[BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14

[Dan Tenenbaum]

----- Original Message -----
> From: "Tom Harrop" <twharrop3 at gmail.com>
> Cc: "bioc-devel" <bioc-devel at r-project.org>, "Bioconductor mailing list" <bioconductor at r-project.org>
> Sent: Tuesday, May 6, 2014 1:25:57 AM
> Subject: Re: [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14
> 
> Hi Dan,
> 
> Thanks a lot for the update.
> 
> I can’t get DESeq2 to load after installing it on my Mavericks build.
> 
> biocLite(‘DESeq2’) runs without error, but library(‘DESeq2’) returns
> the
> error:
> 
> > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
> > versionCheck
> > = vI[[j]]) :
> >  there is no package called ‘annotate’
> > Error: package or namespace load failed for ‘DESeq2’
> 
> biocLite(‘annotate’) or install.packages(‘annotate’) both return:
> 
> > Warning message:
> > package ‘annotate’ is not available (for R version 3.1.0)
> 
> I’ve tried a couple of different CRAN mirrors without luck. Is
> annotate one
> of the packages that still needs to be updated for Mavericks?
> 

Yes, you can tell by going to the annotate landing page (http://www.bioconductor.org/packages/2.14/bioc/html/annotate.html) and seeing whether a Mavericks package is listed under Package Downloads at the bottom. 

I don't think there's a problem with the code in the package; rather, it has issues because its examples try to contact flaky web services. I'll see if we can do something to make this package available.

Thanks,
Dan


> Thanks,
> 
> Tom
> 
> 
> sessionInfo()
> > R version 3.1.0 (2014-04-10)
> > Platform: x86_64-apple-darwin13.1.0 (64-bit)
> > locale:
> > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets
> >  methods
> > [8] base
> > other attached packages:
> > [1] RcppArmadillo_0.4.200.0 Rcpp_0.11.1
> >             GenomicRanges_1.16.3
> > [4] GenomeInfoDb_1.0.2      IRanges_1.22.6
> >          BiocGenerics_0.10.0
> > [7] BiocInstaller_1.14.2
> > loaded via a namespace (and not attached):
> > [1] Biobase_2.24.0     RColorBrewer_1.0-5 stats4_3.1.0
> >       tools_3.1.0
> >
> > [5] XVector_0.4.0
> 
> 
> 
> On 6 May 2014 00:37, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 
> > Hi all,
> >
> > Bioconductor 2.14 (release) packages are now available for the
> > Mavericks
> > (Mac OS X 10.9) build of R.
> >
> > If you install this version of R, you can install Mavericks
> > packages by
> > typing:
> >
> > source("http://bioconductor.org/biocLite.R")
> >
> > ...and then using biocLite() to install the package(s) you want;
> > for
> > example:
> >
> > biocLite("BiocGenerics")
> >
> > There are still a few packages that aren't building on Mavericks.
> > We have
> > been in touch
> > with their maintainers in most cases and hope that they'll be
> > building
> > soon. If you are
> > the maintainer of one of these packages, feel free to contact us on
> > bioc-devel if you
> > need help getting your package to build.
> > Most of the issues have to do with the fact that this version of R
> > uses
> > clang/clang++
> > instead of gcc/g++ to compile C/C++ code.
> >
> > If you need to use a package that's not yet available on Mavericks,
> > you
> > can continue
> > to use the Snow Leopard build of R; it will work fine on Mavericks.
> >
> > Mavericks binaries for BioC-devel (3.0) will be available in the
> > coming
> > weeks.
> >
> > Dan
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> 
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