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

[Renaud]

I never built any package on Mac but you should be able to build the
package via the following command, if R development environment is
installed, which should be the case for Mac OS X:

# create local library
mkdir build_lib
# build package
R CMD INSTALL -l build_lib --build NMF_0.9.tar.gz
# possibly use flag --no-vignettes if the step "creating/re-building
vignettes" seems to take too long.

See
http://cran.r-project.org/doc/manuals/R-exts.html#Building-binary-packages

Renaud


2012/11/11 Gordon Robertson <grobertson at bcgsc.ca>

> Renaud,
>
> I run NMF v0.8.13 on OS X 10.7.5 and on CentOS 5.x. I should be able to
> build a Mac version of v0.9 from the source file, but would need
> instructions. Can you tell me what to do or point me to instructions on the
> web?
>
> 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>
>
>> 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) 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
>>
>> 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
>
>
>
>


-- 

Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
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