@@ -1,6 +1,6 @@

 Package: affxparser

 Version: 1.11.4

-Date: 2007-12-01

+Date: 2008-01-13

 Title: Affymetrix File Parsing SDK

 Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen

 Maintainer: Kasper Daniel Hansen <[email protected]>

@@ -16,6 +16,8 @@

 #    breath-first, in lexicographic order.}

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

 #    file is found, otherwise not.}

+#  \item{allFiles}{If @FALSE, files and directories starting with

+#    a period will be skipped, otherwise not.}

 #  \item{...}{Arguments passed to @see "base::list.files".}

 # }

 #

@@ -41,7 +43,7 @@

 # @keyword IO

 # @keyword internal

 #**/#######################################################################

-findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE, ...) {

+findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE, allFiles=TRUE, ...) {

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

   # Local functions

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

@@ -55,9 +57,22 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

     if (length(paths) == 0)

       return(NULL);

     paths;

-  }

+  } # splitPaths()

+

+  # Checks if a package is loaded or not (should be in the 'base' package)

+  isLoaded <- function(package, version=NULL, ...) {

+    s <- search();

+    if (is.null(version)) {

+      s <- sub("_[0-9.-]*", "", s);

+    } else {

+      package <- manglePackageName(package, version);

+    }

+    pattern <- sprintf("^package:%s$", package);

+    (length(grep(pattern, s)) > 0);

+  } # isLoaded()

+  

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

   # Validate arguments

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

@@ -80,7 +95,7 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

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

   # Prepare list of paths to be scanned

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

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

+  hasRutilsLoaded <- isLoaded("R.utils");

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

   # Don't search the same path twice

@@ -116,7 +131,7 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

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

   pathnames <- c();

   for (path in paths) {

-    files <- list.files(path, all.files=TRUE, full.names=TRUE);

+    files <- list.files(path, all.files=allFiles, full.names=TRUE);

     # Exclude listings that are neither files nor directories

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

@@ -210,6 +225,12 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

 ############################################################################

 # HISTORY:

+# 2008-02-21 [HB]

+# o Added an internal generic isLoaded() function.

+# 2008-02-20 [KH]

+# o Replaced require("R.utils") with a "isLoaded()" feature.

+# 2008-02-14

+# o Added argument 'allFiles=TRUE' to findFiles().

 # 2007-09-17

 # o ROBUSTNESS: Now findFiles() are robust against broken Unix links.

 # 2007-08-30

@@ -1,6 +1,21 @@

 Package: affxparser

 ===================

+Version: 1.11.5 [2008-02-21x]

+o BUG FIX: The code in findFiles() for testing if R.utils is loaded 

+  or not was not correct making it fail to detect R.utils.

+

+

+Version: 1.11.4 [2008-02-20]

+o Now findFiles() and hence findCdf() is only utilizing the R.utils

+  package if it is already loaded.  It will no longer try to load

+  R.utils.

+o Added argument 'allFiles=TRUE' to findFiles().

+o Updated readCcg() according to the newer file format specifications.

+  Now it is possible to do low-level reading of copy-number CNCHP 

+  files generated by the Affymetrix Genotype Console v2.

+

+

 Version: 1.11.3 [2007-12-01]

 o Removed argument 'reorder' from readCel() and  readCelUnits()

   since its name was misleading (the returned value was identical 

@@ -3,6 +3,8 @@

 % 

 %  findFiles.R

 % 

+% on Thu Feb 21 14:05:38 2008.

+% 

 % by the Rdoc compiler part of the R.oo package.

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@@ -16,7 +18,7 @@

  Finds one or several files in multiple directories.

 }

-\usage{findFiles(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE, ...)}

+\usage{findFiles(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE, allFiles=TRUE, ...)}

 \arguments{

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

@@ -25,6 +27,8 @@

    breath-first, in lexicographic order.}

  \item{firstOnly}{If \code{\link[base:logical]{TRUE}}, the method returns as soon as a matching

    file is found, otherwise not.}

+ \item{allFiles}{If \code{\link[base:logical]{FALSE}}, files and directories starting with

+   a period will be skipped, otherwise not.}

  \item{...}{Arguments passed to \code{\link[base]{list.files}}().}

 }

@@ -39,7 +43,7 @@

 }

 \section{Windows Shortcut links}{

-  If package \pkg{R.utils} is available and loaded, 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}}.

 }