mac CI system include directory may collide with user includes

[sounkou-bioinfo]

Hi,

This is more of a notification issue for other people that may encounter the same issue. I have noticed that the r-universe CI for a package was failing https://github.com/r-universe/sounkou-bioinfo/actions/runs/16100968181/job/45443184886 but was working fine with r-lib CI on mac https://github.com/sounkou-bioinfo/Rlibhv/actions/runs/16100845229/job/45429779556. The cause is that i needed to include the openssl library include flags, but at the same location there were headers that collided with the include names of the library i am wrapping, specifically HDF5 herr and hfile headers (to find out this, i have added this to the configure script https://github.com/sounkou-bioinfo/Rlibhv/blob/main/configure#L151). For this package it is not an issue because i will make sure the right include precedence is applied, but hfile.h may be problematic if it collides with for example htslib hfile.h for some other user

Best

[jeroen]

We use the same server configuration and libraries as used on CRAN. You can find these on https://mac.r-project.org/bin/ and also on https://github.com/r-universe-org/macos-libs.

I think generally speaking your package should find and use these libraries, instead of building your own.

This is not just on MacOS: all operating systems have many libraries preinstalled, so if your package includes other versions of those same libraries, they may start to conflict.

[sounkou-bioinfo]

We use the same server configuration and libraries as used on CRAN. You can find these on https://mac.r-project.org/bin/ and also on https://github.com/r-universe-org/macos-libs.

I think generally speaking your package should find and use these libraries, instead of building your own.

This is not just on MacOS: all operating systems have many libraries preinstalled, so if your package includes other versions of those same libraries, they may start to conflict.

Indeed, i ve checked maclibs repo and so the headers there
Version pinning - either to continue to use old versions or upgrade before the system package manager - is the major reason to build from source and statically link the libraries
I guess there is a field specific bias toward "library packages" because it is common to see such packages on Bioconductor or bioconda and to have several versions of the same library installed