similar to: Can I install debs over packages installed via R?

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:

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, everybody. I've got some Centos Linux systems and some Ubuntu Linux systems. R's basically the same in either place, but the packaging of R for Debian systems seems better to me than it is on Fedora/Redhat/Centos. I joined R-sig-debian and we talk about package management issues there sometimes. One of the really handy R packaging ideas they have is to customize R environment so

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

Some packages are available in cran2deb and Debian. After adding cran2deb to my sources.list it seems the cran2deb ones are favored because X.Y-ZcranN is "more recent" than X.Y-Z. In the case of r-cran-rmpi the effect of this was to cause aptitude to want to uninstall all my mpi stuff. Apparently the automatically generated package doesn't have mpi as a dependency. I just put a

Dear all Recently I noticed that there are name clashes between the packages proposed in the Debian testing repos and cran2deb. For example, Synaptic proposes to upgrade from xtable 1.5-6-1cran1 (cran2deb, up-to-date CRAN version) to 1.5.5-1 (testing, older version). Is there anything that can be done about these clashes? Liviu -- Do you know how to read?

Announcing cran2deb: 1700+ Debian packages from almost all of CRAN ------------------------------------------------------------------ Last Friday's presentation at UseR! 2009 was the first really public mention of 'cran2deb'. It provides Debian packages of all of CRAN. It started as Charles' project from last year's Google Summer of Code, was further extended by us over the

Hi all, I'm trying to 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

Hi, I'm using Ubuntu 9.10 amd64 with cran2deb packages (I know it's meant for Debian, it's worked fine for me for many months). Recently apt-get update has to started to complain: ... Hit http://debian.cran.r-project.org testing/ Release Get:1 http://debian.cran.r-project.org testing/ Packages [515kB] Fetched 1B in 3s (0B/s) W: Failed to fetch

Hi, I am curious what will happen to cran2deb: deb http://debian.cran.r-project.org/cran2deb/debian-amd64 testing/ When Squeeze is released? I really hope this service will continue. It has been great being able to aptitude install R packages. Additionally are these packages signed and is there a key? Chris

Dear Michael, I was looking up the status of the cran2deb effort and notice that you now have a PPA where new packages are landing and being built for Ubuntu. It looks like this is still a work in progress, but is already a fantastic resource for me and I hope it is something that you can continue to operate. I'm now installing many of these packages but some things I need are missing.

What is the relation between the cran2deb repository, http://debian.cran.r-project.org/, and the debian repositories at CRAN, http://cran.r-project.org/bin/linux/debian/? I've studied the pages and this list, but am unsure I've got it right. My understanding is that cran2deb had almost all packages, targets testing, and currently is only supported for i386. It appears the debian repo at

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

The cran2deb archives target testing. I just pulled a package from them onto a stable system; the library loaded but said > library(akima) Warning message: package 'akima' was built under R version 2.10.0 Are this and other packages likely to work correctly with different R's (2.7 in the case of stable)? How well are they likely to work with a backported R? The R version would

Hi, I would also be in favor of a stronger stance on licenses. In industry, where we can really get in big trouble for violating a license, we often maintain internal repositories, or need to be careful about filtering what is used from CRAN. I think that is should really be a requirement the package authors commit to stating what the restrictions are on their packages. Nicholas On 10

Dear All, I am running (X)Ubuntu 9.10 for the amd64 architecture on both my laptop e desktop. I came across the posts http://ubuntuforums.org/showthread.php?t=1336062 http://www.mail-archive.com/r-sig-debian at r-project.org/msg00892.html So it looks like that I will not be able to safely use cran2deb together with Ubuntu, but I simply would like to make sure that this is the way things

(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

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