Displaying 20 results from an estimated 1000 matches similar to: "R CMD check --as-cran attempts to hide R_LIBS_USER but fails"
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
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"
2010 Jun 03
1
How to go about getting a change in the SPEC file from which R is built on EPEL?
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
2010 Feb 04
1
Improving RPM packaging for R; ideas gathered from the Debian folks
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
2017 Feb 09
2
R CMD check error
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
2017 Apr 06
3
failure of make check-all
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: .
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
2017 Sep 16
1
R_LIBS_USER not in libPaths
I have not intentionally set R_LIBS_USER. I looked for an Renviron.site
file but did not see it in R/etc or my home directory. The strange part is
that if I print Sud.getenv I see a value for R_LIBS_USER. However, this
directory is not showing under libPaths.
I though .libPaths should contain R_LIBS_USER.
I also noticed that R related variables are not in the system or user
variables because I
2010 Jun 04
0
Renviron settings for Linux Distributions: please tell me R Core's advice
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:
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,
2015 Mar 30
2
Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)
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
2015 Mar 30
2
Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)
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),
2017 Feb 08
2
R CMD check error
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
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]
2017 Apr 06
0
failure of make check-all
You may want to retry that after a make distclean, in case anything changed in the toolchain.
-pd
> On 6 Apr 2017, at 14:43 , Therneau, Terry M., Ph.D. <therneau at mayo.edu> wrote:
>
> 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
2010 Oct 30
2
How to get write permissions for (lib="~/.R/library") ??
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 =
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
2010 Jan 30
2
Can I install debs over packages installed via 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
2017 Feb 09
0
R CMD check error
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
2017 Aug 14
0
workaround for "package building problem Centos 7 & R 3.4.1"
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