BioConductor packages not available for R 3.0.2

Question

[Amit Lavon]

Hello,

When trying to install R package methylkit, I get an error message that says that some bio-packages are not available for my version of R. I am using Ubuntu.

I am new to R, so this probably has to do with me not knowing how to install packages correctly.

Any help will be appreciated.

Thanks, Amit

Code:

# dependencies
options(repos = c(CRAN = "http://cran.rstudio.com"))
install.packages( c("data.table","devtools"))
source("http://bioconductor.org/biocLite.R")
biocLite(c("GenomicRanges"))

# install the package from github
library(devtools)
install_github("al2na/methylKit",build_vignettes=FALSE)

Output:

ERROR: dependencies 'S4Vectors', 'GenomeInfoDb' are not available for package 'methylKit'
* removing '/home/amit/bio/data/shari-g9a/r_libs/methylKit'
Error: Command failed (1)
In addition: Warning message:
packages 'GenomicRanges', 'S4Vectors', 'GenomeInfoDb' are not available (for R version 3.0.2)
Execution halted

[GouthamAtla]

Downloading the zip files and install. It might work.

[Amit Lavon]

What about dependencies?

[GouthamAtla]

You need to install them as well. Sometime its hectic, but its one of the issues, What are the biggest challenges bioinformaticians have with data analysis?, needs to be handled with patience.

[Amit Lavon]

Thanks, but that dependency tree is too much for me to install manually. I'm so tired of struggling with almost every bioinformatic tool installation... :(

[Michael]

Sometimes this can be frustrating, see my update.

[Martin Morgan]

I do not recommend following this advice (download the zips & install), it will only lead to an incomplete or corrupt installation.

Answer 1

[Martin Morgan]

The short answer is to upgrade your version of R to it's current release and try again.

A medium answer is to upgrade your Bioconductor installation to the most recent version of Bioconductor that works with your version of R -- source("http://bioconductor.org/biocLite.R"); biocLite("BiocUpgrade").

A faster answer would (likely) have come by posting on the Bioconductor support site.

Here's the longer explanation:

In the original post, the error is

ERROR: dependencies ‘S4Vectors’, ‘GenomeInfoDb’ are not available for package ‘methylKit’

methylKit is a CRAN package with dependencies on Biocodonductor packages. All CRAN packages that work with the 3.0 series of R currently depend on the most recent released version of the underlying Bioconductor package compatible with the 3.0 series of R.

Bioconductor actually has two versions that work(ed) with the 3.0 versions of R. During the first six months of R 3.0's life, Bioconductor 2.12 was available. During the next six months of 3.0's life, Bioconductor 2.13 was available. There are often substantial changes in (some) Bioconductor packages between releases (this is the motivation for the Bioconductor model of a devel branch and periodic releases -- the release provides a coherent set of stable packages for reproducible results by the end user, while the devel branch provides an opportunity for rapid innovation).

The original poster likely started using R 3.0 / BioC 2.12 (check out BiocInstaller::biocVersion()). Since then of course Bioc 2.13 has come out (on October 15, 2013). Now when the original poster tries to install the CRAN package methylKit, they get the version of methylKit that works with Bioc 2.13 instead of Bioc 2.12. biocLite("BiocUpgrade") will update the user installation to Bioc 2.13 (still more than a year out of date), and the version mismatch will be resolved. Using the most recent R will get the version of methylKit that builds against the current release of Bioconductor (released on October 14, 2014).

Answer 2

[Michael]

Edit: it seems like Bioconductor screwed up the the 3.0 repos and didn't add the missing packages yet.

The same problem is for 3.1.0, GenomicRanges is not avaiable, see https://support.bioconductor.org/p/61960/

I think you should check if it works with the latest R version 3.1.2, if you want it to work this year or check with support.bioconductor.org

​

options(repos = c(CRAN = "http://cran.rstudio.com/"))

I think this is a potential source of problems, why did you set this? are you using R-studio? This is not part of the installation instructions of the package you are trying to install: https://code.google.com/p/methylkit/#Installation

Try to install the package into vanilla R started from the console: R --vanilla

or set the repos back to http://cran.r-project.org/

Please always report on sessionInfo().

[Amit Lavon]

Thanks.

Correcting the repository and running vanilla did not fix the problem. Still the same error.

> sessionInfo()

R version 3.0.2 (2013-09-25)
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=he_IL.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=he_IL.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=he_IL.UTF-8 LC_IDENTIFICATION=C

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

[Amit Lavon]

I'll try upgrading my R installation. Thanks!

[Martin Morgan]

The corrupt repository mentioned in the answer involved the 'devel' repository current at the time; this sort of problem is tolerated in the Bioconductor devel branch and is usually highly transient, typically lasting a single day. The post you point to represented an unusual period of several days during which the various devel versions of packages were in disarray, but this was remedied by the time of the post. The status of the devel branch is not relevant to end users, who will by default be using the stable release branch.