Re: [Rd] Unable to install R on CentOS 64 bit machine

2008-10-04 Thread Prof Brian Ripley
config.log will tell you what is missing.  But most likely it is X11 
headers/libraries in packages like libX11-devel and libXt-devel.  (Note 
that the R-admin manual does tell you this.)


Real names and proper signature blocks are preferred here.

On Fri, 3 Oct 2008, Shantanu Unknown wrote:



Hi all,
I am unable to install R on CentOS5 64 bit machine.

When I do ./configure
I get the message

"checking for X... no
configure: error: --with-x=yes (default) and X11 headers/libs are not available"

from doing a websearch it seems I need to install x11-xorg. But I  could not 
find it when I did a yum install.

I did  "yum list xorg-x11*" and following is what I get
Could someone tell me which is the missing X11 package I need to install for 
CentOS5?
Thanks a lot for any help.
Shantanu

Installed Packages
xorg-x11-apps.x86_64 7.1-4.0.1.el5  installed
xorg-x11-drivers.x86_64  7.1-4.1.el5installed
xorg-x11-drv-acecad.x86_64   1.1.0-2.1  installed
xorg-x11-drv-aiptek.x86_64   1.0.1-2installed
xorg-x11-drv-ast.x86_64  0.81.0-3   installed
xorg-x11-drv-ati.x86_64  6.6.3-3.13.el5 installed
xorg-x11-drv-calcomp.x86_64  1.1.0-1.1  installed
xorg-x11-drv-cirrus.x86_64   1.1.0-2.fc6installed
xorg-x11-drv-citron.x86_64   2.2.0-1.1  installed
xorg-x11-drv-digitaledge.x86_64  1.1.0-1.1  installed
xorg-x11-drv-dmc.x86_64  1.1.0-2installed
xorg-x11-drv-dummy.x86_640.2.0-2.1  installed
xorg-x11-drv-dynapro.x86_64  1.1.0-2installed
xorg-x11-drv-elo2300.x86_64  1.1.0-1.1  installed
xorg-x11-drv-elographics.x86_64  1.1.0-1.1  installed
xorg-x11-drv-evdev.x86_641:1.0.0.5-3.el5installed
xorg-x11-drv-fbdev.x86_640.3.0-2installed
xorg-x11-drv-fpit.x86_64 1.1.0-1.1  installed
xorg-x11-drv-hyperpen.x86_64 1.1.0-2installed
xorg-x11-drv-i810.x86_64 1.6.5-9.13.el5 installed
xorg-x11-drv-jamstudio.x86_641.1.0-1.1  installed
xorg-x11-drv-joystick.x86_64 1.1.0-1.1  installed
xorg-x11-drv-keyboard.x86_64 1.1.0-3installed
xorg-x11-drv-magellan.x86_64 1.1.0-1.1  installed
xorg-x11-drv-magictouch.x86_64   1.0.0.5-2.1installed
xorg-x11-drv-mga.x86_64  1.4.2-7.el5installed
xorg-x11-drv-microtouch.x86_64   1.1.0-1.1  installed
xorg-x11-drv-mouse.x86_641.1.1-1.1  installed
xorg-x11-drv-mutouch.x86_64  1.1.0-2installed
xorg-x11-drv-nv.x86_64   2.1.6-6.el5installed
xorg-x11-drv-palmax.x86_64   1.1.0-1.1  installed
xorg-x11-drv-penmount.x86_64 1.1.0-2.1  installed
xorg-x11-drv-s3.x86_64   0.4.1-2.1  installed
xorg-x11-drv-s3virge.x86_64  1.9.1-2.1  installed
xorg-x11-drv-savage.x86_64   2.1.1-5.fc6installed
xorg-x11-drv-siliconmotion.x86_641.4.1-2.1  installed
xorg-x11-drv-sis.x86_64  0.9.1-7.1.el5  installed
xorg-x11-drv-sisusb.x86_64   0.8.1-4.1  installed
xorg-x11-drv-spaceorb.x86_64 1.1.0-1.1  installed
xorg-x11-drv-summa.x86_641.1.0-1.1  installed
xorg-x11-drv-tdfx.x86_64 1.2.1-3.1  installed
xorg-x11-drv-tek4957.x86_64  1.1.0-1.1  installed
xorg-x11-drv-trident.x86_64  1.2.1-3.fc6installed
xorg-x11-drv-ur98.x86_64 1.1.0-1.1  installed
xorg-x11-drv-vesa.x86_64 1.3.0-8.1.el5  installed
xorg-x11-drv-vga.x86_64  4.1.0-2.1  installed
xorg-x11-drv-via.x86_64  0.2.1-9installed
xorg-x11-drv-vmmouse.x86_64  12.4.0-2.1 installed
xorg-x11-drv-vmware.x86_64   10.13.0-2.1installed
xorg-x11-drv-void.x86_64 1.1.0-3.1  installed
xorg-x11-drv-voodoo.x86_64   1.1.0-3.1  installed
xorg-x11-filesystem.noarch   7.1-2.fc6  installed
xorg-x11-font-utils.x86_64   1:7.1-2installed
xorg-x11-fonts-100dpi.noarch 7.1-2.1.el5installed
xorg-x11-fonts-75dpi.noarch  7.1-2.1.el5installed
xorg-x11-fonts-ISO8859-1-100dpi.noarch   7.1-2.1.el5installed
xorg-x11-fonts-ISO8859-1-75dpi.noarch   

Re: [Rd] Attributes of top level environments clobbered (was Re: [R] possible bug in function 'var' in R 2.7.2?)

2008-10-04 Thread Gabor Grothendieck
On Sat, Oct 4, 2008 at 10:45 AM, laurent <[EMAIL PROTECTED]> wrote:
>
> On Sat, 2008-10-04 at 12:00 +0200, [EMAIL PROTECTED] wrote:
>> Message: 18
>> Date: Fri, 3 Oct 2008 15:35:18 -0500 (CDT)
>> From: Luke Tierney <[EMAIL PROTECTED]>
>> Subject: Re: [Rd] Attributes of top level environments clobbered (was
>>   Re: [R] possible bug in function 'var' in R 2.7.2?)
>> To: Gabor Grothendieck <[EMAIL PROTECTED]>
>> Cc: "r-devel@r-project.org" ,  Martin Maechler
>>   <[EMAIL PROTECTED]>
>> Message-ID: <[EMAIL PROTECTED]>
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>> On Fri, 3 Oct 2008, Gabor Grothendieck wrote:
>>
>> > On Fri, Oct 3, 2008 at 12:46 PM, Luke Tierney <[EMAIL PROTECTED]> wrote:
>> >> On Fri, 3 Oct 2008, Gabor Grothendieck wrote:
>> >>
>> >>> On Fri, Oct 3, 2008 at 11:43 AM, Luke Tierney <[EMAIL PROTECTED]> wrote:
>> 
> [...]
>> > I do appreciate the excellent R software; however, there are a few points 
>> > like
>> > those addressed on the proto home page which do need to be addressed in R
>> > for it to be fully functional.
>>
>> There are some interesting poins on that page that are worth looking
>> into.  Over time I suspect all but the current 3. will be addressed,
>> but 3., which is a variant on the unclass issue, is not likely to be.
>> You can call this a deficiency in R if you like, and I would agree in
>> the sense that I think it is inappropriate to allow attributes to be
>> set but not in a reliable way because they can be inadvertenly
>> removed.  We should have done this differently.  THere were/are two
>> choices:
>>
>>  Make reference values, including environments, special in that they
>>  may not have attributes. This woud have been fairly easy (modulo one
>>  use made in decorating the frames on the search path) and could be
>>  done now to clean things up.
>>
>>  Make R-visible environments in two parts--a wrapper that is passed by
>>  value like standard R objects and could have attributes, and an
>>  internal part that is essentially the current environment object.
>>  This is analogous to the way that character vectors, even of length 1,
>>  consist of an STRSXP wrapper containing CHARSXPs that hold the string.
>>  The STRSXP's are visible at the R level, the CHARSXPs are not.  This
>>  would have been messier to implement, and unfortunately would be very
>>  messy to retro-fit at this point, so it isn't likely to happen unless
>>  there is some other compelling reason to do so.
>
> Couldn't the two options be merged into one for a start ?
>
> - Make reference values either attribute-free entities (seems important,
> as the "poor reliability" of assigning attributes to environment is
> probably not widely known), or generate warnings upon assignment of
> attributes.

Some specifics need to be added to the "poor reliability" phrase relating to
of attributed environments.  The proto package changes the class attribute
of environments (but no other attribute of environments) and proto in turn
underlies large widely used packages which likely exercise it thoroughly yet
through this experience the only places where this was noticeable were
points #1 and #3 of the Avoiding R Bugs section of the proto home page
at http://r-proto.googlecode.com

Neither of these are two points are deal breakers as

- #1 has an easy workaround (just change one line in your DESCRIPTION file) and
  if the promised fix is made even this won't be necesary,

- #3 mostly seems mostly harmless in the context of proto as the only attribute
  change is from a class of  "enviornment" to c("proto",
"environment").  Artificial
  examples can be constructed where this is a problem but substantial experience
  with it suggests that it is not a problem in practice.

(The remaining R problems listed are all related to promises, not environments.)

>
> - Create an R-level class that contains an environment ("Environment" ?,
> "envobj" ?) and implements an environment-like interface by delegation
> (somehow like your option 2. above).
> Gabor could certainly create his own class, but having this administered
> at the R-core level would have the following potential benefits:
> - Anyone with similar needs will think twice before starting to
> implement his own solution.
> - That one class can be moved to a lower level in the internals
> (C-level, with a new given SEXPTYPE) if it proves a working solution,
> and as time permits.
>
> Just a thought,

Actually, I see the main benefit of this or other approach as
providing the missing
elements of S3 support to environments thereby potentially streamlining the
implementation of every package that needs it (proto, tcltk, R.oo, ...) or more
perhaps more accurately allowing tcltk and R.oo and other such packages to
become as streamlined as proto already is.

Each of these packages could then use inheritance rather than
containment thereby
leveraging the S3 OO facilities that one really expects R