[R] SPOT install error

[Duncan Murdoch]

On 21/07/2015 11:43 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
>      * 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

NAMESPACE files have been required in R since R 3.0.0.  If that package
doesn't have one, it sounds as though it hasn't been actively
maintained.  Will definitely be a case of "some assembly required", not
to mention the usual "use at your own risk".

Duncan Murdoch

> 
> (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.)
> 
> 
> William R. Morgan, Ph.D.
> The College of Wooster
> Department of Biology
> Wooster, OH 44691
> 
> 
> 
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