Scott Kostyshak | 24 Apr 22:10 2014
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50% performance of custom R build compared to PPA R for a command

Hi,

I have R installed from the Ubuntu PPA and a local build of R (more
details below). I will refer to these as "R" and "R-devel",
respectively. I've reproduced the following on Ubuntu 13.10 and 14.04.
Below is an example (which requires the bootstrap package) that takes
10 seconds for me to run with R-devel and 5 seconds with R

library(bootstrap)
str(tooth)
theta <- function(ind) {
    easy <- lm(strength ~ E1+E2, data=tooth, subset=ind)
    diffi<- lm(strength ~ D1+D2, data=tooth, subset=ind)
    (sum(resid(easy)^2) - sum(resid(diffi)^2))/13   }
tooth.boot <- bootstrap(1:13, 2000, theta)

I'm wondering if this is due to different compiler flags. For R, when
installing the bootstrap package, I see
gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o
bootstrap.so boott.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR

For R-devel I see:
ccache gcc -shared -L/usr/local/lib -o bootstrap.so boott.o -lgfortran
-lm -lquadmath -L/usr/local/lib/R-devel/lib/R/lib -lR

My install script for the local build is based on Dirk's script [1].
In particular, my configure command is:

R_PAPERSIZE=letter R_BATCHSAVE="--no-save --no-restore"
R_BROWSER=xdg-open PAGER=/usr/bin/pager PERL=/usr/bin/perl
(Continue reading)

Luca Braglia | 24 Apr 01:37 2014
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debian testing CRAN repositories

Dear all,

i've a Debian jessie on my home pcs.

For the repositories of CRAN packages, to the best of my knowledge, there
are

1) http://debian-r.debian.net/

2) http://debian.cran.r-project.org/

3) http://cran.r-project.org/bin/linux/debian/

I'm a bit confused and need a little advice: which better (if one is so)
for my setting? In order to make packages dependencies happy and
integration with the standard debian system "smooth", I "have" to use the
first, right?

Many thanks
  Luca

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Carl Boettiger | 22 Apr 22:55 2014
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Segfaults on Ubuntu 14.04

Hi list,

I've just upgraded my Ubuntu system to 14.04 / Trusty Tahr. I now find that
when I launch the "R" software environment, I immediately get a
segmentation fault with no further warning or error message.

I tried removing the relevant base package, which seemed to successfully
remove R entirely from my system:

    sudo aptitude remove --purge r-base-core

I then simply reinstalled r-base-core, but same error persists.

my sources.list shows:

    deb http://cran.rstudio.com/bin/linux/ubuntu trusty/
    deb-src http://cran.rstudio.com/bin/linux/ubuntu trusty/

I then simply downloaded the Debian wheezy .deb for R 3.1.0 instead and
installed that, which worked just fine.  Just wondering if anyone else has
encountered this problem on the Ubuntu version and/or if I should report
this as a bug, and to whom.  (My apologies, the Debian package information
for the ubuntu .deb file isn't particularly clear on to whom I should
report bugs).

Cheers,

Carl

--

-- 
(Continue reading)

Alex Mandel | 21 Apr 21:39 2014

Re: Ubuntu 13.10 - not able to upgrade R

Looks like you will need to update packages in a specific order. Since
spatial depends on date, date needs to updated first.

update.packages("date")

Then try again and see what it tells you next.
It's a bit of a pain but will eventually work. The other option is to
dump the list of current packages. Uninstall the old and try to install
from the list.

Thanks,
Alex

On 04/21/2014 12:23 PM, claude krzisch wrote:
> Hi,
> Thank you for your response. It was one of the first things I did.
> However, it doesn't work. The error messages are (in french)
> 
> /Les packages source téléchargés sont dans//
> //    '/tmp/Rtmp4IaeBv/downloaded_packages'//
> //essai de l'URL 'http://cran.irsn.fr/src/contrib/spatial_7.3-8.tar.gz'//
> //Content type 'application/x-gzip' length 43593 bytes (42 Kb)//
> //URL ouverte//
> //==================================================//
> //downloaded 42 Kb//
> //
> //Erreur : package 'date' was built before R 3.0.0: please re-install it//
> //Exécution arrêtée//
> //
> //Les packages source téléchargés sont dans//
(Continue reading)

Francesco Brundu | 18 Apr 12:11 2014
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How to use rainbow function without the gamma argument

Hi,
I am using a old code (probably written for R 2.5) and it stops when
calling rainbow() with gamma argument. I saw that gamma argument is not
present in newer version of R rainbow function. How can I translate this
line of code:

rainbow(100, s = 1.0, v = 0.75, start = 0.0, end = 0.75, gamma = 1.5)

?

It fails with:

Error in rainbow(100, s = 1, v = 0.75, start = 0, end = 0.75, gamma = 1.5)
:
  unused argument (gamma = 1.5)
Calls: nmfconsensus ... matrix.abs.plot -> image -> image.default -> rainbow
Execution halted

Thanks

~ Francesco Brundu

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Martin Bel | 18 Apr 10:49 2014

Ubuntu 13.10 - not able to upgrade R

Hi,
I'm having some issues upgrading R. I'm using ubuntu linux 13.10, saucy and would like to upgrade R to the new
version.I'm currently using 3.0.1
I've been following the instructions given in:1.
http://stackoverflow.com/questions/10476713/how-to-upgrade-r-in-ubuntuand2. http://cran.r-project.org/bin/linux/ubuntu/

Here is exactly what i did, following mostly the stackoverflow description:
1) Added the cran mirror link to the sources list(I've actually tryed with 3 different mirrors just in
case)sudo gedit /etc/apt/sources.listdeb http://cran.cnr.berkeley.edu/bin/linux/ubuntu/ saucy/
2) Getting the key step gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9gpg -a --export
E084DAB9 | sudo apt-key add -
3) Run the updates/upgradessudo apt-get update && sudo apt-get upgrade
After a large list of succesful updates i get the following result in the terminal:

W: Failed to fetch http://cran.cnr.berkeley.edu/bin/linux/ubuntu/saucy/InRelease  
W: Failed to fetch http://cran.cnr.berkeley.edu/bin/linux/ubuntu/saucy/Release.gpg  Cannot
initiate the connection to cran.cnr.berkeley.edu:80 (2607:f140:0:8000::201). - connect (101:
Network is unreachable) [IP: 2607:f140:0:8000::201 80]
W: Some index files failed to download. They have been ignored, or old ones used instead.Reading package
lists... DoneBuilding dependency tree       Reading state information... Done0 upgraded, 0 newly
installed, 0 to remove and 0 not upgraded.

I've done this a few times. At this point there are no more updates and the R error is isolated.
Is there a solution to this or should i just re-install R.
Thanks for your time,
Martin
 		 	   		   		 	   		  
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Peter Dotson | 8 Apr 00:14 2014

I am getting 3.1.0 beta instead of 3.0.3

When I use apt-get install r-base, I am getting the 3.1.0 beta instead of
3.0.3

I tried the install from three different mirrors with the same result:

## R repo
deb http://cran.stat.ucla.edu/bin/linux/ubuntu precise/

Setting up r-base (3.0.3.20140328-1precise0) ...
Setting up r-base-dev (3.0.3.20140328-1precise0) ...
Setting up r-base-html (3.0.3.20140328-1precise0) ...
root <at> UNew-SAS:~# R

R version 3.1.0 beta (2014-03-28 r65330) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

## R repo
#deb http://cran.stat.ucla.edu/bin/linux/ubuntu precise/
deb http://ftp.osuosl.org/pub/cran/bin/linux/ubuntu precise/

Setting up r-base-dev (3.0.3.20140328-1precise0) ...
Setting up r-base-html (3.0.3.20140328-1precise0) ...
root <at> UNew-SAS:~# R

R version 3.1.0 beta (2014-03-28 r65330) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

## R repo
(Continue reading)

Francesco Brundu | 7 Apr 17:15 2014
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How to use stable release in Ubuntu

Hi all,
I am writing to you since I think I am experiencing a regression on the
latest beta release, R version 3.1.0 beta (2014-03-28 r65330) -- "Spring
Dance" .. Since I need to check for it before posting, I was searching for
a method to revert to version 3.0.2 in Ubuntu, but I was unable to find it.
Could you please give me some hints?

Thanks
~ Francesco Brundu

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Robert Bruggner | 2 Apr 00:31 2014
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R 3.1.0 Beta installed but I'm not sure how

Hi All, 

I have installed R on Ubuntu 12.04 with apt pointed at my favorite mirror
(http://cran.cnr.berkeley.edu/bin/linux/ubuntu precise/). Today, I ran an apt-get upgrade and now
when I launch R, it tells me that I’m running R version 3.1.0 beta (2014-03-28 r65330) -- "Spring Dance”.

I’m slightly confused as when I look at the package list in
http://cran.r-project.org/bin/linux/ubuntu/precise/, looks as though r-base-core is version
3.0.3. In other words, I’m not sure how I got the the 3.1.0 beta version installed and running instead? 

Perhaps this is related to Paul’s message yesterday
(https://stat.ethz.ch/pipermail/r-sig-debian/2014-April/002245.html) but I’m not sure how to
correct the situation. Apologies if this is something trivial - any help would be greatly appreciated. 

Cheers, 

-Rob
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_______________________________________________
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R-SIG-Debian <at> r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Paul Johnson | 1 Apr 16:07 2014
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Head's up: Renviron change in R_LIBS_USER to 3.1

Hi

Here's a warning for you. If you start R today and it can't find any
packages in your home directory that it did find yesterday, don't
faint. You'll see something like this:
> library(data.table)
Error in library(data.table) : there is no package called 'data.table'

and your user home folder R packages will no longer appear in path:

> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"

Explanation/solution:

Yesterday on Ubuntu 13.10 I ran the package updates and R 3.0.3
installed and it altered the /etc/R/Renviron file to look for packages
here

R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.1'}

But  my packages are still installed in
~/R/x86_64-pc-linux-gnu-library/3.0. This seems unnecessary, on the
face of it, since R is still 3.0.3, not 3.1, but perhaps there's some
binary incompatibility they are worrying about.

I can't say for sure which package caused that particular change, but
I'm suspecting the first or second one here (from the history):

(Continue reading)

Dario Strbenac | 27 Mar 11:00 2014
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mclapply Segmentation Fault for Ubuntu

Running the example in the documentation causes R to crash.

dario <at> bioinfo:~$ R

R version 3.0.3 (2014-03-06) -- "Warm Puppy"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(parallel)
> simplify2array(mclapply(rep(4, 5), rnorm))

 *** caught segfault ***
address 0x7fee2a7229d0, cause 'memory not mapped'

Traceback:
 1: mcexit(0L)
(Continue reading)


Gmane