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@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 <c...@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 <c...@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: c...@witthoft.com > >>>>> The Witthoft Group, Consulting > >>>>> https://witthoftgroup.weebly.com/ > >>>>> > >>>>> _______________________________________________ > >>>>> R-SIG-Mac mailing list > >>>>> R-SIG-Mac@r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>>> > >>> > >> > > > > -- > Sent from my phone. Please excuse my brevity. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
