[R] SPOT install error

William Morgan
Tue, 21 Jul 2015 15:43:15 -0000

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