[R] SPOT install error

[David Winsemius]

On Jul 21, 2015, at 8:43 AM, William Morgan wrote:

> I’m having trouble installing the SPOT R package for microarray image analysis. I’m awaiting a response from the packager developer, but wanted to see if anyone here has successfully used CSIRO’s SPOT software.
> 
> I’ve been following the developer’s "Spot Installation Instructions for Linux and Unix" <http://www.hca-vision.com/Spot_Documentation/Spot_Install_UNIX.pdf>: 
> 
> - Downloaded the Spot package (Spot_3.2_x86_64.tar) to my hard disk.
> 
> - Started R: 
> 
>     R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
>     Copyright (C) 2015 The R Foundation for Statistical Computing
>     Platform: x86_64-apple-darwin13.4.0 (64-bit)
>     …
> 
> - As instructed, executed the command: 
>> install.packages("Spot_3.2_x86_64.tar.gz", CRAN = NULL)
> 
>  This produced:
>     Warning in install.packages :
>       package ‘Spot_3.2_x86_64.tar.gz’ is not available (for R version 3.2.1)
> 
> Presuming that R was looking for the package in a repository and not my hard disk, I modified the command:
>> install.packages("~/Downloads/Spot_3.2_x86_64.tar.gz", repos = NULL, type = "source")
> 
>  This produced:
>     * installing *source* package ‘Spot’ ...
>     ERROR: a 'NAMESPACE' file is required

If your package does not have a NAMESPACE (which was acceptable several R versions ago) then you either need to revert to an older R from the same era as this was written, or you need to edit the source of the package to create a NAMESPACE.

-- 
David.

>     * removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Spot’
>     Warning in install.packages :
>       installation of package ‘/Users/wmorgan/Downloads/Spot_3.2_x86_64.tar.gz’ had non-zero exit status
> 
> (I also tried type = “mac.binary” or “mac.binary.maverick”, but this only produced an error message that it's is not a mac binary file.)
> 
> 


David Winsemius
Alameda, CA, USA