[pkg-bioc] sources.list lines?

[Dirk Eddelbuettel]

On 8 February 2006 at 16:06, elw at stderr.org wrote:
| > anybody got a (current, working) apt-able pkg-bioc repository that's 
| > currently online?
| >
| > i need to bum some packages real quick and don't really want to go through 
| > building today...

I think Steffen's from a few weeks ago may be the best bet.

OTOH I found the quick & dirty way for Quantian to be really straightforward:

For CRAN:

    # options("repos"="http://cran.us.r-project.org")
    # AP <- available.packages()	# CRAN by default, 644 pkgs 
    # IP <- installed.packages()
    # ToInstall <- AP[ ! (AP[,1] %in% IP[,1]) & is.na(AP[,4]), 1 ]
    # install.packages(pkgs=ToInstall, dependencies=TRUE)

You need to then fight the failing one by hand to add Build-Depends etc pp.

For BioC:

    ## > options("repos"="http://www.bioconductor.org")
    ## > AP <- available.packages() 
    ## > IP <- installed.packages() 
    ## > ToInstall <- AP[ ! AP[,1] %in% IP[,1],]   
    ## > ToInstall <- AP[ ! AP[,1] %in% IP[,1] & is.na(AP[,4]),] # excl Bundles
    ## > names(ToInstall[,1])     # about 128 packages
    ## > install.packages(pkgs=ToInstall[,1], dependencies=TRUE)

I think I also tried getBioC.R but ended up not liking it as much.

    ## gets all but 15
    ## > source("http://www.bioconductor.org/getBioC.R")
    ## > getBioC()
    ## which reinstalls all.almost all
    ## still outstanding:  RCurl, msbase, SSOAP, RdbiPgSQL, tilingArray
    ##   GeneTraffic, KEGGSOAP, mmgmos, Rgraphviz
    ## msbase has funny compiler option -ansii  (fix src/Makevars)c
    ## mmgmos had compiler error  (renamed variable)

If your machines are identical enough, you can then just rsync out
/usr/local/lib/R/.

Hth, Dirk

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison