[BioC] Installation of SomaticSignatures

[Julian Gehring]

Hi Sigve,

The problem your are experiencing comes from a problem between R and OS 
mavericks.  With mavericks, some basic build tools were changed.  To 
make a long story short, that means that R package binaries created with 
earlier versions of mac operating systems are not compatible with mavericks.

The 'NMF' package (which comes from CRAN) is still available, but does 
not have a binary build for mavericks yet (see 
http://cran.r-project.org/web/packages/NMF/index.html).  I would expect 
that this will become available soon.  This is in the hands of the CRAN 
repository maintainers, and it seem that waiting is the best strategy.

On the other hand, CRAN has a separate directory with os mavericks 
builds.  I'm not sure why they are not linked to the repo or the web 
page.  You could give it a try and install

http://cran.r-project.org/bin/macosx/contrib/r-release/NMF_0.20.5.tgz

manually.

Best wishes
Julian


On 08.05.2014 10:40, Sigve at embl-heidelberg.de wrote:
> Hi,
>
> I am trying to install the SomaticSignatures using R version 3.1.0. There seems to be a problem with the dependency on NMF:
>
>> biocLite("SomaticSignatures")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0.
> Installing package(s) 'SomaticSignatures'
> Warning: dependency 'NMF' is not available
> trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1/SomaticSignatures_1.0.0.tgz'
> Content type 'application/x-gzip' length 1712756 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
>
> The downloaded binary packages are in
> 	/var/folders/kw/sbc71xm12cz18s24f1mvrzd00000gq/T//RtmpuB97PY/downloaded_packages
> Warning message:
> installed directory not writable, cannot update packages 'MASS'
>
> library(SomaticSignatures)
> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
>    there is no package called 'NMF'
> Error: package or namespace load failed for 'SomaticSignatures'
>
>   -- output of sessionInfo():
>
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin13.1.0 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_3.1.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>