[pkg-bioc] sources.list lines?

[elw at stderr.org]

> | > 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.



I can't seem to find the reference in the archives - if you've got it 
handy, can you paste it into the wiki somewhere?

thanks!


[maybe i should just build a nice mirror here and put it in the wiki 
myself.  ugh, not so much fun.]

--elijah



> 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