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List: r-sig-mac
Subject: Re: [R-SIG-Mac] Corrupt R installation
From: Ken Beath <ken () kjbeath ! com ! au>
Date: 2021-06-11 0:44:32
Message-ID: BBB86A23-F46C-441D-AB06-E9173F3CAF49 () kjbeath ! com ! au
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With RStudio I just quit, restart and then update the packages.
Ken
> On 11 Jun 2021, at 8:07 am, Simon Urbanek <simon.urbanek@R-project.org> wrote:
>
>
> Those errors come from packages that you didn't re-install - anything that uses \
> /usr/local is not from CRAN. So check /Users/Misha/Library/R/4.0/library/
> Best way is to move the entire tree aside (Eg. rename "library" to "old") to make \
> sure you don't pick up old stuff.
> BTW: you can list packages from a tree even if it's not used by R by using lib.loc, \
> so if you renamed the library as above, you can still list all packages in there by \
> using
> pkg=rownames(installed.packages(lib.loc="/Users/Misha/Library/R/4.0/old"))
>
> Cheers,
> Simon
>
> PS: just an aside, avoid using RStudio to perform upgrades as it has issues when \
> packages that it is using get upgraded, using R is safer.
>
> > On 11/06/2021, at 10:01 AM, moleps islon <moleps2@gmail.com> wrote:
> >
> > 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@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@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@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@r-project.org
> > > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > >
> > > _______________________________________________
> > > R-SIG-Mac mailing list
> > > R-SIG-Mac@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@cbs.dk Priv: PDalgd@gmail.com
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> _______________________________________________
> R-SIG-Mac mailing list
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