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

From: "Diego Diez" <diego10ruiz at gmail.com>
To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
Cc: "bioc-devel" <bioc-devel at stat.math.ethz.ch>
Sent: Sunday, April 6, 2014 7:24:09 PM
Subject: Re: [Bioc-devel] Bioconductor packages for R-3.1.0 beta on OSX 10.9

Hi Dan,


On Fri, Apr 4, 2014 at 11:05 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
wrote:

Hi Diego,

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

From: "Diego Diez" <diego10ruiz at gmail.com>
To: "bioc-devel" <bioc-devel at stat.math.ethz.ch>
Sent: Friday, April 4, 2014 12:44:20 AM
Subject: [Bioc-devel] Bioconductor packages for R-3.1.0 beta on
OSX 10.9

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?

Yes, it's not yet supported. We just ordered some Mavericks
machines yesterday which we'll use to build BioC against the new R
binary for Mavericks. We'll announce on the Bioconductor and
Bioc-devel mailing lists when these builds are ready.

Until then, you can run the R binary built on Snow Leopard. It will
work fine on Mavericks and you'll be able to download binary BioC
packages.

Thank you. Also saw your other email sent to the list. What is the
advantage then of having a mavericks build? I guess the problem is
that Xcode 5 builds are not backward compatible.

this did not work either:

biocLite(type="source")

That's puzzling. What about installing an individual package from
source with biocLite()?

Did not work either.

biocLite("Biobase",type="source")

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

here include the output of traceback:

traceback()

11: stop(.msg(...), call. = call.)
10: .stop("'%s' while trying %s", conditionMessage(err), repos, call.
= FALSE)
9: value[[3L]](cond)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch({
       .contribUrl(repos)
   }, error = function(err) {
       version <- getRversion()
       currentVersion <- sprintf("%d.%d", version$major,
       version$minor)
       lowerVersion <- .lowerRVersionString(version)
       oldRepos <- sub(currentVersion, lowerVersion, repos)
       if (oldRepos == repos)
           .stop("'%s' while trying %s", conditionMessage(err),
               repos, call. = FALSE)
       .message("'%s' while trying %s, trying %s",
       conditionMessage(err),
           repos, oldRepos)
       .contribUrl(oldRepos)
   })
5: withCallingHandlers(expr, warning = function(w)
invokeRestart("muffleWarning"))
4: suppressWarnings(tryCatch({
       .contribUrl(repos)
   }, error = function(err) {
       version <- getRversion()
       currentVersion <- sprintf("%d.%d", version$major,
       version$minor)
       lowerVersion <- .lowerRVersionString(version)
       oldRepos <- sub(currentVersion, lowerVersion, repos)
       if (oldRepos == repos)
           .stop("'%s' while trying %s", conditionMessage(err),
               repos, call. = FALSE)
       .message("'%s' while trying %s, trying %s",
       conditionMessage(err),
           repos, oldRepos)
       .contribUrl(oldRepos)
   }))
3: .getContribUrl(biocVersion())
2: bioconductorPackageIsCurrent()
1: biocLite("Biobase", type = "source")

this works (as it did with BiocInstaller)

install.packages("Biobase",repos="http://www.bioconductor.org/packages/2.14/bioc",type="source")

Diego

Dan

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