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

[Diego Diez]

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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>