@@ -1,5 +1,5 @@

 Package: affxparser

-Version: 1.11.3

+Version: 1.11.4

 Date: 2007-12-01

 Title: Affymetrix File Parsing SDK

 Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen

@@ -12,7 +12,7 @@

 # \arguments{

 #  \item{pattern}{A regular expression file name pattern to match.}

 #  \item{paths}{A @character @vector of paths to be searched.}

-#  \item{recursive}{If @TRUE, the directory structure is searched 

+#  \item{recursive}{If @TRUE, the directory structure is searched

 #    breath-first, in lexicographic order.}

 #  \item{firstOnly}{If @TRUE, the method returns as soon as a matching

 #    file is found, otherwise not.}

@@ -25,12 +25,12 @@

 #

 # \section{Paths}{

 #   The \code{paths} argument may also contain paths specified as

-#   semi-colon (\code{";"}) separated paths, e.g. 

+#   semi-colon (\code{";"}) separated paths, e.g.

 #   \code{"/usr/;usr/bin/;.;"}.

 # }

 #

 # \section{Windows Shortcut links}{

-#   If package \pkg{R.utils} is available, Windows Shortcut links (*.lnk)

+#   If package \pkg{R.utils} is available and loaded , Windows Shortcut links (*.lnk)

 #   are recognized and can be used to immitate links to directories

 #   elsewhere.  For more details, see @see "R.utils::filePath".

 # }

@@ -80,7 +80,8 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

   # Prepare list of paths to be scanned

   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-  hasRutils <- suppressWarnings(require(R.utils, quietly=TRUE));

+  hasRutilsLoaded "R.utils:package" %in% sub("_[0-9.-]*", "", search())

+  ## hasRutils <- suppressWarnings(require(R.utils, quietly=TRUE));

   # Don't search the same path twice

   paths <- unique(paths);

@@ -93,7 +94,7 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

     path <- gsub("^[.][/\\]", "", path);

     # Follow Windows shortcut links?

-    if (hasRutils)

+    if (hasRutilsLoaded)

       path <- filePath(path, expandLinks="any");

     # Does the path exist and is it a directory

@@ -131,11 +132,11 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

     # Expand Windows shortcut links?

     files0 <- files;

-    if (hasRutils) {

+    if (hasRutilsLoaded) {

       # Remember these

       files <- sapply(files, FUN=filePath, expandLinks="any", USE.NAMES=FALSE);

     }

- 

+

     # Keep only existing files and directories

     ok <- sapply(files, FUN=function(file) {

       (file.exists(path) && !is.na(file.info(file)$isdir));

@@ -214,7 +215,7 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

 # 2007-08-30

 # o BUG FIX: Pattern matching was done on expanded filenames, whereas they

 #   should really be done on the non-expanded ones.  This, only applies to

-#   Windows shortcuts, but it is not the destination file that is of 

+#   Windows shortcuts, but it is not the destination file that is of

 #   interest, but the name of the shortcut file.

 # o BUG FIX: The recent update was not grep():ing correctly; forgot to

 #   extract the basename().

@@ -226,4 +227,4 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

 # o Removed usage of R.utils for now.

 # 2006-03-14

 # o Created from findCdf.R.

-############################################################################  

+############################################################################

@@ -39,7 +39,7 @@

 }

 \section{Windows Shortcut links}{

-  If package \pkg{R.utils} is available, Windows Shortcut links (*.lnk)

+  If package \pkg{R.utils} is available and loaded, Windows Shortcut links (*.lnk)

   are recognized and can be used to immitate links to directories

   elsewhere.  For more details, see \code{\link[R.utils]{filePath}}.

 }