<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Renaud,<div><br></div><div>I was able to install the v0.9.0 package as source (OS X 10.7.5, R 2.15.1, from RStudio 0.97.168): </div><div><br></div><div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">> install.packages('NMF', repos=c('<a href="http://web.cbio.uct.ac.za/~renaud/CRAN'">http://web.cbio.uct.ac.za/~renaud/CRAN'</a>, getOption('repos')),type='source')</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">Installing package(s) into ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">(as ‘lib’ is unspecified)</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">also installing the dependency ‘rngtools’</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">trying URL '<a href="http://cran.stat.sfu.ca/src/contrib/rngtools_1.0.tar.gz'">http://cran.stat.sfu.ca/src/contrib/rngtools_1.0.tar.gz'</a></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">Content type 'application/x-gzip' length 87523 bytes (85 Kb)</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">opened URL</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">==================================================</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">downloaded 85 Kb</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">trying URL '<a href="http://web.cbio.uct.ac.za/~renaud/CRAN/src/contrib/NMF_0.9.tar.gz'">http://web.cbio.uct.ac.za/~renaud/CRAN/src/contrib/NMF_0.9.tar.gz'</a></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">Content type 'application/x-gzip' length 2526890 bytes (2.4 Mb)</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">opened URL</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">==================================================</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">downloaded 2.4 Mb</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">* installing *source* package ‘rngtools’ ...</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">** package ‘rngtools’ successfully unpacked and MD5 sums checked</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">** R</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">…</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">** testing if installed package can be loaded</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">*** arch - i386</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">*** arch - x86_64</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">* DONE (rngtools)</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">* installing *source* package ‘NMF’ ...</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">** libs</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">*** arch - i386</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">…</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">*** arch - x86_64</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">…</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">** installing vignettes</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"> ‘NMF-unitTests.Rnw’ </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"> ‘NMF-vignette.Rnw’ </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"> ‘heatmaps.Rnw’ </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">** testing if installed package can be loaded</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">*** arch - i386</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">*** arch - x86_64</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">* DONE (NMF)</font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">...</span></font></div></div><div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">> library(NMF)</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">Loading required package: pkgmaker</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">Loading required package: digest</font></div></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">…</font></div><div><span class="Apple-style-span" style="font-family: Courier; font-size: 11px; ">> sessionInfo()</span></div><div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">R version 2.15.1 (2012-06-22)</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">locale:</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">attached base packages:</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">[1] grid parallel stats graphics grDevices utils datasets methods base </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">other attached packages:</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"> [1] NMF_0.9 Biobase_2.16.0 BiocGenerics_0.2.0 RColorBrewer_1.0-5 colorspace_1.2-0 </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"> [6] gridBase_0.4-5 bigmemory_4.3.0 bigmemory.sri_0.1.2 doParallel_1.0.1 iterators_1.0.6 </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">[11] foreach_1.4.0 registry_0.2 rngtools_1.0 pkgmaker_0.9 codetools_0.2-8 </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">[16] stringr_0.6.1 digest_0.5.2 synapseClient_0.19-0 BiocInstaller_1.4.9 </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;"><br></font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">loaded via a namespace (and not attached):</font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">[1] affy_1.34.0 affyio_1.24.0 plyr_1.7.1 preprocessCore_1.18.0 RCurl_1.95-3 </font></div><div><font class="Apple-style-span" face="Courier" style="font-size: 11px;">[6] RJSONIO_1.0-1 tools_2.15.1 xtable_1.7-0 zlibbioc_1.2.0 </font></div></div><div><br></div><div>(I subscribed to nmf-users tonight, but realize now that I did this from my personal email account, so the emails from my GSC account are being held until the moderator approves them. I'll fix this in the morning.)</div><div><br></div><div>Thank you. </div><div><br></div><div>Gordon</div><div><div apple-content-edited="true">
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<br><div><div>On 2012-11-10, at 10:58 PM, Renaud wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Gordon, <br><br>indeed.<br>I forgot to mention that the package is not available for Mac, but this is only because I have no access to a Mac and there is no Mac-builder that I am aware of.<br>If would be nice if someone could build Mac version(s) from the package source though. I could add them to the repository.<br>
Thank you.<br><br>Bests,<br>Renaud.<br><br>PS: Gordon, please subscribe to the mailing list so that you messages can go through.<br><div class="gmail_extra"><br><br><div class="gmail_quote">2012/11/10 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"><div>Renaud,</div><div><br></div><div><div>I can view your CRAN page at <a href="http://web.cbio.uct.ac.za/~renaud/CRAN/" target="_blank">http://web.cbio.uct.ac.za/~renaud/CRAN/</a>, and can download the source file from the NMF page. </div>
</div><div><br></div><div>But I get an error when I try to install v0.9 as you suggested, using R 2.15.1 on OS X 10.7.5, from RStudio. </div><div><br></div><div>Can you help me understand what the problem is? </div><div><br>
</div><div><div><font face="Courier">> install.packages('NMF', repos=c('<a href="http://web.cbio.uct.ac.za/~renaud/CRAN'" target="_blank">http://web.cbio.uct.ac.za/~renaud/CRAN'</a>, getOption('repos')))</font></div>
<div><font face="Courier">Installing package(s) into ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’</font></div><div><font face="Courier">(as ‘lib’ is unspecified)</font></div><div><font face="Courier">Warning in install.packages :</font></div>
<div><font face="Courier"> cannot open: HTTP status was '404 Not Found'</font></div><div><font face="Courier">Warning in install.packages :</font></div><div><font face="Courier"> cannot open: HTTP status was '404 Not Found'</font></div>
<div><font face="Courier">Warning in install.packages :</font></div><div><font face="Courier"> unable to access index for repository <a href="http://web.cbio.uct.ac.za/~renaud/CRAN/bin/macosx/leopard/contrib/2.15" target="_blank">http://web.cbio.uct.ac.za/~renaud/CRAN/bin/macosx/leopard/contrib/2.15</a></font></div>
<div><font face="Courier">Warning in install.packages :</font></div><div><font face="Courier"> package ‘NMF’ is not available (for R version 2.15.1)</font></div><div><br></div><div>Thanks,</div><div><br></div><div>G</div>
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<br><div><div>On 2012-11-10, at 3:21 AM, Renaud wrote:</div><br><blockquote type="cite">Dear NMF enthusiasts,<br><br>following some recent changes/enforcement of CRAN policies the NMF package was archived on mid-September, while I was on leave. As a result it has not been accessible for standard installation ever since. I apologise for the inconvenience and hope it did not affect your research or interest in NMF methodologies.<br>
<br>I have been working hard on a new version, so that it could quickly make its way to CRAN, and bring along a set of improvements developed over the past year, such as a brand new and improved annotated heatmap engine for visualizing NMF results.<br>
<br>The update is now ready and passes all the checks on my system, but for some reason fails on CRAN own machines, and some investigation about this dark magic is necessary until the package is finally back live on CRAN.<br>
<br>It is important that the package is immediately available in some way though, especially given the many enquiries I had about the package and its disappearance from R world. So I put a pre-release version on my personal CRAN-like repository, from which the package can be installed via the following command:<span><br>
<br>install</span><span>.</span><span>packages</span><span>(</span><span>'NMF'</span><span>,</span><span> repos</span><span>=</span><span>c</span><span>(</span><span>'<a href="http://web.cbio.uct.ac.za/~renaud/CRAN" target="_blank">http://web.cbio.uct.ac.za/~renaud/CRAN</a>'</span><span>,</span><span> getOption</span><span>(</span><span>'repos'</span>)))<code></code><br>
<br>I hope you will like this new version and welcome any feedback, bug report, discussion or suggestion, which could improve the package's quality and usability.<br>Note that there is a mailing list dedicated to this (<a href="mailto:nmf-user@lists.r-forge.r-project.org" target="_blank">nmf-user@lists.r-forge.r-project.org</a>) to which you can subscribe, if you have not already:<br>
<br><a href="https://lists.r-forge.r-project.org/mailman/listinfo/nmf-user" target="_blank">https://lists.r-forge.r-project.org/mailman/listinfo/nmf-user</a><br><br>Last but not least, an eye-candy browsable version of the documentation pages is available online at:<br>
<br><a href="http://nmf.r-forge.r-project.org/" target="_blank">http://nmf.r-forge.r-project.org</a><br><br>I will let you know when the package is officially released on CRAN.<br><br>Bests,<br>Renaud<br clear="all"><br>
PS: you are receiving this email because you showed interest in the NMF package, in some way or another. Please send me an email if you do not want to receive any more emails about it.<span class="HOEnZb"><font color="#888888"><br>
<br>-- <br><pre cols="72">Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa</pre><br>
</font></span></blockquote></div><br></div></blockquote></div><br><br clear="all"><br>-- <br><pre cols="72">Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa</pre><br>
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