Question: How to install old version of GO.db in R
0
gravatar for animesh_10kuet
2.7 years 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.

R go.db • 794 views
ADD COMMENTlink modified 2.7 years ago by Martin Morgan ♦♦ 23k • written 2.7 years ago by animesh_10kuet0
Answer: How to install old version of GO.db in R
1
gravatar for Martin Morgan
2.7 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k 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 2.7 years ago by Martin Morgan ♦♦ 23k
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