[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
Mon Apr 8 08:00:50 CEST 2013
Thanks Gordon.
Might be worth investigate via direct emails and post the conclusion, and
hopefully a fix for this, so that the post does not get too messy.
Renaud
2013/4/7 Gordon Robertson <grobertson at bcgsc.ca>
> Thanks Renaud,
>
> Turning shared memory off seems to work. The following was run in the Mac
> terminal. The run with the error was copied from yesterday's screen output.
> The run that follows is from today. I'm happy to work with you offline (or
> on line) to clarify what's happening on OS X, or to make a binary Mac
> package. Just let me know what I can do.
>
> > 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
>
> > nmf.options(shared.memory=FALSE)
> > res <- nmf(esGolub,3,seed=123456,nrun=5,.options='v')
> NMF algorithm: 'brunet'
> Multiple runs: 5
> Mode: parallel (7/8 core(s))
> Runs: |==================================================| 100%
> System time:
> user system elapsed
> 12.603 0.576 4.540
>
> > 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 tools_3.0.0 xtable_1.7-1
>
> G
> --
> Gordon Robertson
> Michael Smith Genome Sciences Centre
> BC Cancer Agency
> Vancouver BC Canada
> www.bcgsc.ca
>
>
> On 2013-04-07, at 12:58 AM, Renaud Gaujoux wrote:
>
> 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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>> nmf-user at lists.r-forge.r-project.org
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>>
>
>
>
> --
>
> Renaud Gaujoux
> Computational Biology - University of Cape Town
> South Africa
>
>
>
--
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
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