[NMF-user] NMF v0.20.5 on OS X gives a error for consensusmap(res) (Gordon Robertson)
Renaud Gaujoux
renaud at cbio.uct.ac.za
Wed May 27 09:12:05 CEST 2015
This is strange.
The CRAN Mac OS binary .tgz file is still on version 0.20.5, but you should
not get the error when installing the source 0.20.6.tar.gz file.
Let's wait and see if the updated Mac binary works.
On 26 May 2015 at 17:42, Gordon Robertson <grobertson at bcgsc.ca> wrote:
> Hello Renaud,
>
> Using the same system that gave errors late last week (OS X 10.7.5, R
> 3.1.3, RStudio 0.99.441), I've just installed v0.20.6 from the
> CRAN .tgz download, then ran the esGolub example. I'm still getting errors
> with coefmap and basismap. I'd be happy to help debug/understand this if
> you would tell me what tests to run.
>
> > install.packages("~/Downloads/NMF_0.20.6.tar.gz", repos = NULL, type =
> "source")
> > library(NMF) # NMF_0.20.5
>
> > sessionInfo()
> R version 3.1.3 (2015-03-09)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> Running under: OS X 10.7.5 (Lion)
>
> 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 stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] RColorBrewer_1.1-2 ggplot2_1.0.1 NMF_0.20.6
> Biobase_2.26.0 BiocGenerics_0.12.1
> [6] cluster_2.0.1 rngtools_1.2.4 pkgmaker_0.22
> registry_0.2 sfsmisc_1.0-27
> [11] matrixStats_0.14.0
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-11 colorspace_1.2-6 digest_0.6.8 doParallel_1.0.8
> foreach_1.4.2 grid_3.1.3
> [7] gridBase_0.4-7 gtable_0.1.2 iterators_1.0.7 magrittr_1.5
> MASS_7.3-40 munsell_0.4.2
> [13] plyr_1.8.2 proto_0.3-10 Rcpp_0.11.5 reshape2_1.4.1
> scales_0.2.4 stringi_0.4-1
> [19] stringr_1.0.0 tools_3.1.3 xtable_1.7-4
> > data("esGolub")
> > esGolub <- esGolub[1:200, ]
> > esGolub$Sample <- NULL
> > res <- nmf(esGolub, 3)
> > res
> <Object of class: NMFfit>
> # Model:
> ...
> Timing:
> user system elapsed
> 0.164 0.005 0.168
> > fit(res)
> <Object of class:NMFstd>
> features: 200
> basis/rank: 3
> samples: 38
> > V.hat <- fitted(res)
> > dim(V.hat)
> [1] 200 38
> > consensusmap(res) # gives a membership heatmap graphic
> > coefmap(res)
> Error in process_tracks(x, tracks, annRow, annCol) :
> Invalid special annotation track name ['basis']. Should partially match
> one of 'basis', ':basis', 'basis:'.
> > basismap(res)
> Error in process_tracks(x, tracks, annRow, annCol) :
> Invalid special annotation track name ['basis']. Should partially match
> one of 'basis', ':basis', 'basis:'.
>
> Thank you,
>
> Gordon
> --
> Gordon Robertson
> Canada's Michael Smith Genome Sciences Centre
> BC Cancer Agency
> Vancouver BC Canada
> www.bcgsc.ca
> T: 604-707-5900 x675416
>
>
>
>
> On 2015-05-23, at 3:00 AM, <nmf-user-request at lists.r-forge.r-project.org>
> <nmf-user-request at lists.r-forge.r-project.org> wrote:
>
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> 1. Re: NMF v0.20.5 on OS X gives a error for consensusmap(res)
> (Gordon Robertson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 22 May 2015 13:05:40 -0700
> From: Gordon Robertson <grobertson at bcgsc.ca>
> To: Renaud <getoxxx at gmail.com>
> Cc: Denise Brooks <dbrooks at bcgsc.ca>,
> "nmf-user at lists.r-forge.r-project.org"
> <nmf-user at lists.r-forge.r-project.org>
> Subject: Re: [NMF-user] NMF v0.20.5 on OS X gives a error for
> consensusmap(res)
> Message-ID: <AA245AAF-0344-4E4E-89A7-68C49F106F49 at bcgsc.ca>
> Content-Type: text/plain; charset="us-ascii"
>
> Renaud,
>
> Thank you for this lightning-fast response! I think I did update stringr
> last week. I'll update and will retry it.
>
> Gordon
>
>
> On 2015-05-22, at 12:59 PM, Renaud wrote:
>
> This comes from a change in stringr, which you probably updated.
> This is fixed in the master and devel branch on GitHub. You can install
> from there to get it right now.
> I will push the fix to CRAN on Monday.
>
> Bests,
> Renaud
>
> On Friday, May 22, 2015, Gordon Robertson <grobertson at bcgsc.ca<mailto:
> grobertson at bcgsc.ca>> wrote:
> To test this further, I did the following, following the user guide
> vignette PDF. I used RStudio (which I do not use for production NMF runs,
> but did for this quick test):
>
> data("esGolub")
> esGolub <- esGolub[1:200, ]
> esGolub$Sample <- NULL
> res <- nmf(esGolub, 3) # finished very quickly
> res #matches vignette
> fit(res) #matches vignette
> V.hat <- fitted(res)
> dim(V.hat) #matches vignette
> summary(res) #matches vignette
> summary(res, target = esGolub) #matches vignette
> w <- basis(res)
> dim(w)
>
> consensusmap(res) #generates a membership heatmap graphic
>
> coefmap(res)
>
> Error in process_tracks(x, tracks, annRow, annCol) :
> Invalid special annotation track name ['basis']. Should partially match
> one of 'basis', ':basis', 'basis:'.
>
> basismap(res)
>
> Error in process_tracks(x, tracks, annRow, annCol) :
> Invalid special annotation track name ['basis']. Should partially match
> one of 'basis', ':basis', 'basis:'.
>
> So I seem able to generate a membership heatmap, but not the other two
> graphics. Until today, I've been able to generate all three.
>
> It's a puzzle.
>
> Gordon
> --
> Gordon Robertson
> Canada's Michael Smith Genome Sciences Centre
> BC Cancer Agency
> Vancouver BC Canada
> www.bcgsc.ca<http://www.bcgsc.ca/>
> T: 604-707-5900 x675416
> Skype: a.gordon.robertson
>
>
>
>
> On 2015-05-22, at 12:23 PM, Gordon Robertson wrote:
>
> Renaud,
>
> On Mac OS X 10.7.5, using R 3.1.3, I'm suddenly getting error messages
> when I ask for a consensus map, basis map, or coefmap.
>
> This is puzzling, as I've used NMF for months without getting these errors.
>
> I re-installed NMF (from RStudio), then rebooted the Mac, then reran the
> small demo clustering job below. I get the same errors regardless of
> whether I run in RStudio (e.g. for the tiny demo), or in a Mac Terminal
> (where I typically run NMF on 7 of 8 threads on an i7 CPU).
>
> Can you offer any insights?
>
> Thank you -
>
> n <- 50;
>
> counts <- c(5, 5, 8);
>
> V <- syntheticNMF(n, counts, noise=TRUE)
>
> res <- nmf( V, 3, nrun=8, .options='tvP', .pbackend=4 )
>
> NMF algorithm: 'brunet'
> Multiple runs: 8
> Mode: parallel (4/8 core(s))
> Runs: |==================================================| 100%
> System time:
> user system elapsed
> 2.282 0.336 1.285
>
> consensusmap(res)
>
> Error in process_tracks(x, tracks, annRow, annCol) :
> Invalid special annotation track name ['basis:', 'consensus:',
> 'silhouette:']. Should partially match one of 'basis:', 'consensus:',
> 'silhouette:'.
>
> basismap(res)
>
> Error in process_tracks(x, tracks, annRow, annCol) :
> Invalid special annotation track name ['basis']. Should partially match
> one of 'basis', ':basis', 'basis:'.
>
> coefmap(res)
>
> Error in process_tracks(x, tracks, annRow, annCol) :
> Invalid special annotation track name ['basis', 'consensus:']. Should
> partially match one of 'basis', 'consensus:', ':basis', 'basis:'.
>
>
> sessionInfo()
>
> R version 3.1.3 (2015-03-09)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> Running under: OS X 10.7.5 (Lion)
>
> 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 stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] doParallel_1.0.8 iterators_1.0.7 foreach_1.4.2 NMF_0.20.5
> Biobase_2.26.0 BiocGenerics_0.12.1
> [7] cluster_2.0.1 rngtools_1.2.4 pkgmaker_0.22
> registry_0.2
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-11 colorspace_1.2-6 compiler_3.1.3 digest_0.6.8
> ggplot2_1.0.1 grid_3.1.3 gridBase_0.4-7
> [8] gtable_0.1.2 magrittr_1.5 MASS_7.3-40 munsell_0.4.2
> plyr_1.8.2 proto_0.3-10 RColorBrewer_1.1-2
> [15] Rcpp_0.11.5 reshape2_1.4.1 scales_0.2.4
> stringi_0.4-1 stringr_1.0.0 tools_3.1.3 xtable_1.7-4
>
>
>
> Gordon
> --
> Gordon Robertson
> Canada's Michael Smith Genome Sciences Centre
> BC Cancer Agency
> Vancouver BC Canada
> www.bcgsc.ca<http://www.bcgsc.ca/>
> T: 604-707-5900 x675416
> Skype: a.gordon.robertson
>
>
>
>
>
>
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--
Renaud Gaujoux, PhD
Systems Immunology - Technion, Haifa, Israel
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