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Question: Bioconductor 3.0 and old versions with R 3.2.0
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gravatar for Cataphractus
2.5 years ago by
Cataphractus0 wrote:

Hello,

I'm having some problems installing the correct version of bioconductor and upgrading packages.

First, when I run the first command to install bioconductor (source(...)) I get this:

Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help
BiocInstaller version 3.0 is too old for R version 3.2.0;
  remove.packages("BiocInstaller") then
  source("http://bioconductor.org/biocLite.R")
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install

It doesn't matter if I follow the suggested instructions, it always ends like that.

The second command (biocLite()) shows this:

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0.
Old packages: 'AnnotationDbi', 'BiocInstaller', 'GenomeInfoDb'
Update all/some/none? [a/s/n]: 

When I press "a", the packages are downloaded and apparently installed (although Biocinstaller shows the previous message of being too old) but if I run biocLite() again in the same R session or a new one, I'm asked again and again. This only happens with those 3 packages.

When I use biocLite("BiocUpgrade"), the message is:

Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

My version, according to R is:

platform       x86_64-unknown-linux-gnu   
arch           x86_64                     
os             linux-gnu                  
system         x86_64, linux-gnu          
status                                    
major          3                          
minor          2.0                        
year           2015                       
month          04                         
day            16                         
svn rev        68180                      
language       R                          
version.string R version 3.2.0 (2015-04-16)
nickname       Full of Ingredients 

And the sessionInfo:

R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Arch Linux

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
 [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     

other attached packages:
[1] BiocInstaller_1.16.5

loaded via a namespace (and not attached):
[1] tools_3.2.0 tcltk_3.2.0


I ommited the steps where R says it cannot write to "/usr/lib/..." and asks for writing on my personal library located on "~/R/...". Also, I also tried to remove that personal dir to start from zero, restarting the session, the computer... 

What can I do to use the latest packages availables?

Thank you.

ADD COMMENTlink written 2.5 years ago by Cataphractus0

Try starting R like this: R --vanilla before running the remove.packages("BiocInstaller") command.

 

ADD REPLYlink written 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k

Same thing.  Tried with R --vanilla, remove.packages, restarting session (with and without --vanilla flag), source && biocLite. Also without restarting session. 

EDIT: seems I have those packages on /usr/lib/R/library. I'm going to try to remove them with sudo  R --vanilla and see what happens.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Cataphractus0

Well, that was it. Seems like in a previous life I installed bioconductor with root privileges and forgot about it, my fault. Sorry for the trouble and thank you for your help :)

ADD REPLYlink written 2.5 years ago by Cataphractus0

I'm having the same issue it seems. After reading your post, I make the calls R --vanilla, remove.packagessource & biocLite. What do you mean when you say you "have those packages on ...". I understand writing to /usr/lib/R/library is sudo protected. What packages are you talking about? Are you saying remove.packages wasn't actually removing the packages because they were sudo-protected?

ADD REPLYlink written 2.5 years ago by jgbradley10

You could try starting R as root and then removing the packages. Be sure to restart R (as a regular user) before trying to reinstall anything.

ADD REPLYlink written 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k

Just tested that and it seems that indeed, remove.packages() has this wonderful feature that it doesn't say a word when it actually fails to properly remove a package because of insufficient privileges! :-/

H.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Hervé Pagès ♦♦ 13k
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