[R] linux gplots install unhappy

[Prof Brian Ripley]

On Tue, 20 Feb 2007, Marc Schwartz wrote:

> On Tue, 2007-02-20 at 10:17 -0800, Randy Zelick wrote:
>> Hello all,
>>
>> I use R on both windows and a "mainframe" linux installation (RedHat
>> enterprise 3.0, which they tell me is soon to be upgraded to 4.0). On
>> windows I installed the package gplots without trouble, and it works fine.
>> When I attempted to do the same on the unix computer, the following error
>> message was forthcoming:
>>
>>
>>
>>
>> downloaded 216Kb
>>
>> * Installing *source* package 'gplots' ...
>> ** R
>> ** data
>> ** inst
>> ** preparing package for lazy loading
>> Loading required package: gtools
>> Warning in library(pkg, character.only = TRUE, logical = TRUE, lib.loc =
>> lib.loc) :
>>           there is no package called 'gtools'
>> Error: package 'gtools' could not be loaded
>> Execution halted
>> ERROR: lazy loading failed for package 'gplots'
>> ** Removing '/n/fs/disk/resuser02/u/zelickr/R/library/gplots'
>>
>> The downloaded packages are in
>>          /tmp/RtmpikM2JW/downloaded_packages
>> Warning messages:
>> 1: installation of package 'gplots' had non-zero exit status in:
>> install.packages("gplots", lib = "~/R/library")
>> 2: cannot create HTML package index in:
>> tools:::unix.packages.html(.Library)
>>
>>
>>
>> Can someone provide the bit of information I need to progress with this?
>>
>> Thanks very much,
>>
>> =Randy=
>
> gplots has a dependency on other packages (gtools and gdata).
>
> Thus, when you install it use:
>
>  install.packages("gplots", dependencies = TRUE, ...)
>
> That will download and install the other packages as well.
>
> There should have been a similar requirement under Windows, so not sure
> what may have been different there, unless there is some confounding due

You don't need gtools to install a binary package, just to use it!
I suspect the menu was used on Windows, where dependencies = TRUE is the 
default.

Come 2.5.0 this sort of query will go away, as the essential dependencies 
become the default on all platforms.

> to your not installing the packages in standard locations, given some of
> the output above. I presume that this is because you don't have root
> access on the Linux server and you are installing to your local user
> path.
>
> HTH,
>
> Marc Schwartz
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595