similar to: Improving RPM packaging for R; ideas gathered from the Debian folks

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

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

I asked a couple of months ago in r-sig-fedora about a difference I noticed between Ubuntu and RedHat/Fedora. Now I think I've figured out the cause is a little issue in packaging but I don't know how to get it fixed. On Ubuntu, the setup is like this. It i is controlled in a file called Renviron R packages built/distributed in RPM are installed to /usr/lib/R/library. R packages built

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 Computing

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,

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"

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

[ Kevin sent this to me but agreed that it's better to have this discussed here. ] On 30 January 2010 at 12:18, Kevin Donnelly wrote: | Hi | | I'm beginning to learn R,a nd I've just discovered cran2deb - what a terrific | resource! Thanks for making it. | | I was wondering what happens if I want to use cran2deb versions instead of the | versions installed via R itself. I'm

Dear R-devel: i have noticed a little wrinkle in R packaging for RPM systems and have communicated with the package maintainer at RedHat Tom Callaway (see far below). Here is the question: Where does R Core Team want packagers to fiddle around with R library paths? Currently, the RPM Spec file used for EPEL's R (For Fedora/Redhat/Centos,etc) adds a line in R_HOME/etc/Renviron like this:

Dear Johannes, Dear Dirk, Thanks a lot for helping. Here is the missing information. Here is how I installed R. This is basically how Martin Maechler showed me to install R under Ubuntu (in several versions so that they are also recognized by ESS). My goal is to adjust this to make it work for Debian: 1) sudo emacs /etc/apt/sources.list # then add: deb

Hi, I have Debian Testing running on a Lenovo Thinkpad X1 Carbon (2015, 3rd gen.). I would like to have a package library independent of the installed R version. Under Ubuntu, I used to have the following line in ~/.Renviron: R_LIBS=/usr/local/R/library:/usr/lib/R/site-library This worked fine and /usr/local/R/library showed up in .libPaths(). However, under Debian (with the same ~/.Renviron),

I have a local library which depends on the expm library. The expm library is loaded into my personal space and I have the environment variable R_LIBS_USER set appropriately. The command "library(expm)" works just fine from the command line, and in fact the package works if I do the source() and dyn.load() commands by hand. The following sequence works: tmt% R CMD build

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]

Dear all, I installed the amd64 cran2deb [1] JGR binaries on a fresh Debian testing, and JGR is missbehaving. When JGR starts up, one core of the CPU goes to 100% and stays there, even though I am keeping it idle and not performing any operation. I tried JGR with both sun-java6-jdk and openjdk-6-jdk, debian-liv:/home/liviu# update-alternatives --config java There are 4 choices for the alternative

(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

This is for the problem I posted about last Friday. First, the happy part, a workaround: $ cd ~/R/x86_64-redhat-linux-gnu-library/3.4 $ ln -sf /usr/share/R/library/* . After that, all of the packages are found by R CMD check. R CMD check looks in the ~/R/x86_64-redhat-linux-gnu-library/3.4 folder for packages, but not in "/usr/share/R/library" (for whatever reason, I do not know

This run was done this AM on my linux box, and older 32 bit Dell optiplex (core 2 duo). The failure message is at the very end. (It's due to be replaced in a couple of weeks.) The sequence of steps was svn up tools/rsync-recommended ./configure make make check-all |& tee zzz Terry T. Result of ./config R is now configured for i686-pc-linux-gnu Source directory: .

On Thu, 2017-02-09 at 09:52 -0600, Therneau, Terry M., Ph.D. wrote: > 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

Hi I am trying to install R-igraph, but when I issue the command : install.packages("igraph", lib="~/.R/library") in the R session, I get the following error: Warning in install.packages("igraph", lib = "~/.R/library") : 'lib = "~/.R/library"' is not writable Error in install.packages("igraph", lib =

This is a follow-up to a post from 2007: https://stat.ethz.ch/pipermail/r-help/2007-April/129009.html Summary of the Problem: Packages are correctly installed and can be loaded when R is opened interactively or using a R script. However, a bash scripts produces an error similar to the following: #!/bin/bash ... R --no-save <<EOF ... library(package) Error in library(package) : there is no