[STATSGRASS] Re: Connecting to databases on Windows using R
Teague O'Mara
Teague.Omara at asu.edu
Thu Mar 17 17:59:12 EST 2005
I followed the directions from bioconductor FAQ/Windows section and using
getBioC was able to get Rbdi again, but RdbiPgSQL isn't appearing (or
Rdbi.PgSQL). It will open the site and load everything else that I want/need,
but RdbiPgSQL isn't to be found.
R returns the message:
Unable to locate the requested package(s) in any known repository
getBioC("database") should be loading Rdbi and RdbiPgSQL, but when I try to call
them up through R, Rdbi will work, but RdbiPgSQL isn't in the library.
Using install.packages2("RdbiPgSQL") gets the same response: it can't find the
package.
I also tried to install RMySQL, which is supposed to be supported for R on
Windows, but isn't in the CRAN repository.
Teague
Quoting Craig Aumann <caumann at ualberta.ca>:
> What the heck is install.packages2?? And where does one get it?
>
> On Thu, 2005-03-17 at 15:14, Markus Neteler wrote:
> > OK, found something:
> >
> > install.packages2("Rdbi")
> > install.packages2("RdbiPgSQL")
> >
> > seems to do the trick (was looking at getBioC.R).
> >
> > Then I also found:
> > http://www.bioconductor.org/data/downloading.html
> >
> > I'll update my docs tomorrow after another test (or your
> > confirmation).
> >
> > Markus
> >
> > On Thu, Mar 17, 2005 at 01:54:10PM -0700, Craig Aumann wrote:
> > >
> > > Well I'm curious to know what R on Windows actually does with the
> > > following commands:
> > >
> > >
>
install.packages(contriburl="http://www.bioconductor.org/repository/devel/package/Source/","Rdbi")
> > >
>
install.packages(contriburl="http://www.bioconductor.org/repository/devel/package/Source/","RdbiPgSQL")
> > >
> > > Does it successully install the packages, or complain loudly?
> > >
> > >
> > > On Thu, 2005-03-17 at 13:30, Markus Neteler wrote:
> > > > Hi
> > > >
> > > > (for me) it's strange that Rdbi doesn't appear on CRAN but
> > > > I was already notified once not to discuss Rdbi questions on
> > > > the R Mailing lists... (so better to ask here :-)
> > > >
> > > > Anyway, I have compiled some usage instructions here:
> > > > http://grass.itc.it/statsgrass/r_and_dbms.html
> > > > which should be more or less still valid.
> > > >
> > > > Maybe a bit helpful, also comparing speed of Rdbi and RODBC.
> > > > However, it doesn't cover MS-Win installation...
> > > >
> > > > Best
> > > >
> > > > Markus
> > > >
> > > > On Thu, Mar 17, 2005 at 11:33:02AM -0700, Craig Aumann wrote:
> > > > > See Teague's question below. As a linux person, I don't know
> the answer
> > > > > to this so am forward this message to the list.
> > > > >
> > > > > Having looked also at http://www.bioconductor.org/ - which
> links off of
> > > > > the main R web page, I see a Windows version of Rdbi (click
> "What is
> > > > > Bioconductor" and scroll down till you find the heading:
> "Database
> > > > > Interaction"). I'm seeing a RDBI for Windows, but no windows
> version of
> > > > > RdbiPgsql which is a problem!
> > > > >
> > > > > Have you tried sending a message to the R-Help list about this -
> how do
> > > > > windows users access PGSQL databases from R? (R website ->
> mailing
> > > > > lists.)
> > > > >
> > > > > On the CRAN site, just searching databases, I saw the
> following:
> > > > > DBI, RMySQL, RODBC, ROracle. Not sure if windows versions exist
> for any
> > > > > of these.
> > > > >
> > > > > Also have a look at the links in
> > > > > http://cran.r-project.org/doc/manuals/R-data.html .
> > > > >
> > > > > Afraid that's all I know about attaching to Databases on Windows
> - which
> > > > > ain't much I'm afraid.
> > > > >
> > > > > Cheers!
> > > > > Craig
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Thu, 2005-03-17 at 10:40, Teague O'Mara wrote:
> > > > > > Hi Craig. I came back across this email from awhile ago. I'm
> attempting to
> > > > > > look at cluster of points in GRASS and have been using the
> script that Michael
> > > > > > Barton wrote, but I'd like to look at a few other things and
> it seems that using
> > > > > > R and my GRASS data will be much easier. I have been using R
> for basic
> > > > > > statistics, but am far from being fluent with it. If you have
> a moment, can you
> > > > > > help me out with some R issues? I'm using an XP machine with
> R 2.0.1.
> > > > > >
> > > > > > I'm having a problem downloading and installing Rdbi and
> RdbiPgSQL. I can't
> > > > > > find these two sets, or any SQL interface that will download
> from CRAN. I was
> > > > > > able to download these directly from sourcforge (tar.gz
> format), but I'm not
> > > > > > sure what to do with them now. Is it an issue with this
> version of R?
> > > > > >
> > > > > > Thanks for any help you can offer.
> > > > > >
> > > > > > Cheers--
> > > > > > Teague
> > > > > >
> > > > > >
> > > > > >
> > > > > > Teague O'Mara
> > > > > > Department of Anthropology
> > > > > > Arizona State University
> > > > > > Box 872402
> > > > > > Tempe, AZ 85287-2402
> > > > > > 480.965.6213
> > > > > >
> > > > > >
> > > > > > Quoting Craig Aumann <caumann at ualberta.ca>:
> > > > > >
> > > > > > > In glancing at your script, I wondered why you didn't just
> import the
> > > > > > > stuff into a statistical package like R and then use all
> the
> > > > > > > clustering
> > > > > > > routines it has. See www.r-project.org
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > ## Key commands in R are:
> > > > > > >
> > > > > > > ## Load the packages to access the database, in particular
> the PgSQL
> > > > > > > ##
> > > > > > > database
> > > > > > > require(Rdbi)
> > > > > > > require(RdbiPgSQL)
> > > > > > >
> > > > > > > ## Load some clustering routines
> > > > > > >
> > > > > > > require(cluster)
> > > > > > > require(mclust)
> > > > > > >
> > > > > > >
> > > > > > > ### Connect to the database and read in a points data set
> "jogis"
> > > > > > > ## and read in the dataset "wells_att".
> > > > > > >
> > > > > > >
> > > > > > > conn <- dbConnect(PgSQL(), dbname="jogis", user="caumann")
> > > > > > > wells <- dbReadTable(conn, "wells_att")
> > > > > > > dbDisconnect(conn)
> > > > > > >
> > > > > > > ## Now you can apply any clustering or kernel smoothing
> technique you
> > > > > > > want to the dataset.
> > > > > > >
> > > > > > > If this is of any help, let me know and I can provide more
> details.
> > > > > > > Cheers!
> > > > > > > Craig
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > _______________________________________________
> > > > > statsgrass mailing list
> > > > > statsgrass at grass.itc.it
> > > > > http://grass.itc.it/mailman/listinfo/statsgrass
>
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Teague O'Mara
Department of Anthropology
Arizona State University
Box 872402
Tempe, AZ 85287-2402
480.965.6213
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