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Question: How to install old version of GO.db in R
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gravatar for animesh_10kuet
17 months ago by
animesh_10kuet0 wrote:

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.

ADD COMMENTlink modified 17 months ago by Martin Morgan ♦♦ 21k • written 17 months ago by animesh_10kuet0
1
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

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.

 

ADD COMMENTlink written 17 months ago by Martin Morgan ♦♦ 21k
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