New release that fixes building on WIN64, plus manual page edits to s…

…atisfy new parser.

git-svn-id: https://hedgehog.fhcrc.org/compbio/r-dbi@451 dcde13d4-9b1b-0410-ac9e-ef07de68c835

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: RMySQL
-Version: 0.7-4
-Date: 2009-04-07
+Version: 0.7-5
+Date: 2010-07-13
 Title: R interface to the MySQL database
 Author: David A. James and Saikat DebRoy
-Maintainer: Jeffrey Horner <jeff.horner@vanderbilt.edu>
+Maintainer: Jeffrey Horner <jeffrey.horner@gmail.com>
 Description: Database interface and MySQL driver for R.
    This version complies with the database interface 
    definition as implemented in the package DBI 0.2-2.

configure.win

@@ -1,10 +1,8 @@
-echo "configure.win:"
-echo ""
 echo -n "checking for \$MYSQL_HOME... "
 if test -z "$MYSQL_HOME" ; then
 	echo "not found... searching registry..."
 	echo ""
-	${R_HOME}/bin${R_ARCH_BIN}/Rscript < inst/FindMySQLhome.R
+	"${R_HOME}/bin${R_ARCH_BIN}/Rscript" inst/FindMySQLhome.R
 	echo ""
 	exit 1
 else
@@ -14,4 +12,9 @@ else
 	  exit 2
 	fi
 fi
-echo ""
+x86=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e 'cat(.Machine$sizeof.pointer==4)'`
+if test $x86 = "TRUE"; then
+	cp src/Makevars.win32 src/Makevars.win
+else
+	cp src/Makevars.win64 src/Makevars.win
+fi

man/MySQL.Rd

@@ -148,7 +148,6 @@ On meta-data:
 \code{\link[DBI]{dbGetStatement}}
 \code{\link[DBI]{dbHasCompleted}}
 \code{\link[DBI]{dbGetRowCount}}
-\code{\link[DBI]{dbGetAffectedRows}}
 }
 \examples{\dontrun{
 # create a MySQL instance and create one connection.

man/RMySQL-package.Rd

@@ -173,7 +173,6 @@ See the documentation at the MySQL Web site
 \seealso{
 On database managers:
 
-\code{\link[DBI:DBI-package]{DBI}} 
 \code{\link[DBI]{dbDriver}}
 \code{\link[DBI]{dbUnloadDriver}}
 
@@ -204,7 +203,6 @@ On meta-data:
 \code{\link[DBI]{dbGetStatement}}
 \code{\link[DBI]{dbHasCompleted}}
 \code{\link[DBI]{dbGetRowCount}}
-\code{\link[DBI]{dbGetAffectedRows}}
 }
 \examples{\dontrun{
 # create a MySQL instance and create one connection.

man/dbEscapeStrings-methods.Rd

@@ -28,7 +28,7 @@
   \code{\link[DBI]{dbSendQuery}},
   \code{\link[DBI]{dbGetQuery}},
   \code{\link[DBI]{fetch}},
-  \code{\link[DBI]{dbNextResult}},
+  \code{\link{dbNextResult}},
   \code{\link[DBI]{dbCommit}},
   \code{\link[DBI]{dbGetInfo}},
   \code{\link[DBI]{dbReadTable}}.

man/dbReadTable-methods.Rd

@@ -68,13 +68,13 @@
 
   \code{header} is a logical indicating whether the first data line
   (but see \code{skip}) has a header or not.  If missing, it value
-  is determined following \code{\link[base]{read.table}} convention,
+  is determined following \code{\link{read.table}} convention,
   namely, it is set to TRUE if and only if the first row has one
   fewer field that the number of columns.
 
   \code{row.names} is a logical to specify whether the first column
   is a set of row names.  If missing its default follows the 
-  \code{\link[base]{read.table}} convention.
+  \code{\link{read.table}} convention.
 
   \code{col.names} a character vector with column names (these names
   will be filtered with \code{\link[DBI]{make.db.names}} to 

man/safe.write.Rd

@@ -16,7 +16,7 @@ safe.write(value, file, batch, ...)
   \item{\dots}{any other arguments are passed to \code{write.table}.}
 }
 \details{
-   The function has a while loop invoking \code{\link[base]{write.table}}
+   The function has a while loop invoking \code{\link{write.table}}
    for subsets of \code{batch} rows of \code{value}.  Since this is
    a helper function for \code{\link[RMySQL]{mysqlWriteTable}}, it has 
    hardcoded other arguments to \code{write.table}.
@@ -26,7 +26,7 @@ safe.write(value, file, batch, ...)
 }
 \note{No error checking whatsoever is done.}
 
-\seealso{\code{\link[base]{write.table}}} 
+\seealso{\code{\link{write.table}}} 
 
 \examples{\dontrun{
    ctr.file <- file("dump.sqloader", "w")

src/Makevars.win64

@@ -0,0 +1,2 @@
+PKG_CPPFLAGS = -I"${MYSQL_HOME}"/include
+PKG_LIBS = "${MYSQL_HOME}"/bin/libmySQL.dll

src/RS-DBI.h

@@ -31,17 +31,16 @@ extern "C" {
 
 #include "S4R.h"
 
-/* Microsoft Visual C++ uses int _getpid()  */
-#ifdef MSVC
+/* WIN32 uses int _getpid()  */
+#if defined WIN32
 #include <process.h>
-#define getpid _getpid
-#define pid_t int
+ /* #define getpid _getpid */
+#include <ctype.h>
+ /* #define pid_t int */
 #else           
 #include <unistd.h>
 #endif
 
-pid_t getpid(); 
-
 /* We now define 4 important data structures:
  * RS_DBI_manager, RS_DBI_connection, RS_DBI_resultSet, and
  * RS_DBI_fields, corresponding to dbManager, dbConnection,
@@ -260,7 +259,7 @@ void RS_na_set(void *ptr, Stype type);
 int  RS_is_na(void *ptr, Stype type);
 extern const struct data_types RS_dataTypeTable[];
 
-int isalpha(int c);
+/* int isalpha(int c); */
 
 #ifdef __cplusplus 
 }

src/RS-MySQL.h

@@ -24,7 +24,7 @@
 extern  "C" {
 #endif
 
-#ifdef WIN32
+#if defined WIN32
 # include <windows.h>
 # undef ERROR
 #endif