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

----- Original Message -----

From: "Leonardo Collado Torres" <lcollado at jhu.edu>
To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
Cc: bioc-devel at r-project.org
Sent: Sunday, November 2, 2014 9:26:25 PM
Subject: Re: [Bioc-devel] Can't seem to use useDevel();	biocLite() for BioC 3.1

Thanks, I incorrectly thought that I was using the same R version as
the Bioc-build machines since the "r66923" part matched. Now I
realize
that this tag is used in all of the newest R builds at
http://r.research.att.com/.

It's admittedly confusing;

the question of whether to use R-devel with Bioc-devel has a different answer every six months, but the answer can always be found here:

http://www.bioconductor.org/developers/how-to/useDevel/

Also, when looking at the devel build report, you should probably focus more on the version portion of the "R version" column than on the SVN revision number.

Dan

On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:

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