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

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> To: "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 7:33:01 AM
> Subject: Re: [Bioc-devel] [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14
> 
> 
> 
> ----- 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.
> 

annotate should now be available for Mavericks, via
biocLite("annotate")

Thanks,
Dan


> 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
> > >
> > 
> > 	[[alternative HTML version deleted]]
> > 
> > 
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