Issue installing hdf5r on MacBook Pro with M3 Pro chip (only when using `renv`)
lucygarner opened this issue · comments
Hi,
I have been helping a colleague to set up their R environments on a new MacBook Pro with M3 Pro chip. However, we are having difficulties installing hdf5r when using renv. hdf5r installs fine into the "System Library" (outside of renv).
However, inside an RStudio project with renv, we get the following initial error:
In file included from const_export.c:23: In file included from ./const_export.h:22: ./global.h:23:10: fatal error: 'hdf5.h' file not found #include <hdf5.h> ^~~~~~~~ 1 error generated. make: *** [const_export.o] Error 1 ERROR: compilation failed for package ‘hdf5r’ * removing ‘/Users/user1/Documents/R/new_project/renv/library/R-4.3/aarch64-apple-darwin20/hdf5r’
This error was fixed using the following command, as discussed hhoeflin/hdf5r#171:
install.packages("hdf5r", configure.args = c("--with-hdf5=/opt/homebrew/bin/h5cc"))
However, we then have the following error:
ld: library 'hdf5_hl' not found clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [hdf5r.so] Error 1 ERROR: compilation failed for package ‘hdf5r’ * removing ‘/Users/user1/Documents/R/new_project/renv/library/R-4.3/aarch64-apple-darwin20/hdf5r’
Do you have any idea why we are specifically getting these errors when in an RStudio project using renv? And how we might fix them?
Best wishes,
Lucy
To confirm -- when the package is installed outside of renv, is the package still being installed from sources? Or is a binary copy of the package being installed?
My best guess is that the PATH might differ between what you see in an renv project, and what you see in a regular R session outside of renv. Can compare what:
writeLines(strsplit(Sys.getenv("PATH"), .Platform$path.sep)[[1]])
reports in each case? I ask because I think the hdf5r package includes a configure script that tries to find some of these binaries and tools on the PATH, and so the issue may be related.
It may also be helpful to see the full output produced during package installation (so I can see what library paths are included, and what seems to be missing)
I have the same issue on my Macbook pro M1 (OS: Monterrey). My R version is 4.3 (x86-84), handled using Rswitch. Did anyone solve this issue?