<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello Renaud,<div><br></div><div>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. </div><div><div><br></div><div>> install.packages("~/Downloads/NMF_0.20.6.tar.gz", repos = NULL, type = "source")</div><div>> library(NMF) # NMF_0.20.5</div><div><br></div><div>> sessionInfo()</div><div>R version 3.1.3 (2015-03-09)</div><div>Platform: x86_64-apple-darwin10.8.0 (64-bit)</div><div>Running under: OS X 10.7.5 (Lion)</div><div><br></div><div>locale:</div><div>[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8</div><div><br></div><div>attached base packages:</div><div>[1] parallel stats graphics grDevices utils datasets methods base </div><div><br></div><div>other attached packages:</div><div> [1] RColorBrewer_1.1-2 ggplot2_1.0.1 <font class="Apple-style-span" color="#ff4013">NMF_0.20.6</font> Biobase_2.26.0 BiocGenerics_0.12.1</div><div> [6] cluster_2.0.1 rngtools_1.2.4 pkgmaker_0.22 registry_0.2 sfsmisc_1.0-27 </div><div>[11] matrixStats_0.14.0 </div><div><br></div><div>loaded via a namespace (and not attached):</div><div> [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 </div><div> [7] gridBase_0.4-7 gtable_0.1.2 iterators_1.0.7 magrittr_1.5 MASS_7.3-40 munsell_0.4.2 </div><div>[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 </div><div>[19] <font class="Apple-style-span" color="#ff4013">stringr_1.0.0</font> tools_3.1.3 xtable_1.7-4 </div><div>> data("esGolub")</div><div>> esGolub <- esGolub[1:200, ]</div><div>> esGolub$Sample <- NULL</div><div>> res <- nmf(esGolub, 3)</div><div>> res</div><div><Object of class: NMFfit></div><div> # Model:</div><div> ...</div><div> Timing:</div><div> user system elapsed </div><div> 0.164 0.005 0.168 </div><div>> fit(res)</div><div><Object of class:NMFstd></div><div>features: 200 </div><div>basis/rank: 3 </div><div>samples: 38 </div><div>> V.hat <- fitted(res)</div><div>> dim(V.hat)</div><div>[1] 200 38</div><div>> consensusmap(res) # gives a membership heatmap graphic</div><div>> coefmap(res)</div><div><font class="Apple-style-span" color="#ff4013">Error in process_tracks(x, tracks, annRow, annCol) : </font></div><div><font class="Apple-style-span" color="#ff4013"> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.</font></div><div>> basismap(res)</div><div><font class="Apple-style-span" color="#ff4013">Error in process_tracks(x, tracks, annRow, annCol) : </font></div><div><font class="Apple-style-span" color="#ff4013"> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.</font></div><div><br></div></div><div>Thank you,</div><div><br></div><div>Gordon<br><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>--</div><div>Gordon Robertson</div><div>Canada's Michael Smith Genome Sciences Centre</div><div>BC Cancer Agency </div><div>Vancouver BC Canada</div><div><a href="http://www.bcgsc.ca">www.bcgsc.ca</a></div></div><div><div>T: 604-707-5900 x675416</div><div><br></div></div></div></span></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<br><div><div>On 2015-05-23, at 3:00 AM, <<a href="mailto:nmf-user-request@lists.r-forge.r-project.org">nmf-user-request@lists.r-forge.r-project.org</a>> <<a href="mailto:nmf-user-request@lists.r-forge.r-project.org">nmf-user-request@lists.r-forge.r-project.org</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Send nmf-user mailing list submissions to<br><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:nmf-user@lists.r-forge.r-project.org">nmf-user@lists.r-forge.r-project.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span class="Apple-tab-span" style="white-space:pre"> </span>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/nmf-user<br>or, via email, send a message with subject or body 'help' to<br><span class="Apple-tab-span" style="white-space:pre"> </span>nmf-user-request@lists.r-forge.r-project.org<br><br>You can reach the person managing the list at<br><span class="Apple-tab-span" style="white-space:pre"> </span>nmf-user-owner@lists.r-forge.r-project.org<br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of nmf-user digest..."<br><br><br>Today's Topics:<br><br> 1. Re: NMF v0.20.5 on OS X gives a error for consensusmap(res)<br> (Gordon Robertson)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Fri, 22 May 2015 13:05:40 -0700<br>From: Gordon Robertson <grobertson@bcgsc.ca><br>To: Renaud <getoxxx@gmail.com><br>Cc: Denise Brooks <dbrooks@bcgsc.ca>,<br><span class="Apple-tab-span" style="white-space:pre"> </span>"nmf-user@lists.r-forge.r-project.org"<br><span class="Apple-tab-span" style="white-space:pre"> </span><nmf-user@lists.r-forge.r-project.org><br>Subject: Re: [NMF-user] NMF v0.20.5 on OS X gives a error for<br><span class="Apple-tab-span" style="white-space:pre"> </span>consensusmap(res)<br>Message-ID: <AA245AAF-0344-4E4E-89A7-68C49F106F49@bcgsc.ca><br>Content-Type: text/plain; charset="us-ascii"<br><br>Renaud,<br><br>Thank you for this lightning-fast response! I think I did update stringr last week. I'll update and will retry it.<br><br>Gordon<br><br><br>On 2015-05-22, at 12:59 PM, Renaud wrote:<br><br>This comes from a change in stringr, which you probably updated.<br>This is fixed in the master and devel branch on GitHub. You can install from there to get it right now.<br>I will push the fix to CRAN on Monday.<br><br>Bests,<br>Renaud<br><br>On Friday, May 22, 2015, Gordon Robertson <grobertson@bcgsc.ca<mailto:grobertson@bcgsc.ca>> wrote:<br>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):<br><br>data("esGolub")<br>esGolub <- esGolub[1:200, ]<br>esGolub$Sample <- NULL<br>res <- nmf(esGolub, 3) # finished very quickly<br>res #matches vignette<br>fit(res) #matches vignette<br>V.hat <- fitted(res)<br>dim(V.hat) #matches vignette<br>summary(res) #matches vignette<br>summary(res, target = esGolub) #matches vignette<br>w <- basis(res)<br>dim(w)<br><br>consensusmap(res) #generates a membership heatmap graphic<br><br><blockquote type="cite">coefmap(res)<br></blockquote>Error in process_tracks(x, tracks, annRow, annCol) :<br> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.<br><br><blockquote type="cite">basismap(res)<br></blockquote>Error in process_tracks(x, tracks, annRow, annCol) :<br> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.<br><br>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.<br><br>It's a puzzle.<br><br>Gordon<br>--<br>Gordon Robertson<br>Canada's Michael Smith Genome Sciences Centre<br>BC Cancer Agency<br>Vancouver BC Canada<br>www.bcgsc.ca<http://www.bcgsc.ca/><br>T: 604-707-5900 x675416<br>Skype: a.gordon.robertson<br><br><br><br><br>On 2015-05-22, at 12:23 PM, Gordon Robertson wrote:<br><br>Renaud,<br><br>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.<br><br>This is puzzling, as I've used NMF for months without getting these errors.<br><br>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).<br><br>Can you offer any insights?<br><br>Thank you -<br><br><blockquote type="cite">n <- 50;<br></blockquote><blockquote type="cite">counts <- c(5, 5, 8);<br></blockquote><blockquote type="cite">V <- syntheticNMF(n, counts, noise=TRUE)<br></blockquote><blockquote type="cite">res <- nmf( V, 3, nrun=8, .options='tvP', .pbackend=4 )<br></blockquote>NMF algorithm: 'brunet'<br>Multiple runs: 8<br>Mode: parallel (4/8 core(s))<br>Runs: |==================================================| 100%<br>System time:<br> user system elapsed<br> 2.282 0.336 1.285<br><blockquote type="cite">consensusmap(res)<br></blockquote>Error in process_tracks(x, tracks, annRow, annCol) :<br> Invalid special annotation track name ['basis:', 'consensus:', 'silhouette:']. Should partially match one of 'basis:', 'consensus:', 'silhouette:'.<br><blockquote type="cite">basismap(res)<br></blockquote>Error in process_tracks(x, tracks, annRow, annCol) :<br> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.<br><blockquote type="cite">coefmap(res)<br></blockquote>Error in process_tracks(x, tracks, annRow, annCol) :<br> Invalid special annotation track name ['basis', 'consensus:']. Should partially match one of 'basis', 'consensus:', ':basis', 'basis:'.<br><br><br><blockquote type="cite">sessionInfo()<br></blockquote>R version 3.1.3 (2015-03-09)<br>Platform: x86_64-apple-darwin10.8.0 (64-bit)<br>Running under: OS X 10.7.5 (Lion)<br><br>locale:<br>[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8<br><br>attached base packages:<br>[1] parallel stats graphics grDevices utils datasets methods base<br><br>other attached packages:<br> [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<br> [7] cluster_2.0.1 rngtools_1.2.4 pkgmaker_0.22 registry_0.2<br><br>loaded via a namespace (and not attached):<br> [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<br> [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<br>[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<br><blockquote type="cite"><br></blockquote><br>Gordon<br>--<br>Gordon Robertson<br>Canada's Michael Smith Genome Sciences Centre<br>BC Cancer Agency<br>Vancouver BC Canada<br>www.bcgsc.ca<http://www.bcgsc.ca/><br>T: 604-707-5900 x675416<br>Skype: a.gordon.robertson<br><br><br><br><br><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://lists.r-forge.r-project.org/pipermail/nmf-user/attachments/20150522/06031df9/attachment-0001.html><br><br>------------------------------<br><br>_______________________________________________<br>nmf-user mailing list<br>nmf-user@lists.r-forge.r-project.org<br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/nmf-user<br><br>End of nmf-user Digest, Vol 9, Issue 2<br>**************************************<br></div></blockquote></div><br></div></body></html>