G'day, Several MZmine modules rely on R for their processing - these include Baseline Correction, XCMS and CAMERA Search.
Configuring the Java-R interface used by MZmine can be tricky and there are regular posts to this mailing-list asking for help with this. The user manual contains instructions on how to configure the MZmine start-up script to use R, see https://bit.ly/MZmineManual#h.1pys305nsw0o The salient steps are as follows: 1. Install R (http://http://www.r-project.org) 2. The following packages must be installed in your R distribution: rJava, ptw, gplots, xcms and CAMERA. To install them, run the following commands in R: install.packages(c("rJava", "ptw", "gplots")) source("http://bioconductor.org/biocLite.R";) biocLite("xcms") biocLite("CAMERA") 3. Set the following parameters according to your R configuration: R_HOME This is the directory where R is installed, e.g. for Windows it will be something like C:\Program Files\R\R-2.15.0 R_LIBS_USER This is the directory in which R installs third-party packages. It's usually a sub-directory of your personal directory, e.g. for Windows it will be something like %USERPROFILE%\Documents\R\win-library\2.15. For some R installations it might the library sub-directory of R_HOME, e.g. %R_HOME%\library. PATH Append the directory that contains R's libraries. It will be a sub-directory of %R_HOME%, e.g. for 32-bit Windows it will be something like %R_HOME%\bin\i386 or for 64-bit Windows %R_HOME%\bin\x64 JRI_LIB_PATH This is the directory where rJava has installed its JRI libraries. It will be a sub-directory of %R_LIBS_USER%, e.g. for 32-bit Windows it will be something like %R_LIBS_USER%\rJava\jri\i386 or for 64-bit Windows %R_LIBS_USER%\rJava\jri\x64 If, after performing these steps, MZmine is still unable to use R, then please post a message to this list with details of your MZmine and R configuration. Follow the guidelines in the user manual, see https://bit.ly/MZmineManual#h.ieegr3ccm53e With regard to your R configuration please include the following information: What version of R have you installed? Where is R installed? Do you have a 32-bit or 64-bit operating system? Are you running the 32-bit or 64-bit version of R? Run R from the command-line (this is how MZmine uses R). For 32-bit Windows, the command will be something like: C:\Program Files\R\R-2.15.2\bin\i386\R.exe and for 64-bit Windows: C:\Program Files\R\R-2.15.2\bin\x64\R.exe Then send us the output of the following R commands. .libPaths() packageDescription("xcms") packageDescription("ptw") packageDescription("rJava") Finally, please let us know the settings you've configured in your MZmine start-up script for the variables listed above (or simply attach the script to your message). Thanks, Chris. This 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. ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
