[Bioc-devel] Windows binaries for the new release?

[James W. MacDonald]

On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> On 04/26/2017 10:00 AM, James W. MacDonald wrote:
>
>> I see the binaries on the respective web pages, but biocLite seems not to:
>>
>
> I'm not 100% sure but can you try again in a new R session? I think you
> have a cached version of the repository index.
>

At a command prompt, using --vanilla:

C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(BiocInstaller)
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'Biobase', 'IRanges', 'S4Vectors'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions are later:
           binary source needs_compilation
Biobase    2.35.1 2.36.0              TRUE
IRanges    2.9.19 2.10.0              TRUE
S4Vectors 0.13.17 0.14.0              TRUE

Do you want to install from sources the packages which need compilation?
y/n:

Is there a way to remove the cache manually? I have already uninstalled and
re-installed BiocInstaller.

Jim




> Martin
>
>
>> biocLite()
>>>
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
>> installation path not writeable, unable to update packages: foreign
>> Old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics', 'biomaRt',
>> 'IRanges',
>>   'S4Vectors'
>> Update all/some/none? [a/s/n]: a
>>
>>   There are binary versions available but the source versions are later:
>>                binary source needs_compilation
>> AnnotationDbi  1.37.4 1.38.0             FALSE
>> Biobase        2.35.1 2.36.0              TRUE
>> BiocGenerics   0.21.3 0.22.0             FALSE
>> biomaRt       2.31.10 2.32.0             FALSE
>> IRanges        2.9.19 2.10.0              TRUE
>> S4Vectors     0.13.17 0.14.0              TRUE
>>
>> Do you want to install from sources the packages which need compilation?
>> y/n:
>>
>> sessionInfo()
>>>
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 14393)
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] BiocInstaller_1.26.0
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.0 tools_3.4.0
>>
>>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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