[R] RMySQL on win32

[Martin Morgan]

Pete Cap <peteoutside at yahoo.com> writes:

> List,
>
> I am still unable to compile RMySQL on XP and would appreciate any
> assistance anyone could provide.
>
> I know that setting up RMySQL on win32 is not easy.  The
> installation instructions are supposedly contained in
> ../src/README.win.  They give instructions on creating a file,
> libmysql.a, which I was able to do successfully.
>
> Here is where the instructions basically break down.  The creation
> of this file all occurs in \MySQL\..\lib\opt, after which the reader
> is instructed to copy libmysql.a to ..\lib\opt (huh?  You mean,
> where it already is?).  Then the reader is instructed to build the
> binaries with Rcmd build --binary RMySQL.
>
>>From the windows command shell, the result is:
>
> C:\>Rcmd build --binary RMySQL
> * checking for file 'RMySQL/DESCRIPTION' ... OK
> * preparing 'RMySQL':
> * checking DESCRIPTION meta-information ...'sh' is not recognized as an internal  or external command, operable program or batch file.
>  OK
> * cleaning src

> 'sh' is not recognized as an internal or external command, operable program or batch file.
> Error: cannot open file 'c:/TEMP/Rout381268676' for reading

> Apparently R is trying to call some shell script (from the windows
> prompt??) so I attempted this in cygwin.  Results:

Is this because you do not have the R tool chain required for building
R packages on Windows correctly installed? See the R Installation and
Administration Guide

http://cran.r-project.org/doc/manuals/R-admin.html

section 3 (Installing R under Windows); also perhaps

http://wiki.fhcrc.org/bioc/HowTo/Build_R_on_Windows

You'll eventually want Rtools\bin ahead of any cygwin paths in your
PATH variable, so that

c:\> which sh

('which' is a cygwin command, cygwin is not technically required to
install R packages on Windows) points to the R version of sh.

I seem to remember having some trouble finding reimp (used by
configure.win), with the link here

http://www.mingw.org/mingwfaq.shtml

providing some help -- you'll want reimp available in the bin
directory of MinGW; this might not be relevant.

Martin

> Can't locate R/Dcf.pm in @INC (@INC contains: c \PROGRA~1\R\R-24~1.1\share\perl; /usr/lib/perl5/5.8/cygwin /usr/lib/perl5/5.8 /usr/lib/perl5/site_perl/5.8/cygwin /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/site_perl/5.8/cygwin /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/cygwin /usr/lib/perl5/vendor_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/cygwin /usr/lib/perl5/vendor_perl/5.8 .) at c:\PROGRA~1\R\R-24~1.1/bin/build line 29.
> BEGIN failed--compilation aborted at c:\PROGRA~1\R\R-24~1.1/bin/build line 29.
>
> Dcf.pm is actually located in C:\Program Files\R\R-2.4.1\share\perl\R.  I wonder if the variable @INC is simply incorrect (it's looking under R-24~1.1, not sure if the truncated value is actually correct) but I have no idea in which file it may be located.
>
> Anyone have any ideas?
> I have installed mingw-utils while attempting to get this up and running, if it matters.
>
> If there is a simply better solution that I should try, I would appreciate hearing about it as well.  All I really need to do at this point is send select and join queries to the local server--perhaps I should just install RSQLite from CRAN?
>
> Thanks in advance,
>
> Pete
>
>  
> ---------------------------------
> Be a PS3 game guru.
>
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>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org