[R] SPOT install error

Duncan Murdoch
Tue, 21 Jul 2015 16:01:48 -0000

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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