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

[Duncan Murdoch]

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/
>>>
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>>
>