search for: r_libs_site

Displaying 20 results from an estimated 60 matches for "r_libs_site".

2014 Apr 25
0
Preventing $R_HOME/site-library/ via R_LIBS_SITE=":" (no other way?)
(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...
2020 Mar 19
2
R CMD check --as-cran attempts to hide R_LIBS_USER but fails
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...
2020 Mar 19
1
R CMD check --as-cran attempts to hide R_LIBS_USER but fails
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=...
2010 Jun 03
1
How to go about getting a change in the SPEC file from which R is built on EPEL?
...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...
2010 Jun 04
0
Renviron settings for Linux Distributions: please tell me R Core's advice
...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...
2020 Mar 19
0
R CMD check --as-cran attempts to hide R_LIBS_USER but fails
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...
2015 Jul 29
1
Installing/updating packages on a lab network
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...
2013 Nov 21
1
R CMD check (v-3.0.2) not loading $R_CHECK_ENVIRON
...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 $R_CHECK_ENVIRON /root/.R/check.Renviron Still no luck. Finally, I just set R_LIBS globally (which, was empty) before running the check and the dependencies are then found....
2010 Feb 04
1
Improving RPM packaging for R; ideas gathered from the Debian folks
...management issues there sometimes. One of the really handy R packaging ideas they have is to customize R environment so that there are several directories in the package path. It adjusts the etc/Renviron file so that it has: R_LIBS_USER=${R_LIBS_USER-'~/R/i486-pc-linux-gnu-library/2.10'} R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} That would be pretty easy to add into the R packaging for RPM systems. The benefit is as follows. If an unprivileged user tries to install an R package, there's no error, but rather it installs t...
2010 Jan 30
2
Can I install debs over packages installed via R?
...e | versions go into /usr/lib/R/library, while the R versions go | into /usr/local/lib/R/site-library. Is it OK just to delete them from the | site-library, and reinstall from cran2deb? 1) These are different locations, so there is no conflict. 2) R looks at the variables R_LIBS (or rather, R_LIBS_SITE and R_LIBS_USER). On Debian/Ubuntu, R_LIBS is set in /etc/R/Renviron to # edd Apr 2003 Allow local install in /usr/local, also add a directory for # Debian packaged CRAN packages, and finally the default dir # edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS R_LIBS_SITE=$...
2015 Jul 28
2
Installing/updating packages on a lab network
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
2017 Aug 14
0
workaround for "package building problem Centos 7 & R 3.4.1"
...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...
2011 Mar 05
1
Multiple LibPaths in Fresh Install
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]
2015 Aug 29
2
Having both R-current and R-devel installed on Ubuntu
...\ > > > #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...
2012 Apr 15
1
R CMD check with non-standard .libPaths
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
2008 Sep 10
0
Package installation in Windows - Urgent!
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...
2012 Oct 17
1
Rcmd_environ and R_LIBS_{USER,SITE}
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...
2013 Jan 18
1
maintaining multiple R versions
(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...
2010 May 09
2
running a locally built R-devel with libraries from Debian installation
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
2017 Feb 09
2
R CMD check error
...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...