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Question: Problem using BiocUpgrade
0
gravatar for dianmante
3.8 years ago by
dianmante0
United States
dianmante0 wrote:

Hello everybody,

I tried to upgrade all my installed bioconductor packages using BiocUpgrade, but it shows this error:
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

However, I have installed R version 3.1.1. In fact, when I run just biocLite() it recognizes my R version correctly.

Any advice?

Thanks,
Diana

 

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
> biocLite("BiocUpgrade")
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.16.0

loaded via a namespace (and not attached):
[1] tools_3.1.1

ADD COMMENTlink modified 3.8 years ago by Dan Tenenbaum ♦♦ 8.2k • written 3.8 years ago by dianmante0
2

Maybe there's a bit of confusion between 'updating' your packages to the latest available for your version of Bioconductor (which the command biocLite() invoked with no arguments does; maybe your packages are currently up-to-date?) versus 'upgrading' to a new version of Bioconductor (for the current release this would require using the 'devel' version of R; Bioconductor 2.14 could be updated to version 3.0 without changing version of R)?

ADD REPLYlink written 3.8 years ago by Martin Morgan ♦♦ 22k
3
gravatar for Dan Tenenbaum
3.8 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

You are already running the most recent release version of Bioconductor. So you do not need to upgrade.

The only exception would be if you are developing a package or want to use cutting edge features in existing packages. In that case you would want to use the "devel" version of Bioconductor (Bioconductor 3.1). That version only works with R-devel (which will become R-3.2 when it is released next Spring).

So if you want to use Bioc-devel, install R-devel. You can have more than one version of R on your machine.

See this page:

 

http://www.bioconductor.org/developers/how-to/useDevel/

Or perhaps what you are trying to do is just update all your packages to their most recent version within the bioconductor release? If that is the case, just call biocLite() with no arguments.

Dan

 

ADD COMMENTlink written 3.8 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for dianmante
3.8 years ago by
dianmante0
United States
dianmante0 wrote:

Thanks Dan,

That means that this "error" message will show if I have the last version of Bioconductor, right?

So it is normal that I am having the same "error" message when using R-devel because I already have Bioconductor 3.1. right?

Thanks, 
Diana

 

> biocLite("BiocUpgrade")
Error: Bioconductor version 3.1 cannot be upgraded with R version 3.2.0
> sessionInfo()
R Under development (unstable) (2014-10-29 r66891)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_1.6.1       BiocInstaller_1.17.1

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

ADD COMMENTlink written 3.8 years ago by dianmante0
0
gravatar for Dan Tenenbaum
3.8 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

This is a different error message that you are seeing for a different reason. It's saying that you already have the most recent version of Bioconductor for the version of R you are using. And since the version of R you are using is the absolute most recent (R-devel), you really can't go forward any more. 

Dan

 

ADD COMMENTlink written 3.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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