gmane.comp.lang.r.debian

Re: trouble installing ess 13.04 ubuntu package on64bit system

Dirk Eddelbuettel — 2013-05-17T19:31:54

Hi Chris,

On 17 May 2013 at 15:10, Chris Sims wrote:
| 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.

My apologies -- there was a slight mishap with someone in ESS Core committed
'post-release' too soon, which Martin Maechler caught and reverted before
alerting me to the new release.  Problem was, one file was left o

trouble installing ess 13.04 ubuntu package on 64bit system

Chris Sims — 2013-05-17T19:10:18

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

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

Paul Johnson — 2013-05-14T14:13:40

Thanks very much for the packaging.

I think I found the answer about missing glyphs.  I followed the debugging
advice that BDR put in that bugzilla entry mentioned in my last note.  The
culprit was a copy of the microsoft symbol.ttf was in my user account font
folder.  That used to be a good thing, but apparently no more.  It causes
1) R to not be able to display lceil and other large braces and 2) Evince
cannot display some sizes of "mu" and "<=".  As soon as that file is
removed, then everything seems to display just fine.

Oh, one more thing. I can confirm the claim in that bug report that R
itself is writing proper PDF output, the problem is only in the display on
screen in a given system.  Embedding the fonts always solves this trouble,
however, so if one is unable to remove a troubled font or fiddle around it,
there is still a straightforward fix.

pj


On Sun, May 12, 2013 at 12:08 PM, Johannes Ranke <jranke< at >uni-bremen.de>wrote:

Upcoming repository for R 3.0 on wheezy

Johannes Ranke — 2013-05-12T22:43:57

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

Re: R 3 and Debian Testing

Lorenzo Isella — 2013-05-12T18:31:40

Hello,
Well, it turned out that I had exactly nothing to do.
Since my repos point constantly towards the latest testing, I had just to  
wait till today and I got R 3.0 installed on my box. No need to add any  
extra repository.
Cheers

Lorenzo


On Tue, 07 May 2013 18:53:32 +0200, Dirk Eddelbuettel <edd< at >debian.org>  
wrote:

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

Johannes Ranke — 2013-05-12T17:08:55

Hi,

The R 3 packages for wheezy are currently being built for i386 and amd64. If 
all goes well, they will be available within the next two days.

As for R on Debian wheezy, I just checked demo(plotmath) on the default R 
2.15.1 on wheezy, and it produced all the nice plotting symbols I would expect 
in good quality. I realize this does not help you, I just want to make clear 
that wheezy is not the problem here.

I will check the wheezy backport for proper functioning of plotmath.

Kind regards,

Johannes


Am Sonntag, 12. Mai 2013, 15:09:59 schrieb Paul Johnson:

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

Paul Johnson — 2013-05-12T13:09:59

Thanks Charles, but ... (below)


On Sat, May 11, 2013 at 6:28 PM, Charles Plessy <charles-r-nospam< at >plessy.org

I agree to your interpretation of the packaging problem. I can post the R
packages for Wheezy on my website if anybody wants them.

Now, back to the "no glyph" problem. Does


work for you on Debian 7?

Here's a re-producible example that generates bad on-screen output for me.

plot(0~0, type = "n")
text(.4, expression(group(lceil,x, rceil)), cex=0.5)

The glyphs for the left and right braces look like "dominoes".

I found a thread from 2010 about a similar problem, but that case blamed
the Wine fonts. Now I suspect some other bad symbol font has found its way
to the front of my path.

https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14355

That thread points out that using the Xlib version of the X11 device SOLVES
the problem, but at the price of slightly lower quality of output. If I
want to use the default Cairo device, apparently I have to fiddle something.

I am experimenting with the debu

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

Charles Plessy — 2013-05-11T23:28:08

Le Sat, May 11, 2013 at 04:25:14PM -0500, Paul Johnson a écrit :
 

Dear Paul,

the packages in the squeeze-cran3 folder are built for the Debian "Squeeze"
(6.0) distribution.  The liblzma2 package exists in Squeeze, but not in Wheezy
(Debian 7.0, the distribution you used for your fresh install).  Downgrades
are not supported, as exemplified by your problem.

Debian Wheezy was released just one week ago, so I guess it is only a matter of
time before a "wheezy-cran" folder will be provided.

Best regards,

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

Paul Johnson — 2013-05-11T21:25:14

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

Re: R 3 and Debian Testing

Chris Evans — 2013-05-10T14:24:48

I think that only gets us R >= 3.0.0 if the full line is 

  http://cran.r-project.org/bin/linux/debian/ squeeze-cran3/

I had squeeze-cran/ not squeeze-cran3/ so I wasn't getting the update to 3.0.0.  I think I must have been missing some Emails alerting us.

Very best all and many, many thanks to the stars who make all this work for lusers like myself.

Chris

----- Original Message -----

Re: R 3 and Debian Testing

Johannes Ranke — 2013-05-10T06:16:02

Robert,

good question. I have not been doing so, and I am afraid it is a bit
much for me. I will make an extra effort to include some more...

In case anyone would like to help in upgrading my simple build system,
here it is:

http://kriemhild.uft.uni-bremen.de/viewvc/r-backports

I am currently travelling and very busy with teaching, so it may take a
bit longer this time.

Kind regards,

Johannes


On Fri, May 10, 2013 at 10:12:39AM +1000, Robert King wrote:

Re: R 3 and Debian Testing

Robert King — 2013-05-10T00:12:39

Thanks Johannes!  It's great to be able to combine latest R & stable
debian.

Is your plan to include all the r-cran-* packages currently in stable?

Regards,
Robert


On 10 May 2013 09:52, Johannes Ranke <jranke< at >uni-bremen.de> wrote:


[[alternative HTML version deleted]]

Re: R 3 and Debian Testing

Johannes Ranke — 2013-05-09T23:52:55

Dear Lorenzo,

Am Dienstag, 7. Mai 2013, 18:33:12 schrieb Lorenzo Isella:


Yes, I believe R 3 will enter testing at some point and you will get it this 
way. 

I am currently preparing a wheezy repository on CRAN with R 3.0, so you could 
also use that once it is there. However, at the moment there are r-cran-* 
packages (e.g. r-cran-abind) and other things (e.g. python-rpy2) in jessie 
(testing) that are not compatible with R 3.0, as the versions rebuilt using R 
3.0 have not propagated to testing yet.

Kind regards,

Johannes

Re: R 3 and Debian Testing

Dirk Eddelbuettel — 2013-05-07T16:53:32

On 7 May 2013 at 18:33, Lorenzo Isella wrote:
| 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.

The repository mirrored at every CRAN mirror with base page at 

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

has been at your disposal for at least half a decade.  Thanks to Johannes, R
3.0.0 is only one apt-get update away, and so will R 3.0.1 come May 16 (plus
a few days for compiling and mir

R 3 and Debian Testing

Lorenzo Isella — 2013-05-07T16:33:12

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

Backporting R 3.0.0 to Quantal, Precise, and Lucid

Michael Rutter — 2013-05-04T12:48:08

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).

R 3.0.0 and Raring Ringtail (Ubuntu 13.04)

Michael Rutter — 2013-04-30T01:44:00

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 stil

Re: naming r-base files Ubuntu precise builds

Michael Rutter — 2013-04-29T16:27:09


On 04/29/2013 08:53 AM, Tobias Verbeke wrote:

Tobias,

That "feature" of the naming convention is a function of the process 
used to build the deb packages for Ubuntu.  I use a Launchpad PPA to 
build the binaries, then mirror them to CRAN.  Using Launchpad allows 
for the packages to be built on multiple architectures (386 and amd64 
and others in the future) without me having to maintain all those build 
machines.

The strange naming is one potential downside.  Every once in a while I 
need to upload a release of R twice to the PPA in order to fix a bug. 
Sometimes, this will result in names like you see above.  Once the 
package is built, I cannot fix the names.  However, it should not be 
causing any problems as apt/synaptic should install that as the latest 
version of R.  In my experience, it is only cosmetic and does not effect 
the upgrade process.

Hope this helps,
Michael

naming r-base files Ubuntu precise builds

Tobias Verbeke — 2013-04-29T12:53:27

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.gz02-Mar-2013 14:09 79K 
r-base_2.15.3-1precise0precise1.dsc02-Mar-2013 14:09 2.4K 
r-base_2.15.3-1precise0precise1_all.deb02-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

Re: r-base-core on Ubuntu 13.04 x86_64

Dirk Eddelbuettel — 2013-04-29T11:55:37

On 29 April 2013 at 11:42, Rune Juhl wrote:
| r-base-core 3.0.0-2raring2 (among other packages) is only available
| for i386 at the moment. Will the repo be updated in the "nearest"
| future? Is there a problem compiling v3 on x86_64?

Yes. All architectures supported by these builder should provide binaries
if and when they had a chance to catch up.

In the meantime just point to the quantal variant. I have R 3.0.0 from
those on 32 and 64 bit Ubuntu.

There was an issue with tcl/tk under raring which needed a different
Build-Depends which is why these are a little behind.  

But it all should catch up.  Michael is doing a very nice job with these
rebuilds based on my Debian packages, and I am a heavy user of this myself.

Dirk

Re: r-base-core on Ubuntu 13.04 x86_64

Michael Rutter — 2013-04-29T11:43:18


On 04/29/2013 05:42 AM, Rune Juhl wrote:

Rune,

I had one small configuration error in my CRAN setup.  The amd64 builds 
will appear in the next mirror sync on CRAN.  If you need those deb 
packages now, head over to the Launchpad PPA:

https://launchpad.net/~marutter/+archive/rrutter

Thanks for finding my error,
Michael