[R] update.packages() fails due to searching for old versions of packages

[Michael McQuaid]

When I try to update packages, the package manager appears to search for
old versions of the packages, despite seemingly knowing about the existence
of newer versions. Here is an example where I try to update the e1071
package and it seems to recognize that the current version is 1.7-17 but
then searches for and fails to find 1.7-16. This happens for every package
I try to update, I've just included one here for brevity. I have tried
several mirrors including wustl, utk, and iastate. I wonder if there is
some file on my system pointing to the old version. I also tried updating
from R 4.5.1 to 4.5.2, but the issue persists. I am on macOS Tahoe 26.2 on
an M1 Macbook Pro.

$ Rscript -e 'update.packages(oldPkgs=c("e1071"))'
e1071 :
 Version 1.7-16 installed in /Users/mm223266/Library/R/arm64/4.5/library
 Version 1.7-17 available at https://cloud.r-project.org
Update? (Yes/no/cancel)
trying URL '
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz
'
Error in download.file(urls, destfiles, "libcurl", mode = "wb", ...) :
  cannot open URL '
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz
'
In addition: Warning messages:
1: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) :
  downloaded length 0 != reported length 279
2: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) :
  cannot open URL '
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz':
HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘e1071’ failed

	[[alternative HTML version deleted]]