With RStudio I just quit, restart and then update the packages.
Ken
> On 11 Jun 2021, at 8:07 am, Simon Urbanek <simon.urba...@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 <mole...@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 <pda...@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.urba...@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 <nos...@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
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>>>
>>> _______________________________________________
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>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd....@cbs.dk Priv: pda...@gmail.com
>>
>> _______________________________________________
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>
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