similar to: Trouble installing modified package

I started using r2u (see https://eddelbuettel.github.io/r2u) recently and thought I was having a problem in that I was getting out-of-date versions of packages. I made enquiries of Dirk Eddelbuettel about this, and he enlightened me as to what the problem really was. I was seeing old versions of packages that were stored in a library, different from /usr/lib/R/site-library. I have a personal

Hi, Sorry for posting a question that has been asked before but I couldn't quite find the right answer in previous help topics. I am trying to set my library path to a user-specified library ("C:/Users/K/Documents/Work/RLib"). I have used .libPaths("C:/Users/K/Documents/Work/RLib") but when I check the .libPaths(), both the user-specified and default libraries appear. It

I am updating the Bioconductor package, LMGene. Thus I am modifying someone else's package, editing or writing new documentation, etc. When I modify the man files in LMGene and install the library, it doesn't change the 'help' that R gives you. The 'help' you actually get in R is the same as before. I haven't been able to find an explanation in "Writing R

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"

I am working on a SLES 10 cluster with R available on it. To better use my resources, I want to use Rmpi, but I am having a difficult time installing it. I have set the $R_LIBS variable correctly. The MPI libraries are available through the PGI compiler, but this R instance was compiled with GCC. The Rmpi package can be compiled and installed with %R CMD INSTALL Rmpi_0.5-5.tar.gz

Hi, I'm updating the LMGene package from Bioconductor. "Writing R Extensions" suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R.

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

Hi there, I'm in the following directory: ~/Documents/Rstuff/diceFiles/dice_1.1 The directory "dice" is in this directory, with all the usual build files (DESCRIPTION, NAMESPACE, etc). I'm trying to run the following command: R CMD check dice (where "dice" is the name of the package I'm checking), and I get the following: * checking package dependencies ...

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

Works for me. Which shell are you using? Are you setting .libPaths elsewhere? Peter-Dalgaards-MacBook-Air:F pd$ R_LIBS=~/tmp Rscript -e '.libPaths()' [1] "/Users/pd/tmp" [2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library" Peter-Dalgaards-MacBook-Air:F pd$ export R_LIBS=~/tmp

I want my local libraries to have priority over the system installed ones, which, as far as I can make out from help(".libPaths"), means they have to come first in that list (it doesn't actually_say_ so, but that seems to be the idea). We have R_LIBS_USER which looks made for specifying where I keep my own libraries. Unfortunately it comes last in .libPaths() [which appears to

Good day, I believe from the documentation that folders in R_LIBS should appear in the output of .libPaths, but they do not. The documentation contains "The library search path is initialized at startup from the environment variable R_LIBS ..." However, $ export R_LIBS=/users/stgrad/dario/tmp/ $ Rscript -e ".libPaths()" [1] "/dskh/nobackup/biostat/Bioconductor"

Doing help("R_LIBS") brings up a help file (the same one as help(library)), but the help file doesn't mention R_LIBS. It does have a link to .libPaths, which does document R_LIBS. The quickest fix would be for help("R_LIBS") to bring up the .libPaths help file. --please do not edit the information below-- Version: platform = i386-pc-mingw32 arch = i386 os = mingw32

As from R 2.5.0 users can install packages in their home directories, in directory specified by the environment variable R_LIBS_USER. It's a great feature. But I have a problem with this feature, when R_LIBS is defined. It works well the first time, when R creates the directory defined in R_LIBS_USER. > install.packages('BayesTree') Warning in

On 07/24/2018 07:50 AM, Martin Maechler wrote: >>>>>> Benjamin Tyner >>>>>> on Sat, 21 Jul 2018 13:42:43 -0400 writes: > > Not sure whether it is the same issue as was raised here: > > https://stat.ethz.ch/pipermail/r-devel/2010-October/058729.html > > > but in any case perhaps the problem could partially be remedied on

I was flummoxed for a long time by errors generated when I did something like install.packages(foo,lib="Rlib") where ``Rlib'' is my personalized directory of R packages, which lives in my home directory (from which I started R before issuing the foregoing install.packages() call. Recently someone (I forget who, but thanks very much to whomever it was) pointed out that I

I've just installed version 1.4.0 of R, and am experiencing a puzzling phenomenon with the library() function. I have .lib.loc set as follows: > .lib.loc [1] "/usr/local/lib/R/library" "/home/faculty/rolf/Rlib" If I invoke > library(melvin) I get the error message Error in library(melvin) : There is no package called `melvin' but if I invoke >

>>>>> Benjamin Tyner >>>>> on Fri, 20 Jul 2018 19:42:09 -0400 writes: > Here's a trick/workaround; if lib.loc is the path to your > library, then prior to calling library(), >> environment(.libPaths)$.lib.loc <- lib.loc Well, that is quite a "trick" -- and potentially a pretty dangerous one, not intended when making

Not sure whether it is the same issue as was raised here: https://stat.ethz.ch/pipermail/r-devel/2010-October/058729.html but in any case perhaps the problem could partially be remedied on line 245 of src/library/base/R/library.R by passing the lib.loc to .getRequiredPackages2() ...here is a patch (untested) Index: src/library/base/R/library.R

On 24.07.2018 23:37, Benjamin Tyner wrote: > > > On 07/24/2018 07:50 AM, Martin Maechler wrote: >>>>>>> Benjamin Tyner >>>>>>> ???? on Sat, 21 Jul 2018 13:42:43 -0400 writes: >> ???? > Not sure whether it is the same issue as was raised here: >> ???? > https://stat.ethz.ch/pipermail/r-devel/2010-October/058729.html >>