[NMF-user] error running NMF_0.16.2 in R 3.0.0 on OS X 10.7.5

Sun Apr 7 02:47:26 CEST 2013

Renaud,

With R 3.0.0, I get an error when I try to run a test. I'm likely missing something simple. Could you help me resolve this?

> 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 [OK] | Cores 7/8
> library(RColorBrewer)
> n <- 100; counts <- c(10, 5, 8); p <- sum(counts)
> V <- syntheticNMF(n, counts, noise=TRUE)
> groups <- as.factor(do.call('c', lapply(seq(3), function(x) rep(x, counts[x]))))
> res <- nmf(V, 3, nrun=100)
Error: NMF::nmf - 100/100 fit(s) threw an error.
# Error(s) thrown:
  - run #1: Fatal error in attach: big.matrix could not be attached.
Timing stopped at: 31.804 1.025 5.987

> 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
[8] methods   base

other attached packages:
 [1] doParallel_1.0.1    iterators_1.0.6     foreach_1.4.0
 [4] RColorBrewer_1.0-5  NMF_0.16.2          synchronicity_1.1.0
 [7] bigmemory_4.4.3     BH_1.51.0-0         bigmemory.sri_0.1.2
[10] Biobase_2.20.0      BiocGenerics_0.6.0  digest_0.6.3
[13] rngtools_1.2        pkgmaker_0.15.2     registry_0.2

loaded via a namespace (and not attached):
[1] codetools_0.2-8  colorspace_1.2-1 compiler_3.0.0   gridBase_0.4-6
[5] stringr_0.6.2    xtable_1.7-1

--
I'm able to run simple jobs.
> x <- rmatrix(20,10)
> res <- nmf(x, 2)
> res <- nmf(x, 2, 'lee')

--
But possibly larger jobs hit the error?
> data(esGolub)
> res <- nmf(esGolub,3,seed=123456)
> res <- nmf(esGolub,3,seed=123456,nrun=20)
Error: NMF::nmf - 20/20 fit(s) threw an error.
# Error(s) thrown:
  - run #1: Fatal error in attach: big.matrix could not be attached.
Timing stopped at: 71.596 1.011 14.788

> res <- nmf(esGolub,3,seed=123456,nrun=5,.options='v')
NMF algorithm: 'brunet'
Multiple runs: 5
Mode: parallel (7/8 core(s))
Runs: |==================================================| 100%
Error: NMF::nmf - 5/5 fit(s) threw an error.
# Error(s) thrown:
  - run #1: Fatal error in attach: big.matrix could not be attached.
Timing stopped at: 13.673 0.579 4.927

Thank you,

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

On 2013-04-06, at 12:47 PM, Gordon Robertson wrote:

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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