R SIG Debian - Mar 2012 - 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"

On 22 March 2012 at 14:02, Scott Smith wrote:
| 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
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

You would need to uninstall r-cran-proto, which seems outdated. But you
can't, as r-cran-ggplot2 depends on it.

The /usr/local/lib/R setup comes to the rescue:  just do a manual

   install.packages("proto")   # or 'R CMD INSTALL proto_*.tar.gz

and you will have a newer, better one /ahead/ of the broken one in your
.libPath.

Dirk



| 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"
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
"Outside of a dog, a book is a man's best friend. Inside of a dog, it
is too
dark to read." -- Groucho Marx

On 03/22/2012 03:02 PM, Scott Smith wrote:
> 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
This was an issue with a bunch of packages when R moved to the 2.14 
series.  A number of packages had to be rebuilt to fix the NAMESPACE issue.

So this is an issue with your r-cran-ggplot2 package.  The problem is I 
am not sure where you are getting the package from.  ggplot2 is not on 
the CRAN Ubuntu pages and my cran2deb4ubutu project does not support 
lucid.  Where are you downloading the r-cran-ggplot2 package from?

Michael

> 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"
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
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

Hi Scott,

I like apt-get and dpkg.

They made administering my Debian box much more
convenient.

However, I was surprised some time ago to see that
Debian's package management technology was failing
to keep up with new releases of R packages.

It seemed to me that R's packages were evolving
faster than Debian's archives were updated.

I had to used R's built in package management
tool.

If I recall correctly, it's named something like
update_package() or update_packages() and
it downloads new R code from CRAN.

If you haven't already considered R's built in
package management, you may want to try it.

I hope that helps,
Kingsley

I realize my last mail lacked an explicit question: Does anyone on this list
know why this fails?

We have Ubuntu Linux on a large compute cluster at The Genome Institute, and
I'm attempting to move people off of a bunch of privately managed R
installations to a single dpkg-based one.

My experience with cran2deb is at less than a week, so I hope you'll forgive
my ignorance.  Any suggestions you have would be appreciated.

Thanks!
Scott

--
Scott Smith
Manager, Application Programming and Development
Analysis Pipeline
The Genome Institute
Washington University School of Medicine

On Mar 22, 2012, at 2:02 PM, Scott Smith wrote:
> 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"
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Don,

On Tuesday 27 March 2012 00:50:01 Don Armstrong wrote:
> On Mon, 26 Mar 2012, Johannes Ranke wrote:
> > Dear Dirk, dear all,
> > 
> > > | Perhaps an indication that this cran2deb stuff is very green?
> > > 
> > > It has been inoperational for years as you could have noticed by
> > > looking at the version numbers of the packages you were getting,
> > > relative to CRAN.
> > > 
> > > Use http://debian-r.debian.net, which is a pretty new, well done
> > > "reboot" of the same idea.
> > 
> > This indeed looks nice - I wonder how hard it would be to make the
Debian
> > stable/squeeze variant work...
> 
> I need to fix a few things, and then I will be doing the rebuilds for
> stable too. Probably two weeks or so.
This sounds really nice... Looking forward,

Johannes
> 
> 
> Don Armstrong