Sorry for the delay here, just catching up on changes coming back from break.

Based on my research, it looks like Apple may just intentionally not be providing support for the C++17 filesystem API in its pre-2019 operating systems, even for versions of Clang that could otherwise support it: https://stackoverflow.com/a/58668083

I can't really fix this on the BPCells side, though once we hit CRAN most Mac users won't need to compile it themselves. As a stopgap measure, I've implemented a clearer error message up-front when an incompatible compiler is detected prior to package installation.

Short of upgrading your computer's OS version to a more recent release, the actual fix on your end would be to use a clang / gcc version not distributed by Apple.

Just to outline those steps for users who are unsure:
[BEGIN EDIT 4/29/2023]
From my own testing, it seems conda is not a great way to install a newer compiler on an old macOS version.

Here is an approach that I used successfully on a 2015 iMac running macOS 12.6.4 Monterey. This should only be necessary if your first install attempt gets the error:

Unable to compile program with C++17 std::filesystem.
Please install a newer compiler version and set CC and CXX in ~/.R/Makevars

Steps I used:

Install homebrew
Install hdf5 and llvm through homebrew: brew install hdf5 llvm (llvm is the project that clang and clang++ are part of)

Use brew info llvm to get the folder where llvm binaries are installed.

Output from brew info llvm

bparks@DN52emcl dotfiles % brew info llvm
==> llvm: stable 16.0.2 (bottled), HEAD [keg-only]
Next-gen compiler infrastructure
https://llvm.org/
/usr/local/Cellar/llvm/16.0.2 (6,779 files, 1.6GB)
Poured from bottle using the formulae.brew.sh API on 2023-04-28 at 15:45:24
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/llvm.rb
License: Apache-2.0 with LLVM-exception
==> Dependencies
[I cut off the rest of the output since it's not needed here]

Here we see the main install folder of /usr/local/Cellar/llvm/16.0.2, so we update ~/.R/Makevars to have

Confirm that hdf5 headers are visible in /usr/local/include:

ls -l /usr/local/include/hdf5.h

BPCells % ls -l /usr/local/include/hdf5.h
lrwxr-xr-x   1 bparks  admin  38 Apr 28 15:48 /usr/local/include/hdf5.h -> ../Cellar/hdf5/1.12.2_2/include/hdf5.h

Update ~/.R/Makevars to include both the compiler path for clang/clang++ and the include path for the hdf5 libraries

CC=/usr/local/Cellar/llvm/16.0.2/bin/clang
CXX=/usr/local/Cellar/llvm/16.0.2/bin/clang++
CFLAGS=-I/usr/local/include
CXXFLAGS=-I/usr/local/include

Install BPCells using remotes::install_github("bnprks/BPCells")

For some reason I had trouble using the conda hdf5 with this setup, so I'd recommend using homebrew for both the compiler and hdf5 installation, and deactivate any conda environment you have active prior to installation.
[END EDIT 4/29/2023]

Old instructions prior to 4/29/2023 edit

~~Install clang via conda: conda install -c conda-forge clang~~ EDIT 4/28/2023: I think installing via homebrew might be more robust brew install llvm. Then in the following instructions replace clang-cpp with clang++
Find the paths for conda's clang and clang-cpp by running which clang and which clang-cpp in your conda env
Edit the file ~/.R/Makevars adding the lines CC=[path-to-clang] and CXX=[path-to-clang-cpp] (more info available in this manual)
Try installing the package again, verifying that the compiler commands printed are calling your conda environment's copy of clang or clang-cpp

I'm closing this for now, but feel free to re-open with a comment if this outlined solution doesn't work for you.

Compilation issues on macOS #3

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