xcmsPapply {xcms} | R Documentation

## Deprecated: xcmsPapply

### Description

This function is deprecated, use `bplapply` instead.

An apply-like function which uses Rmpi to distribute the processing evenly across a cluster. Will use a non-MPI version if distributed processing is not available.

### Usage

        xcmsPapply(arg_sets, papply_action, papply_commondata = list(),
               show_errors = TRUE, do_trace = FALSE, also_trace = c())

### Arguments

`arg_sets` | a list, where each item will be given as an argument to papply\_action
`papply_action` | A function which takes one argument. It will be called on each element of arg\_sets
`papply_commondata` | A list containing the names and values of variables to be accessible to the papply\_action. 'attach' is used locally to import this list.
`show_errors` | If set to TRUE, overrides Rmpi's default, and messages for errors which occur in R slaves are produced.
`do_trace` | If set to TRUE, causes the papply\_action function to be traced. i.e. Each statement is output before it is executed by the slaves.
`also_trace` | If supplied an array of function names, as strings, tracing will also occur for the specified functions.

### Details

Similar to apply and lapply, applies a function to all items of a list, and returns a list with the corresponding results.

Uses Rmpi to implement a pull idiom in order to distribute the processing evenly across a cluster. If Rmpi is not available, or there are no slaves, implements this as a non-parallel algorithm.

`xcmsPapply` is a modified version of the papply function from package papply 0.2 (Duane Currie). Parts of the slave function were wrapped in try() to make it failsafe and progress output was added.

### Value

A list of return values from papply\_action. Each value corresponds to the element of arg\_sets used as a parameter to papply\_action

### Note

Does not support distributing recursive calls in parallel. If papply is used inside papply\_action, it will call a non-parallel version

### Author(s)

Duane Currie <duane.currie@acadiau.ca>, modified by Ralf Tautenhahn <rtautenh@ipb-halle.de>.

### Examples

    ## Not run:
    library(Rmpi)
    library(xcms)

    number_lists <- list(1:10,4:40,2:27)

    mpi.spawn.Rslaves(nslaves=2)

    results <- xcmsPapply(number_lists,sum)
    results

    mpi.close.Rslaves()

    ## End(Not run)

[Package xcms version 3.10.2 Index]