[Bioc-devel] using devel bug

[Kasper Daniel Hansen]

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.

Best,
Kasper

On Tue, Mar 10, 2015 at 3:50 PM, Henrik Bengtsson <henrik.bengtsson at ucsf.edu
> wrote:

> On Tue, Mar 10, 2015 at 12:30 PM, Martin Morgan <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> 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 mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
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> >
> >
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