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 However, after biocLite gets done installing an individual package, it looks for other out-of-date packages and asks whether I want to update all, some or none.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] ? 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 -------------------------------------------------------------------

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 However, after biocLite gets done installing an individual package, it looks for other out-of-date packages and asks whether I want to update all, some or none.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? Martin > > 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 > > > ------------------------------------------------------------------- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793