[Bioc-devel] Rdbi namespace issue

[John Zhang]

>>
>> I just tried loading RbdiPgSQL and then Rdbi and found these errors with
>> Rdbi from the devel repository.  Any ideas on how to fix this?  I'm cc'ing
>> the bioc-devel list in case there is something interesting to be learned
>> from the discussion, given the state of namespaces.

It was fine on my machine but my R is a few days older than yours. I will update 
my R and try again.



>
>Just looking a bit, it seems that Rdbi has this statement in 'zzz.R':
>.onLoad <- function(lib, pkg) {
>  # Changed by JZ from Rdbi.PgSQL to RdbiPgSQL
>  autoload("PgSQL", "RdbiPgSQL")
># autoload("MySQL", "Rdbi.MySQL")
>.....
>
>And in RdbiPgSQL NAMESPACE:
>import(Rdbi)
>
>Is this causing the circular dependency?
>
>
>> > > library(Rdbi) 
>>
>> Loading required package: Rdbi
>> Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
>> keep.source) :
>> 	cyclic name space dependencies are not supported
>> Error: package 'Rdbi' could not be loaded
>> Error: .onLoad failed in 'loadNamespace' for 'Rdbi'
>> Error: package/namespace load failed for 'Rdbi'
>>
>> > sessionInfo()
>>
>> R version 2.4.0 alpha (2006-09-13 r39286)
>> 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=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NA
>>ME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATIO
>>N=C
>>
>> attached base packages:
>> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
>> [7] "base"
>>
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084