R/sFsnowfall-internal.R

Defines functions onLoad debug simpleAssign absFilePath getNamedArguments fetchNames errHandler checkFunction checkTryErrorAny deleteRestoreFiles addRestoreFile dirCreateStop startedWithSfCluster fetchDirName setVar getVar setOption

## Functions copied from package snowfall (http://cran.r-project.org/web/packages/snowfall/index.html)
## as the package was removed from the CRAN repository.


##*****************************************************************************
## Unordered internal helper functions.
##*****************************************************************************

##*****************************************************************************
## Helpers for managing the internal variables in the package namespace without
## awake the R CMD check for later R versions (which basically blaims many
## global assignings).
##
## The given solution has an advantage: only writing is affected. Reading of the
## objects can remain the same (thanks to Uwe Ligges for the tipp):
##   reading:  .sfOption$parallel
##   writing:  setOption("parallel", TRUE)
##*****************************************************************************

##*****************************************************************************
## Set an option in the cn.farms option list.
## (Basically this is the setting of a list entry).
## key - character: object name
## val - object (everything is allowed, even NULL)
##*****************************************************************************
setOption <- function( key=NULL, val=NULL ) {
  if( !is.null(key) && is.character( key ) ) {
    option <- getVar( ".sfOption" )   ## Get from NS
    option[[key]] <- val
    setVar( ".sfOption", option )     ## Write to NS
    
    return( invisible( TRUE ) )
  }
  
  stop( "key or val is NULL or key no string." )
}

##*****************************************************************************
## Get a specific variable from the cn.farms namespace.
## var - character: object name
##*****************************************************************************
getVar <- function( var=NULL ) {
  if( !is.null( var ) && is.character( var ) ) {
    tmp <- try( getFromNamespace( var, "cn.farms" ) )
    
    if( inherits( tmp, "try-error" ) )
      stop( paste( "Object", var, "not found in package" ) )
    
    return( tmp )
  }
  
  stop( "var is NULL or not a string." )
}

##*****************************************************************************
## Write a specific variable to the cn.farms namespace.
## var - character: object name
## arg - object (NULL allowed)
##*****************************************************************************
setVar <- function( var=NULL, arg=NULL ) {
  if( !is.null( var ) && is.character( var ) ) {
    assignInNamespace( var, arg, "cn.farms" )
    
    return( invisible( TRUE ) )
  }
  
  stop( "var is NULL or no character" );
}

##*****************************************************************************
## Replaces the tilde operator in file/directory names with the system
## depending counterpart.
## Used for configuration files mainly.
##
## PARAMETER: String directory
## RETURN:    String directory replaced
##*****************************************************************************
fetchDirName <- function( dir ) {
  return( gsub( "~", Sys.getenv( "HOME" ), dir ) )
}

##*****************************************************************************
## Is this cn.farms session started through sfCluster?
## As a backward compatible solution there is only the LOCKFILE option open
## (as there is no default for it and setable through commandline).
##
## PARAMETER: -
## RETURN:    Boolean True (running with sfCluster), False
##*****************************************************************************
startedWithSfCluster <- function() {
  if( !exists( ".sfOption" ) )
    return( FALSE )
  else
    return( !is.null( .sfOption$LOCKFILE ) && ( .sfOption$LOCKFILE != '' ) )
}

##*****************************************************************************
## Creates a directory (recursive) if needed and stops on failure.
##
## PARAMETER: String directory
## RETURN:    Boolean success (true, on fail, execution stops)
##*****************************************************************************
dirCreateStop <- function( dir=NULL ) {
  if( !is.null( dir ) && !file.exists( dir ) ) {
    if( dir.create( dir, recursive=TRUE ) ) {
      message( "Created directory: ", dir )
      return( invisible( TRUE ) );
    }
    else
      stop( "UNABLE to create directory: ", dir )
  }
  
  ## Never reached.
  return( invisible( FALSE ) );
}

##***************************************************************************
## Add a file (with absolute path) to remove list after sfStop().
## Used for save/restore-files.
##
## PARAMETER: file String abs. filepath
##***************************************************************************
addRestoreFile <- function( file=NULL ) {
  if( !is.null( file ) )
    if( is.vector( .sfOption$RESTOREFILES ) )
      ## Check if file is already in the list. If yes: no add.
      if( length( grep( file, .sfOption$RESTOREFILES ) ) == 0 )
        setOption( "RESTOREFILES", c( .sfOption$RESTOREFILES, file ) )
      else
        setOption( "RESTOREFILES", c( file ) )
  
  debug( paste( "Added file for delete: ", file, "\n" ) )
  
  return( invisible( length( .sfOption$RESTOREFILES ) ) )
}

##***************************************************************************
## Clean up save/restore files after successfull cluster shutdown.
##***************************************************************************
deleteRestoreFiles <- function() {
  if( !is.null( .sfOption$RESTOREFILES ) ) {
    ## File names are absolute: just unlink all.
    ##    lapply( .sfOption$RESTOREFILES, unlink )
    for( file in .sfOption$RESTOREFILES ) {
      ## Does file exist?
      if( file.exists( file ) ) {
        if( unlink( file ) != 0 )
          cat( "Unable to delete save/restore file:", file, "\n" )
        else
          cat( "Deleted save/restore file:", file, "\n" )
      }
    }
    
    setOption( "RESTOREFILES", NULL )
  }
}

##***************************************************************************
## Check if any element of a given list produced a stop or try-error.
## RETURN: Vector of logicals (true: ok, false: try error caught).
##***************************************************************************
checkTryErrorAny <- function( res ) {
  return( sapply( res,
          function( x ) {
            if( inherits( x, "try-error" ) )
              return( FALSE )
            else
              return( TRUE )
          }
      ) )
}

##***************************************************************************
## Check if given argument is a function.
##***************************************************************************
checkFunction <- function( fun, stopOnError=TRUE ) {
  return( TRUE )
  
  state <- FALSE
  
  try( if( !exists( as.character( substitute( fun ) ), inherits=TRUE ) ||
          !is.function( fun ) ||
          is.null( get( as.character( substitute( fun ) ), inherits=TRUE ) ) ||
          !is.function( fun ) ) state <- TRUE )
  
  if( !state ) {
    ##    if( !is.function( fun ) ) cat( "FAIL SYMBOL\n" )
    ##    if( !exists( as.character( substitute( fun ) ), inherit=TRUE ) ) cat( "FAIL EXIST\n" )
    ##    if( is.null( get( as.character( substitute( fun ) ), inherit=TRUE ) ) ) cat( "FAIL GET\n" )
    ##    if( !is.function( fun ) ) cat( "FAIL FUNCTION\n" )
    
    if( stopOnError )
      stop( paste( "Not a function in sfCluster function call: '", fun, "'" ) )
  }
  
  return( state )
}

errHandler <- function( ... ) {
  print( "ERROR IN HANDLING STUFF!\n" )
}

##***************************************************************************
## Treat given three dot arguments as strings (for names listings
## like in sfExport).
## Ripped from buildin R function rm (by XXX).
## Returns list with names, stops on errors.
##***************************************************************************
fetchNames <- function( ... ) {
  ## Dot argument to list of characters: ripped from rm()...
  dots <- match.call(expand.dots = FALSE)$...
  
  if( length(dots) &&
      !all( sapply( dots, function(x) is.symbol(x) || is.character(x) ) ) )
    stop( "... must contain names or character strings in function ",
        as.character( sys.call( -1 ) ) )
  ## end ripp.
  
  return( sapply(dots, as.character) )
}

##***************************************************************************
## Create named list with all parameters from an function call.
## Idea somewhere from R-help (not tracked).
## This does not work if above env is not global env!
##***************************************************************************
getNamedArguments <- function( ... ) {
  pars <- as.list( substitute( {...} )[-1] )
  
  ##  pars <- as.list( substitute( {...} )[-1] )
  ##  pars <- lapply( pars, function( x ) {
  ##                                        if( is.atomic( x ) )
  ##                                          return( x )
  ##                                        else
  ##                                          return( deparse( x ) )
  ##                                      } )
  
  return( pars )
}

##***************************************************************************
## Ensure a given filename contains an absolute path.
## Kind of silly and lame. But works in most cases.
##***************************************************************************
absFilePath <- function( file ) {
  ## If not starting with separator, path is most likely relative.
  ## Make it absolute then.
  ## On Windows absolute path can contain drive chars.
  if( .Platform$OS.type == "windows" ) {
    if( ( substr( file, 1, 1 ) != .Platform$file.sep ) &&
        ( substr( file, 2, 2 ) != ":" ) )
      file <- file.path( getwd(), file )
  }
  else
  if( substr( file, 1, 1 ) != .Platform$file.sep )
    file <- file.path( getwd(), file )
  
  return( file )
}

simpleAssign <- function( name=NULL, value ) {
  message( paste( "simpleAssign called: ", name, "VAL:", value ) )
  
  if( is.null( name ) || !is.character( name ) || ( nchar( name ) == 0 ) ) {
    warning( "NULL assign on simpleAssign()" )
    return( NULL )
  }
  else {
    assign( name, value, envir = globalenv() )
    return( NULL )
  }
}

##***************************************************************************
## Internal debug printer (globally disable using package variable DEBUG).
##***************************************************************************
debug <- function( txt='' ) {
  if( DEBUG )
    message( txt )
}

.onLoad <- function( lib, pkg ) {
  ##  options( "error"=errHandler )
}
Bioconductor-mirror/cn.farms documentation built on June 1, 2017, 6:35 a.m.