<div dir="ltr"><div><div><div>Hi Gordon,<br><br></div>I believe the warning you get is because you manually set repos=NULL. The warning message says that package <font color="#db5127">‘~/software/clustering/NMF/R/NMF/v0.16.2/NMF_0.16.2.tar.gz’ </font>(the whole string) is not available from CRAN, which is true.<br>
</div>So no issues here.<br><br></div><div>Bests,<br></div>Renaud<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/4/6 Gordon Robertson <span dir="ltr"><<a href="mailto:grobertson@bcgsc.ca" target="_blank">grobertson@bcgsc.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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 (...<span style="color:rgb(219,81,39)">is not available (for R version 3.0.0)</span>). </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 color="#db5127">Warning in install.packages :</font></div>
<div><font 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'" target="_blank">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 style="white-space:pre-wrap"> </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>
<div style="word-wrap:break-word"><div style="word-wrap:break-word">--</div><div style="word-wrap:break-word">Gordon Robertson<br>Michael Smith Genome Sciences Centre</div><div style="word-wrap:break-word">BC Cancer Agency<br>
Vancouver BC Canada<br><a href="http://www.bcgsc.ca" target="_blank">www.bcgsc.ca</a><br><br></div></div>
</div>
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<pre cols="72">Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa</pre>
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