I recently updated R to 4.3.2 and reinstalled HDF5Array with no problem, but now running library(HDF5Array) crashes my R Studio session with the "R Session Aborted. R encountered a fatal error." popup.

I then tried running library(HDF5Array) in R on the terminal and got the following traceback:

 *** caught segfault ***
address 0x600000020, cause 'invalid permissions'

Traceback:
 1: H5Pcreate("H5P_FILE_ACCESS")
 2: H5Fcreate(file)
 3: h5createFile(filepath)
 4: .get_dump_autofile()
 5: setHDF5DumpDir()
 6: fun(libname, pkgname)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(fun(libname, pkgname), error = identity)
11: runHook(".onLoad", env, package.lib, package)
12: loadNamespace(package, lib.loc)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return && !quietly)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
17: library(HDF5Array)

I am not sure which permissions are invalid, as I can run commands like write.csv() to the current directory with no problems.

Here is my session info:

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.3.2

Any help troubleshooting this would be greatly appreciated!

Based on the error message this looks like the "invalid permissions" are referring to something in memory rather than your file system. If the only command you're running before the crash is H5Pcreate("H5P_FILE_ACCESS") then it doesn't even try to create any files. This is pretty mysterious as I've never seen this issue before, but HDF5Array is used by a lot of people so I'd have expected it to be reported before if there was a simple oversight in the rhdf5 package. I've tried to find the problem this morning, but drawn a blank so far.

Maybe you could try installing the packages from source, so they are compiled on your computer, rather than downloading the pre-built versions from Bioconductor. You can do that with the following command:

BiocManager::install(c("Rhdf5lib", "rhdf5"), force=TRUE, type = "source")

That might work straight away, or you might need to install some additional tools for doing the compiling. If that's the case I think you can follow the "Mandatory Tools" section of https://mac.r-project.org/tools/ to get the things you'll need.