I can't upgrade BiocInstaller :
root@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
Strangely,
dario@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@bioinfo:~/Documents$ which sudo R
/usr/bin/sudo
/usr/bin/R
dario@bioinfo:~/Documents$ su root
root@bioinfo:/home/dario/Documents# which R
/usr/bin/R
root@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/
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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