[Bioc-devel] using devel bug

[Martin Morgan]

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you'll be told BiocInstaller is out-of-date and (b) the current devel 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.bengtsson at ucsf.edu
> <mailto:henrik.bengtsson at ucsf.edu>> wrote:
>
>     On Tue, Mar 10, 2015 at 12:30 PM, Martin Morgan <mtmorgan at fredhutch.org
>     <mailto:mtmorgan at 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 <
>      >> kasperdanielhansen at gmail.com <mailto:kasperdanielhansen at 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 at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>      >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>      >>
>      >
>      >
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>
>


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