[Bioc-sig-seq] Rsamtools installation

[Hervé Pagès]

Hi Guy,

[I'm cc'ing the bioc-sig-seq list]

Tillinghast, Guy, M.D. wrote:
> Dr. Pages,
>  
> I am looking for the set of MS-DOS commands for installing Rsamtools, 
> via Rtools, onto my version of R.

Just to clarify, Rsamtools has little to do with Rtools.

Rsamtools is an R package (R extension), more precisely a Bioconductor
package. Rtools is not an R extension, it's a set of tools for Windows
that first need to be installed on your system before you can install
R extensions *from source*.

Installing Rtools can be tricky and is considered something that only
advanced users should do. The primary source of information for
this is section "3 Installing R under Windows" of the "R Installation
and Administration" manual:

http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Windows

Note that problems with Rtools installation are not Bioconductor
related. Therefore questions concerning it are better addressed to
the R-devel mailing list. But before you do so, you need to make sure
that you've followed exactly the steps described in the above
documentation. If the problem persists, then report it with at much
details as you can (saying "trying 'R CMD INSTALL Rsamtools' does
not work" is not enough).

Once you've managed to install Rtools on your Windows box, you should
be able to install most CRAN or Bioconductor package with (from within
R):

   biocLite("pkgname", type="source")

Make sure you try this first (with, let's say, the IRanges package)
before you go any further. If that doesn't work, then something is
wrong with your Rtools installation.

Note that, most of the times, Windows users don't need to install
Rtools, because, for most CRAN and Bioconductor packages, a Windows
binary is available. So they can just do:

   biocLite("pkgname")

Now in the case of Rsamtools, the situation is a little bit more
complicated because it is not part of our devel builds yet so
biocLite() won't find it (with or without 'type="source"'). That
means you need to retrieve a working copy of its source tree via
svn with:
   svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
(user: readonly, pass: readonly).

and then install with: R CMD INSTALL Rsamtools

It's important that you use a recent R devel for this (R-2.11)
because the current Rsamtools (v 0.1.45) is designed to work with
BioC 2.6 + R 2.11.

But that also means that you are venturing on a tough road when another
*much* easier option for you would be to wait a week or two when the
Rsamtools package will be added to our devel builds. Then, if everything
goes well, a Windows binary will become available and you'll be able
to install it with just:

   biocLite("pkgname")

(again from within R 2.11).

Cheers,
H.


>  
> I have seen a set of commands for the MAC (which seems to employ the 
> commands HOME,INCLUDE,LIB,PATH, MSVSPATH, ROOTSYS,R_LIBS, and TMPDIR) 
> and have perused the sequencing list-server to find the commands for 
> windows.
>  
> In this list of MAC commands, I recognize PATH, which I have set up for 
> my Windows XP with:
> path=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;c:\MiKTeX2.8\miktex\bin;c:\R\bin;c:\Rsamtools
>  
> However, it appears that I need to translate the other seven commands.  
> [trying 'R CMD INSTALL Rsamtools' does not work.]
>  
> I have Rtools, perl, MinGW,and miktex installed.  I have a circa 
> November, 2009 copy of Rsamtools on my hard drive, though could use 
> Subversion to obtain another version if needed.  
>  
> It appears the additional 7 MS-DOS commands are needed to enable Rtools 
> to parse my Rsamtools folder on my hard drive and accomplish the 
> installation. 
>  
> Guy
> 
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-- 
Hervé Pagès

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