Hi Chris,
I think the way you chose is good, but please make sure your changes do not
break the current functionality for people without R. That is, the scripts
should still run even when R is not installed.
Best,
Tomas
On Dec 6, 2010, at 7:21 PM, Pudney Chris (ext) GBJH wrote:
> G'day,
>
> I'm finishing off a module that uses an R package to perform baseline
> correction of raw data files.
>
> I want to know how to best package this module given that it introduces
> a dependency on R and some R packages. In order for the module to work
> the system needs:
>
> 1. R installed (64-bit if 64-bit JRE is running MZmine 2)
>
> 2. rJava package installed in R
>
> 3. ptw package installed in R
>
> Then the following lines need to be added/changed in startMZmine_Linux.sh:
>
> # Set R environment variables.
> export R_HOME=/usr/lib64/R
> export R_SHARE_DIR=/usr/share/R/share
> export R_INCLUDE_DIR=/usr/share/R/include
> export R_DOC_DIR=/usr/share/R/doc
> export LD_LIBRARY_PATH=${R_HOME}/lib:${R_HOME}/bin
>
> # Set JRI path: the directory holding the JRI JAR files and library.
> JRI_PATH=${HOME}/R/x86_64-pc-linux-gnu-library/2.10/rJava/jri
>
> # It is not necessary to modify the following section
> LOGGING_CONFIG_FILE=conf/logging.properties
> JAVA_PARAMETERS="-XX:+UseParallelGC -Djava.io.tmpdir=$TMP_FILE_DIRECTORY
> -Djava.util.logging.config.file=$LOGGING_CONFIG_FILE $USE_64_BIT
> -Xms${HEAP_SIZE}m -Xmx${HEAP_SIZE}m -Djava.library.path=${JRI_PATH}"
> CLASS_PATH=MZmine2.jar:${JRI_PATH}/JRIEngine.jar:${JRI_PATH}/JRI.jar:${JRI_PATH}/REngine.jar
>
> (similarly for Windows and MacOS).
>
> In fact, I've created separate start scripts rather than mess with the
> originals. Is this neat enough for contribution?
>
> Regards,
> Chris.
>
>
>
>
> Syngenta Limited, Registered in England No 2710846
> Registered Office : Syngenta Limited, European Regional Centre, Priestley
> Road, Surrey Research Park, Guildford, Surrey, GU2 7YH, United Kingdom
>
> message may contain confidential information. If you are not the designated
> recipient, please notify the sender immediately, and delete the original and
> any copies. Any use of the message by you is prohibited.
>
>
> ------------------------------------------------------------------------------
> What happens now with your Lotus Notes apps - do you make another costly
> upgrade, or settle for being marooned without product support? Time to move
> off Lotus Notes and onto the cloud with Force.com, apps are easier to build,
> use, and manage than apps on traditional platforms. Sign up for the Lotus
> Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d
> _______________________________________________
> Mzmine-devel mailing list
> Mzmine-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology
1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
TEL: +81-98-966-8684
------------------------------------------------------------------------------
What happens now with your Lotus Notes apps - do you make another costly
upgrade, or settle for being marooned without product support? Time to move
off Lotus Notes and onto the cloud with Force.com, apps are easier to build,
use, and manage than apps on traditional platforms. Sign up for the Lotus
Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
