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

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.

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

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