similar to: R CMD check (v-3.0.2) not loading $R_CHECK_ENVIRON

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

Dear List, Further to my earlier email, I note that, for me at least, R CMD check is *not* reading R_LIBS from ~/.R/check.Renviron on R 2.15.2 patched (r61228) and R Under Development (r61660). The only way I can get R CMD check to look for packages in a user-supplied library is by explicitly exporting R_LIBS set to the relevant directory. R CMD build *does* read R_LIBS from ~/.R/build.Renviron

Dear List, I'm having considerable trouble setting up my environment (Linux, Fedora 16, Bash) to build and check packages under R Under Development (r61660). I'm doing this to better get a handle on difference in the output from running checks on examples in one of my packages. Note I compiled R Under Development myself The problem I am now having is whenever I try to build my analogue

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

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

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),

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

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 ask them to

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

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

> .expand_R_libs_env_var("poof/%p/%v") [1] "poof/x86_64-w64-mingw32/3.4" Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Jan 12, 2018 at 4:49 AM, Loris Bennett <loris.bennett at fu-berlin.de> wrote: > Hi, > > When I install a package as a non-root user, it gets saved in a path > such as > > ~/R/x86_64-unknown-linux-gnu-library/3.4 >

Hi, When I install a package as a non-root user, it gets saved in a path such as ~/R/x86_64-unknown-linux-gnu-library/3.4 for any R version 3.4.x. Thus, if I want to install the packages somewhere else, as root say, I might do install.packages("somepackage","/some/where/else/R/site-library/3.4") In this case I would then want to construct the appropriate path in, say,

Martyn, No, that didn't work. One other thing in the mix (which I don't think is the issue) is that I call one of the C-entry points of expm. So the DESCRIPTION file imports expm, the NAMESPACE file imports expm, and the init.c file is #include "R.h" #include "R_ext/Rdynload.h" /* Interface to expm package. */ typedef enum {Ward_2, Ward_1, Ward_buggy_octave}

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:

Hello, Dirk (and everybody): I have Ubuntu on some systems and I notice there's a very nice thing you do with your R packages. The system is setup so that packages installed from deb go into /usr/lib/R, while packages built from scratch by root go into /usr/local/.., and if the user runs install.packages(), then it gets dumped into the user's own account. I'm much more familiar with

Hi there, Moving this request for info over from an R-HPC-SIG list thread as the issue is less HPC than something that has bitten me as a result of trying to install HPC (read CUDA) R packages. Background to this is that I have both a Ubuntu host for a Tesla card that some researchers are looking to do CUDA-related R computation on, and a prototype, RHEL-based, cluster that is being used to

I have a local library 'dart' that imports "httr". It has routines that access central patient data such as birth date, so it is heavily used locally but of no interest to anyone else. The httr library (and 300 others) are in a shared directory, referenced by everyone in the biostatistics group via adding this location to the .libPaths in their default .Rprofile.

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 =