[STATSGRASS] Re: Connecting to databases on Windows using R
Markus Neteler
neteler at itc.it
Thu Mar 17 16:18:09 EST 2005
On Thu, Mar 17, 2005 at 02:11:16PM -0700, Teague O'Mara wrote:
> Craig and Markus:
>
> Just trying it I get the same complaint for both:
>
> trying URL `http://www.bioconductor.org/repository/devel/package/Source//PACKAGES'
> Error in download.file(url = paste(contriburl, "PACKAGES", sep = "/"), :
> cannot open URL
> `http://www.bioconductor.org/repository/devel/package/Source//PACKAGES'
> In addition: Warning message:
> cannot open: HTTP status was `404 Not Found'
>
> Apparently the page has moved, or the packages have been taken off?
the packages *are* there, but they have disabled the nice installation method
somehow. I am googling for > 20min now, to no avail.
http://www.bioconductor.org/repository/devel/package/html/index.html
-> Rdbi -> Source package download
-> RdbiPgSQL -> Source package download
Save to disk. Then first install Rdbi, then RdbiPgSQL.
Ah, for MS-Win you want to grab the .zip files instead.
> Also, Rdbi will load, but I get the following message:
> Loading required package: Rdbi
> [1] TRUE
> Warning message:
> package 'Rdbi' was built under R version 2.1.0
>
> I searched around for a new version of R, but it seems that 2.0.1 is the latest
> version. Or is 2.1 new source code for Linux?
Maybe the maintainer of the package is a bit ahead?
According to http://cran.at.r-project.org/ the version 2.0.1 is current.
Worth a mail to the maintainer of Rdbi/RdbiPgSQL.
Markus
> Teague
>
>
>
>
> Quoting Craig Aumann <caumann at ualberta.ca>:
>
> >
> > 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
> >
> > _______________________________________________
> > statsgrass mailing list
> > statsgrass at grass.itc.it
> > http://grass.itc.it/mailman/listinfo/statsgrass
> >
>
>
>
> Teague O'Mara
> Department of Anthropology
> Arizona State University
> Box 872402
> Tempe, AZ 85287-2402
> 480.965.6213
--
Markus Neteler <neteler itc it> http://mpa.itc.it
ITC-irst - Centro per la Ricerca Scientifica e Tecnologica
MPBA - Predictive Models for Biol. & Environ. Data Analysis
Via Sommarive, 18 - 38050 Povo (Trento), Italy
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