[NMF-user] error running NMF_0.16.2 in R 3.0.0 on OS X 10.7.5
Renaud Gaujoux
renaud at cbio.uct.ac.za
Sun Apr 7 09:58:36 CEST 2013
Hi,
I saw this error on CRAN's Mac check logs as well. This seems to be linked
with the shared.memory feature when running parallel computations, on Mac
only.
I have no Mac to thoroughly check and asked the author of bigmemory to see
if he could reproduce the error: he could not when running the example in
an R console, but got an error when running the checks.
So this will need further investigations.
Did you reinstall all packages, specially bigmemory, after upgrading to
R-3.0.0?
You should still be able to run parallel computations but disabling
shared.memory by:
nmf.options(shared.memory=FALSE)
If you do not want to remember/type this every time you load NMF, you could
simply uninstall the synchronicity package, which you probably do not need
otherwise. The shared memory feature will then be disabled for good.
Bests,
Renaud
2013/4/7 Gordon Robertson <grobertson at bcgsc.ca>
> 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
>
>
> 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
>
>
>
>
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>
--
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
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