Hi Harry.
Thanks for providing the details about the plan. I'll try to take
a look at some of the Open Office documents in the next week. For the
most part, the inter-system interfaces are the same and only the
mechanics are specific to the host.
I hope OO doesn't require that we add _all_ S functions to a menu.
If for no other reason, the user will be overwhelmed. Gnumeric
requires that we register them with the function manager at run-time
which means we can tailor them to the particular session/application.
What one typically wants is a way to tell OO that if it is looking for
a function, ask R does it have that function. There are a variety of
issues about argument types, etc. These aside, what we typically want
to have is a that R is embedded in OO and the R-OO bridge provides a
way to marshall a call from OO to R. And we also want a bi-directional
interface so that R can access the OO sheet, etc. from R functions.
I'll try to briefly address the libR.so issues.
> Some of the (many) things that I do not have a good grasp on are:
> - which R functions are available to the calling app. There is a list of
> functions listed in Chapter 5 of the "Writing R Extensions" doc.
> But there is also a function defined as:
> call_R(char*, long, void**, char**, long*, char**, long, char**);
> which appears to provide access to all R functions. Is this the case?
- If we have a routine that is responsible for marshalling all calls
from OO to R, we can have it use call_R or alternatively construct and
evaluate an R expression directly in C code. If you look in the
RGnumeric.c file and specifically at the routine
RGnumeric_fixedArgCall(), you'll see an example of the marshalling
routine. This is a more explicit and flexible version of call_R()
and will do error handling correctly!
>
> - how do R and optional R packages (such as Bioconductor) interact via
libR.so?
- If you think of libR.so as simply being a way to embedd R into
another application (just like we can load a library into R), then
that version of R inside a host application runs exactly as it would
as a stand-alone. One loads any [optional] R package using the
library() function in R and the R engine will take care of all the
details, e.g. loading the .so/.dll for that library, the S code, etc.
The only important thing is that packages in which the C/Fortran code
use routines in R must be installed after R has been built with
libR.so enabled. This is the default when R is configured with the
--enable-R-shlib option and packages are subsequently installed. Any
package installed before R was built as a shared library may not work.
>
> - Do all optional packages have to be defined when building libR.so? (this
> doesn't sound right) Or if not, how is libR.so informed that it has to
load an
> additional package?
No. They can be installed whenever needed.
Somebody will have to tell R to load that additional package when it
is needed. This can be done either in the startup script for R
(i.e. Rprofile) or by the "user" of OO. Typically, you will add a
function to OO that will load the relevant R packages. This function
is your OO wrapper to the R functionality.
>
> - Is this process integral to the runtime so that once Bioconductor or
other
> package is installed via 'R INSTALL ..', libR.so can access them
just like R?
Yes. R and libR.so are almost exactly the same. From one point of
view, the difference is how they start - R is a stand alone
application that starts itself; libR.so is started by some other
application.
This should be very interesting. I'll try to find some time to read
the OO docs and help out.
D.
Harry Mangalam wrote:> Hi All,
>
> A group of about 3-4 of us are looking into the possibility of
incorporating R
> into OpenOffice's (OO) spreadsheet component (sc) . We wish to use
OO's nice
> ODBC ability to query a postgresql-based gene expression database thus
> populating an OO sc and then use Bioconductor via R to analyse
user-selected
> parts of this spreadsheet.
>
> We've looked at and compiled and used RGnumeric (with Duncan's
help) to see
> what's possible under Gnumeric, but AFAIK gnumeric won't have DB
connectivity
> for some time and has neither the finish nor the integration of OO.
>
> We've reviewed quite a few documents that describe the integration
approach and
> while it seems to be a bit complex (mostly due to UNO - OO's CORBA-like
> integration strategy), it seems to be quite doable.
>
> We envision it working ike this:
>
> - build R as a shared lib - libR.so [trivial - the R team has done this for
us]
>
> - use the UNO framework to direct the writing of an IDL that allows libR.so
to
> be linked into the OO sc runtime [time consuming to digest all the docs and
get
> a feel for how to do this, altho there are some introductory docs at:
> http://sc.openoffice.org/addin_howto.html
>
> - write code that will automate the insertion of available R functions into
the
> OO sc menu system. [possibly tricky but mostly tedious..?]
>
> - write the query interface to the database within OO [pretty easy]
>
> Some of the (many) things that I do not have a good grasp on are:
> - which R functions are available to the calling app. There is a list of
> functions listed in Chapter 5 of the "Writing R Extensions" doc.
> But there is also a function defined as:
> call_R(char*, long, void**, char**, long*, char**, long, char**);
> which appears to provide access to all R functions. Is this the case?
>
> - how do R and optional R packages (such as Bioconductor) interact via
libR.so?
>
> - Do all optional packages have to be defined when building libR.so? (this
> doesn't sound right) Or if not, how is libR.so informed that it has to
load an
> additional package?
>
> - Is this process integral to the runtime so that once Bioconductor or
other
> package is installed via 'R INSTALL ..', libR.so can access them
just like R?
>
>
>
> --
> Cheers, Harry
> Harry J Mangalam - 949 856 2847 (v&f) - hjm@tacgi.com
> <<plain text preferred>>
>
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