Hello,
Inline.
Às 10:36 de 28/05/2026, Karl Schilling escreveu:
Thank you everybody so much for your help.
I adjusted my CRAN mirror in my etc/Profile.site file as suggested by
Rui Barradas - that solved the issue with the twice repeated question of
which repository to use.
I'm glad it was helpful.
Whenever I have problems with update.packages() the following script
usually works. No guarantees, though.
inst_pack <- function(pkgs, lib = .libPaths()[1],
repos = "https://cloud.r-project.org";,
Ncpus = 1L){
utils::install.packages(
pkgs = pkgs,
lib = lib,
repos = repos,
Ncpus = Ncpus
)
}
repo_default <- "https://cran.r-project.org";
repo_cloud <- "https://cloud.r-project.org";
## set repo, use default if you prefer it
local({r <- getOption("repos")
r["CRAN"] <- repo_cloud
options(repos=r)
})
#
inst_pkgs <- installed.packages(priority = NA_character_)
inst_pkgname <- inst_pkgs[, "Package"]
inst_version <- inst_pkgs[, "Version"]
#
avail_pkgs <- available.packages(repos = repo_cloud)
avail_pkgname <- avail_pkgs[, "Package"]
avail_version <- avail_pkgs[, "Version"]
i <- which(avail_pkgname %in% inst_pkgname)
j <- which(inst_pkgname %in% avail_pkgname)
any(avail_pkgname[i] != inst_pkgname[j])
# FALSE
# coerce the version strings to real version numbers
avail_version <- package_version(avail_version)
inst_version <- package_version(inst_version)
# which packages to update
i_update <- which(avail_version[i] > inst_version[j])
length(i_update)
ncores <- 1L
# ncores <- max(1L, parallel::detectCores() - 4L)
to_update <- avail_pkgname[i][i_update]
inst_pack(to_update, Ncpus = ncores)
Hope this helps,
Rui Barradas
It did not resolve, however, the issue that all
packages were flagged as not actual.
So I followed the advice of Jeff Newmiller - actually I went one step
further and completely de-installed my R version, re-installed it, and
then downloaded the packages I need. That solved the problem.
One point that I still do not understand is why AFTER updating my
original R 4.5 packages to 4.6, those were still identified as not up-to
date. So why I was in this "ndless" loop of ineffective (?) updating.
But maybe I should be pragmatic and be satisfied that it now works again.
Again, thank you all for your help.
Best,
Karl Schillng
On 28.05.2026 00:33, Uwe Ligges wrote:
On 28.05.2026 00:02, Jeff Newmiller wrote:
So can we interpret this to mean that update.packages() will fix
(replace) old packages that were copied into the new library? What if
one or more packages were dropped/archived or pulled from non-
standard package sources?
No, not if a package is archived from CRAN or downloaded from a
repository that is not declared. update.packages() won't find that the
update is needed in such a case
I talked about active CRAN packages.
Best,
Uwe Ligges
On May 27, 2026 2:06:12 PM PDT, Uwe Ligges <[email protected]
dortmund.de> wrote:
On 27.05.2026 18:01, Karl Schilling wrote:
I am running R under Windows 11. recently updated R to the
4.6patchhed version. I then copied my packages from my previous
version (4.5) to the library of 4.6. Then I updated all
packages.
Since then, I see the following behavior:
Each time I run
"update.packages(ask='graphics',checkBuilt=TRUE)" I am asked
TWICE
"--- Please select a CRAN mirror for use in this session ---".
And, more embarrassingly, all my Cran and Bioconductor are said
to require an update. That also happens when I run
"update.packages", say, one hour after my last update.
And when I run "old.packages()", it seems that all my packages
are identified as being old.
Any suggestions what might be going on?
For a major version change (as from 4.5.x to 4.6.y) we do not
guarantee API compatibility, hence we cannot guarantee that a
package built for 4.5.x will work under 4.6.y. As a consequence,
update.packages() knows that everything has to be reinstalled.
Best,
Uwe Ligges
Thank you so much in advance,
Karl Schilling
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