[R] SPOT install error

[William Morgan]

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

(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