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Ubuntu Lucid, R 2.14.2, and ggplot2

13 messages · Scott Smith, Michael Rutter, Kingsley G. Morse Jr. +3 more

Original
Scott Smith
# 
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"
Dirk Eddelbuettel
#
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You would need to uninstall r-cran-proto, which seems outdated.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
Michael Rutter
#
On 03/22/2012 03:02 PM, Scott Smith wrote:
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

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Kingsley G. Morse Jr.
    

    

      
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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

  
  


  


      

    

    

      
      

        


  

        

      Scott Smith
    

    

      
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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:

        

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Scott Smith
    

    

      
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So I did:
sudo apt-get install r-cran-proto

And it appears to be "on the latest version".

I could go the "install.packages" route, but was trying to stick with the cran2deb packages as the rest of our system uses those.  Is the cran2deb system just untrustworthy at this point?  It seems to be re-built every evening.

        
On Mar 22, 2012, at 2:15 PM, Dirk Eddelbuettel wrote:

        

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Scott Smith
    

    

      
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Yeah, it seems like maybe the cran2deb stuff is not quite ready for prime time?

It's a shame because we are making .deb packages for everything we develop internally, and I'd like to be able to indicate where R or some subset of it is a dependency.

        
On Mar 22, 2012, at 2:21 PM, Kingsley G. Morse Jr. wrote:

        

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 22 March 2012 at 12:21, Kingsley G. Morse Jr. wrote:

        
| 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.

You need to carefully think through /which distro version/ with which release
cycle you want.

I keep what I maintain (R itself, dozens of r-cran-* package /very current/
but that goes into Debian unstable, and then after a few days into Debian
testing.  "Testing" is a good compromise.

Debian stable does only get much less infrequently.  As "stable" means no updates.

Ubuntu is somewhere in the middle.

Now, cran2deb (as in Michael's cran2deb4ubuntu or the new debian-r.debian.net
by Don) is orthogonal to both.

Dirk

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

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 22 March 2012 at 14:53, Scott Smith wrote:

        
|

        
| On Mar 22, 2012, at 2:15 PM, Michael Rutter wrote:

        
|

        
| > 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 I'm new to R packaging.  
| 
| If this works (It's still running for me, but others have done this and reported it works using the /usr/bin/R 2.14.2):
| R_LIBS=$HOME/myR R -e 'install.packages('ggplot2', dep = TRUE, lib="/gscuser/ssmith/myR", repos="http://cran.us.r-project.org")'
| 
| Why does cran2deb make a package (daily?) which is incompatible?
| 
| 
| > 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?
| 
| I got it here:
| http://bioinformatics.rri.sari.ac.uk/cran2deb/rep/dists/testing/main/binary-amd64/
| 
| I also installed it from this server a few days ago, but the server went away, then came back again today with a different repo name, which did not exist.  This page is now down again.
| http://debian.cran.r-project.org
| 
| 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.

In case you use Ubuntu, stick to Michael's cran2deb4ubuntu.

Do not mix Debian and Ubuntu.

Dirk

| 
| It's a shame because we are funded to release our bioinformatics pipelines, and they are all carefully Debian packaged.  I can make a big blob of R_LIBS for each one of them instead of specifying R modules as dpkg dependencies, but it feels like a terrible hack.
| 
| 
| > 
| > 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
| > 
| > _______________________________________________
| > R-SIG-Debian mailing list
| > R-SIG-Debian at r-project.org
| > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
| 
| 	[[alternative HTML version deleted]]
| 
| 
| ----------------------------------------------------------------------
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

  
    

      
      
    

  


  


      

    

    
3 days later

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Dear Dirk, dear all,

            

      
      
      
    

        
This indeed looks nice - I wonder how hard it would be to make the Debian 
stable/squeeze variant work...

Kind regards,

Johannes

            

      
      
      
    

        
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      Don Armstrong
    

    

      
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On Mon, 26 Mar 2012, Johannes Ranke wrote:

            

      
      
      
    

        
I need to fix a few things, and then I will be doing the rebuilds for
stable too. Probably two weeks or so.


Don Armstrong

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Don,

        
On Tuesday 27 March 2012 00:50:01 Don Armstrong wrote:

            

      
      
      
    

        
This sounds really nice... Looking forward,

Johannes