Martin Maechler
2022-Jun-01 08:35 UTC
[R] R_LIBS var needed to be set after upgrade to R 4.2.2
>>>>> Ashim Kapoor >>>>> on Wed, 1 Jun 2022 11:24:21 +0530 writes:> Dear All,> I upgraded to R 4.2.2 on Debian 10 today.Well, I assume you mean R 4.2.0 .. at least that one exists. > The R shell incantation worked fine and all libraries would load but, > I needed to point the R_LIBS variable to > /usr/local/lib/R/site-library/ in order for the R --vanilla < myfile.R > incantation to find the libraries. you mean other installed *packages* > May I ask, why was this ? I never needed to do this on any previous > upgrade to R. Well, for me, the R --vanilla form also only sees the 29 (14 "base" + 15 "Recommended") packages that come with R. Debian (& Ubuntu etc) have used a similar setup where the default {R-level} .libPaths() has contained three libraries, via R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} see https://cloud.r-project.org/bin/linux/debian/#pathways-to-r-packages also for much more. Note (also from the above CRAN page https://cloud.r-project.org/bin/linux/debian/ [ Remember "menu" "Binaries" -> "Linux" -> "Debian" ] The good thing about the Debian (and derivatives) setup is that it also separates (as I do) the "packages that come with R" in one library (= /usr/lib/R/library) from packages that are installed differently. > Many thanks, > Ashim
Ashim Kapoor
2022-Jun-01 09:00 UTC
[R] R_LIBS var needed to be set after upgrade to R 4.2.2
Dear Sir,> > I upgraded to R 4.2.2 on Debian 10 today. > > Well, I assume you mean R 4.2.0 .. at least that one exists.My bad, yes I made a typo. I did mean R 4.2.0.> > The R shell incantation worked fine and all libraries would load but, > > I needed to point the R_LIBS variable to > > /usr/local/lib/R/site-library/ in order for the R --vanilla < myfile.R > > incantation to find the libraries. > > you mean other installed *packages* > > > May I ask, why was this ? I never needed to do this on any previous > > upgrade to R. > > Well, for me, the R --vanilla form also only sees the > 29 (14 "base" + 15 "Recommended") packages that come with R.Has this ALWAYS been the case for you ? Even with prior versions of R ?> Debian (& Ubuntu etc) have used a similar setup where the > default {R-level} .libPaths() has contained three libraries, > via > > R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} > > see > > https://cloud.r-project.org/bin/linux/debian/#pathways-to-r-packages > > also for much more. > Note (also from the above CRAN page > https://cloud.r-project.org/bin/linux/debian/ > [ Remember "menu" "Binaries" -> "Linux" -> "Debian" ] > > The good thing about the Debian (and derivatives) setup is that > it also separates (as I do) the "packages that come with R" in > one library (= /usr/lib/R/library) from packages that are > installed differently.My confusion is : Earlier R --vanilla incantation was working fine, even without my intervening and adding to R_LIBS. That is why I was confused. My main query is : Is there anything special to R 4.2.0 which needs R_LIBS to be setup seperately? THAT is my query. Best Regards, Ashim