[Bioc-devel] Environment/RSqlite db interaction

[James W. MacDonald]

Hi,

I have stumbled upon a weird interaction between the SQlite-based 
annotation packages and the old environment-based packages.

The annaffy package has a function is_dbpackage() that is used to strip 
off the .db at the end of the SQlite packages, using something like this:

tmp <- as.environment(paste("package", chip, sep=":"))
exists("db_conn", tmp)

If a SQlite package is loaded first, this test fails:

 > library(GO.db)
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: RSQLite
 > library(mouse4302)
 > tmp <- as.environment("package:mouse4302")
 > exists("db_conn", tmp)
[1] TRUE

But if the env-based package is loaded first, it works:

 > library(mouse4302)
 > library(GO.db)
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: RSQLite
 > tmp <- as.environment("package:mouse4302")
 > exists("db_conn", tmp)
[1] FALSE

I can get around this behavior for now by remembering to load the envs I 
need to use with annaffy first. However, for end users this won't 
necessarily be an option, and annaffy fails miserably if you load things 
in the 'wrong' order.

Is this something that needs to be fixed in annaffy, or should this test 
reliably detect the difference between an env or SQlite based package?

Best,

Jim

Oh yeah, I almost forgot:

 > sessionInfo()
R version 2.6.0 alpha (2007-09-11 r42820)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
[1] GO.db_1.17.1         AnnotationDbi_0.1.15 RSQLite_0.6-0
[4] DBI_0.2-3            Biobase_1.15.33      mouse4302_1.17.0
[7] rcompgen_0.1-15

---
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623