Hi Joseph,

not sure what your issue is. Can you connect using Crispin's latest  
version? Both v2.0.0 and 2.0.01 works for me; I have my port as "4094"

Can you please provide us with the output of sessionInfo()?

\Heidi

On 9 Dec 2008, at 17:10, Joseph Fass wrote:

> Hi Heidi - it seems that whenever I try to specify 3306 in the  
> "databases.txt" file, I get this error message:
>
> > xmapConnect()
> Select a database to connect to:
>
> 1: Human ('homo_sapiens_core_50_36l')
>
> Selection: 1
> Error in mysqlNewConnection(dbDriver(drv), ...) :
>   Argument port must be an integer value
>
> ... this occurs whether I put double quotes around 3306 or not (all  
> other values - not headings - in "databases.txt" have double quotes  
> around them).
>
> Did Crispin's message mean that he fixed this particular issue?   
> Why might I be having this issue, whereas I'm assuming other people  
> have been using 2.0.01 successfully?
>
> ~Joe
>
> PS - I'm not very familiar with R's internals, but I went looking  
> for the xmapConnect function, because I could run the particular line:
> con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3],  
> host = a[5], port = port, client.flag = "196608")
> ... if I changed it to:
> con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3],  
> host = a[5], port = port, client.flag = 196608)
> but apparently function code isn't stored in plain text ...
>
> UPDATE: with the help of someone more competent, we removed the  
> quotes from 196608 in the package before re-installing, which fixed  
> my issue ... I'm guessing this is what Crispin changed?
>
>
>
>
>
>
>
>
> On Mon, Dec 8, 2008 at 11:31 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:
> Hi Joseph,
>
> quick question; do you get the same error message when you specify  
> which
> port to use in your databases.txt file? In your first email you  
> used 3306,
> does that still apply?
>
> \Heidi
>
> > Just wanted to add that I noticed I had exonmap 2.0.0, ... so I  
> installed
> > 2.0.01, and am seeing the same error:
> >
> >
> >> > 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
> >>
> >
> >
> > --
> > Joseph Fass
> > Bioinformatics Programmer
> > UC Davis Bioinformatics Core
> > joseph.fass -at- gmail.com (professional)
> > 970.227.5928 (c)  ||  530.752.2698 (w)
> >
>
>
>
>
>
> -- 
> 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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