Cannot Install Latest Version Of Deseq

Question

[Pasta]

Hi,

I am using R 2.12.1 and I would like to use the new function estimateDispersions() of from DESeq package 1.4.1.

The problem I am facing is that I am running the version 1.2.1 of DESeq but cannot update to the last version ... Typically, to update I use:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq")

but that doesnt work ... I read somewhere that I need r-dev to make it work, it is installed but that doesnt change a thing.

Any help is appreciated. Thanks

sessionInfo()

R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-linux-gnu (64-bit)

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=C              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] DESeq_1.2.1     locfit_1.5-6    lattice_0.19-13 akima_0.5-4    
[5] Biobase_2.10.0 

loaded via a namespace (and not attached):
 [1] annotate_1.28.1      AnnotationDbi_1.12.1 DBI_0.2-5           
 [4] genefilter_1.32.0    geneplotter_1.28.0   grid_2.12.1         
 [7] RColorBrewer_1.0-5   RSQLite_0.9-4        splines_2.12.1      
[10] survival_2.36-2      tools_2.12.1         xtable_1.5-6

EDIT: I tried to manually install DESeq 1.4.1 but I get this error:

Error : package 'Biobase' 2.10.0 was found, but >= 2.13.6 is required by 'DESeq'
ERROR: lazy loading failed for package ‘DESeq’

but I cannot find BioBase 2.13.6 anywhere :(

[Michael Schubert]

Please also post the error message you get when trying to install DESeq 1.4.1 and the OS you are running.

[Pasta]

@Michael: I am running Ubuntu 11.04. I do no get any error message when I install DESeq as it installs OK but not the latest version...

[Pasta]

@Michael: I am running Ubuntu 11.04. I do no get any error message when I install DESeq, it just doesnt install the latest version

Answer 1

[Ning-Yi Shao]

Now the latest Biobase is 2.13.7.

And I think you should install R 2.14, and use bioclite to install the package.

Ref

Answer 2

[Michael]

You can't do it that way, you have to update your R installation to the latest version (atm 2.13.1, or devel version 2.14) to be able to install the latest version of Bioconductor. The Bioconductor versions are tightly linked with the R version. Manually installing single bioconductor packages on top of an older R version almost never works because of version requirements not met with other packages.

If you always need the newest BioC packages, one possible way is to regularly build the latest R version yourself from source. Unfortunately, none of the Linux distributions I know can keep pace with the R version updates for their compiled R binaries.

Much less hassle for you: use the Ubuntu repositories of cran to install the latest binary version using your package manager, follow the instructions here.

In short (for your ubuntu version 11.04 Natty), add a line to /etc/apt/sources.list file

deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu natty/

Then run apt-get to install the latest R:

sudo apt-get update
sudo apt-get install r-base

Then, from inside R, install Bioconductor packages using biocLite as you did before.

[Pasta]

Thanks a lot - works like a charm !

Answer 3

[Ryan Dale]

I read somewhere that I need r-dev to make it work, it is installed but that doesnt change a thing

It's kind of confusing, but Ubuntu's r-dev is the "developer's package" which contains the source code that you can use to compile the version Ubuntu ships (R 2.12.1).

For the latest DESeq (1.5.1+, with the new estimateDispersions and GLM framework) you need BioConductor 2.9, which depends on the development version of R, 2.14 . . . which isn't available in any Ubuntu repos that I know of (including the CRAN mirror repos which currently go up to R 2.13.1).

So you'll need to compile R 2.14 yourself. Once that's done, make sure you start up your new version of R, and then from in there the following should work:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq")

Answer 4

[Darked89]

Not sure if this is your case, but mixing Ubuntu/Debian packages installed by apt-get with R packages installed directly from CRAN may cause problems. If you must have the latest versions you may need to have your own (user version) R/Bioconductor versions and update any package as required.

Answer 5

[Dado]

After installing Ubuntu oneiric server and R 2.14 (using apt-get) I still get this error when trying to install DESeq!

package 'DESeq' is not available for R version 2.14.0

the installer is using R version 2.14.0 and biocinstall version 2.5.10 and tries to install Bioconductor 2.5 packages for some odd reason.

Any idea how to fix this?

Cheers,

Dado

[Eva_Maria]

You can install DESeq via Bioconda using this command

conda install bioconductor-deseq2

[Ram]

This is a 7 year old post :-)