[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

[Kasper Daniel Hansen]

You should not be using R-3.1.2 patched with the current devel version of
Bioconductor; use R-devel.

Best,
Kasper

On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres <lcollado at jhu.edu>
wrote:

> Hi,
>
> I can't seem to install devel packages via biocLite() and I wonder if
> something is broken or if I'm missing something. For example, take
> GenomeInfoDb which is at 1.3.6 and is passing all checks.
>
> The usual code using a fresh R 3.1.2-patched install isn't working as
> it downloads the latest release version (1.2.2):
>
> > source("http://bioconductor.org/biocLite.R")
> Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> ## Was expecting 3.1 here
> > useDevel()
> Error: 'devel' version already in use
> > biocLite('GenomeInfoDb')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2.
> Installing package(s) 'GenomeInfoDb'
> trying URL '
> http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz
> '
> Content type 'application/x-gzip' length 404120 bytes (394 KB)
> opened URL
> ==================================================
> downloaded 394 KB
>
>
> The downloaded binary packages are in
>
> /var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//Rtmpxp29xo/downloaded_packages
> >
> > sessionInfo()
> R version 3.1.2 Patched (2014-11-01 r66923)
> ## Note that it matches the current R version used by the Bioc-devel
> build machines
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.16.0 colorout_1.0-2
>
> loaded via a namespace (and not attached):
> [1] tools_3.1.2
>
>
>
> For my computer it's not problem because I can download the pkg via
> svn and install locally. But it breaks my tests in TravisCI which
> relies on biocLite().
>
> Cheers,
> Leo
>
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