[R-SIG-Mac] Corrupt R installation

[moleps islon]

Allright - I´m way beyond believing I could save my packages and ended up
removing everything (including all versions in R.framework dir.) I
reinstalled from CRAN. But there is still something out of the ordinary.
After installing some of them : Some work, others (meaning most) display

"Error: package or namespace load failed for ‘tidyr’ in dyn.load(file,
DLLpath = DLLpath, ...):
 unable to load shared object
'/Users/Misha/Library/R/4.0/library/glue/libs/glue.so':
  dlopen(/Users/Misha/Library/R/4.0/library/glue/libs/glue.so, 6): Library
not loaded: /usr/local/opt/r/lib/R/lib/libR.dylib
  Referenced from: /Users/Misha/Library/R/4.0/library/glue/libs/glue.so
  Reason: image not found"

- but the library is listed both when I run installed.packages() from R and
when I enter the correct directory from the terminal. Moreover - all
privileges are OK within the directory.

I promise I´ll never try another shortcut in updating R--must have taken me
better part of a week to try and sort this out.




On Thu, Jun 10, 2021 at 8:34 AM peter dalgaard <pdalgd using gmail.com> wrote:

> Yep. (In the first form, you likely want a stoplist for base and
> recommended packages.)
>
> You can also base it on a listing of the library directory. This has the
> advantage that you can fairly easily twiddle it to look at older versions
> after the upgrade.
>
> > .libPaths()
> [1] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library"
> > list.files("/Library/Frameworks/R.framework/Versions")
> [1] "3.0"     "3.1"     "3.2"     "3.3"     "3.4"     "3.5"     "3.6"
> [8] "4.0"     "Current"
> >
> list.files("/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
>   [1] "assertthat"            "backports"             "base"
>
>   [4] "base64enc"             "BH"                    "bitops"
>
>   [7] "boot"                  "caTools"               "chron"
>
>  ...
> >
> setdiff(list.files("/Library/Frameworks/R.framework/Versions/3.6/Resources/library"),rownames(installed.packages()))
> [1] "caTools"      "dplyr"        "plogr"        "translations"
>
> (Notice that "translations" is not a package, so  a red herring in this
> context)
>
> -pd
>
> > On 10 Jun 2021, at 00:26 , Simon Urbanek <simon.urbanek using r-project.org>
> wrote:
> >
> >
> > Um, this is actually a lot easier purely with R - if you want to keep
> track of your favorite packages it is as simple as
> >
> > pkgs = rownames(installed.packages())
> > writeLines(pkgs, "packages.txt")
> >
> > and oyu have a list of all packages that you can edit if desired. if you
> ever want to re-install then simply
> >
> > pkgs = readLines("packages.txt")
> > install.packages(pkgs)
> >
> > and if you only want to install missing it's simply
> >
> > missing.pkgs = pkgs[!pkgs %in% rownames(installed.packages())]
> > install.packages(missing.pkgs)
> >
> > All trivially done in R. It is always beyond me why people come up with
> incredibly convoluted solutions to simple things ..
> >
> > Cheers,
> > Simon
> >
> >
> >
> >> On 9/06/2021, at 8:55 PM, Dr Eberhard Lisse <nospam using lisse.NA> wrote:
> >>
> >> On 08/06/2021 22:46, moleps islon wrote:
> >> [...]
> >>> I have no idea why, but my R installation (Mac OS X - Big Sur)
> >>> automatically updates causing havoc with my libraries each time.  My
> >>> Mac is under administration from the university and their software
> >>> center, but they claim it is not their fault - but I still suspect
> >>> them for causing all the trouble.
> >> [...]
> >>
> >> Sounds like Homebrew to me.  If so, or anyway, create a file (before
> >> updating) which contains something like
> >>
> >>       #!/usr/bin/env Rscript --vanilla
> >>       #
> >>       # set the Mirror
> >>       #
> >>       local({
> >>              r <- getOption("repos")
> >>               r["CRAN"] <- "https://cloud.r-project.org/"
> >>              options(repos = r)
> >>       })
> >>       install.packages(c(
> >>                "lubridate",
> >>                "tidyverse"
> >>       ), dependencies = TRUE)
> >>
> >>
> >> or similar and run it if the additional libraries disappear.
> >>
> >> You can fill this with something like
> >>
> >>       grep -h library *R \
> >>       |awk -F 'library' '{print $2}' \
> >>       |sed 's/(//g;s/)//g' \
> >>       |sort -u \
> >>       |awk '{print "\"" $1 "\","}'
> >>       |sed '$ s/,$//'
> >>
> >> or in a few lines of the language of your choice generate the whole
> >> script. And of course refine to your liking with something like
> >>
> >>       find ~/R -name '*.R' -exec grep -h library {} ';' \
> >>       ...
> >>
> >> greetings, el
> >>
> >> --
> >> To email me replace 'nospam' with 'el'
> >>
> >> _______________________________________________
> >> R-SIG-Mac mailing list
> >> R-SIG-Mac using r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
>
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