[BioC] specifications for exonmap database config file?

[Crispin Miller]

Hi,
I've just updated exonmap to version (2.0.03; 2.1.03 devel), which should
fix this. Thanks for pointing it out...
Crispin
 


On 09/12/2008 18:41, "Joseph Fass" <joseph.fass at gmail.com> wrote:

> 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;L
> C_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 at 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 at 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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