[Bioc-devel] biocUpgrade Wrongly Infers R Version

[Dan Tenenbaum]

----- Original Message -----
> From: "Dario Strbenac" <dstr7320 at uni.sydney.edu.au>
> To: bioc-devel at r-project.org
> Sent: Monday, April 27, 2015 10:00:10 PM
> Subject: [Bioc-devel] biocUpgrade Wrongly Infers R Version
> 
> I can't upgrade BiocInstaller :
> 
> root at bioinfo:/home/dario/Documents# R
> 
> R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
> Copyright (C) 2015 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>   Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> > source("http://bioconductor.org/biocLite.R")
> Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help
> A new version of Bioconductor is available after installing the most
> recent
>   version of R; see http://bioconductor.org/install
> > biocLite("BiocUpgrade")
> Error: Bioconductor version 3.0 cannot be upgraded with R version
> 3.1.0
> > sessionInfo()
> R version 3.2.0 (2015-04-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.10
> 
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BiocInstaller_1.16.4
> 
> loaded via a namespace (and not attached):
> [1] tools_3.2.0
> 

Start R with "R --vanilla" then

remove.packages("BiocInstaller")
source("http://bioconductor.org/biocLite.R")
useDevel()




> Strangely,
> 
> dario at bioinfo:~/Documents$ sudo R
> R version 3.1.1 (2014-07-10) -- "Sock it to Me"
> Copyright (C) 2014 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
> dario at bioinfo:~/Documents$ which sudo R
> /usr/bin/sudo
> /usr/bin/R
> dario at bioinfo:~/Documents$ su root
> root at bioinfo:/home/dario/Documents# which R
> /usr/bin/R
> root at bioinfo:/home/dario/Documents# R
> R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
> Copyright (C) 2015 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> 



> Also, why does GO.db not appear in the build and check reports ?
> http://www.bioconductor.org/checkResults/release/bioc-LATEST/


Those reports are for software and experiment data packages; GO.db is an annotation package, those do not have build reports.

Unless your question has something to do with package development you should post to

https://support.bioconductor.org

Dan



> 
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> 
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