Hi Heidi,

Thanks again for your responsiveness.  I haven't tried v2.0.02; instead I
had some help, and changed those lines in the xmapConnect code (see below)
before installing 2.0.01 again, and I no longer have a problem (I can
connect to my local copy of the database, and do analysis, etc.).  The port
was not a problem if I left its field in "databases.txt" as "" ... (and 3306
is the correct default for me) ... maybe this was only not a problem because
there was a correct default to rely on, but in the case of client.flag, it
was hardcoded into the function, and not interpreting the double quotes
correctly (??)

Did you mean a more recent sessionInfo?  Did you get the sessionInfo and
traceback results I replied with previously?  sessionInfo now says:

> 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_2.0.01     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

~Joe







On Tue, Dec 9, 2008 at 10:11 AM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:

> 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)
>
>
>


-- 
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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