[BioC] flowClust package - how to get it installed

[Martin Morgan]

(sorry for the re-send, the first didn't make it to the list)

"Kort, Eric" <Eric.Kort at vai.org> writes:

Hi Eric -- a couple of suggestions below...

> Anne writes:
> Rgui, the following worked for me (on Windows XP, R 2.7):
>
> install.packages("flowClust")
>
> And I presume this will work also:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("flowClust")

Follow the second approach (source + biocLite). This will ensure, for
instance, that your R / bioc packages are compatible, that you're
accessing the correct repository, that you're getting necessary
dependencies, etc. It'll also give others on the list, including the
pacakge maintainer, confidence that the package has been installed in
a reproducible way.

> However, you WILL need the GSL libraries installed (libgsl.dll and
> libgslcblas.dll).  I got them from here:
>
> http://gnuwin32.sourceforge.net/downlinks/gsl-bin-zip.php
>
> Unzip that file and simply copy bin/libgsl.dll and bin/libgslcblas.dll
> to some location on your PATH.  (The simplest thing to do is just to
> copy these two files to
> c:/whereever/you/installed/R/library/flowClust/libs.)

While simple, this'll bring you grief in the long run, e.g., when you
update R or GSL, want to use GSL libraries for some other purpose,
etc. I'd follow the recommendations in gsl-bin-zip.php, and add the
path to the .dll to a PATH environment variable.

Martin

> Having done that, I was able to load the library and run the examples.
>
> -Eric
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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