[NMF-user] NMF v0.20.5 on OS X gives a error for consensusmap(res)

[Renaud Gaujoux]

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> 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
> 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
> T: 604-707-5900 x675416
> Skype: a.gordon.robertson
>
>
>
>
>
>
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