[Bioc-devel] using devel bug
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bumps in end-of-life, devel-to-release, and new-devel branches of BiocInstaller, so (a) you'll be told BiocInstaller is out-of-date and (b) the current devel IS_UPGRADEABLE=FALSE will become IS_UPGRADEABLE=TRUE and you'll be able to upgrade.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]]
>>
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>>
>
>
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