Thanks for your amazingly fast reply, Heidi! ...


On Mon, Dec 8, 2008 at 2:57 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:

> Hi Joseph
>
> > I can't find consistent or complete documentation on how to set up a
> > config
> > file for communicating with a local ensembl database using exonmap.  The
> R
> > help page for xmapConnect says that the function uses a file called
> > "databases.txt", and points me to the package installation instructions
> to
> > find out how to set it up.  But the package (exonmap_1.0.07.tar.gz)
> > installation instructions only talk about config files called, for
> > example,
> > "human.mycnf", and refer to example configuration files available at
> > http://xmap.picr.man.ac.uk, which I can't find.
>
> First of all, you'll want to update your exonmap package! The current
> version is something like 2.0.01, and it's undergone fairly extensive
> changes. One of those changes is how to connect to the database. It used
> to be via an "human.mycnf" file in earlier versions of exonmap, but this
> has now been replaced by "databases.txt". An example is given in
> INSTALL.pdf at
> http://www.bioconductor.org/packages/2.3/bioc/html/exonmap.html


Yikes!  I was looking at an old documentation page <smacks forehead> ... but
I *do* have exonmap 2.0.0 installed.  Thanks for the heads-up.  I altered my
"databases.txt" file to be:
name    species    db.name    type    host    port    username    password
"Human"    "human"    "homo_sapiens_core_50_36l"    "core"    "
tao.genomecenter.ucdavis.edu"    ""     "<ASK>"    "<ASK>"

and now:

> xmapConnect()
Select a database to connect to:

1: Human ('homo_sapiens_core_50_36l')

Selection: 1
username:***
password:***
Error in mysqlNewConnection(dbDriver(drv), ...) :
  Argument client.flag must be an integer value
*
*
... but the client.flag value is hardcoded into the function, right? ... I
was also getting a warning about R_XMAP_CONF_DIR not being set ... I set it
and the warning went away, but no change in the above error ...
traceback and sessionInfo:

> traceback()
9: stop("Argument client.flag must be an integer value")
8: mysqlNewConnection(dbDriver(drv), ...)
7: is(object, Cl)
6: is(object, Cl)
5: .valueClassTest(standardGeneric("dbConnect"), "DBIConnection",
       "dbConnect")
4: dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = a[5],
       client.flag = "196608")
3: FUN(newX[, i], ...)
2: apply(dbs, 1, function(a) {
       port <- a[6]
       if (is.na(port)) {
           con <- dbConnect("MySQL", user = un, password = pw, dbname =
a[3],
               host = a[5], client.flag = "196608")
       }
       else {
           con <- dbConnect("MySQL", user = un, password = pw, dbname =
a[3],
               host = a[5], port = port, client.flag = "196608")
       }
   })
1: xmapConnect()

and ...

> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] exonmap_2.0.0      RMySQL_0.7-2       DBI_0.2-4
RColorBrewer_1.0-2
[5] genefilter_1.22.0  survival_2.34-1    affy_1.20.0
Biobase_2.2.1

loaded via a namespace (and not attached):
[1] affyio_1.10.1        annotate_1.20.1      AnnotationDbi_1.4.2
[4] preprocessCore_1.4.0 RSQLite_0.7-1


Thanks again,
~Joe




-- 
Joseph Fass
Bioinformatics Programmer
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

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