On 03/10/2015 01:01 PM, Kasper Daniel Hansen wrote:
Yeah, I basically have one version of R devel which is re-compiled every morning and then all packages are updated. This is probably happening around the transition from R-devel using one version of BiocInstaller to another. Reading the code, it seems weird to me that IS_UPGRADABLE gets set at install time; this is something that will depend on query time, at least for R-devel.
IS_UPGRADEABLE (also useDevel()) is meant to key off the version of BiocInstaller, under the assumption that BiocInstaller is correct for the version of R in use. Each release is accompanied by version bumps in end-of-life, devel-to-release, and new-devel branches of BiocInstaller, so (a) you'll be told BiocInstaller is out-of-date and (b) the current devel IS_UPGRADEABLE=FALSE will become IS_UPGRADEABLE=TRUE and you'll be able to upgrade.
It isn't really simpler to think in terms of the version of R in use, either, e.g., BiocInstaller under R-3.1 was initially (Bioc version 2.15) not upgradeable, until our Bioc 3.0 came out.
BiocInstaller could / should detect that it was running on the wrong version of R for Kasper's and Henrik's case.
Martin
Best, Kasper On Tue, Mar 10, 2015 at 3:50 PM, Henrik Bengtsson <henrik.bengts...@ucsf.edu <mailto:henrik.bengts...@ucsf.edu>> wrote: On Tue, Mar 10, 2015 at 12:30 PM, Martin Morgan <mtmor...@fredhutch.org <mailto:mtmor...@fredhutch.org>> wrote: > On 03/10/2015 11:08 AM, Kasper Daniel Hansen wrote: >> >> Ok, I had to manually remove the BiocInstaller package, restart R and then >> run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0 > > > any idea how BiocInstaller 1.16.x was installed in the R-3.2 library? I > think install.packages() will actually currently do the wrong thing... I think *when* could also be an important lead. See my troubleshooting on this in Bioc devel thread '[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1' on Nov 17, 2014: https://stat.ethz.ch/pipermail/bioc-devel/2014-November/006670.html Maybe related? /Henrik > > >> >> Clearly, there is some issue with the IS_UPGRADEABLE variable which (I >> guess) is initialized at install time. >> >> On Tue, Mar 10, 2015 at 2:01 PM, Kasper Daniel Hansen < >> kasperdanielhan...@gmail.com <mailto:kasperdanielhan...@gmail.com>> wrote: >> >>> Using R-devel, I get >>> >>> R-devel >>> >>> R Under development (unstable) (2015-03-09 r67969) -- "Unsuffered >>> Consequences" >>> Copyright (C) 2015 The R Foundation for Statistical Computing >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>> **************************** >>> ** Hopkins NEWS and Notes ** >>> **************************** >>> >>> News and updates for the R installation will be sent to bit-help, so >>> consider subscribing >>> >>> An automatic user library has been created (in case it did not already >>> exist) as >>> ~/R/x86_64-unknown-linux-gnu-library/3.2 >>> install.packages and R CMD INSTALL will automatically install to this >>> directory, so there is no need for a -l or a lib argument to these >>> functions. >>> >>> Loading required package: utils >>> none >>>> >>>> source("http://www.bioconductor.org/biocLite.R";) >>> >>> Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help >>> >>> >>> Why? In the past it would auto-detect my R version and automatically use >>> Bioc devel. Also, I get >>> >>>> useDevel(TRUE) >>> >>> Error: 'devel' version requires a more recent R >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: useDevel(TRUE) >>> 2: .stop("'devel' version requires a more recent R") >>> >>> Best, >>> Kasper >>> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > -- > 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> > > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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