[R] SPOT install error

David Winsemius
Tue, 21 Jul 2015 19:49:31 -0000

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