[Bioc-devel] using devel bug

[Martin Morgan]

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-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
>>
>>
>
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>
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