[Bioc-devel] using devel bug
mtmorgan at fredhutch.org
Tue Mar 10 20:30:27 CET 2015
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...
> 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 Under development (unstable) (2015-03-09 r67969) -- "Unsuffered
>> 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
>> 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
>> Loading required package: utils
>> 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
>> 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")
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