[BioC] Library installation: odd error

[Michael Bauer]

On 7/12/2011 4:06 PM, Steve Lianoglou wrote:
> Hi Michael,
>
> On Tue, Jul 12, 2011 at 3:47 PM, Michael Bauer<mjbauer at eecs.tufts.edu>  wrote:
>> I am a system administrator at a site with several R users.  In response to
>> a previous set of questions, we were encouraged to have individual users set
>> up R library directories in their home directories and use the R environment
>> variables to direct R to put auto-installed libraries there.
>>
>> However, we've run across one consistent problem: the library that prompted
>> this whole string will not install on Linux.  (It installs just fine in R on
>> Windows.)  When presented with a writable library directory to install into,
>> it the installation invariably fails with the error:
>>
>> Error in ret[i, ]<- c(pkgs[i], lib, desc) :
>>   number of items to replace is not a multiple of replacement length
> I'll cut here.
>
> This has happened to me recently. Any time I tried to install
> *anything* I would get this error.
>
> So, first question: is it only when you try to install a particular
> package that this happens, or are all package-installs now hosed?
>
> I'm going to assume that all package installs are not working.
>
> This error was happening to me because there is a package that is
> *already* installed in the system which is "corrupt". I had installed
> a library that "hand crafted" its own installation, and I guess the
> meta-data that R requires a package to have has changed over time
> causing this custom-installed-package to trip things up.
>
> The details of my situation and how I fixed it are here:
> http://thread.gmane.org/gmane.comp.ai.machine-learning.shogun/2020
>
> The details of your problem are likely different -- but maybe this
> will help you find the offending package (if one exists)?
>
> Is there some package that was installed in a non-traditional manner?
>
> If you compare the output of `installed.packages()`[*] between your
> linux and windows install, you can find which packages are installed
> on the linux machine and not the windows machine that might be causing
> these problems.
>
> HTH,
>
> -steve
>
> [*] you probably want to use `installed.packages()[,1]` since the
> object returned from the function call is a matrix.

So far as I know, I'm the only one who would have altered our 
system-wide installation of R, and I've followed installation 
instructions on each occasion.  I'll check out the one that caused you 
havoc (sg) as we also have that one installed, but the datestamp on it 
is from 2009, and we've successfully installed quite a bit since then.

That datestamp, on the other hand, makes me suspect that several of our 
R libraries are significantly out of date.  As a simple check, I'm 
building R from scratch in an alternate directory and will see if it can 
handle installs.

One question: is there any R configuration directory that I should be 
looking in for environment changes, or is everything handled through 
environment variables in the appropriate shell configuration?

MJB