Entering edit mode
Hello;
I recently upgraded to R 3.2.0 and yet R seems to revert back to an older version of Bioconductor 2.13. I am trying to get Bioc 3.1 installed which is to my understanding what pairs with the new R version that I have.
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> version$version.string [1] "R version 3.2.0 (2015-04-16)"
However if I try the below, I am successful in installing Bioc 3.0 (which is a good fix for nw, but ideally I would like 3.1)
> remove.packages("BiocInstaller")
> biocLite("BiocUpgrade")
Would you like to use a personal library instead? (y/n) y
I thought maybe it has to do with my library paths, so I have that here and my sessionInfo() for after Bioc 3.0 is installed.
> .libPaths() [1] "/home/mistrm82/R/x86_64-pc-linux-gnu-library/3.2" "/usr/local/lib/R/site-library" [3] "/usr/lib/R/site-library" "/usr/lib/R/library"
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.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
If anyone has any thoughts on this, your help would be much appreciated. Thank you,
Meeta
Looks like you upgraded to 3.2.0 and had an old (Bioconductor 2.13) version of BiocInstaller installed.
Seems like you were on the right track when you uninstalled BiocInstaller. Does that work in R-3.2.0?
remove.packages("BiocInstaller") source("http://bioconductor.org/biocLite.R")?
I think that, although the package is removed, the code from the package is still available. Remove the package and restart R.
So I have tried all of the above. When I remove BiocInstaller and then source('http://bioconductor.org/biocLite.R'). I get the following error;
Error in utils::packageVersion("BiocInstaller") : package ‘BiocInstaller’ not foundIf I restart R after removing the package.and I source, I get the following. It's very weird that it keeps going back to Bioc2.13 - I thought maybe it was installing via the other libPaths but when I try removing BiocIntsaller and specifying the other paths the package is not found.
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for helpWhen you restart R (after removing BiocInstaller), try restarting as follows:
R --vanillaDoes that work?
It's also possible that you have more than one copy of BiocInstaller installed in different library locations. After starting R with
R --vanilla, repeat the commandremove.packages("BiocInstaller")until it says there is no such package. If you get a different error, it may be suggesting that it can't remove BiocInstaller due to insufficient permissions. So you could try running R as root:sudo R --vanilla.I've tried it from R --vanilla and removed it until it says no such package. When I source I get Bioconductor 2.13 temporarily loaded. Same as before...
source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for helpThanks so much for all your help so far. I have found another copy of BiocInstaller at
/usr/local/lib/R/site-library/BiocInstaller/<font face="monospace">How should I go about removing that? </font>
Please post your
sessionInfo()as it is before doing thesource()command. Something weird is going on.Hi,
for me just a log out from the R-shell after
remove.packages("BiocInstaller")
and then a log in resolve this issue
arnome