[NMF-user] installing NMF in R 3.0.0 on OS X

[Gordon Robertson]

Hi Renaud,

I thought I'd send these notes on the chance that they'd be helpful to others. I installed NMF, but have not yet run it. The one thing that was a bit odd is the warning (...is not available (for R version 3.0.0)).

I've been using v0.9 for some time on R v2.15.x, on OS X 10.7.5. Today I updated R to v3.0.0, and got an error message when installing from the v0.9 .tgz from the latest RStudio (which is how I'd installed NMF on v2.15.x).

RStudio did not recognize that v0.16.2 was available at CRAN (seeing only NMFN available, but not NMF), and after trying to install a few .tar.gz versions from your CRAN-like web page (but failing to achieve a loadable library), a Google search suggested I look at CRAN. From there I downloaded v0.16.2's tar.gz, and installed it from RStudio's GUI installer.  All seemed OK.

> install.packages("~/software/clustering/NMF/R/NMF/v0.16.2/NMF_0.16.2.tar.gz", repos = NULL, type = "source")
Warning in install.packages :
  package ‘~/software/clustering/NMF/R/NMF/v0.16.2/NMF_0.16.2.tar.gz’ is not available (for R version 3.0.0)
...
> library(NMF)
Loading required package: pkgmaker
Loading required package: registry

Attaching package: ‘pkgmaker’

The following object is masked from ‘package:utils’:

    packageName

Loading required package: rngtools
Loading required package: digest
Loading required package: grid
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 7/8
  To enable shared memory capabilities, try: install.extras('NMF')

> install.extras('NMF')
Loaded extra package: bigmemory
trying URL 'http://cran.stat.sfu.ca/bin/macosx/contrib/3.0/synchronicity_1.1.0.tgz'
Content type 'application/x-gzip' length 206844 bytes (201 Kb)
opened URL
==================================================
downloaded 201 Kb


The downloaded binary packages are in
/var/folders/x5/l6f5m2j91vdd99wy2gchtld40000gn/T//RtmpLXt3yC/downloaded_packages
Loading required package: synchronicity
Loaded extra package: Biobase

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] synchronicity_1.1.0  NMF_0.16.2           bigmemory_4.4.3      BH_1.51.0-0          bigmemory.sri_0.1.2
 [6] Biobase_2.20.0       BiocGenerics_0.6.0   digest_0.6.3         rngtools_1.2         pkgmaker_0.15.2
[11] registry_0.2         BiocInstaller_1.10.0

loaded via a namespace (and not attached):
 [1] codetools_0.2-8    colorspace_1.2-1   doParallel_1.0.1   foreach_1.4.0      gridBase_0.4-6
 [6] iterators_1.0.6    RColorBrewer_1.0-5 stringr_0.6.2      tools_3.0.0        xtable_1.7-1


Gordon
--
Gordon Robertson
Michael Smith Genome Sciences Centre
BC Cancer Agency
Vancouver BC Canada
www.bcgsc.ca<http://www.bcgsc.ca>


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