@@ -1,8 +1,8 @@

 Package: affxparser

-Version: 1.37.0

+Version: 1.37.1

 Depends: R (>= 2.6.0)

-Suggests: R.utils (>= 1.29.8), AffymetrixDataTestFiles

-Date: 2014-04-11

+Suggests: R.oo (>= 1.18.0), R.utils (>= 1.32.4), AffymetrixDataTestFiles

+Date: 2014-08-25

 Title: Affymetrix File Parsing SDK

 Authors@R: c(

   person("Henrik", "Bengtsson", role=c("aut")),

@@ -13,7 +13,7 @@ Authors@R: c(

 Author: Henrik Bengtsson [aut], James Bullard [aut], Robert Gentleman [ctb], Kasper Daniel Hansen [aut, cre], Martin Morgan [ctb]

 Maintainer: Kasper Daniel Hansen <[email protected]>

 Description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR).  It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK.  Both ASCII- and binary-based files are supported.  Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL).  These files can be read either in full or in part.  For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

-FusionDetails: Fusion SDK v1.1.2

+Note: Fusion SDK v1.1.2

 License: LGPL (>= 2)

 LazyLoad: yes

 biocViews: Infrastructure, DataImport

@@ -1,6 +1,10 @@

 Package: affxparser

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

+Version: 1.37.1 [2014-08-25]

+o CLEANUP: Removed R CMD check NOTEs that appeared in recent R versions.

+

+

 Version: 1.37.0 [2014-04-11]

 o The version number was bumped for the Bioconductor devel version,

   which is now BioC v2.15 for R (>= 3.1.0).

@@ -41,7 +41,10 @@

 # @keyword internal

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

 arrangeCelFilesByChipType <- function(pathnames=list.files(pattern="[.](cel|CEL)$"), path="celFiles/", aliases=NULL, ...) {

-  require("R.utils") || throw("Package not loaded: R.utils");

+  # To please R CMD check

+  Arguments <- isFile <- filePath <- NULL;

+  rm(list=c("Arguments", "isFile", "filePath"));

+  require("R.utils") || stop("Package not loaded: R.utils");

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

   # Validate arguments

@@ -98,6 +101,8 @@ arrangeCelFilesByChipType <- function(pathnames=list.files(pattern="[.](cel|CEL)

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

 # HISTORY:

+# 2014-08-25

+# o Now using stop() instead of throw().

 # 2012-09-01

 # o Added argument 'aliases' to arrangeCelFilesByChipType(), e.g.

 #   arrangeCelFilesByChipType(..., aliases=c("Focus"="HG-Focus")).

@@ -44,6 +44,9 @@

 # @keyword internal

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

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

+  # To please R CMD check

+  filePath <- NULL; rm(list="filePath");

+

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

   # Local functions

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

@@ -72,7 +75,7 @@ findFiles <- function(pattern=NULL, paths=NULL, recursive=FALSE, firstOnly=TRUE,

    (pattern %in% s);

   }

-  

+

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

   # Validate arguments

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

@@ -56,6 +56,10 @@

 # @keyword "internal"

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

 readCdfUnitsWriteMap <- function(filename, units=NULL, ..., verbose=FALSE) {

+  # To please R CMD check

+  Arguments <- enter <- exit <- NULL;

+  rm(list=c("Arguments", "enter", "exit"));

+

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

   # Validate arguments

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

@@ -78,6 +78,10 @@

 # @keyword "IO"

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

 readCelUnits <- function(filenames, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"), cdf=NULL, ..., addDimnames=FALSE, dropArrayDim=TRUE, transforms=NULL, readMap=NULL, verbose=FALSE) {

+  # To please R CMD check

+  Arguments <- enter <- exit <- NULL;

+  rm(list=c("Arguments", "enter", "exit"));

+

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

   # Local functions

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

@@ -31,7 +31,7 @@

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

   # Default version is 1 (one) [1]

   if (is.null(header$version))

-    header$version <- as.integer(1); 

+    header$version <- as.integer(1);

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

@@ -64,11 +64,11 @@

 # dependency so as to traverse across the entire parentage of a file.

 # This information will provide the entire history of how a file came

 # to be.

-# 

-# The first data header section immediately follows the file header 

+#

+# The first data header section immediately follows the file header

 # section.

 #

-# Item Type  Description 

+# Item Type  Description

 # 1    GUID  The data type identifier. This is used to identify the type

 #            of data stored in the file. For example:

 #            * acquisition data (affymetrix-calvin-scan-acquisition)

@@ -81,14 +81,17 @@

 #            Example: When a  user manually aligns the grid in a DAT file

 #            the grid coordinates are updated in the DAT file and the file

 #            is given a new file identifier.

-# 3 DATETIME Date and time of file creation. 	

+# 3 DATETIME Date and time of file creation.

 # 4   LOCALE The locale of the operating system that the file was created on.

-# 5 	   INT The number of name/type/value parameters. 	

+# 5 	   INT The number of name/type/value parameters.

 # 6 	 WVT[] Array of parameters stored as name/value/type triplets.

 #            WVT[]=(WSTRING/VALUE/TYPE)[]

-# 7 	   INT Number of parent file headers. 	

+# 7 	   INT Number of parent file headers.

 # 8 	 GDH[] Array of parent file headers. GDH[]=GenericDataHeader[]

 .writeCcgDataHeader <- function(con, header, ...) {

+  # To please R CMD check

+  charToInt <- NULL; rm(list="charToInt");

+

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

   # Local functions

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

@@ -105,7 +108,7 @@

   }

   writeString <- function(con, str, ...) {

-    # A 1 byte character string. A string object is stored as an INT 

+    # A 1 byte character string. A string object is stored as an INT

     # (to store the string length) followed by the CHAR array (to store

     # the string contents).

     str <- as.character(str);

@@ -131,8 +134,8 @@

   writeWString <- function(con, str, ...) {

     # A UNICODE string. A string object is stored as an INT (to store the

-    # string length) followed by the WCHAR array (to store the string 

-    # contents).    

+    # string length) followed by the WCHAR array (to store the string

+    # contents).

     str <- as.character(str);

     nchars <- as.integer(nchar(str));

     writeInt(con, value=nchars);

@@ -164,7 +167,7 @@

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

   # Default version is 1 (one) [1]

   if (is.null(header$version))

-    header$version <- as.integer(1); 

+    header$version <- as.integer(1);

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

@@ -198,8 +201,8 @@

 # 2012-05-18

 # o Now using stop() instead of throw().

 # 2007-08-16

-# o This file only contains a stub, so there is currently no 

+# o This file only contains a stub, so there is currently no

 #    writeCcgHeader() or writeCcg().

 # 2006-11-06

 # o Created.

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

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