[BioC] Running R without X11?

[Sean Davis]

On Sat, Sep 6, 2008 at 2:12 AM, ALok <foralok at gmail.com> wrote:
> The problem you mentioned
>
>  unable to load shared library
> '/usr/local/lib/R/library/tcltk/libs/tcltk.so':
>
> One option is to install R by using tar package.
> to  configure R in share library mode
> you can use the option
> ../configure --enable-R-shlib
> This will allow you to share the R library

Alok,

The --enable-R-shlib will compile the R library as a shared library so
that it can be included in other programs.  However, it does not
affect library building for R, so reconfiguring will not improve
matters.  In other words, R uses shared libraries with foreign
language packages (C, Fortran code), which is what the error message
is implying is a problem.  In additino, R can be a shared library
itself for other programs, and the -enable-R-shlib enables this.

Sean


> On Sat, Sep 6, 2008 at 3:07 AM, Amy Johnson <a7johnson at gmail.com> wrote:
>
>> Hi, I'm trying to run batch R scripts that is triggered online with PHP
>> code:
>>
>> exec(R --no-save -q < myscript.r > output.txt 2>&1);
>>
>> However, as there are some R libraries, e.g. qvalue, webbioc needs X11
>> (tcltk) loaded, I got the following errors:
>>
>> Loading Tcl/Tk interface ... Error in dyn.load(file, DLLpath = DLLpath,
>> ...)
>> :
>>  unable to load shared library
>> '/usr/local/lib/R/library/tcltk/libs/tcltk.so':
>>  /usr/lib/libXft.so.2: undefined symbol: FT_GlyphSlot_Embolden
>> Error : .onLoad failed in 'loadNamespace' for 'tcltk'
>> Error: package/namespace load failed for 'tcltk'
>> Execution halted
>>
>> I have no problem to run the script on the shell when X11 is lauched. How
>> do
>> I launch X11 before running R scripts in batch from the web? Is there a way
>> to avoid loading tcltk when loading R libraries like qvalue and webbioc? As
>> far as I remember, the old versions of qvalue and webbioc do not require
>> tcltk.
>>
>> Thanks
>>
>> Amy.
>>
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>
>
>
> --
> Ph.D scholar
> Centre of Computational Biology and Bioinformatics
> School of Information Technology
> JNU New Delhi
>
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