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)

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

Gmane