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

[Renaud Gaujoux]

Hi Gordon,

I believe the warning you get is because you manually set repos=NULL. The
warning message says that package
‘~/software/clustering/NMF/R/NMF/v0.16.2/NMF_0.16.2.tar.gz’
(the whole string) is not available from CRAN, which is true.
So no issues here.

Bests,
Renaud


2013/4/6 Gordon Robertson <grobertson at bcgsc.ca>

> 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
>
>
>
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>



-- 

Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
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