Sean Southard | 11 May 22:49 2015
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Foreach %dopar% operator incorrectly load balancing

Dear R-SIG-Debian,

I am using R version 3.1.2 with rstudio-server 0.98.113 on debian build
3.2.0-4-amd64 #1 SMP Debian 3.2.68-1+deb7u1 x86_64 GNU/Linux.

I often use the %dopar% operator in from the foreach package to run code in
parallel. However, the only other use on the box seemingly installed a few
items and suddenly %dopar% will use far more than the number of cores I am
specifying and seems to load balance between all of them. The issue with
this is that it doesn't actually seem to perform non-trivial tasks at all
anymore.

This is an example of testing code I've been using for testing the %dopar%
 loop.

library(iterators)
library(foreach)
library(doParallel)
library(Parallel)
nCores <- 4

cl <- makeCluster(nCores)
registerDoParallel(cl)
trials = 100000

x <- iris[which(iris[,5] != "setosa"),c(1,5)]
    t2 <- system.time({
    r2 <- foreach(icount(trials), .combine=cbind) %dopar% {
    ind <- sample(100,100,replace= TRUE)
    results1 <- glm(x[ind,2]~x[ind,1],family=binomial(logit))
(Continue reading)

Natalia Morandeira | 8 May 04:10 2015
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Unable to install packages: "/usr/bin/ld: cannot find -lgfortran"

Dear all,

I'm using R version 3.2.0 in Ubuntu 12.04 LTS.

 While trying to install any package I get the error: "/usr/bin/ld: cannot 
find -lgfortran"

If I open a Terminal and run "ldconfig -p | grep libgfortran"​, I get:​
"libgfortran.so.3 (libc6,x86-64) => 
/usr/lib/x86_64-linux-gnu/libgfortran.so.3"

I've been an R user for two years and this is the first time I get this 
error. I've uninstalled R and re-installed it but the problem was not 
solved. 

I'll be very grateful for any help or suggestions to solve the problem.

Best regards,

Natalia Morandeira
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"Dr. Stefan Röttger" | 7 May 09:39 2015
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Problems installing packages with R 3.2.0 on Linux Mint 17.1

Dear R-SIG-Debians,

I have difficulties installing packages from within R through 
install.packages(). R version is 3.2.0 and OS is Linux Mint 17.1.

For most packages, a lot of error messages come up which seem to be 
related to compilation. Installing packages provided by the ubuntu 
distro through apt-get works just fine.

I followed all directions given in CRAN's /bin/linux/ubuntu/readme.html, 
but the problem persists.

Entering install.packages("sem") in R, for example, produces the output 
below.

I would be happy if anyone could give me a hint or recommendation on how 
to get the compilation going.

Best regards,
Stefan

 > install.packages("sem")
Installing package into ‘/home/stefan/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
versuche URL 'http://cran.rstudio.com/src/contrib/sem_3.1-5.tar.gz'
Content type 'application/x-gzip' length 146831 bytes (143 KB)
==================================================
downloaded 143 KB

* installing *source* package ‘sem’ ...
(Continue reading)

Vincent Lemoine | 20 Apr 14:26 2015

Dependency problem with "python-rpy2" package

Hello,

I have a problem with package "python-rpy2" with Debian Wheezy repository.

I use this repo :
deb http://cran.r-project.org/bin/linux/debian wheezy-cran3/

This package depends on "python-singledispatch" but it doesn't exist in official Debian repo...

Could you help me to fix this issue ?

Thanks a lot,
kamaraju kusumanchi | 20 Apr 00:10 2015
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R-SIG-Debian Info Page is down

I am getting a "Error 503" when I go to
https://stat.ethz.ch/mailman/listinfo/r-sig-debian . Could you please
take a look?

thanks
raju
--

-- 
Kamaraju S Kusumanchi | http://raju.shoutwiki.com/wiki/Blog
kamaraju kusumanchi | 19 Apr 23:58 2015
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running unit tests on the stringr package

I am trying to learn how  to run the unit tests in the stringr package
and have the following questions.

1) The r-cran-stringr package does not suggest/depend on the
r-cran-testthat package . Would it make sense to add such a thing
since after all the tests in /usr/lib/R/site-library/stringr/tests
rely on testthat package?

2) I am getting the following error when trying to run the unit tests

% R
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
...
> library('testthat')
> library('stringr')
> test_dir('/usr/lib/R/site-library/stringr/tests')
String and pattern checks : 123
Counting matches : ....
Detecting patterns : ..........
Duplicating strings : ......
Extract patterns : ..
Joining strings : ......
String length : .........
Locations : ............
Matching groups : ..............
Test padding : ....
Splitting strings : .........................
Extracting substrings : ...................
Trimming strings : ........

(Continue reading)

Timothy Harding | 16 Apr 05:53 2015
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Cannot Install R to Trusty 14.04

Hello,

I've followed the instructions at several different how to sites:
http://cran.r-project.org/
http://r-interface.blogspot.com/2012/04/install-r-jgr-and-deducer-in-ubuntu.html
http://stackoverflow.com/questions/28273441/receiving-unmet-dependency-while-installing-r-base-on-ubuntu-14-10

I've installed R to various Ubuntu's before, including trusty, but recently
it has stopped working:

dhis <at> tmctpsql:~$ sudo apt-get install r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-base-dev : Depends: r-base-core (>= 3.1.3.20150410-1trusty) but it is
not going to be installed
E: Unable to correct problems, you have held broken packages.

Any ways around this? Does anyone else have issues with installing to a
brand new trusty install?

Timothy Harding
RPCV Vanuatu
(Continue reading)

kamaraju kusumanchi | 13 Apr 04:07 2015
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list of available R packages

This is a very minor point. But thought I would bring it to your
attention anyway...

According to http://cran.r-project.org/bin/linux/debian/ , the list of
available R packages can be found by

apt-cache search ^r-.*

This seems to work in bash but not in zsh. As a work around, I found out that

apt-cache search "^r-.*"

works in both zsh and bash.

--

-- 
Kamaraju S Kusumanchi | http://raju.shoutwiki.com/wiki/Blog
Skye Bender-deMoll | 7 Apr 19:52 2015
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Rmpi install issues

Hi Folks,
  I've recently transitioned to Debian 8.0 and was having a hard time 
getting Rmpi to work.

I believed I'd successfully installed dependencies via

 > sudo apt-get install r-cran-rmpi

 > apt-show-versions r-cran-rmpi
r-cran-rmpi:amd64/jessie 0.6-5-1 uptodate

but when installing the package I was still getting

checking mpi.h presence... no
checking for mpi.h... no
configure: error: "Cannot find mpi.h header file"
ERROR: configuration failed for package ‘Rmpi’

I discovered that /usr/lib/openmpi/include/ was missing

In hindsight, it is obvious that header files are only included when the 
dev version of openmpi is intalled:

 > sudo apt-get install libopenmpi-dev

After which Rmpi package installed without error.

I'm not very familiar with debian package management, but wouldn't most 
debian R users be building package from source?  If so, maybe 
libopenmpi-dev should be added as a dependency of r-cran-rmpi ?  If not, 
(Continue reading)

Marius Hofert | 2 Apr 20:34 2015
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Re: Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)

On Thu, Apr 2, 2015 at 5:49 AM, Johannes Ranke <jranke <at> uni-bremen.de> wrote:
> Hi Marius,
>
> thanks for your reply.
>
>> > So maybe you could modify your instructions to the case where someone
>> > wants to have R-devel in addition to the released R version, if that is
>> > what you are aiming at? I could then add it to the README for Debian on
>> > CRAN.
>>
>> That sounds good. I just modified the instructions to R-devel and used
>> a more "Kurt-like" naming convention:
>
>> 1) sudo nano /etc/apt/sources.list
>>    deb http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/
>>    deb-src http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/
>
> ...
>
>> 9) Create a (symbolic) link (don't use 'make install'):
>>    cd ..
>>    ln -s /usr/local/R/R-devel_build/bin/R /usr/local/R/R-devel
>
> Why not put a link into /usr/local/bin which is already in the path?

... I think the reason was that ESS auto-recognizes everything in
/usr/local/R if your main R version in use is installed there, see C-h
k ess-rterm-version-paths...

>
(Continue reading)

Marius Hofert | 2 Apr 03:17 2015
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Re: Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)

On Tue, Mar 31, 2015 at 2:05 AM, Johannes Ranke <jranke <at> uni-bremen.de> wrote:
> Dear Marius,
>
> thanks for sharing your thoughts on this. I am not very happy that you provide
> instructions to install R 3.1.3 from sources when binaries are already
> provided on CRAN.

Dear Johannes,

... no one in his/her clear mind would go that way unless necessary. I
have given reasons for when and why it is necessary.

> The installation instructions you share bring more work and
> a more non-standard setup, unless you want two different copies of R. But your
> instructions do not cover that case!

... because it is trivial from the procedure I described. Replace the
version number by 'devel' or 'rc' (for patched) and the rest remains
pretty much the same (obviously adapting the download link).

>
> From my point of view it could be interesting if it were modified for keeping
> an up to date copy of R-devel in addition to the released version,

yes, that's a use case. Or if you need >= 2 R versions to check back
with older versions or if a user with a different R version reports a
bug and you can not reproduce it with the version you have etc...

>  but in the
> way you are giving it here I think it may lead people to be distracted from
(Continue reading)


Gmane