ERROR: compilation failed for package ‘flowCore’

[Biomiha]

Hi there,

I am trying to get all my cytoverse packages up to the latest version, however I keep hitting against compilation issues.
I am running an Apple M1 Pro and Sonoma 14.2.1.
I tried to compile flowCore and got the following error during compilation:

1 error generated.
make: *** [fcsTextParse.o] Error 1
ERROR: compilation failed for package ‘flowCore’

Before this there was also a line saying:

on.hpp:38:27: fatal error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?

The latter was to do with the {cytolib} package.

There don't seem to be any available binaries for the M1 (arm64) architecture for the current version and there is no way of finding old binaries (e.g. Bioconductor version 3.17) so I am a bit stuck.
I imagine there are quite a few people running M1 and M2 chips these days that will be stuck in a similar limbo to me. Any ideas for where to find a binary?

Thanks ever so much in advance,
Miha

[LTLA]

Pinging this.

binary_function was removed from the C++ standard library in C++17, which is now the default C++ specification for R package builds. The easiest solution is for flowCore to mandate the use of an earlier specification... which it seems to do in the SystemRequirements (C++11), but this is contradicted by the C++17 requirement in the Makevars.

[Edomenegaz]

Same problem over here. I've tried through BiocManager and directly from this repo, but I get the same error.

[Edomenegaz]

I think I've figured out what caused the problem. Apparently, having R installed through Homebrew on macOS is prone to all kinds of compiling issues, since it implements a different pipeline than the default one by CRAN. For me, removing my Homebrew R installation and reinstalling R from scratch from the official CRAN webpage, solved the issue and made life a lot easier with other plugins, too.