headers
Martin Maechler | 15 Jun 2013 11:47
Picon
Favicon
Gravatar

r-cran-rjava (ubuntu 13.04 ?) -- missing dependencies?

I am really no java lover, but for some reason had interested to look
at an R package that depends on  rJava...
and when I tried, I was *again* (it is my usual experience for more
than 10 years)
unable to get rJava installed,
as indeed, also   'R CMD javareconf'  ended  in an error that  jni.h
was not found.

I see the issue here,
http://stackoverflow.com/questions/16438073/unable-to-install-rjava-in-r-3-0-in-ubuntu-13-04

including the proposed solution

   sudo apt-get install openjdk-7-*

which installs 690 MB (!) of stuff (not counting the "basic openjdk-7"
installed previously)...
...
and indeed solves the problem  {i.e.  'R CMD javareconf'  then succeeds}.

---
Summary: I think  r-cran-rjava  needs the full (or at least more than now of)
'openjdk-7-*' in its (debian) dependencies.

Martin
Permalink | Reply | 2 comments |
headers
John Blischak | 13 Jun 2013 21:41
Picon

Cannot install XML package with R 3.0 and Ubuntu 12.04

Hi,

I am unable to install the R package XML using R 3.0.1 on Ubuntu 12.04 LTS
(64-bit). After the installation failed using install.packages, I followed
previous directions for installing R packages on Ubuntu
(R-SIG-Debian<http://grokbase.com/t/r/r-sig-debian/127nwwez27/package-xml-does-not-load-in-r-2-15-1>,
StackOverflow<http://stackoverflow.com/questions/7765429/unable-to-install-r-package-in-ubuntu-11-04>)
by running sudo apt-get install r-cran-xml. However, this is not usable
with R 3.0, and update.packages(oldpkgs = 'XML') failed as well. Lastly, it
is not available on the RutteR
PPA<https://launchpad.net/~marutter/+archive/rrutter/+index?batch=75&direction=backwards&start=600>
.

Is there a way to solve this? Thanks in advance!

John

P.S. In case it could be helpful, here is my session info:

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
LC_ADDRESS=C
(Continue reading)

Permalink | Reply | 5 comments |
headers
Michael Rutter | 12 Jun 2013 22:19
Picon

cran2deb4ubuntu Updated for R 3.0.1 and Ubuntu 13.04

It has taken a long time, but cran2deb4ubuntu has been updated for R 
3.0.1.  Over 1000 R packages are available as .deb files (with 
dependencies) for Ubuntu 13.04 (raring), 12.10 (quantal) and 12.04 
(precise).

These packages can be found at the [c2d4u 
PPA](https://launchpad.net/~marutter/+archive/c2d4u).  Instructions on 
how to install the PPA can be found on this webpage.

Hopefully, I have updated every package.  If one has slipped through the 
cracks, please let me know via mail.  The package list is based on the 
the CRAN Task Views, so if a package you use is missing, the best way to 
get it into c2d4u is to get it added to an appropriate Task View.

Michael
--

-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
4205 College Drive
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter
mar36 <at> psu.edu
Permalink | Reply | 0 comments |
headers
Giuseppe Pagnoni | 7 Jun 2013 11:01
Picon
Gravatar

Function nlme::lme in Ubuntu (but not Win or OS X): "Non-positive definite approximate variance-covariance"

Dear all,

I am estimating a mixed-model in Ubuntu Raring (13.04ΒΈ amd64), with the
code:

fm0 <- lme(rt ~ run + group * stim * cond,
                 random=list(
                   subj=pdSymm(~ 1 + run),
                   subj=pdSymm(~ 0 + stim)),
                 data=mydat1)

When I check the approximate variance-covariance matrix, I get:

> fm0$apVar
[1] "Non-positive definite approximate variance-covariance"

*However*, if I do the same on a Windows or a Mac OS X machine, I get:

> fm0$apVar
               reStruct.subj1 reStruct.subj2 reStruct.subj3 reStruct.subj1
reStruct.subj1   1.952757e-01   3.130089e-01   5.766955e-01  -0.1034862377
reStruct.subj2   3.130089e-01   5.703211e-01   9.864047e-01  -0.1937902915
reStruct.subj3   5.766955e-01   9.864047e-01   1.861434e+00  -0.3303689957
reStruct.subj1  -1.034862e-01  -1.937903e-01  -3.303690e-01   0.0941652375
reStruct.subj2  -3.464557e-03  -5.933008e-03  -1.102904e-02   0.0163847582
reStruct.subj3  -6.826057e-01  -1.186231e+00  -2.122872e+00   0.3705613715
lSigma          -2.058254e-06  -4.764783e-06   1.653583e-05  -0.0000146693
               reStruct.subj2 reStruct.subj3        lSigma
reStruct.subj1  -3.464557e-03  -6.826057e-01 -2.058254e-06
reStruct.subj2  -5.933008e-03  -1.186231e+00 -4.764783e-06
(Continue reading)

Permalink | Reply | 2 comments |
headers
Chris Sims | 17 May 2013 21:10
Picon
Favicon

trouble installing ess 13.04 ubuntu package on 64 bit system

I'm finding installation of the ess raring0 package fails, on two 
different 64-bit kubuntu systems.  Installing from the command line 
using apt-get produces, after apparently going through most of the 
installation without problems:

ERROR: install script from ess package failed
dpkg: error processing ess (--configure):
  subprocess installed post-installation script returned error exit status 1
Errors were encountered while processing:
  ess
E: Sub-process /usr/bin/dpkg returned an error code (1)

If I install from within Synaptic, there is an additional error 
message:  E: Internal Error, No file name for ess:amd64

After the installation process ends with this error, ess is not 
available within emacs.

Chris Sims
Permalink | Reply | 1 comment |
headers
Johannes Ranke | 13 May 2013 00:43
Picon
Picon
Favicon

Upcoming repository for R 3.0 on wheezy

Dear all,

I have done the backport of R 3.0 to wheezy in the usual way and it is on its 
way to CRAN.

If you are interested in installing it, be aware that the debianized R 
packages availabe in wheezy that are not in the list of packages recompiled 
for CRAN will not work with this backport. This is explained in more detail in 
the README, which will appear in an updated version together with the 
wheezycran3 repository folder.

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

I realize that it is not optimal to just support only such a small proportion 
of the R related packages in Debian.

To move forward, I see two options:

a) One or more Debian developers could start to upload r-base and the reverse 
dependencies to the official Debian wheezy-backports repository. For wheezy, 
this is pretty straightforward at first as no adaptations are currently 
necessary to make the packages from testing (I am actually backporting from 
unstable) build on wheezy. But one needs to be a debian developer to upload 
and commit to the job of keeping these backports working.

b) Alternatively the build scripts I am using could be improved or rewritten. 
It seems sbuild is recommended over pbuilder nowadays, and there are several 
points that could be improved to make the backporting procedure more efficient.

Of course it would be nice to have more (like cran2deb repositories for more R
(Continue reading)

Permalink | Reply | 0 comments |
headers
Paul Johnson | 11 May 2013 23:25
Picon

clean wheezy, R intrigue, squeeze-cran3 requires liblzma2?

Hi.

On the release version of Debian Wheezy, I am missing symbols for left and
right brackets in plotmath. Anybody see similar trouble while reviewing
demo(plotmath)?

This is a completely clean, fresh install.  I've not installed any peculiar
libraries or packages, except R, the installation of which still puzzles
me.

I configured a CRAN mirror for packages using squeeze-cran3 folder, and
that's where the first funny thing happened.  I noticed same when R-2.15.3
came out, but I thought I had this trouble because my system was all junked
up with unusual libraries.  But now, on a clean system, I get this error,
which indicates I need a package liblzma2, which does not exist in Debian:

pauljohn <at> pjlap-d7:amd64$ sudo apt-get install r-base-core
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-core : Depends: liblzma2 (>= 4.999.9beta+20091116) but it is not
installable
               Recommends: r-recommended but it is not going to be installed
(Continue reading)

Permalink | Reply | 4 comments |
headers
Lorenzo Isella | 7 May 2013 18:33
Picon

R 3 and Debian Testing

Dear All,
I am using Debian testing on multiple machine machines at home.
This is my source list

  deb http://ftp.ch.debian.org/debian/ testing main contrib non-free
  deb-src http://ftp.ch.debian.org/debian/ testing main non-free contrib

  deb http://security.debian.org/ testing/updates main contrib non-free
  deb-src http://security.debian.org/ testing/updates main contrib non-free

So, my repositories always point to the latest Debian testing, even now  
after the new release of Debian 7.
I am wondering if, after the new release of Debian 7, R 3 will become  
routinely available to me, without the need to add any specific repository.
Cheers

Lorenzo
Permalink | Reply | 6 comments |
headers
Michael Rutter | 4 May 2013 14:48
Picon

Backporting R 3.0.0 to Quantal, Precise, and Lucid

Today (May 4, 2013) I will begin the process of backporting R 3.0.0 to
Quantal, Precise, and Lucid.  This will include all the recommended
packages and the packages for R found in the universe repository for
Ubuntu.  Things to keep in mind:

- If you do not want to receive these upgrades and you use the CRAN
repositories or my Launchpad PPA, please remove them from your apt/synaptic
sources lists.  This will keep you on your current versions.

- You could pin the old versions (search google for "apt pinning"), but
since updates will only be coming for R 3.0.0, it is easier to just remove
the repositories.

- This should be complete by Monday, but it may take longer depending on
server load.

After the update process, base R and the recommended packages will be found
on [CRAN](http://cran.r-project.org/bin/linux/ubuntu/) while all the other
packages can be found at my [PPA](
https://launchpad.net/~marutter/+archive/rrutter).

--

-- 
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

	[[alternative HTML version deleted]]
(Continue reading)

Permalink | Reply | 0 comments |
headers
Michael Rutter | 30 Apr 2013 03:44
Picon

R 3.0.0 and Raring Ringtail (Ubuntu 13.04)

New .deb packages for R 3.0.0 on Raring Ringtail (13.04) are available 
on both [CRAN](http://cran.us.r-project.org/bin/linux/ubuntu/) and my 
[Launchpad PPA](https://launchpad.net/~marutter/+archive/rrutter).  Some 
notes for this release.

- The initial build for Raring Ringtail did not come with Tcl/Tk being 
supported.  This issue has been addressed and the current release 
supports Tcl/Tk.

- Due to a small configuration error on my server, the amd64 packages 
for Raring Ringtail did not sync to CRAN.  This has been fixed and the 
64-bit packages should be available soon on a CRAN mirror near you.

- As has been previously discussed, R 3.0.0 requires that all packages 
be rebuilt against it. Therefore, all the r-cran-* packages found in the 
Ubuntu universe repository will not work with R 3.0.0.  In an effort to 
rectify this, I have rebuilt a number of those packages against R 3.0.0 
and they can be found at the [RRutter 
PPA](https://launchpad.net/~marutter/+archive/rrutter), but not CRAN.  I 
am still having issues with a couple of packages, but I am working on those.

- R 3.0.0 is still available for older Ubuntu releases on my [RDev 
PPA](https://launchpad.net/~marutter/+archive/rdev).  The plan is to 
upgrade Lucid, Precise, and Quantal this Friday evening (May 3rd, 2013) 
as well as many of the r-cran-* packages available in universe.  If you 
do not want to upgrade to R 3.0.0, please remove the appropriate 
repository from you sources list.

--

-- 
Dr. Michael A. Rutter
(Continue reading)

Permalink | Reply | 0 comments |
headers
Tobias Verbeke | 29 Apr 2013 14:53
Picon
Favicon

naming r-base files Ubuntu precise builds

L.S.

The Ubuntu precise builds of R 2.15.3 at

http://cran.r-project.org/bin/linux/ubuntu/precise/

have names for the r-base package that seem erroneous

r-base_2.15.3-1precise0precise1.diff.gz	02-Mar-2013 14:09 	79K	 
r-base_2.15.3-1precise0precise1.dsc	02-Mar-2013 14:09 	2.4K	 
r-base_2.15.3-1precise0precise1_all.deb	02-Mar-2013 17:49 	37K

Should this be

r-base_2.15.3-1precise1.diff.gz
r-base_2.15.3-1precise1.dsc
r-base_2.15.3-1precise1_all.deb

and, if yes, can this be fixed?

Many thanks in advance!

Best wishes,
Tobias
Permalink | Reply | 1 comment |

Gmane