double*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) const in rcppplanc_nmf.cpp.o
      void HighFive::SliceTraits<HighFive::Selection>::read<unsigned long long>(unsigned long long*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) const in rcppplanc_nmf.cpp.o
  "_H5Dwrite", referenced from:
      void HighFive::SliceTraits<HighFive::Selection>::write_raw<double>(double const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in rcppplanc_nmf.cpp.o
      void HighFive::SliceTraits<HighFive::Selection>::write_raw<unsigned long long>(unsigned long long const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in rcppplanc_nmf.cpp.o
      void HighFive::SliceTraits<HighFive::Selection>::write_raw<double>(double const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in conversion.cpp.o
      void HighFive::SliceTraits<HighFive::Selection>::write_raw<int>(int const*, HighFive::DataType const&, HighFive::PropertyList<(HighFive::PropertyType)5> const&) in conversion.cpp.o
  "_H5Eclear2", referenced from:
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataSetException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::PropertyException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataSpaceException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataTypeException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::FileException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::FileException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in conversion.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::PropertyException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in conversion.cpp.o
      ...
  "_H5Eget_auto2", referenced from:
      HighFive::File::File(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<HighFive::DataSetException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::PropertyException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataSpaceException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataTypeException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::FileException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::FileException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in conversion.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::PropertyException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in conversion.cpp.o
      ...
  "_H5Eget_major", referenced from:
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataSetException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataSpaceException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataTypeException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      ...
  "_H5Eget_minor", referenced from:
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataSetException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataSpaceException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataTypeException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      ...
  "_H5Eset_auto2", referenced from:
      HighFive::File::File(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in rcppplanc_nmf.cpp.o
      std::__1::unique_ptr<HighFive::SilenceHDF5, std::__1::default_delete<HighFive::SilenceHDF5>>::~unique_ptr[abi:ue170006]() in rcppplanc_nmf.cpp.o
      HighFive::File::File(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o
      std::__1::unique_ptr<HighFive::SilenceHDF5, std::__1::default_delete<HighFive::SilenceHDF5>>::~unique_ptr[abi:ue170006]() in conversion.cpp.o
  "_H5Ewalk2", referenced from:
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataSetException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::PropertyException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataSpaceException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::DataTypeException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::FileException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in rcppplanc_nmf.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::FileException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in conversion.cpp.o
      void HighFive::HDF5ErrMapper::ToException<HighFive::PropertyException>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) in conversion.cpp.o
      ...
  "_H5Fcreate", referenced from:
      HighFive::File::File(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<HighFive::DataSet>::PathTraits() in rcppplanc_nmf.cpp.o
      HighFive::PathTraits<HighFive::DataSet>::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<HighFive::DataSet>::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<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned int, HighFive::PropertyList<(HighFive::PropertyType)1> const&, HighFive::PropertyList<(HighFive::PropertyType)2> const&) in conversion.cpp.o
      HighFive::PathTraits<HighFive::DataSet>::PathTraits() in conversion.cpp.o
      ...
  "_H5P_CLS_DATASET_CREATE_ID_g", referenced from:
      void HighFive::PropertyList<(HighFive::PropertyType)3>::add<HighFive::Chunking>(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)3>::add<HighFive::Chunking>(HighFive::Chunking const&) in conversion.cpp.o
  "_H5P_CLS_LINK_CREATE_ID_g", referenced from:
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(HighFive::CreateIntermediateGroup const&) in conversion.cpp.o
  "_H5Pcreate", referenced from:
      void HighFive::PropertyList<(HighFive::PropertyType)3>::add<HighFive::Chunking>(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)3>::add<HighFive::Chunking>(HighFive::Chunking const&) in conversion.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(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>(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)3>::add<HighFive::Chunking>(HighFive::Chunking const&) in conversion.cpp.o
  "_H5Pset_create_intermediate_group", referenced from:
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(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<unsigned long const*>, std::__1::__wrap_iter<unsigned long const*>>(std::__1::__wrap_iter<unsigned long const*>, std::__1::__wrap_iter<unsigned long const*>) in rcppplanc_nmf.cpp.o
      HighFive::DataSpace::DataSpace<unsigned long const*, unsigned long const*>(unsigned long const*, unsigned long const*) in rcppplanc_nmf.cpp.o
      HighFive::DataSpace::DataSpace<unsigned long const*, unsigned long const*>(unsigned long const*, unsigned long const*) in conversion.cpp.o
      HighFive::DataSpace::DataSpace<std::__1::__wrap_iter<unsigned long const*>, std::__1::__wrap_iter<unsigned long const*>>(std::__1::__wrap_iter<unsigned long const*>, std::__1::__wrap_iter<unsigned long const*>) 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<double>() in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<double>() in conversion.cpp.o
  "_H5T_NATIVE_INT_g", referenced from:
      HighFive::DataType HighFive::create_and_check_datatype<int>() in conversion.cpp.o
  "_H5T_NATIVE_ULLONG_g", referenced from:
      HighFive::DataType HighFive::create_and_check_datatype<unsigned long long>() 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<double>() in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<unsigned long long>() in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<double>() in conversion.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<int>() 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<double>() in rcppplanc_nmf.cpp.o
      HighFive::DataType::getSize() const in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<unsigned long long>() in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<double>() in conversion.cpp.o
      HighFive::DataType::getSize() const in conversion.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<int>() in conversion.cpp.o
  "_H5Tis_variable_str", referenced from:
      HighFive::DataType HighFive::create_and_check_datatype<double>() in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<unsigned long long>() in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<double>() in conversion.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<int>() in conversion.cpp.o
  "_H5check_version", referenced from:
      HighFive::File::File(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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<HighFive::DataSetException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataSpaceException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::DataTypeException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in rcppplanc_nmf.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::FileException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      int HighFive::HDF5ErrMapper::stackWalk<HighFive::PropertyException>(unsigned int, H5E_error2_t const*, void*) in conversion.cpp.o
      ...
  "_H5open", referenced from:
      HighFive::DataType HighFive::create_and_check_datatype<double>() in rcppplanc_nmf.cpp.o
      HighFive::DataType::isReference() const in rcppplanc_nmf.cpp.o
      HighFive::DataType HighFive::create_and_check_datatype<unsigned long long>() in rcppplanc_nmf.cpp.o
      HighFive::File::File(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> 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>(HighFive::Chunking const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)13>::add<HighFive::CreateIntermediateGroup>(HighFive::CreateIntermediateGroup const&) in rcppplanc_nmf.cpp.o
      void HighFive::PropertyList<(HighFive::PropertyType)3>::add<HighFive::Chunking>(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
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theAeon commented Sep 1, 2024 

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
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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
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theAeon commented Sep 1, 2024

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.

conda-forge/staged-recipes#25904

if you want to help me pester them

@theAeon
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theAeon commented Sep 1, 2024

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

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