Question: Cannot Install Latest Version Of Deseq
2
gravatar for Pasta
7.7 years ago by
Pasta1.3k
Switzerland
Pasta1.3k wrote:

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 :(

R deseq • 5.4k views
ADD COMMENTlink modified 4.7 years ago by Biostar ♦♦ 20 • written 7.7 years ago by Pasta1.3k

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

ADD REPLYlink written 7.7 years ago by Michael Schubert6.9k

@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...

ADD REPLYlink written 7.7 years ago by Pasta1.3k

@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

ADD REPLYlink written 7.7 years ago by Pasta1.3k
4
gravatar for Ning-Yi Shao
7.7 years ago by
Ning-Yi Shao380
United States
Ning-Yi Shao380 wrote:

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

ADD COMMENTlink modified 6 months ago by RamRS21k • written 7.7 years ago by Ning-Yi Shao380
4
gravatar for Michael Dondrup
7.7 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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.

ADD COMMENTlink modified 6 months ago by RamRS21k • written 7.7 years ago by Michael Dondrup46k

Thanks a lot - works like a charm !

ADD REPLYlink written 7.7 years ago by Pasta1.3k
2
gravatar for Ryan Dale
7.7 years ago by
Ryan Dale4.8k
Bethesda, MD
Ryan Dale4.8k wrote:

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")
ADD COMMENTlink modified 6 months ago by RamRS21k • written 7.7 years ago by Ryan Dale4.8k
1
gravatar for Darked89
7.7 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

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.

ADD COMMENTlink written 7.7 years ago by Darked894.2k
0
gravatar for Dado
7.4 years ago by
Dado0
Dado0 wrote:

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

ADD COMMENTlink written 7.4 years ago by Dado0

You can install DESeq via Bioconda using this command

conda install bioconductor-deseq2
ADD REPLYlink modified 6 months ago by RamRS21k • written 6 months ago by akhilvbioinfo130

This is a 7 year old post :-)

ADD REPLYlink written 6 months ago by RamRS21k
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