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Question: Problems getting Bioc 3.1 after upgrade to R_3.2.0
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gravatar for meeta.mistry
2.6 years ago by
meeta.mistry10
United States
meeta.mistry10 wrote:

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

 

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by meeta.mistry10

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")

?

 

ADD REPLYlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k

I think that, although the package is removed, the code from the package is still available. Remove the package and restart R.

ADD REPLYlink written 2.6 years ago by Martin Morgan ♦♦ 20k

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 found

If 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 help

ADD REPLYlink written 2.6 years ago by meeta.mistry10

When you restart R (after removing BiocInstaller), try restarting as follows:

R --vanilla

Does that work?

ADD REPLYlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k
2

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 command remove.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 .

ADD REPLYlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k

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 help

 

ADD REPLYlink written 2.6 years ago by meeta.mistry10

Thanks 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>

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by meeta.mistry10

Please post your sessionInfo() as it is before doing the source() command. Something weird is going on.

 

ADD REPLYlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k

Hi,

for me just a log out from the R-shell after

remove.packages("BiocInstaller")

 and then a log in resolve this issue

arnome

ADD REPLYlink modified 20 months ago • written 20 months ago by Arnaud Mounier40
1
gravatar for meeta.mistry
2.6 years ago by
meeta.mistry10
United States
meeta.mistry10 wrote:

I've figured it out, it seems that after removing the package from my personal library R reverts back to an older Bioc installed in /usr/local/lib/R/site-library/`

I removed the directory and then source() which results in in the installation of Bioc 3.1 and all the associated package updates. Thanks so much for all your help!

ADD COMMENTlink written 2.6 years ago by meeta.mistry10
0
gravatar for meeta.mistry
2.6 years ago by
meeta.mistry10
United States
meeta.mistry10 wrote:
Sorry about that, this is the sessionInfo() prior to the source

> 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              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] 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     
> 
ADD COMMENTlink written 2.6 years ago by meeta.mistry10
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