[BioC] useDevel and update all packages - wrong library location?

Martin Morgan mtmorgan at fhcrc.org
Wed Aug 15 23:02:39 CEST 2012

On 08/15/2012 11:41 AM, Janet Young wrote:
> Hi there,
> Until now I haven't used the devel versions of bioc packages at all, but after looking at the instructions at http://www.bioconductor.org/developers/useDevel/  I've started to do that (I want to maintain parallel release and devel installations).
> Installing individual packages with biocLite e.g.
> 	source("http://bioconductor.org/biocLite.R")
> 	biocLite("Rsamtools")
> worked OK - it put the new packages in the right location. It worked well a couple of times in a row.
> However, after biocLite gets done installing an individual package, it looks for other out-of-date packages and asks whether I want to update all, some or none. I reply "all" and it then installs devel versions of the packages in the wrong place - in my release version library dir rather than the devel version library dir.
> My Rdevel is aliased to "setenv R_LIBS_USER /home/jayoung/traskdata/lib_linux_gizmo/Rdevel ; R"
> and from my Rdevel session, here are a couple of possibly useful outputs:
> .libPaths()
> [1] "/home/btrask/traskdata/lib_linux_gizmo/Rdevel"
> [2] "/home/btrask/traskdata/lib_linux_gizmo/R/library"

> .Library
> [1] "/home/btrask/traskdata/lib_linux_gizmo/R/library"
> Is .Library what's used as the destination dir - shouldn't it be the same as .libPaths()[1] ?

Hi Janet -- I think the confusion here is that update.packages() (which 
is used when you ask for a package to be updated) tries to do the update 
in the directory where the out-of-date package is installed. I think 
this is the right thing to do.

I guess you have some Bioc packages in both locations [1] and [2], and 
that you're expecting [2] to contain just release versions of the 
package. But that's a version of R with some release, some devel 
versions of Bioc packages, which is not what you want.

Here's the content of my .libPaths()[2]

 > dir(.libPaths()[2])
  [1] "base"       "boot"       "class"      "cluster"    "codetools"
  [6] "compiler"   "datasets"   "foreign"    "graphics"   "grDevices"
[11] "grid"       "KernSmooth" "lattice"    "MASS"       "Matrix"
[16] "methods"    "mgcv"       "nlme"       "nnet"       "parallel"
[21] "rpart"      "spatial"    "splines"    "stats"      "stats4"
[26] "survival"   "tcltk"      "tools"      "utils"

just base and recommended packages, whose update status is not tied to 
Bioc version.

Not sure if that clarifies or not?


> I wonder if I've misunderstood something here - any tips?
> thanks very much,
> Janet
> -------------------------------------------------------------------
> Dr. Janet Young
> Tapscott and Malik labs
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., C3-168,
> P.O. Box 19024, Seattle, WA 98109-1024, USA.
> tel: (206) 667 1471 fax: (206) 667 6524
> email: jayoung  ...at...  fhcrc.org
> -------------------------------------------------------------------
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