EDIT 4 (2023/06/22)
I'm trying to create a PK model using rxode2 package. Unfortunately, I got an error message stating error building model when using rxode({...}) function. Since I'm using a Mac (OS version 12.6.6, Intel processor), I followed the instructions here and here since I saw the message that rxode2 has not detected OpenMP support and will run in single-threaded mode after I loaded the package.
At the end, this is what I did (for reproduction):
- Reinstall Xcode Command Line Tools:
sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select --install
However, this results in installing older sdk versions as well. I don't know if this could be related to Xcode that was used in the past. I have reinstalled Xcode but I still have my old projects showing up at Xcode startup and these may have been targeted to previous SDK versions. I'm not sure how to perform a complete removal (not only Xcode but also any settings/configuration files that could be linked to sdk ressources somewhere in my computer).
- Check libomp:
brew update && brew install libomp
--> Warning: libomp 16.0.5 is already installed and up-to-date
- Update Makevars file:
Of note (1): I first made a mistake creating this file (a simple txt file using textedit and removing the .txt extention) in my working R directory. I then created it in (what I hope is the good location...) the .r folder located in my$HOME (/Users/username/.r/Makevars)
Of note (2): R could not locate gfortran./usr/local/bin/gfortranis a symlink asls -l /usr/local/bin/gfortranprints/usr/local/bin/gfortran -> ../Cellar/gcc/13.1.0/bin/gfortran. I then modified Makevars accordingly. Currently, the Makevars file looks like this:
LOC=/usr/local/Cellar/gcc/13.1.0
CC=$(LOC)/bin/gcc-13 -fopenmp
CXX=$(LOC)/bin/g++-13 -fopenmp
CXX11=$(LOC)/bin/g++-13 -fopenmp
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L$(LOC)/lib -Wl,-rpath,$(LOC)/lib,-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/current/
CPPFLAGS=-I$(LOC)/include -I/usr/local/include
FLIBS=-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/13/gcc/x86_64-apple-darwin21 -L/usr/local/Cellar/gcc/13.1.0/lib/gcc/current/ -lgfortran -lquadmath -lm
CXX1X=$(LOC)/bin/g++-13
CXX98=$(LOC)/bin/g++-13
CXX14=$(LOC)/bin/g++-13
CXX17=$(LOC)/bin/g++-13
- Install
data.tablepackage from source to see if something's going wrong.
Aside from many warnings (-pedantic flag enabled), I get the following error (as we can see, it uses MacOSX12.sdk even though the last version available is MacOSX13.1.sdk, cf image above):
install.packages("data.table", type = "source")
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
- Reorder $PATH
As pointed out in this post, the 'tapi file' issue can be caused by the wrongld commandbeing used when'$HOME/anaconda3/bin/ld'path is preceding'$HOME/usr/bin'.
Sincewhich -a ldreturnsUsers/username/anaconda3/bin/ld(I have Anaconda activated), I addedexport PATH=/usr/bin:$PATHat the end of the.bash_profilefile in $HOME and then runsource ~\.bash_profileinto the terminal to have it take effect.
.bash_profile file
export JAVA_HOME=$(/usr/libexec/java_home)
# Setting PATH for Python 3.7
# The original version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.7/bin:${PATH}"
export PATH
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/username/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/Users/username/anaconda3/etc/profile.d/conda.sh" ]; then
. "/Users/username/anaconda3/etc/profile.d/conda.sh"
else
export PATH="/Users/username/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
export PATH=/usr/bin:$PATH
And now
$ which -a ld
/usr/bin/ld # it is now preceding $HOME/anaconda3/bin/ld
/Users/username/anaconda3/bin/ld
/usr/bin/ld
But still install.packages("data.table", type = "source") returns
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
- Remove older SDK files
After removing MacOSX11* and MacOSX12* .sdk files:
install.packages("data.table", type = "source") returns
ld: library not found for -lz
Could it be that the system is looking for MacOSX12.sdk exclusively? After it has been removed, it cannot target the most recent sdk files. MacOSX.sdk and MacOSX13.sdk are symlinks pointing to MacOSX13.1.sdk
ls -l /Library/Developer/CommandLineTools/SDKs/
total 0
lrwxr-xr-x 1 root wheel 14 15 jui 10:03 MacOSX.sdk -> MacOSX13.1.sdk
drwxr-xr-x 7 root wheel 224 12 nov 2022 MacOSX13.1.sdk
lrwxr-xr-x 1 root wheel 14 15 jui 10:02 MacOSX13.sdk -> MacOSX13.1.sdk
I tried to google related issues, and I found this post where it looks like Xcode and SDK versions need to be closely related. Maybe could this problem arise because the MacOS SDK version that is used is MacOSX12 ? Any idea why MacOSX.sdk/MacOSX13.*.sdk cannot be targeted ?
- Trying with macrtools
I installed the development version ofmacrtoolsR package from GitHub (as it has superseded the r-macos-rtools installer package). I followed these instructions after removing the Command line tools folder containing all MacOSX* .sdk files:
remotes::install_github("coatless-mac/macrtools")
macrtools::macos_rtools_install()
# Congratulations!
# Xcode CLI, Gfortran, and R developer binaries have been installed successfully.
But then two new elements come up:
i) In contrast with xcode-select --install, macrtools::macos_rtools_install() only installs MacOSX12 and MacOSX13 sdk files (not MacOSX11).
ii) However:
macrtools::is_xcode_cli_installed()
# FALSE
It says that Xcode CLI is not installed (even though SDK files are now present). The same thing occurs after trying to specifically install Xcode CLI:
macrtools::xcode_cli_install()
# Finding available software
# Downloading Command Line Tools for Xcode
# Downloaded Command Line Tools for Xcode
# Installing Command Line Tools for Xcode
# Done with Command Line Tools for Xcode
# Done.
macrtools::is_xcode_cli_installed()
# FALSE
macrtools::is_gfortran_installed()
# TRUE
macrtools::recipes_binary_install('r-base-dev')
# No error
install.packages("data.table", type = "source")
# ** R
# ** inst
# ** byte-compile and prepare package for lazy loading
# ** help
# *** installing help indices
# ** building package indices
# ** installing vignettes
# ** testing if installed package can be loaded from temporary location
# ** checking absolute paths in shared objects and dynamic libraries
# ** testing if installed package can be loaded from final location
# ** testing if installed package keeps a record of temporary installation path
# * DONE (data.table)
I'm not getting the message error unsupported tapi file type anymore :). But still, OpenMP is not detected:
> library(data.table)
# data.table 1.14.8 using 1 threads (see ?getDTthreads). Latest news: r-datatable.com
# **********
# This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode.
- Running {rxode2}
It is now possible to build a PK model without getting an error. However, many similar warnings show up (because of the -pedantic flag in Makevars ?) and I was wondering if they were related to OpenMP non-detection:
ppk_mode = rxode({
centr(0) = 0;
TVCl = THETA_Cl*(CLCREAT/120)^0.8*(0.7^DIAL);
TVVc = THETA_Vc*(WT/70) *(0.5^DIAL);
TVVp = THETA_Vp;
...
})
# /usr/local/include/stdlib.h:291:20: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]
# int cgetnext(char **, char **);
# ^
# /usr/local/include/stdlib.h:291:20: note: insert '_Nullable' if the pointer may be null
# int cgetnext(char **, char **);
# ^
# _Nullable
# /usr/local/include/stdlib.h:291:20: note: insert '_Nonnull' if the pointer should never be null
# int cgetnext(char **, char **);
# And many other similar warnings.
- gfortran reinstallation and Makevars update
After uninstalling and reinstalling gfortran with {macrtools}, it is still located at the same location/usr/local/Cellar/gcc/13.1.0/...
ls -l /usr/local/bin/gfortran
# lrwxr-xr-x [...] /usr/local/bin/gfortran -> ../Cellar/gcc/13.1.0/bin/gfortran
And
ls /usr/local/gfortran/lib/gcc/
# No such file or directory
Also, running set into the terminal prints x86_64-apple-darwin21 which is different from the platform mentioned by sessionInfo() in R that displays x86_64-apple-darwin20. I'm not sure what {macrtools} did at the end.
This is how the current Makevars file looks like:
LOC=/usr/local/Cellar/gcc/13.1.0
CC=$(LOC)/bin/gcc-13 -fopenmp
CXX=$(LOC)/bin/g++-13 -fopenmp
CXX11=$(LOC)/bin/g++-13 -fopenmp
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L$(LOC)/lib -Wl,-rpath,$(LOC)/lib,-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/current/
CPPFLAGS=-I$(LOC)/include -I/usr/local/include
FLIBS=-L/usr/local/Cellar/gcc/13.1.0/lib/gcc/13/gcc/x86_64-apple-darwin21/13 -L/usr/local/Cellar/gcc/13.1.0/lib/gcc/current/ -lgfortran -lquadmath -lm
CXX1X=$(LOC)/bin/g++-13
CXX11=/usr/local/gfortran/bin/g++
CXX98=$(LOC)/bin/g++-13
CXX14=$(LOC)/bin/g++-13
CXX17=$(LOC)/bin/g++-13
Unfortunately I get again the tapi error with MacOSX12.sdk that is used:
install.packages("data.table", type = "source")
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
I followed the same {macrtools} instructions as before, but I cannot get rid this time of the tapi error message and MacOSX12.sdk issue. During this {macrtools} process, I noticed that it downloaded resources in a darwin20 folder from 'mac.R-project.org' (cf below)
Downloading Command Line Tools for Xcode
Downloaded Command Line Tools for Xcode
Installing Command Line Tools for Xcode
Done with Command Line Tools for Xcode
Done.
gfortran was already installed! ...
Downloading https://mac.R-project.org/bin/REPOS ...
Using repository https://mac.R-project.org/bin/darwin20/x86_64 ...
Downloading index https://mac.R-project.org/bin/darwin20/x86_64/PACKAGES ...
Downloading binary: https://mac.R-project.org/bin/darwin20/x86_64/xz-5.4.2-darwin.20-x86_64.tar.xz ...
trying URL 'https://mac.R-project.org/bin/darwin20/x86_64/xz-5.4.2-darwin.20-x86_64.tar.xz'
Content type 'application/octet-stream' length 559568 bytes (546 KB)
==================================================
downloaded 546 KB
Installing: xz-5.4.2-darwin.20-x86_64.tar.xz into '/opt/R/x86_64' ...
...
For a reason I cannot explain, reproducing the same steps with macrtools results now again in the tapi error. Could it be related to any darwin version discrepancy ?
Of note, I upgraded MacOS to Monterey a few days ago. I reinstalled XQuartz as well. Is there a way to get rid of all these gfortran/gcc, command line tools and SDK-related issues to start from scratch with a clean R / Fortan / SDK / etc. environment ?
- Extra information - SessionInfo()
It shows that x86_64-apple-darwin20 platform version is used (and not darwin21 that is installed on my computer and that is the one in Makevars). But changing 21 to 20 in Makevars does not seem to have an influence.
- Cleaning and starting again
Since things look complicated, I uninstalledlibomp,lightgbm,llvm,Xcode command line toolsandanaconda.
brew uninstall libomp
Error: Refusing to uninstall /usr/local/Cellar/libomp/16.0.5
because it is required by lightgbm, which is currently installed.
You can override this and force removal with:
brew uninstall --ignore-dependencies libomp
brew uninstall lightgbm
Uninstalling /usr/local/Cellar/lightgbm/3.3.5... (98 files, 18.1MB)
brew uninstall libomp
Uninstalling /usr/local/Cellar/libomp/16.0.5... (7 files, 1.7MB)
brew uninstall llvm
Uninstalling /usr/local/Cellar/llvm/16.0.5... (6,779 files, 1.6GB)
Regarding Anaconda cleaning, I followed instructions here
conda install anaconda-clean
anaconda-clean --yes
Backup directory: /Users/username/.anaconda_backup/2023-06-22T181652
rm -rf ~/anaconda3
I also removed this in ~/.bash_profile
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/username/opt/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /de$
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/Users/username/opt/anaconda3/etc/profile.d/conda.sh" ]; then
. "/Users/username/opt/anaconda3/etc/profile.d/conda.sh"
else
export PATH="/Users/username/opt/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
Now, bash_profile looks like this:
export JAVA_HOME=$(/usr/libexec/java_home)
# Setting PATH for Python 3.7
# The original version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.7/bin:${PATH}"
export PATH
$PATH
-bash: /Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin: No such file or directory
However, I noticed that in addition to have anaconda3 files in ~/anaconda3, I also found them in /opt/anaconda3 as mentioned in bash_profile, along with gfortran (among others):
I also found that libomp.dylib is in /opt/anaconda3/lib:
Is this strange or is it something expected ? Should I also remove anaconda3 from this folder ?
which gfortran
# returns nothing, (i.e., expected since /opt is not in $PATH ?)
And lastly,
rm -rf /Library/Developer/CommandLineTools
xcode-select --install
Now, I reinstalled a few things and followed these instructions from here and here:
curl -O https://mac.r-project.org/openmp/openmp-14.0.6-darwin20-Release.tar.gz # since my Apple clang version is 1400.x
sudo tar fvxz openmp-14.0.6-darwin20-Release.tar.gz -C /
After unpacking, I indeed find these files:
/usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h
I added the following lines to $HOME/.R/Makevars that now contains only these lines:
CPPFLAGS += -I/usr/local/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/lib -lomp
As proposed here (item 6), I created and compiled omp_test.c, and then called the compiled C function from R, and got:
OpenMP threads available: 8
- Testing with data.table and rxode2
Aftef being so excited that OpenMP seems to work, I checked withdata.tableandrxode2packages
install.packages("data.table", type = "source")
# Many warnings like /usr/local/include/stdlib.h:346:37: note: insert '_Nonnull' if the pointer should never be null
# But installation successful
library(data.table)
# data.table 1.14.8 using 4 threads (see ?getDTthreads). Latest news: r-datatable.com
Becoming more and more confident, I tried with rxode2. However...
install.packages("rxode2", type = "source")
[...]
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
**using SDK: ‘MacOSX13.1.sdk’ ----> which was empty previously, this is good news!**
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:26: error: no template named 'numeric_limits'
bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:60: error: no template named 'numeric_limits'
bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:18: error: no template named 'numeric_limits'
int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:50: error: no template named 'numeric_limits'
int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:648:17: error: no template named 'numeric_limits'
static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:25: error: no template named 'numeric_limits'
return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:58: error: no template named 'numeric_limits'
return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:661:16: error: no template named 'numeric_limits'
using _Lim = numeric_limits<_IntT>;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:664:12: error: use of undeclared identifier '_Lim'
return _Lim::max();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:665:21: error: use of undeclared identifier '_Lim'
} else if (__r <= _Lim::lowest()) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:666:12: error: use of undeclared identifier '_Lim'
return _Lim::min();
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:138:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int abs(int) __pure2;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:853:1: error: declaration conflicts with target of using declaration already in scope
abs(const complex<_Tp>& __c)
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: target of using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:9: note: using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:910:16: error: reference to unresolved using declaration
return abs(__c.real());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:912:16: error: reference to unresolved using declaration
return abs(__c.imag());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:969:16: error: reference to unresolved using declaration
__re = abs(__re);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1022:29: error: reference to unresolved using declaration
return complex<_Tp>(log(abs(__x)), arg(__x));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1049:23: error: reference to unresolved using declaration
return polar(sqrt(abs(__x)), arg(__x) / _Tp(2));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:65:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1174:33: error: reference to unresolved using declaration
return complex<_Tp>(abs(__x.real()), __x.imag());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘rxode2’
Unfortunately, there seems to be something missing when trying to install rxode2. Did I forget to reinstall anything ? I also found here some problems related to a wrong value of CMAKE_OSX_SYSROOT and heard about header files to link to usr/local/include. Or even something missing in ~/.R/Makevars ? I really don't know what sould be done next.
