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how to get old packages to work on R 2.12.1

4 messages · Joseph Boyer, Marc Schwartz, Joshua Wiley +1 more

Marc Schwartz
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On Jan 19, 2011, at 9:49 AM, Joseph Boyer wrote:

            

      
      
      
    

        
The burden of determining when and how you update R and any contributed packages is on you, not the R Core developers. R's SDLC is well known and is also documented in:

  http://www.r-project.org/doc/R-FDA.pdf

Specifically as it pertains to contributed packages, the total burden is on the package authors/maintainers to keep their packages up to date with  R as new versions are released. If a new version of R "breaks" an old package as a result of core functionality changes, then the contributed package authors and maintainers have been remiss in not keeping up to date with R's development process, since such changes are announced well in advance and beta releases of R are made available for testing prior to release. 

There is no absolute guarantee that a contributed package will work for all future versions of R. A package maintainer may elect to stop maintaining the package at any time, by choice or otherwise. We are all volunteers and mortal...

Frankly, that is no different than if you were using a commercial package with third party contributed functionality.

You don't indicate what OS you are running on, but according to CRAN, deSolve is available in both source and binary package form:

  http://cran.us.r-project.org/web/packages/deSolve/index.html

for current versions of R. 

With respect to yags, AFAICS, it is not on CRAN, but on R-Forge:

  https://r-forge.r-project.org/R/?group_id=329

which means that you may need to contact the package maintainer regarding whether or not his package is being actively maintained and available for your unstated OS and perhaps why it is not on CRAN, which would improve availability. The tests on R-Forge would seem to suggest that it is working with 2.12.1.

The general solution may be as simple as running update.packages(...) depending upon your OS. If on Windows, see:

  http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f

That being said, in general, it is best to cleanly install both a new version of R and the associated contributed packages that you require.

HTH,

Marc Schwartz

  
  


  


      

    

    

      
      

        


  

        

      Joshua Wiley
    

    

      
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Dear Joe,

        
On Wed, Jan 19, 2011 at 7:49 AM, Joseph Boyer <joseph.g.boyer at gsk.com> wrote:

            

      
      
      
    

        
This is not an option for your current problem, but if backwards
compatibility is important, keep backups.  I borrowed this idea from
Debian which has stable and unstable versions.  The stable ones are
"frozen"---no more updates are done (not 100% true, but that is the
gist).  R is very well behaved about having multiple installs, so I
typically install new versions in a new directory and then install all
my packages again (I keep an R script for this).  Once I am satisfied
that everything I want to do works in the latest and greatest version
of R + updated packages, I can delete the old versions, otherwise, I
just keep both.  Storage is available cheaply (< .05 USD per
gigabyte), so unless you're installing all of CRAN, it should not cost
much to keep duplicates.

            

      
      
      
    

        
I do not believe that packages are invalidated because of their
version.  There are instances where old code no longer works, and some
newer packages may also require more modern versions of packages
because either the package maintainers know the older package versions
do not work as they want, or they are unsure and unwilling to deal
with the hassle.  In any case, everything I have seen suggests that
the R core team is very aware of compatibility issues and does as much
as possible to keep R core stable and compatible.  There have been
quite a few discussions on the R-devel list about new features etc.
that invariably include a discussion of what the ramifications of
change would be and whether or not it is justified.

            

      
      
      
    

        
I think many would, do, and will.  Improvement and progress
necessitate change (I suspect most developers are thrilled not to be
stuck using paper tape in batch mode [and my sincerest condolences to
those who still fondly remember and lament the loss]).  The R core
team is very good about giving advance warning and providing R-devel
before it is officially released which allows software developers to
start working with the new code and updating their programs if
necessary before the latest version of R is rolled out to general
users.

I know it is frustrating and a hassle when something that used to work
stops (I currently work with Windows 7 x64, Windows XP x32, and Debian
unstable---trying to keep all three up-to-date and working similarly
keeps me on my toes and if half the things I've muttered under my
breath about computers at 2am actually came to pass.....), but also
consider that the R core team already freely volunteer their time and
(vast) skill to provide us this wonderful software.  I do not think it
is too much to ask that software developers and users be willing to
put in some of their own time to update when there are changes and
improvements to R that are, ultimately, benefiting us anyways.  If it
is truly too much bother and hassle for minor improvements, it may be
better to only upgrade R versions at major releases (1, 2, 3, etc.).
My school seems to have taken this approach and still has 1.8.1, I
think, loaded on their lab computers.

My $.02 (or$.05)

Sincerely,

Josh

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Robert Baer
    

    

      
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Did you do:
update.packages(checkBuilt=TRUE)

Rob
--------------------------------------------------
From: "Joshua Wiley" <jwiley.psych at gmail.com>
Sent: Wednesday, January 19, 2011 11:43 AM
To: "Joseph Boyer" <joseph.g.boyer at gsk.com>
Cc: <r-help at r-project.org>
Subject: Re: [R] how to get old packages to work on R 2.12.1