MASS is blocked for R 2.15.0

I updated R to R 2.15.0 via apt-get and received the message that 
r-cran-mass was blocked.
I recently tried apt-get update/ apt-get safe-upgrade and received the 
same message, for
r-cran-mass-7.3.16-1lucid0

I currently have MASS 7.3-7 installed

How can I figure out what is wrong and correct it?

thx,

--

-- 
Michael Friendly     Email: friendly <at> yorku.ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://datavis.ca
Toronto, ONT  M3J 1P3 CANADA

Re: GotoBLAS2 breaks lapack

Dirk Eddelbuettel <edd <at> debian.org> writes:

> One last follow-up.  Debian's Atlas maintainer has started to work in the
> OpenGoto packaging.  There will be proper Goto packages now that the license
> is better, but it may take a while. It took years to get Atlas packaged
> 'right' so don;t expect anything too soon.  The gotoblas2-helper package is
> still useful for the 'here and now'.

Unfortunately it is broken :(

Link not found at ./getGotoBLAS2 line 83

Installing LaTeX class files not available in Debian packages

I apologize for abusing the list somewhat but there is some connection
to R.  Several of the example files in the knitr package for R use the
tufte-handout class, which, AFAICS, is not available in Ubuntu or
Debian packages (please correct me if I am wrong).

The source files are available at tufte-latex.googlecode.com (a.k.a.
code.google.com/p/tufte-latex) and I presume they should end up in a
subdirectory of /usr/local/share/texmf or something like that.  Is
there a standard approach to adding unpackaged class files?

ez package installation fails - ubuntu 12.04

Hello everyone,

I've just installed ubuntu 12.04 and the package named 'ez' fails to
install because of a dependency.
The error messages are:

Error : package ‘Matrix’ 1.0-2 is loaded, but >= 1.0.3 is required by ‘ez’
ERROR: lazy loading failed for package ‘ez’
* removing ‘/usr/local/lib/R/site-library/ez’

The downloaded packages are in
    ‘/tmp/Rtmp38etdB/downloaded_packages’
Mensagens de aviso perdidas:
In install.packages("ez") :
  installation of package ‘ez’ had non-zero exit status

I'm not sure if this is the proper way to report a bug. I hope it helps.

Is there anything I can do to get it working?

Thanks in advance.
Flavio Bastos

	[[alternative HTML version deleted]]

_______________________________________________
R-SIG-Debian mailing list
R-SIG-Debian <at> r-project.org

A guide to R packages for Ubuntu

As per a request, here is a brief guide to what is available to R users 
as packages in Ubuntu.

Each release of Ubuntu includes the latest version of R and the 
recommended packages.  In addition, there are approximately 80 
additional r-cran packages available in the default repositories.  The 
limitation to these packages is that they are not updated and reflect 
the current version of the program or package when that version of 
Ubuntu was released.

If you want to have current versions of R and the recommended packages, 
there are two repositories to choose from:

CRAN: http://cran.r-project.org/bin/linux/ubuntu/
Launchpad PPA: https://launchpad.net/~marutter/+archive/rrutter

Both sites have the same packages (the PPA packages are mirrored on 
CRAN), but there may be a reason to use one over the other.

CRAN Advantages:
- A local mirror may be faster in terms of internet speed.
- Older versions of the packages are available, so if an update to R or 
a core package breaks your code, you can reinstall an older version via 
synaptic or apt.

PPA Advantages:
- Quickest way to get the updates (only by about 24 hours however)
- Easy to install (sudo add-apt-repository ppa:marutter/rrutter)

If you have been using CRAN, then there is no reason to change to the 

R packages for Ubuntu 12.04 LTS Precise Pangolin now available

Ubuntu users,

The latest version of Ubuntu (12.04 LTS: Precise Pangolin) has been 
released.  Current R packages are also available from the following 
locations:

The CRAN repository
http://cran.r-project.org/bin/linux/ubuntu/

My Launchpad PPA (feeds CRAN, has a few more packages)
https://launchpad.net/~marutter/+archive/rrutter

cran2deb4ubuntu (over 1000 packages found in CRAN Taskviews, not all 
uploaded yet)
https://launchpad.net/~marutter/+archive/c2d4u

If you have any questions, please let me know.
Michael

--

-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter

Error installing libraries (eg RODBC) on R-2.15.0 : cannot find 'config.log'

Dear list,

as I started installing R-2.15.0 on a Red Hat 4.5.1-4 as well a Ubuntu
10.04.3 systems.
While the basic installation went fine (like the previous R-2.14.2), now
I'm having trouble installing almost one third of the additional libraries
I want (which installed flawlessly with R-2.14.2), among them RODBC for
which I show the message below (obtained on Ubuntu) :

surf_forInstallation_≥ R  CMD INSTALL RODBC_1.3-5.tar.gz
* installing to library '/linux/biolo/R_surf/R-2.15.0/lib64/R/library'
* installing *source* package 'RODBC' ...
** package 'RODBC' successfully unpacked and MD5 sums checked
checking for gcc...
gcc -std=gnu99
checking for C compiler default output file name... configure: error: C
compiler cannot create executables
See `config.log' for more details.
ERROR: configuration failed for package 'RODBC'
* removing '/linux/biolo/R_surf/R-2.15.0/lib64/R/library/RODBC'

In fact, I get identical messages on our Red Hat 4.5.1-4 and the Ubuntu
10.04.3 systems mentioned above.
Obviously something with our C compiler(s) didn't work out.
In order to learn more about the problem I tried to look at config.log
mentioned in the installation-message above, however, I cannot find
the file, neither in my current path nor in
 /linux/biolo/R_surf/R-2.15.0/lib64/R/library .
Obviously the RODBC directory doesn't exist any more when the installation
attempt ends.

Dependency problem bug with r-cran-vr

Hi,

I was trying to connect GRASS with R, following the guidelines described here:

http://grass.osgeo.org/wiki/R_statistics

The line in my /etc/apt/sources.list is like:

deb http://ftp.iitm.ac.in/cran/bin/linux/debian squeeze-cran/

But when I tried to install r-cran-vr, I got an unmet dependency
problem with r-cran-mass and r-cran-class.
But these two packages were already installed. Then why it happen?
--------------------------------------------------------------
jaisen <at> debian:~$ sudo apt-get install r-cran-vr
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-cran-vr : Depends: r-cran-mass but it is not going to be installed
             Depends: r-cran-class but it is not going to be installed
E: Broken packages
jaisen <at> debian:~$
--------------------------------------------------------------

symbol lookup error

Hi all,

I am on debian testing with pre-packaged R (2.14.1) installed.  I started
getting weird crashes.  Now I have a reproducible example:

# R
R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

> save(/usr/lib/R/bin/exec/R: symbol lookup error: /usr/lib/R/lib/libR.so: undefined symbol: _pcre_valid_utf8
# 

Right after entering 'save(' I pressed TAB.

Any help on this would be highly appreciated.

Regards,
Andreas

Ubuntu Lucid, R 2.14.2, and ggplot2

I've just updated to the latest R (2.14.2) on my Ubuntu Lucid box, and now the ggplot2 installed as a .deb
package fails to work.

$ R -e 'library(ggplot2)'
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : 
  package ‘proto’ does not have a NAMESPACE and should be re-installed
Calls: library -> .getRequiredPackages2 -> library
Execution halted

Here is what I did to ensure the packages were up-to-date:

$ sudo apt-get update
$ sudo apt-get install r-base r-base-core r-cran-ggplot2 r-cran-proto

Here is what my sources list and dpkg list looks like:

$ cat /etc/apt/sources.list.d/r-cran.list 
deb http://cran.wustl.edu/bin/linux/ubuntu lucid/

$ dpkg -l r-base r-base-core r-cran-ggplot2 r-cran-proto
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                      Version                   Description
+++-=========================-=========================-==================================================================
ii  r-base                    2.14.2-3lucid0            GNU R statistical computation and graphics system
ii  r-base-core               2.14.2-3lucid0            GNU R core of statistical computation and graphics system
ii  r-cran-ggplot2            0.8.9-1cran1              GNU R package "An implementation of the Grammar of
ii  r-cran-proto              0.3-9-1cran1              GNU R package "Prototype object-based programming"

Secure apt

I am trying to add Michael Rutter's ppa to my
repository.  I cannot do this from the command
line.  I think I may be behind a firewall so copying
the key to a text file is my best option.  When I
search for the key at 

http://keyserver.ubuntu.com:11371/

the search fails.  Tried typing and 
cutting and pasting E084DAB9 into 
the search box without success.  How 
can I get the key?