Marius Hofert | 31 Mar 02:42 2015
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Re: Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)

Dear Dirk, Dear Johannes,

Thanks for helping, I could solve the problem.

By reading your posts, I got a bit of the impression that questions
beyond the 'standard installation' process are not really welcome on
R-SIG-Debian. If this is the case, I'm sorry for my post. I wasn't
aware of this, but Dirk makes it clear why on
https://stat.ethz.ch/pipermail/r-sig-debian/2013-March/002062.html.

As Dirk also mentioned on
http://stackoverflow.com/questions/8343686/how-to-install-2-different-r-versions-on-debian
installing from source is the only practical way in case one needs
several R versions. I now went back to Chapter 2 of
http://cran.r-project.org/doc/manuals/r-release/R-admin.html to read
more about it and to see whether I have done something substantially
wrong. This seemed not to be the case.

Next, Dirk's wonderful little example helped... I could check that
.Renviron is indeed found. Then it was easy: my local
version-independent library was not found simply because .libPaths()
only contains those folders which physically exist (also mentioned on
?.libPaths). And indeed, I had not checked that.

Here is thus the final solution that worked (in case useful for others
or being improved upon [slightly expanded in comparison to the
original one, e.g., also addressing how to obtain a key -- the server
is different than keys.gnupg.net mentioned on CRAN.]):

1) sudo emacs /etc/apt/sources.list # then add: deb
(Continue reading)

Marius Hofert | 30 Mar 18:30 2015
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Re: 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 http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/
   deb-src http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/

2) sudo apt-get build-dep r-base

3) sudo mkdir /usr/local/R
   sudo chown mhofert:mhofert /usr/local/R

   cd /usr/local/R
   wget http://cran.r-project.org/src/base/R-3/R-3.1.3.tar.gz
   tar -xzf R-3.1.3.tar.gz
   mv R-3.1.3 R-3.1.3-source

   mkdir R-3.1.3-build
   cd R-3.1.3-build
   ../R-3.1.3-source/configure

   make
   make check
   make pdf
(Continue reading)

Marius Hofert | 30 Mar 08:24 2015
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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), my .libPaths()
just shows "/usr/local/R/R-3.1.3-build/library" which is the
version-dependent library (this used to come at 3rd position in
.libPaths()). Does R on Debian not look for ~/.Renviron? I also
tried R_LIBS_USER but no luck here either (although, as far as I
understand Section 6.2 of "R Installation and Administration",
R_LIBS or R_LIBS_USER should work (?))

Cheers, Marius

PS: I found two sites which seem to be related, but it was still
not quite clear to me how to approach the problem:
https://stat.ethz.ch/pipermail/r-sig-debian/2005-December/000050.html
https://stat.ethz.ch/pipermail/r-sig-debian/2010-May/001146.html
Mathieu Basille | 26 Feb 21:49 2015

Suggestions to improve the info page of /bin/linux/debian

After Johannes set up the CRAN repository for Jessie, I had quite some 
trouble figuring out what any user should do to have a running and 
up-to-date R in Debian (particularly Testing). Part of the problem is, I 
think, the overwhelming documentation on the page "DEBIAN PACKAGES OF R 
SOFTWARE" which is provided on CRAN at /bin/linux/debian. Some information 
is also lacking in places.

So here are a few suggestions to try to arrange this page. The main one is 
actually a reorganization of the whole page, which should make it easier 
from a user perspective. Note that I think all information I added is 
correct, but it might not be entirely accurate.

I think the page in itself would benefit largely from the inclusion of a 
table of contents (with links to sections). With the page reorganized, that 
would follow this:

INSTALLATION
    ADMINISTRATION AND MAINTENANCE
    PATHWAYS TO R PACKAGES
BACKPORTS ON CRAN
    SUPPORTED PACKAGES
    DEBIAN WHEEZY (STABLE)
    DEBIAN JESSIE (TESTING)
    DEBIAN SQUEEZE (OLD STABLE)
    DEBIAN SID (UNSTABLE)
    SECURE APT
    SUPPORTED PLATFORMS
REPORTING PROBLEMS
BACKPORTING FOR DEBIAN
ACKNOWLEDGEMENT
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Carl Boettiger | 16 Jan 22:44 2015
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Unable to install R 3.1.2 on Debian:Testing

Dear Johannes, R-sig-debian list,

Along with Dirk Eddelbuettel I've been maintaining Debian-based Docker
containers for R. Recently our container installing r-base has started to
fail. This seems to be due to a problem with the libjpeg dependencies. The
example I show below was working with debian:jessie on Jan 5th, but has
been failing since then.  (https://registry.hub.docker.com/u/rocker/r-base/
)

>From a vanilla install of debian:testing (or jessie or squeeze) I add the
CRAN repository for the latest R version for debian, and then I then try to
install `r-base-core` 3.1.2:

    apt-key adv --keyserver keys.gnupg.net --recv-key 381BA480
    echo "deb http://cran.rstudio.com/bin/linux/debian wheezy-cran3/" >
/etc/apt/sources.list.d/r-cran.list

    apt-get install r-base-core=3.1.2*

and I get the error:

*Selected version '3.1.2-1~wheezycran3.0' (CRAN Backports:wheezy-cran3
[amd64]) for 'r-base-core'Some packages could not be installed. This may
mean that you haverequested an impossible situation or if you are using the
unstabledistribution that some required packages have not yet been
createdor been moved out of Incoming.The following information may help to
resolve the situation:*

*The following packages have unmet dependencies: r-base-core : Depends:
libjpeg8 (>= 8c) but it is not installable*
(Continue reading)

kamaraju kusumanchi | 21 Dec 12:37 2014
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How to get fortunes in R

I was going through
http://dirk.eddelbuettel.com/papers/r_package_development_nov2014.pdf
and found this on pg-3

> fortunes::fortune(92)
##
## If you don't go with R now, you will someday.
## -- David Kane (on whether to use R or S-PLUS)
## R-SIG-Finance (November 2004)

However, when I tried it on my machine, I get

rajulocal <at> hogwarts:~/work/r_programming$ R -q
> fortunes::fortune(92)
Error in loadNamespace(name) : there is no package called ‘fortunes’

What package(s) do I need to install to get fortune in R? I tried
doing a "apt-cache search fortune R" but none of the hits look
promising. I am using Debian Jessie.

rajulocal <at> hogwarts:~/work/r_programming$ dpkg -l \*fortune\* r-base | grep ^ii
ii  fortune-mod       1:1.99.1-7   amd64        provides fortune
cookies on demand
ii  fortunes-min      1:1.99.1-7   all          Data files containing
selected fortune cookies
ii  r-base            3.1.1-1      all          GNU R statistical
computation and graphics system

thanks
--

-- 
(Continue reading)

Nussbaum Madlene | 16 Dec 14:10 2014
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BLAS/LAPACK routine 'DLASCL' gave error code -4 in liblapack3 Version 3.5.0


Dear all

Some computations gave a matrix. The single value decomposition of it worked fine previously, after an
system upgrade I get the following error:
-----
> La.svd(x,256,256)
Error in La.svd(x, nu, nv) :
  BLAS/LAPACK routine 'DLASCL' gave error code -4
-----
Erroneous Matrix: ftp://usys-ftp.ethz.ch/ITES/STEP/nussbaum/R/matrix-lapack-error4.RData /.csv
Operating System: Debian 8
Previous version:    liblapack3   3.4.1 (running without error)
New version:          liblapack3   3.5.0-4 (gives error above)
How do I track down this error code?
Is this a bug in liblapack3 or what did change?
Thank you!
M. Nussbaum

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Seb R | 5 Nov 09:48 2014
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Latest version of R from CRAN for utopic (14.10)

Hi,
I am not in a hurry, but I would like to upgrade my ubuntu to utopic.
However, for now, the latest version of R that can be installed from CRAN
mirrors is not available for utopic.
Indeed, I am not sure I understand this sentence :

> UBUNTU PACKAGES FOR R
> R packages for Ubuntu on i386 and amd64 are available for all stable
> Desktop releases of Ubuntu until their official end of life date. However,
> only the latest Long Term Support (LTS) release is fully supported. As of
> October 17, 2013, the supported releases are Trusty Tahr (14.04), Precise
> Pangolin (12.04; LTS), and Lucid Lynx (10.04; LTS).
>
Does this mean that from now only LTS version will get the latest version
of R, or the non-LTS will be partially supported ?
If, as I think I understand, non-LTS can also get latest R, is there any
schedule for utopic ?
I don't have any idea of how long and complicated it is for you developpers
to make it available after, I suppose, a stability testing period...
Thank you

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David Ibarra Gómez | 22 Oct 10:22 2014
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Problems to compile examples of RInside

Hello,

                I have some problems to migrate to R  >3.0 my devel machine (R.2.15.2). So I decided to start from scratch with
a brand new virtual machine.

Downloaded latest network install of debian testing, not stable (jessie/sid, SMP Debian 3.16.3-2
(2014-09-20) x86_64 GNU/Linux) installed only with ssh-server and basic utilities (no X).

Then I installed R by:

apt-get install r-base-dev

Then from R, I installed the needed (for me) packages by:

install.packages(c("Rcpp","RInside","forecast", "quadprog", "tseries", "fracdiff", "zoo", "RcppArmadillo","randomForest","RInside","lubridate","quantmod","nnet","caret"),type="source")

Session info extract (Rcpp and RInside libraries loaded):

R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
(Continue reading)

Ali Youssef | 30 Sep 20:09 2014

Re: String Kernel for R 3.1.1


Dear all , 

May you inform me how  to use the function of gapweightkernel() from stringkernel Library . where the
library is not for R 3.1.1 . I am using R 3.1.1 .

sincerely 
 		 	   		   		 	   		  
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Miguel Angel Barros | 30 Sep 14:24 2014
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error in Ubuntu

Hello,
I've got this error while I'm try to install R on Ubuntu 12.04. The cran
that I used was from Argentina.
"E:Type 'http://cran.r-project.org/bin/linux/ubuntu' is not known on line
60 in source list /etc/apt/sources.list  "

So, please, Could everyone help me with this error.

Thank you so much

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Gmane