[R-SIG-Mac] upgraded to 4.5 (mac x86), errors

[Kevin Ushey]

Not to be pithy, but R includes version components in its user library
paths by default for a reason...

On Sat, May 31, 2025, 8:35 AM Jeff Newmiller via R-SIG-Mac <
r-sig-mac using r-project.org> wrote:

> Carl: "Doctor, it hurts when I don't upgrade properly..."
> Duncan: "... then don't do that."
> Carl: "But I didn't... rather I did"
>
> Carl, copying ANY previously-installed packages over to the upgraded
> library is a no-no. Just because you did it previously and got lucky does
> not mean it is okay to do it whenever you upgrade... and your troubles here
> stem directly from this bad practice.
>
> Put your broken library directory in the trash and start over from scratch.
>
> On May 31, 2025 4:48:23 AM PDT, Carl Witthoft <carl using witthoft.com> wrote:
> >Good guess, but that isn't what happened here.  I carefully did NOT
> replace the "base" package set that's installed along with 4.5 .  It was
> only the "contributed" collection that I copied over from 4.4 and then ran
> 'update' on. I apologize for not making that clear earlier.
> >
> >So, in fact the menu update command did not successfully "clean out"
> references to dylib files in the 4.4 directory, as the error messages
> showed. This despite my getting a full set of messages reporting successful
> download of the latest versions of all the "contributed" packages.
> >
> >On 5/31/25 7:34 AM, Duncan Murdoch wrote:
> >> You shot yourself in the foot as Peter said.
> >>
> >> There are 3 classes of packages in R:  base, recommended, and
> contributed.  Base packages are really part of R itself, and are only
> changed when you update R.
> >>
> >> Contributed packages are add-ons, and can be updated independently of
> R.   They do need to be reinstalled when an R update changes x or y in the
> x.y.z R version number.  The update.packages() function or the
> corresponding menu items will do that.
> >>
> >> Recommended packages are contributed packages that are distributed with
> R.  update.packages() will handle them, too.
> >>
> >> The base packages will never be updated by update.packages() (which is
> used by "update all"), so you were trying to use R 4.4 base packages with R
> 4.5.0.
> >>
> >> It would probably make sense to store base packages separately from
> contributed packages to avoid even the possibility of this kind of user
> error.
> >>
> >> You might think having update.packages() reinstall base packages would
> be a good idea, but if the base packages are messed up, R is broken, and
> update.packages() probably won't work properly.
> >>
> >> Duncan Murdoch
> >>
> >> On 2025-05-31 6:38 a.m., Carl Witthoft wrote:
> >>> I did this sequence: copy over all 4.4 packages and then selected
> >>> "update all" from the R-gui menu.  Since several CRAN packages (per
> >>> initial posting) still failed, I guess there's something inside
> >>> update.packages that doesn't get cleaned out.
> >>>
> >>> Once I removed all the "updated" libraries and did a fresh install,
> >>> things seem to be OK.
> >>> Thanks to P.D. and D. M. for your suggestions.
> >>>
> >>> On 5/31/25 4:42 AM, peter dalgaard wrote:
> >>>> Works fine here.
> >>>>
> >>>> Did you do something with your packages after installing?
> >>>>
> >>>> Reason that I ask: A number of people have been shooting themselves
> in the foot by copying old package directories over new ones - including
> the non-CRAN system packages that update.packages() can't fix.
> >>>>
> >>>> Or, if you have packages in a separate non-versioned library, then
> you may need update.packages(checkBuilt=TRUE).
> >>>>
> >>>> -pd
> >>>>
> >>>>> On 30 May 2025, at 23.00, Carl Witthoft <carl using witthoft.com> wrote:
> >>>>>
> >>>>> I suspect this is something simple I forgot to update or delete, but:
> >>>>> iMac x86 recently upgraded to 15.5 Sequoia.
> >>>>>
> >>>>> I installed R 4.5 from CRAN.
> >>>>> then tried to install the "gmp" library and:
> >>>>>
> >>>>> Error: package or namespace load failed for ‘gmp’ in get(Info[i, 1],
> envir = env):
> >>>>> lazy-load database
> '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/gmp/R/gmp.rdb'
> is corrupt
> >>>>> In addition: Warning message:
> >>>>> In get(Info[i, 1], envir = env) :
> >>>>>    internal error 1 in R_decompress1 with libdeflate
> >>>>>
> >>>>> Then,
> >>>>> library(ggplot2)
> >>>>> Error: package or namespace load failed for ‘ggplot2’ in
> dyn.load(file, DLLpath = DLLpath, ...):
> >>>>> unable to load shared object
> '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/glue/libs/glue.so':
> >>>>>
> dlopen(/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/glue/libs/glue.so,
> 0x0006): Library not loaded:
> /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib
> >>>>>    Referenced from: <E900C54A-FB6D-371D-B50B-512EB8D2F868>
> /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/glue/libs/glue.so
> >>>>>    Reason: tried:
> '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib'
> (no such file),
> '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib'
> (no such file),
> '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib'
> (no such file), '/usr/local/lib/libR.dylib' (no such file),
> '/usr/lib/libR.dylib' (no such file, not in dy
> >>>>>
> >>>>> So I need to clear something out that's pointing to the 4.4 paths.
> But aged me forgets what that is.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Carl Witthoft
> >>>>> personal: carl using witthoft.com
> >>>>> The Witthoft Group, Consulting
> >>>>> https://witthoftgroup.weebly.com/
> >>>>>
> >>>>> _______________________________________________
> >>>>> R-SIG-Mac mailing list
> >>>>> R-SIG-Mac using r-project.org
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>
> >>
> >
>
> --
> Sent from my phone. Please excuse my brevity.
>
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