search for: r_libs_site

(As a non-root/non-admin), I've just tried to figure out how to prevent a default $R_HOME/site-library/ to be added to the library path. The solution I found was to environment variable R_LIBS_SITE to ":" (preferably in ~/.Renviron). Note that setting R_LIBS_SITE to en empty string will cause it to fall back to using $R_HOME/site-library/. This "hack" is based on the following in help(".Library.site"): .Library.site is a (possibly empty) character vector givin...

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 ".lib...

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=...

...my Ubuntu Renviron file, I have this at the end: R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/2.11'} # edd Apr 2003 Allow local install in /usr/local, also add a directory for # Debian packaged CRAN packages, and finally the default dir # edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} I wondered why the RedHat/Fedora install of the R RPM don't see same/similar options. On Fedora/RedHat using R from RPM as distributed on EPEL, all the packages go into /us...

...has some bad effects. It seems to block R_LIBS_USER, so users who try to install packages are not invited to install them in ~/R/i386... as they are invited to do on Ubuntu. On Ubuntu, Renviron file has been modified thus: R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/2.11'} R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} That has a nice effect. They set the default install library to /usr/local/lib/R/site-library, so things that local admin builds are separate from the packaged stuff, which goes into /usr/lib/R/librar...

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 th...

On 7/28/2015 1:32 PM, Uwe Ligges wrote: > Just add the line > > R_LIBS_SITE=F:/R/library > > to the file R_HOME/etc/x64/Renviron.site Thanks, Uwe I have no way to test this and our IT people who do the installation know nothing of R, so follow-up questions: * There is no R_HOME/etc/x64/Renviron.site file, but there is a R_HOME/etc/Rprofile.site I can modify and...

...o check a package using R CMD check --as-cran <package>. When I do so, the check fails upon not finding the dependencies which I have installed in a non-standard location. Per the manual, I created ~/.R/check.Renviron : $ cat ~/.R/check.Renviron R_LIBS=/usr/lib64/R/library:/usr/lib64/R/var R_LIBS_SITE=/usr/lib64/R/library:/usr/lib64/R/var No luck. I tried explicitly pointing R_CHECK_ENVIRON to ~/.R/check.Renviron: $ echo $R_CHECK_ENVIRON /root/.R/check.Renviron Still no luck. Finally, I just set R_LIBS globally (which, was empty) before running the check and the dependencies are then found....

...management issues there sometimes. One of the really handy R packaging ideas they have is to customize R environment so that there are several directories in the package path. It adjusts the etc/Renviron file so that it has: R_LIBS_USER=${R_LIBS_USER-'~/R/i486-pc-linux-gnu-library/2.10'} R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} That would be pretty easy to add into the R packaging for RPM systems. The benefit is as follows. If an unprivileged user tries to install an R package, there's no error, but rather it installs t...

...e | versions go into /usr/lib/R/library, while the R versions go | into /usr/local/lib/R/site-library. Is it OK just to delete them from the | site-library, and reinstall from cran2deb? 1) These are different locations, so there is no conflict. 2) R looks at the variables R_LIBS (or rather, R_LIBS_SITE and R_LIBS_USER). On Debian/Ubuntu, R_LIBS is set in /etc/R/Renviron to # edd Apr 2003 Allow local install in /usr/local, also add a directory for # Debian packaged CRAN packages, and finally the default dir # edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS R_LIBS_SITE=$...

I'm the faculty member in my department who advises our IT staff on the details of installing R for students and faculty on our Windows 7 lab network. We are about to upgrade from R 3.1.1 to R 3.2.1, and once that is done, this version of R and all installed packages will be frozen in the image that appears in C:/Program Files/R/R-3.2.1/ on every lab computer, and this image is refreshed

...between Centos and Debian. In Centos /usr/lib64/R/etc/Renviron we have the EPEL version of the settings that Dirk Eddelbuettel worked out with R Core for Debian packaging way back in the beginning of, well, the century: R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-redhat-linux-gnu-library/3.4'} R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib64/R/library:/usr/share/R/library'} R_LIBS_SITE looks good in that file. I know (for sure) these settings were put in as adaptation to Dirk's Debian package because I sent them to Spot Calloway back in the ea...

Using: natty alpha-2 Could anyone englighten me (or point me to a self-enlightment page) as to why when installing R using: > apt-get install revolution-mkl r-revolution-revobase revolution-r r-base-core There are 4 library paths available (installed by default): > .libPaths() [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" [3]

...\ > > > #make svnonly > make > > echo "*** Done -- now run 'make install'" > > > > > ## --snip here ------------------------------------------------------------------------------ > ## ~/bin/R-devel.sh > > #!/bin/bash > > export R_LIBS_SITE=${R_LIBS_SITE-'/usr/lib/R-devel/lib/R/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library::/usr/lib/R/library'} > export PATH="/usr/local/lib/R-devel/bin:$PATH" > R "$@" > > -- > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.co...

Does anyone have advice on how to instruct R CMD check to use a non-standard set of libraries? Here's the situation: I'm trying to do some automated checking on package dependencies of a package I maintain. In order to do that I've written code that takes the list of the dependent packages and for each package (1) downloads the most recent/available .tar.gz file; (2) installs the

Thanks for your response. However, I need more guidance. 1) I searched the archives of this list back to June 1. I found no discussion on this subject as I examined all the subject titles for the string [Ww]in. 2) I tried (what I understand) to be you suggestion. I created etc/Renviron.site: R_LIBS_SITE="C:\Program Files\R\R-2.7.2\library:C:\Program Files\R\R-2.7.2\Packages" 3) As a test, downloading a package resulted in it being stored in: C:\Documents and Settings\[USER]\Local Settings\Temp\RtmpO7pcpi\downloaded_packages 4) From the documantation of Renviron: Unix versions of R have...

Is there a fundamental reason why I cannot set either one of ## add local library path -- doesn't work either R_LIBS_USER="c:/opt/R-library" R_LIBS_SITE="c:/opt/R-library" in $R_HOME/etc/Rcmd_environ even though I can seemingly set other things here? It breaks "R CMD check" for me as I prefer NOT to install packages in a versioned path. FWIW, defaulting to a versioned path is (to this no-longer-bemused user) as much a perme...

(somewhat related to thread [Rd] R CMD check not reading R_LIBS ) For many years I have maintained R versions by building R (./configure ; make) in a directory indicating the version number, putting the directory/bin on my path, and setting R_LIBS_SITE. It seems only one version can easily be installing in /usr/bin, and in any case that requires root, so I do not do that. There may be an advantage to installing somewhere in a directory with the version number, but that does not remove the need to set my path. (If there is an advantage to ins...

Hi, What is the best way to tell a locally-built R-devel (somewhere in the user home directory) to use the libraries from the Debian installation (i.e. /usr/local/lib/R/site-library and /usr/lib/R/site-library). I suppose this would take setting one or all of R_LIBS, R_LIBS_SITE, R_LIBS_USER in ~/.Renviron, but that would also affect the Debian R in the system so is not an option. How do R Debianers handle this situation? Cheers, -- Seb

...ns 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 Computing Platform: x86_64-pc-linux-gnu (64-bit) > system("printenv | grep R_LIBS") R_LIBS_SITE= R_LIBS_USER=/people/biostat2/therneau/Rlib So, per the manual R CMD check inherits the path. The question is why does it ignore it? Terry T. On 02/09/2017 02:54 AM, Martyn Plummer wrote: > On Wed, 2017-02-08 at 15:51 -0600, Therneau, Terry M., Ph.D. wrote: >> I have a local library w...