[Nmf-user] [ANN] NMF version 0.9 pre-release - install error - resolved

Gordon Robertson grobertson at bcgsc.ca
Sun Nov 11 08:24:54 CET 2012 

Renaud,

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):

> install.packages('NMF', repos=c('http://web.cbio.uct.ac.za/~renaud/CRAN', getOption('repos')),type='source')
Installing package(s) into ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
(as ‘lib’ is unspecified)
also installing the dependency ‘rngtools’

trying URL 'http://cran.stat.sfu.ca/src/contrib/rngtools_1.0.tar.gz'
Content type 'application/x-gzip' length 87523 bytes (85 Kb)
opened URL
==================================================
downloaded 85 Kb

trying URL 'http://web.cbio.uct.ac.za/~renaud/CRAN/src/contrib/NMF_0.9.tar.gz'
Content type 'application/x-gzip' length 2526890 bytes (2.4 Mb)
opened URL
==================================================
downloaded 2.4 Mb

* installing *source* package ‘rngtools’ ...
** package ‘rngtools’ successfully unpacked and MD5 sums checked
** R
…
** testing if installed package can be loaded
*** arch - i386
*** arch - x86_64

* DONE (rngtools)
* installing *source* package ‘NMF’ ...
** libs
*** arch - i386
…
*** arch - x86_64
…
** installing vignettes
   ‘NMF-unitTests.Rnw’
   ‘NMF-vignette.Rnw’
   ‘heatmaps.Rnw’
** testing if installed package can be loaded
*** arch - i386
*** arch - x86_64

* DONE (NMF)
...
> library(NMF)
Loading required package: pkgmaker
Loading required package: digest
…
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] NMF_0.9              Biobase_2.16.0       BiocGenerics_0.2.0   RColorBrewer_1.0-5   colorspace_1.2-0
 [6] gridBase_0.4-5       bigmemory_4.3.0      bigmemory.sri_0.1.2  doParallel_1.0.1     iterators_1.0.6
[11] foreach_1.4.0        registry_0.2         rngtools_1.0         pkgmaker_0.9         codetools_0.2-8
[16] stringr_0.6.1        digest_0.5.2         synapseClient_0.19-0 BiocInstaller_1.4.9

loaded via a namespace (and not attached):
[1] affy_1.34.0           affyio_1.24.0         plyr_1.7.1            preprocessCore_1.18.0 RCurl_1.95-3
[6] RJSONIO_1.0-1         tools_2.15.1          xtable_1.7-0          zlibbioc_1.2.0

(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.)

Thank you.

Gordon


On 2012-11-10, at 10:58 PM, Renaud wrote:

Hi Gordon,

indeed.
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.
If would be nice if someone could build Mac version(s) from the package source though. I could add them to the repository.
Thank you.

Bests,
Renaud.

PS: Gordon, please subscribe to the mailing list so that you messages can go through.


2012/11/10 Gordon Robertson <grobertson at bcgsc.ca<mailto:grobertson at bcgsc.ca>>
Renaud,

I can view your CRAN page at http://web.cbio.uct.ac.za/~renaud/CRAN/, and can download the source file from the NMF page.

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.

Can you help me understand what the problem is?

> install.packages('NMF', repos=c('http://web.cbio.uct.ac.za/~renaud/CRAN', getOption('repos')))
Installing package(s) into ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository http://web.cbio.uct.ac.za/~renaud/CRAN/bin/macosx/leopard/contrib/2.15
Warning in install.packages :
  package ‘NMF’ is not available (for R version 2.15.1)

Thanks,

G


On 2012-11-10, at 3:21 AM, Renaud wrote:

Dear NMF enthusiasts,

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.

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.

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.

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:

install.packages('NMF', repos=c('http://web.cbio.uct.ac.za/~renaud/CRAN', getOption('repos')))

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.
Note that there is a mailing list dedicated to this (nmf-user at lists.r-forge.r-project.org<mailto:nmf-user at lists.r-forge.r-project.org>) to which you can subscribe, if you have not already:

https://lists.r-forge.r-project.org/mailman/listinfo/nmf-user

Last but not least, an eye-candy browsable version of the documentation pages is available online at:

http://nmf.r-forge.r-project.org<http://nmf.r-forge.r-project.org/>

I will let you know when the package is officially released on CRAN.

Bests,
Renaud

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.

--

Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa





--

Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa


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