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?

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@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@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

