<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Renaud,</div><div><br></div>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?<div><br></div><div><div>> library(NMF)</div><div>Loading required package: pkgmaker</div><div>Loading required package: registry</div><div><br></div><div>Attaching package: ‘pkgmaker’</div><div><br></div><div>The following object is masked from ‘package:utils’:</div><div><br></div><div> packageName</div><div><br></div><div>Loading required package: rngtools</div><div>Loading required package: digest</div><div>Loading required package: grid</div><div>NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 7/8</div><div>> library(RColorBrewer)</div><div>> n <- 100; counts <- c(10, 5, 8); p <- sum(counts) </div><div>> V <- syntheticNMF(n, counts, noise=TRUE)</div><div>> groups <- as.factor(do.call('c', lapply(seq(3), function(x) rep(x, counts[x]))))</div><div>> res <- nmf(V, 3, nrun=100)</div><div><font class="Apple-style-span" color="#db5127">Error: NMF::nmf - 100/100 fit(s) threw an error.</font></div><div><font class="Apple-style-span" color="#db5127"># Error(s) thrown:</font></div><div><font class="Apple-style-span" color="#db5127"> - run #1: Fatal error in attach: big.matrix could not be attached.</font></div><div>Timing stopped at: 31.804 1.025 5.987 </div><div><br></div><div>> sessionInfo()</div><div>R version 3.0.0 (2013-04-03)</div><div>Platform: x86_64-apple-darwin10.8.0 (64-bit)</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 grid stats graphics grDevices utils datasets </div><div>[8] methods base </div><div><br></div><div>other attached packages:</div><div> [1] doParallel_1.0.1 iterators_1.0.6 foreach_1.4.0 </div><div> [4] RColorBrewer_1.0-5 NMF_0.16.2 synchronicity_1.1.0</div><div> [7] bigmemory_4.4.3 BH_1.51.0-0 bigmemory.sri_0.1.2</div><div>[10] Biobase_2.20.0 BiocGenerics_0.6.0 digest_0.6.3 </div><div>[13] rngtools_1.2 pkgmaker_0.15.2 registry_0.2 </div><div><br></div><div>loaded via a namespace (and not attached):</div><div>[1] codetools_0.2-8 colorspace_1.2-1 compiler_3.0.0 gridBase_0.4-6 </div><div>[5] stringr_0.6.2 xtable_1.7-1 </div><div><br></div><div>--</div><div>I'm able to run simple jobs. </div><div><div>> x <- rmatrix(20,10)</div><div>> res <- nmf(x, 2)</div><div>> res <- nmf(x, 2, 'lee')</div><div><br></div></div><div>--</div><div>But possibly larger jobs hit the error?</div><div><div>> data(esGolub)</div><div>> res <- nmf(esGolub,3,seed=123456)</div><div>> res <- nmf(esGolub,3,seed=123456,nrun=20)</div><div><font class="Apple-style-span" color="#db5127">Error: NMF::nmf - 20/20 fit(s) threw an error.</font></div><div><font class="Apple-style-span" color="#db5127"># Error(s) thrown:</font></div><div><font class="Apple-style-span" color="#db5127"> - run #1: Fatal error in attach: big.matrix could not be attached.</font></div><div>Timing stopped at: 71.596 1.011 14.788 </div><div><div><br></div><div>> res <- nmf(esGolub,3,seed=123456,nrun=5,.options='v')</div><div>NMF algorithm: 'brunet'</div><div>Multiple runs: 5</div><div>Mode: parallel (7/8 core(s))</div><div>Runs: |==================================================| 100%</div><div><font class="Apple-style-span" color="#c03917">Error: NMF::nmf - 5/5 fit(s) threw an error.</font></div><div><font class="Apple-style-span" color="#c03917"># Error(s) thrown:</font></div><div><font class="Apple-style-span" color="#c03917"> - run #1: Fatal error in attach: big.matrix could not be attached.</font></div><div>Timing stopped at: 13.673 0.579 4.927 </div></div></div><div><br></div><div><br></div><div>Thank you,</div><div><br></div><div>G</div><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; ">--</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Gordon Robertson<br>Michael Smith Genome Sciences Centre</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">BC Cancer Agency<br>Vancouver BC Canada<br><a href="http://www.bcgsc.ca">www.bcgsc.ca</a><br><br></div></div>
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<br><div><div>On 2013-04-06, at 12:47 PM, Gordon Robertson wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Renaud,<div><br></div><div>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)). </div><div><br></div><div>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). </div><div><br></div><div>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. </div><div><div><br></div><div>> install.packages("~/software/clustering/NMF/R/NMF/v0.16.2/NMF_0.16.2.tar.gz", repos = NULL, type = "source")</div><div><font class="Apple-style-span" color="#db5127">Warning in install.packages :</font></div><div><font class="Apple-style-span" color="#db5127"> package ‘~/software/clustering/NMF/R/NMF/v0.16.2/NMF_0.16.2.tar.gz’ is not available (for R version 3.0.0)</font></div></div><div>...</div><div><div>> library(NMF)</div><div>Loading required package: pkgmaker</div><div>Loading required package: registry</div><div><br></div><div>Attaching package: ‘pkgmaker’</div><div><br></div><div>The following object is masked from ‘package:utils’:</div><div><br></div><div> packageName</div><div><br></div><div>Loading required package: rngtools</div><div>Loading required package: digest</div><div>Loading required package: grid</div><div>NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 7/8</div><div> To enable shared memory capabilities, try: install.extras('NMF')</div><div><br></div><div>> install.extras('NMF')</div><div>Loaded extra package: bigmemory</div><div>trying URL '<a href="http://cran.stat.sfu.ca/bin/macosx/contrib/3.0/synchronicity_1.1.0.tgz'">http://cran.stat.sfu.ca/bin/macosx/contrib/3.0/synchronicity_1.1.0.tgz'</a></div><div>Content type 'application/x-gzip' length 206844 bytes (201 Kb)</div><div>opened URL</div><div>==================================================</div><div>downloaded 201 Kb</div><div><br></div><div><br></div><div>The downloaded binary packages are in</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>/var/folders/x5/l6f5m2j91vdd99wy2gchtld40000gn/T//RtmpLXt3yC/downloaded_packages</div><div>Loading required package: synchronicity</div><div>Loaded extra package: Biobase</div></div><div><br></div><div><div>> sessionInfo()</div><div>R version 3.0.0 (2013-04-03)</div><div>Platform: x86_64-apple-darwin10.8.0 (64-bit)</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 grid stats graphics grDevices utils datasets methods base </div><div><br></div><div>other attached packages:</div><div> [1] synchronicity_1.1.0 NMF_0.16.2 bigmemory_4.4.3 BH_1.51.0-0 bigmemory.sri_0.1.2 </div><div> [6] Biobase_2.20.0 BiocGenerics_0.6.0 digest_0.6.3 rngtools_1.2 pkgmaker_0.15.2 </div><div>[11] registry_0.2 BiocInstaller_1.10.0</div><div><br></div><div>loaded via a namespace (and not attached):</div><div> [1] codetools_0.2-8 colorspace_1.2-1 doParallel_1.0.1 foreach_1.4.0 gridBase_0.4-6 </div><div> [6] iterators_1.0.6 RColorBrewer_1.0-5 stringr_0.6.2 tools_3.0.0 xtable_1.7-1 </div></div><div><br></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; ">--</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Gordon Robertson<br>Michael Smith Genome Sciences Centre</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">BC Cancer Agency<br>Vancouver BC Canada<br><a href="http://www.bcgsc.ca/">www.bcgsc.ca</a><br><br></div></div>
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