On 04/10/2013 06:26 PM, Kasper Daniel Hansen wrote: > > > > On Wed, Apr 10, 2013 at 9:18 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 04/10/2013 05:43 PM, Kasper Daniel Hansen wrote: > > Right now, I get that R-devel uses BiocInstaller 1.10.0 and points to > Bioconductor 2.12, the same as R-3.0. Shouldn't it point to Bioconductor > 2.13 for R-devel? > > > Hi Kasper -- remember that, because R is now on a yearly release cycle, > we're using R-3.0.x for both release and devel for the next ~6 months, see > > http://bioconductor.org/__developers/useDevel/ > <http: bioconductor.org="" developers="" usedevel=""/> > > and after > > source("http://bioconductor.__org/biocLite.R > <http: bioconductor.org="" bioclite.r="">") > useDevel() > > > Point taken; Bioc devel should be using the R-3-0-branch. > > Nevertheless, if I use R-devel, I should be getting the Bioc devel version, > which I don't. I have > R Under development (unstable) (2013-04-10 r62546) -- "Unsuffered Consequences" > Copyright (C) 2013 The R Foundation for Statistical Computing > Platform: x86_64-apple-darwin12.3.0 (64-bit) > > which is from right now. If you're looking to correct this, then useDevel() or remove.packages("BiocInstaller"); source("http://bioconductor.org/biocLite.R"). One would get the correct version if installing a new R-devel. You do have an edge case and we'll fix it, thanks. Martin > > Kasper > > > But actually, I think your R-devel is a little out of date and that with > something more recent than > > ------------------------------__------------------------------ __------------ > r62488 | ligges | 2013-04-03 16:12:25 -0700 (Wed, 03 Apr 2013) | 1 line > > update BioC devel to 2.13 > ------------------------------__------------------------------ __------------ > > you'll get > > > source("http://bioconductor.__org/biocLite.R > <http: bioconductor.org="" bioclite.r="">") > Installing package into > ?/home/mtmorgan/R/x86_64-__unknown-linux-gnu-library/3.1? > (as ?lib? is unspecified) > trying URL > 'http://www.bioconductor.org/__packages/2.13/bioc/src/__contrib/ BiocInstaller_1.11.0.__tar.gz > <http: www.bioconductor.org="" packages="" 2.13="" bioc="" src="" contrib="" bioc="" installer_1.11.0.tar.gz="">' > > ... > > Martin > > > > Best, > Kasper > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <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 <tel:%28206%29%20667-2793> > > -- 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