search for: r_libs_us

AFAIU, 'R CMD check --as-cran' tries to hide any site and user package libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary to R_LIBS_SITE, it fails for R_LIBS_USER and the user's personal library is still available for test scripts. Should I revise my assumptions, or is that intentional? The short version. Shouldn't: $ R_LIBS_USER='' Rscript --vanilla -e ".libPaths()"...

On Wed, Mar 18, 2020 at 8:04 PM Dirk Eddelbuettel <edd at debian.org> wrote: > > > On 18 March 2020 at 19:19, Henrik Bengtsson wrote: > | AFAIU, 'R CMD check --as-cran' tries to hide any site and user package > | libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary > > What makes you think that? AFAIK --as-cran just sets a bunch of the (nearly > countless) environment variables (all described in R Inst+Admin, as I recall) > to a set of values "close to" values CRAN uses. 1. --as-cran sets R_LIBS_SITE='no_such_d...

On 18 March 2020 at 19:19, Henrik Bengtsson wrote: | AFAIU, 'R CMD check --as-cran' tries to hide any site and user package | libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary What makes you think that? AFAIK --as-cran just sets a bunch of the (nearly countless) environment variables (all described in R Inst+Admin, as I recall) to a set of values "close to" values CRAN uses. | to R_LIBS_SITE, it fails for R_LIBS_USER and the user's p...

I have not intentionally set R_LIBS_USER. I looked for an Renviron.site file but did not see it in R/etc or my home directory. The strange part is that if I print Sud.getenv I see a value for R_LIBS_USER. However, this directory is not showing under libPaths. I though .libPaths should contain R_LIBS_USER. I also noticed that R related...

Hi, Having currently a big problem with R 2.10.1 vanilla (Solaris): As soon as the R_LIBS_USER env var gets bigger than 1023 chars R completely ignores it and uses the default: > Sys.getenv('R_LIBS_USER'); R_LIBS_USER "${R_LIBS_USER-~/R/i386-pc-solaris2.11-library/2.10}" The strange thing is, if I set another envar to the...

I'm not sure I follow what.the problem is. Are you trying to set R_LIBS_USER but R does not acknowledge it, or do you observe something in R that you didn't expect to be there and you are trying to figure out why that is / where that happens? Henrik On Sep 16, 2017 07:10, "Rene J Suarez-Soto" <rene.j.suarez at gmail.com> wrote: > I have a compute...

I have a computer where R_LIBS_USER is not found in libPaths. This is for Windows (x64). I ran R from the command line, RGui and RStudio and I get the same results. I also ran R --vanilla and I still get the discrepancy. The only thing I found interesting was that I also ran SET from the command line and the "R related variab...

I've found that the HTML help system started via help.start() requires all forward slashes in R_LIBS_USER otherwise the Packages page is corrupt/non-working. Note that by default R_LIBS_USER is set by R on startup. Example 1: With R_LIBS_USER=C:/Users/JohnDoe/R/win-library/2.10 > help.start() [and go to "Packages"] If nothing happens, you should open 'http://127.0.0.1:6850/doc/html...

Dear all, the recent update to R-3.4.1 kind of screwed the path to the libraries installed on a user basis. The previous version of the file /etc/R/Renviron had the following line activated: R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.4'} This one is commented in the current one which means that the path to the libraries installed previously is not found. I never touched this file before. Was that on purpose or did that happen accidentally? Cheers, STefan ------...

As from R 2.5.0 users can install packages in their home directories, in directory specified by the environment variable R_LIBS_USER. It's a great feature. But I have a problem with this feature, when R_LIBS is defined. It works well the first time, when R creates the directory defined in R_LIBS_USER. > install.packages('BayesTree') Warning in install.packages("BayesTree") : argument 'lib...

> Your best bet really to govern your .libPaths from your Rprofile.site and Renviron.site ... To do this for any version of R, one can add: R_LIBS_USER=~/.local/share/R/%p-library/%v to ~/.Renviron or the Renviron.site file. This automatically expands to the platform and R x.y version early on when R starts up, e.g. ~/.local/share/R/x86_64-pc-linux-gnu-library/4.2. > rather than asking a few million R users to adjust from past practice. We...

I would appreciate ideas about MS Windows install issues. I'm at our stats summer camp and have been looking at a lot of Windows R installs and there are some wrinkles about R_LIBS_USER. On a clean Win7 or Win8 system, with R-3.0.1, we see the user library for packages defaulting to $HOME/R/win-library. I think that's awesome, the way it should be. Yea! But it does not appear that way on all systems, and I think it is because of lingering after-effects of previous R insta...

I'm relaying a question from my institute's sysadmin: Would it be possible to modify update.packages() and related functions so that 'lib.loc' accepts integer values to specify a library from the .libPaths() vector? Many Linux users want to update all user packages (inside the R_LIBS_USER directory, e.g. ~/r/library) and none of the system packages (inside the /usr directory, e.g. /usr/lib64/R/library), because they don't have write privileges to update the system packages. Currently, this can be done by pressing 'y RET' for all the user packages and 'RET'...

On 16 March 2023 at 13:39, Felipe Contreras wrote: | I see R by default installs packages in ~/R. I know I can change the | default directory with R_LIBS_USER, but software shouldn't be | polluting the home directory. | | For example both python and node install packages to ~/.local/lib, | ruby to ~/.local/share. They don't install to for example ~/node. | | R should do the same: it should install packages to somewhere inside | ~/.local by de...

Hi An upgrade to R 3.4.1 on Ubuntu removed the default setting of R_LIBS_USER in /etc/R/Renviron. What's the rationale behind this? Thanks. Best regards Kirill

I want my local libraries to have priority over the system installed ones, which, as far as I can make out from help(".libPaths"), means they have to come first in that list (it doesn't actually_say_ so, but that seems to be the idea). We have R_LIBS_USER which looks made for specifying where I keep my own libraries. Unfortunately it comes last in .libPaths() [which appears to me to be a bug (1) if that means last in the search order and (2) because install.packages() defaults to the first element in .libPaths() while I think most users would...

...> .libPaths() [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" [3] "/usr/lib/R/library" Explanation/solution: Yesterday on Ubuntu 13.10 I ran the package updates and R 3.0.3 installed and it altered the /etc/R/Renviron file to look for packages here R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.1'} But my packages are still installed in ~/R/x86_64-pc-linux-gnu-library/3.0. This seems unnecessary, on the face of it, since R is still 3.0.3, not 3.1, but perhaps there's some binary incompatibility they are worrying about. I ca...

Martin, I am aware of --vanilla; I use it myself for some testing. In this case R_LIBS_USER was set externally (part of my login) and does not involve any of the R scripts. That means it is inherited by any subprocess. For example: tmt1495% R --vanilla --no-environ R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Comp...

On 2 July 2017 at 23:24, Kirill M?ller wrote: | On 02.07.2017 22:01, Dirk Eddelbuettel wrote: | > On 2 July 2017 at 21:39, Kirill M?ller wrote: | > | Hi | > | | > | An upgrade to R 3.4.1 on Ubuntu removed the default setting of | > | R_LIBS_USER in /etc/R/Renviron. What's the rationale behind this? Thanks. | > | > Pretty much exactly what I told you in person last week :) | > | > - idea is to prefer /usr/local/lib/R/site-library/ | > - multi-user more important than per-user | > | > Also see https://bugs.debian.o...

On 3 July 2017 at 15:35, Stefan L?dtke wrote: | the recent update to R-3.4.1 kind of screwed the path to the libraries | installed on a user basis. | | The previous version of the file /etc/R/Renviron had the following line | activated: | | R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.4'} | | This one is commented in the current one which means that the path to the | libraries installed previously is not found. I never touched this file before. | | Was that on purpose or did that happen accidentally? i) Wrong ven...