Re: Running R from Unix Command Line

>I have a CGI PERL Script that needs to
>invoke the R program on the command line
>of UNIX and send commands to it.

>Can I do this using the normal system command?

Yes.

>Would this work?

Yes.

>If so, how can I specify the commands without clashing
>with the double quotes of perl and that of R?

I had perl create an R script as a file. I used a template and the Perl Template Toolkit to do this. Then, I call R like this:

my $cmd = qq( <R executable> CMD BATCH <R script> );
my $errorlevel = system($cmd);

You can check if it worked like this:

if ($errorlevel) {

    # handle errors

}

Regards,
Michael.

--
-----------------------------------------------------------
Dipl.-Inform. Michael Nuhn
Bioinformatik
Zentrum für Nanostrukturtechnologie und
Molekularbiologische Technologie

+49 (0)631 - 205 4334
[email protected]
http://www.nuhn.net
-----------------------------------------------------------

  ----- Original Message ----- 
  From: Shalini Sridhar 
  To: [email protected] 
  Sent: Thursday, August 03, 2006 12:41 PM
  Subject: [Biodevelopers] Running R from Unix Command Line


  Hello all,

  If someone can please throw a light on this I would be eternally greatful :

  I have a CGI PERL Script that needs to invoke the R program on the command line of UNIX and send commands to it.

  Can I do this using the normal system command? Would this work? If so, how can I specify the commands without clashing with the double quotes of perl and that of R?

  If not, could someone please suggest an alternative to this ?

  Thanks

  Shalini









   






----------------------------------------------------------------------------
    From: João Miguel Fernandes <[email protected]>
    Reply-To: Programming for bioinformatics <[email protected]>
    To: [email protected]
    Subject: [Biodevelopers] CfP: MOMPES 2007, published by IEEE CS Press
    Date: Sat, 8 Jul 2006 15:26:20 +0100
    >[Apologies for multiple copies]
    >
    >******************************************************************
    > CALL FOR PAPERS
    >
    > 4th International Workshop on Model-based Methodologies for
    > Pervasive and Embedded Software (MOMPES 2006)
    >
    > http://www.di.uminho.pt/mompes
    >
    > within the
    >7th European Joint Conferences on Theory and Practice of Software
    > (ETAPS 2007)
    > http://www.di.uminho.pt/etaps07/
    > Braga - Portugal
    > March 31, 2007
    >******************************************************************
    >Model Based Development (MBD) comprises approaches to software
    >development, which heavily rely on modelling and the systematic
    >transition from models to executable code. One of these approaches
    >is the OMG's Model Driven Architecture (MDA), which is based on
    >the separation between the specification of a system and its
    >implementation using specific platforms.
    >
    >This workshop focuses on the theoretical and practical aspects
    >related with the adoption of MDA and other MBD methodologies
    >(notation, process, methods, and tools) for supporting the
    >construction of computer-based systems, and more specifically,
    >pervasive and embedded software.
    >
    >Suggested areas of interest in the workshop include, but are not
    >restricted to:
    >
    >Suggested areas of interest in the workshop include, but are not
    >restricted to:
    >- Specification of Platform Independent Models (PIMs) and Platform
    > Specific Models (PSMs)
    >- PIM to PSM transformations
    >- MBD process for embedded and pervasive software
    >- Automatic code generation in MBD
    >- Testing and validation in MBD
    >- Tools for MBD of embedded and pervasive software
    >- Model-based development of hardware and software systems
    >- Model-based architectures
    >- Meta-Models for MBD
    >- System evolution and maintenance
    >- Precise semantics and consistency checks in MBD
    >- Integration of feature modelling
    >- Case studies on the application of MBD
    >- Models and techniques to enhance the security of embedded and
    > pervasive software
    >
    >The official language is English.
    >Authors are requested to submit a PDF version of their papers in
    >IEEE 8.5"x11" Two-Column format (see "Information for Authors" tab 
    >at
    >http://www.computer.org/portal/site/cscps/index.jsp).
    >Papers should not exceed 10 pages, including figures, references,
    >and appendices.
    >Submitted papers will be reviewed by at least 3 PC members.
    >Authors of accepted papers must sign the IEEE copyright form.
    >Full papers exceeding 10 pages will be charged for pages in excess.
    >At least one author of each accepted submission must register
    >and present the paper at the workshop.
    >The proceedings will be published by IEEE Computer Society Press.
    >Position papers will be published online.
    >For details about the paper submission process, please consult the
    >workshop website.
    >
    >******************************************************************
    >Important Dates:
    >- Submission of full papers: 23.Oct.2006
    >- Notification of acceptance: 27.Nov.2006
    >- Camera-ready paper version: 29.Dec.2006
    >- Workshop at ETAPS 2007: 31.Mar.2007
    >
    >******************************************************************
    >Organizing Committee:
    >- João M. Fernandes U Minho (PT)
    >- Ricardo J. Machado U Minho (PT)
    >- Siobhan Clarke Trinity CD (IE)
    >- Ridha Khedri McMaster U (CA)
    >
    >Programme Committee:
    >- Jean Bézivin U Nantes (FR)
    >- Siobhan Clarke Trinity CD (IE)
    >- Jörg Desel KU Eichs.-Ingolstadt (DE)
    >- Dov Dori Technion (IL)
    >- João M. Fernandes U Minho (PT)
    >- Robert B. France Colorado SU (US)
    >- Antônio A. Fröhlich UF Santa Catarina (BR)
    >- Lidia Fuentes U Malaga (ES)
    >- Hassan Gomaa George Mason U (US)
    >- Luís Gomes UN Lisboa (PT)
    >- David Harel Weizmann I (IL)
    >- Mike Hinchey NASA (US)
    >- Jens B. Jorgensen U Aarhus (DK)
    >- Ridha Khedri McMaster U (CA)
    >- Pericles Loucopoulos UMIST (UK)
    >- Ricardo J. Machado U Minho (PT)
    >- Dirk Muthig IESE (DE)
    >- Franz Rammig U Paderborn (DE)
    >- Bran Selic IBM Rational Software (CA)
    >- João P. Sousa CMU (US)
    >- Dragos Truscan TUCS (FI)
    >- Arie van Deursen CWI (NL)
    >******************************************************************
    >
    >--
    >Joao M. Fernandes, PhD.
    >Dept. Informatics
    >Universidade do Minho
    >4710-057 Braga, PORTUGAL
    >
    >Phone: +351-253604454/9
    >Fax: +351-253604471
    >Email: jmf(AT)di(DOT)uminho(DOT)pt
    >Web: www.di.uminho.pt/~jmf
    >
    >

    ><< smime.p7s >> 


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