Error with C Stack Usage when installing packages - r

Question

I haven't touched R in a while, and just tried running some old Bioconductor code on my new Mac (M1, 2020, running OS Monterey 12.2.1).
I am able to run the beginning of my script (where I install packages) seemingly without issue:
library("knitr")
.cran_packages <- c("ggplot2", "gridExtra")
.bioc_packages <- c("dada2", "phyloseq", "DECIPHER", "phangorn", "msa")
.inst <- .cran_packages %in% installed.packages()
if(any(!.inst)) {
install.packages(.cran_packages[!.inst])
}
.inst <- .bioc_packages %in% installed.packages()
if(any(!.inst)) {
BiocManager::install(.bioc_packages[!.inst])
}
However, when I go to actually load the packages, like so:
sapply(c(.cran_packages, .bioc_packages), require, character.only = TRUE)
many of the bioconductor packages fail to load, with this readout:
Loading required package: dada2
Error: package or namespace load failed for ‘dada2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Loading required package: phyloseq
Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Loading required package: DECIPHER
Loading required package: Biostrings
Failed with error: ‘package ‘S4Vectors’ required by ‘Biostrings’ could not be found’
In addition: Warning message:
In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
cannot open compressed file '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/DESCRIPTION', probable reason 'No such file or directory'
Loading required package: msa
Loading required package: Biostrings
Failed with error: ‘package ‘S4Vectors’ required by ‘Biostrings’ could not be found’
In addition: Warning message:
In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
cannot open compressed file '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/DESCRIPTION', probable reason 'No such file or directory'
ggplot2 gridExtra dada2 phyloseq DECIPHER phangorn msa
TRUE TRUE FALSE FALSE FALSE TRUE FALSE
Based on this result, I have tried re-installing ‘GenomeInfoDbData’ and ‘S4Vectors’ separately. It looks like the issue with installing ‘GenomeInfoDbData’ is the version of ‘S4Vectors’. When I choose to skip updating S4Vectors, I get this error message:
> BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for
details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’
trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz'
Content type 'application/x-gzip' length 11193674 bytes (10.7 MB)
==================================================
downloaded 10.7 MB
Error: C stack usage 7953728 is too close to the limit
Execution halted
The downloaded source packages are in
‘/private/var/folders/84/4fxygqsd07zcn8kzy9yh8t2c0000gn/T/RtmppKV5Cc/downloaded_packages’
Old packages: 'S4Vectors'
Update all/some/none? [a/s/n]:
n
Warning message:
In .inet_warning(msg) :
installation of package ‘GenomeInfoDbData’ had non-zero exit status
and when I choose to proceed with updating S4Vectors (from binary), I get a similar error:
Old packages: 'S4Vectors'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
S4Vectors 0.32.3 0.32.4 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) n
trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/S4Vectors_0.32.3.tgz'
Content type 'application/x-gzip' length 2099211 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
The downloaded binary packages are in
/var/folders/84/4fxygqsd07zcn8kzy9yh8t2c0000gn/T//RtmppKV5Cc/downloaded_packages
Warning message:
In .inet_warning(msg) :
installation of package ‘GenomeInfoDbData’ had non-zero exit status
This also, for some reason seems to involve an issue with my C-stack usage, which I cannot get to the bottom of. I have tried un-installing and re-installing R and R studio, trying both the version for the M1 macs and the Intel macs. Here's my system info at the moment:
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1