I used R version (2.5.0) . I want to install GO.db but it gives error like

> source("http://bioconductor.org/getBioC.R")
Error in value[[3]](cond) : could not find function "numeric_version"

> source("http://bioconductor.org/biocLite.R")
Error in get(x, envir, mode, inherits) : variable ".BioC_version_associated_with_R_version" was not found

If i install R version(2.7.0) and install GO.db. I gives error after loading the GO.db

library(GO.db)
Error:
>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)'.
>Error: package 'DBI' required by 'AnnotationDbi' could not be found

I need to use older version of R version (2.5.0) with GO.db.

1. How can I install GO.db with older version of R?
2. Is there any better way to install older GO.db packages with new version of R? Please Help.

From the release announcements, it seems that R-2.5 (from 2007) was associated with Bioconductor 2.0. There is no 'GO.db' in that release, only 'GO'. The old version of GO will not work with current R / Bioconductor packages.

The relevant repositories are

repos = c(
    "http://cran.r-project.org",
    "http://bioconductor.org/packages/2.0/bioc",  
    "http://bioconductor.org/packages/2.0/data/annotation", 
    "http://bioconductor.org/packages/2.0/data/experiment", 
    "http://bioconductor.org/packages/2.0/extra")

So you might try, in R-2.5,

install.packages("GO", repos=repos)

Replace 2.0 with 2.2 in the repos for R-2.7, where there now a package GO.db.

If you're aiming for long-term reproduciblity, I think the only hope (and it does no good retrospectively) is to archive a system image of the original software installation.