[Bioc-devel] Bioconductor packages for R-3.1.0 beta on OSX 10.9

[Diego Diez]

Dear all,

sorry if double posting this. I sent it two days ago using a different
email not registered at bioc-devel and it seems (as for the archives)
it has not reached destination.

FYI, it seems the OSX build R 3.1.0 beta has split into snowleopard
and mavericks builds:

http://r.research.att.com

When installing the later and trying to install Bioconductor I get the
following:

> source("http://bioconductor.org/biocLite.R")
Warning: unable to access index for repository
http://www.bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1

   package 'BiocInstaller' is available as a source package but not as a binary

'biocLite.R' failed to install 'BiocInstaller', use
  'install.packages("BiocInstaller",
  repos="http://www.bioconductor.org/packages/2.14/bioc")'
Warning message:
package 'BiocInstaller' is not available (for R version 3.1.0 beta)


then did the following:


> install.packages("BiocInstaller",
+   repos="http://www.bioconductor.org/packages/2.14/bioc",type="source")
trying URL 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz'
Content type 'application/x-gzip' length 14183 bytes (13 Kb)
opened URL
==================================================
downloaded 13 Kb

* installing *source* package 'BiocInstaller' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
'/private/var/folders/dm/96krztk175d19vx9rcsgd2qc0000gn/T/RtmpMt3iRo/downloaded_packages'


and after that did:

> biocLite()
Error: 'no packages in repository (no internet connection?)' while trying
  http://bioconductor.org/packages/2.14/bioc

which failed, presumably  because the new repository structure is not
yet supported?

this did not work either:

> biocLite(type="source")

Best,
Diego

> sessionInfo()
R version 3.1.0 beta (2014-03-31 r65343)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.13.3

loaded via a namespace (and not attached):
[1] tools_3.1.0