Dear all,

I am having some issues with the installation of some packages. I have written an R package that I would like to share with some computer-reluctant biologists. To make it easy, I have written a simple R function to install all required packages (see below with limited number of packages for the example).

install_packages <- function(){

    # Open R and install packages
    local({r <- getOption("repos")
        r["CRAN"] <- "http://cran.r-project.org" 
        options(repos=r)
    })

    # Define a vector with the names of all required packages
    package <- c( 'AnnotationDbi', 'caTools', 'edgeR', 'GenomicRanges', 'GenomicAlignments', 'gtools', 'Rsamtools', 'VennDiagram' )
     
    # Install required packages
    for(k in 1:length(package)){
           cat("\n\t\t", k, ".\t Installing ", package[k], sep='')
           install.packages(package[k], dependencies=TRUE);
     }

}


It works well for most standard packages, but some packages are problematic, giving me error messages of this kind:

package ‘edgeR’ is not available (for R version 3.1.2)

I have tried a gazillion things, but I can’t figure out why I get these ‘warnings’ and don’t understand why they are not ‘errors’. Any help would be greatly appreciated.
Thanks,

Patrick

PS: I know that these packages are installed on my machine, but I am trying to do this for other computers. Thanks.
 

sessionInfo()

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      parallel  stats4    stats     graphics  grDevices utils    
[8] datasets  methods   base     

other attached packages:
[1] VennDiagram_1.6.9       gtools_3.4.1            GenomicAlignments_1.2.1
[4] Rsamtools_1.18.2        Biostrings_2.34.1       XVector_0.6.0          
[7] GenomicRanges_1.18.4    edgeR_3.8.5             limma_3.22.4           
[10] caTools_1.17.1          AnnotationDbi_1.28.1    GenomeInfoDb_1.2.4     
[13] IRanges_2.0.1           S4Vectors_0.4.0         Biobase_2.26.0         
[16] BiocGenerics_0.12.1    

loaded via a namespace (and not attached):
[1] base64enc_0.1-2    BatchJobs_1.5      BBmisc_1.9         BiocParallel_1.0.3
[5] bitops_1.0-6       brew_1.0-6         checkmate_1.5.1    codetools_0.2-10  
[9] DBI_0.3.1          digest_0.6.8       fail_1.2           foreach_1.4.2     
[13] iterators_1.0.7    RSQLite_1.0.0      sendmailR_1.2-1    stringr_0.6.2     
[17] tools_3.1.2        zlibbioc_1.12.0   

You are re-inventing the wheel here. Plus, install.packages() is quite happy to install using a vector of package names.

A simpler thing would be to write a script like so, and save it as, say 'installme.R'

source("https://www.bioconductor.org/biocLite.R")

biocLite(c('AnnotationDbi', 'caTools', 'edgeR', 'GenomicRanges', 'GenomicAlignments', 'gtools', 'Rsamtools', 'VennDiagram' ), ask = FALSE)

Then tell your recalcitrant biologist types to open R and then do

source("installme.R")

But do note that if your reluctant biologist friends are getting hung up on something like installing packages, you most likely have much larger problems...

You haven't specified a bioconductor repository. Also, install.packages() works on a vector. Why not simply

## Install & / or load 'BiocInstaller', then use biocLite()
source("http://bioconductor.org/biocLite.R")
BiocInstaller::biocLite(packages)

? This works for CRAN and Bioconductor packages. Alternatively, set up an AMI or use a pre-configured docker instance running Rstudio!

Sweet! worked perfectly. Thanks so much!

PS: weird thing though: when i installed BiocInstaller, I got the same warning message:

Warning message:

package ‘BiocInstaller’ is not available (for R version 3.1.2)

Is this a known bug???

Thanks again!

You are right, it had something to do with how I installed BiocLite. Martin's solution works. Thanks guys!