[Bioc-devel] Bioconductor packages for R-3.1.0 beta on OSX 10.9
Dan Tenenbaum
dtenenba at fhcrc.org
Mon Apr 7 04:29:55 CEST 2014
----- Original Message -----
> 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.
>
Well, there's that, but also, apparently the gcc Snow Leopard builds are not forward-compatible with the Mavericks build.
The advantage of the Mavericks build as I understand it is that it uses clang, which is officially supported by apple, and is much newer than the version of gcc that was used before, so it supports C++ 11.
I believe that the Snow Leopard builds will eventually be phased out.
I'm not the best person to ask about the advantages/disadvantages since this was a decision taken by R-core. You could ask on R-sig-mac.
Dan
> >>
> >> 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
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
>
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