[NMF-user] NMF v0.20.5 on OS X gives a error for consensusmap(res) (Gordon Robertson)
Gordon Robertson
grobertson at bcgsc.ca
Tue May 26 17:42:57 CEST 2015
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<http://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<mailto:nmf-user-request at lists.r-forge.r-project.org>> <nmf-user-request at lists.r-forge.r-project.org<mailto: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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