[Genabel-commits] r1509 - in pkg/ProbABEL/src: . include include/R_ext
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Dec 28 22:46:42 CET 2013
Author: lckarssen
Date: 2013-12-28 22:46:42 +0100 (Sat, 28 Dec 2013)
New Revision: 1509
Removed:
pkg/ProbABEL/src/include/Colors.h
pkg/ProbABEL/src/include/Defn.h
pkg/ProbABEL/src/include/Errormsg.h
pkg/ProbABEL/src/include/Fileio.h
pkg/ProbABEL/src/include/Graphics.h
pkg/ProbABEL/src/include/GraphicsBase.h
pkg/ProbABEL/src/include/IOStuff.h
pkg/ProbABEL/src/include/Internal.h
pkg/ProbABEL/src/include/Makefile.in
pkg/ProbABEL/src/include/Makefile.win
pkg/ProbABEL/src/include/Parse.h
pkg/ProbABEL/src/include/Print.h
pkg/ProbABEL/src/include/RBufferUtils.h
pkg/ProbABEL/src/include/README
pkg/ProbABEL/src/include/R_ext/Applic.h
pkg/ProbABEL/src/include/R_ext/BLAS.h
pkg/ProbABEL/src/include/R_ext/Callbacks.h
pkg/ProbABEL/src/include/R_ext/GetX11Image.h
pkg/ProbABEL/src/include/R_ext/GraphicsDevice.h
pkg/ProbABEL/src/include/R_ext/GraphicsEngine.h
pkg/ProbABEL/src/include/R_ext/Lapack.h
pkg/ProbABEL/src/include/R_ext/Linpack.h
pkg/ProbABEL/src/include/R_ext/Makefile.in
pkg/ProbABEL/src/include/R_ext/Parse.h
pkg/ProbABEL/src/include/R_ext/PrtUtil.h
pkg/ProbABEL/src/include/R_ext/QuartzDevice.h
pkg/ProbABEL/src/include/R_ext/R-ftp-http.h
pkg/ProbABEL/src/include/R_ext/RConverters.h
pkg/ProbABEL/src/include/R_ext/RStartup.h
pkg/ProbABEL/src/include/R_ext/Rdynload.h
pkg/ProbABEL/src/include/R_ext/Riconv.h
pkg/ProbABEL/src/include/R_ext/Visibility.h
pkg/ProbABEL/src/include/R_ext/eventloop.h
pkg/ProbABEL/src/include/R_ext/rlocale.h
pkg/ProbABEL/src/include/R_ext/stats_package.h
pkg/ProbABEL/src/include/R_ext/stats_stubs.h
pkg/ProbABEL/src/include/Rconnections.h
pkg/ProbABEL/src/include/Rdefines.h
pkg/ProbABEL/src/include/Rdevices.h
pkg/ProbABEL/src/include/Rdynpriv.h
pkg/ProbABEL/src/include/Rembedded.h
pkg/ProbABEL/src/include/Rgraphics.h
pkg/ProbABEL/src/include/Rinlinedfuns.h
pkg/ProbABEL/src/include/Rinterface.h
pkg/ProbABEL/src/include/Rinternals.h
pkg/ProbABEL/src/include/Rmath.h0.in
pkg/ProbABEL/src/include/Rmodules/
pkg/ProbABEL/src/include/S.h
pkg/ProbABEL/src/include/Startup.h
pkg/ProbABEL/src/include/config.h.in
pkg/ProbABEL/src/include/memcheck.h
pkg/ProbABEL/src/include/stamp-h.in
pkg/ProbABEL/src/include/valgrind.h
Modified:
pkg/ProbABEL/src/coxph_data.cpp
Log:
Delete unused R include files from ProbABEL. These files are not used anywhere and weren't even listed in src/Makefile.am, so were never distributed with the source anyway.
Modified: pkg/ProbABEL/src/coxph_data.cpp
===================================================================
--- pkg/ProbABEL/src/coxph_data.cpp 2013-12-27 23:29:13 UTC (rev 1508)
+++ pkg/ProbABEL/src/coxph_data.cpp 2013-12-28 21:46:42 UTC (rev 1509)
@@ -259,7 +259,6 @@
*/
void coxph_data::remove_snp_from_X()
{
-
if (ngpreds == 1)
{
X.delete_row(X.nrow -1);
Deleted: pkg/ProbABEL/src/include/Colors.h
===================================================================
--- pkg/ProbABEL/src/include/Colors.h 2013-12-27 23:29:13 UTC (rev 1508)
+++ pkg/ProbABEL/src/include/Colors.h 2013-12-28 21:46:42 UTC (rev 1509)
@@ -1,53 +0,0 @@
-/*
- * R : A Computer Language for Statistical Data Analysis
- * Copyright (C) 1998--2008 R Development Core Team
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 2 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, a copy is available at
- * http://www.r-project.org/Licenses/
- */
-
-#ifndef COLORS_H_
-#define COLORS_H_
-
-/* This is a private header, possibly temporary */
-
-#define COLOR_TABLE_SIZE 1024
-
-/* always remap private functions */
-#define isNAcol Rf_isNAcol
-
-/* hsv2rgb and rgb2hsv are in Utils.h */
-
- /* Miscellaneous (from colors.c) */
-
-Rboolean isNAcol(SEXP col, int index, int ncol); /* used in plot[3d].c */
-
-
-#ifdef UNUSED
-#define char2col Rf_char2col
-#define CheckColor Rf_CheckColor
-#define rgb2col Rf_rgb2col
-#define RGB2rgb Rf_RGB2rgb
-#define RGBA2rgb Rf_RGBA2rgb
-#define ScaleColor Rf_ScaleColor
-unsigned int char2col(const char *); /* rgb2col() or name2col() */
-unsigned int rgb2col(const char *);
-unsigned int ScaleColor(double x);
-unsigned int CheckColor(int x);
-char *RGB2rgb(unsigned int, unsigned int, unsigned int);
-char *RGBA2rgb(unsigned int, unsigned int, unsigned int, unsigned int);
-#endif
-
-#endif
-
Deleted: pkg/ProbABEL/src/include/Defn.h
===================================================================
--- pkg/ProbABEL/src/include/Defn.h 2013-12-27 23:29:13 UTC (rev 1508)
+++ pkg/ProbABEL/src/include/Defn.h 2013-12-28 21:46:42 UTC (rev 1509)
@@ -1,1243 +0,0 @@
-/*
- * R : A Computer Language for Statistical Data Analysis
- * Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka
- * Copyright (C) 1998--2008 The R Development Core Team.
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 2 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, a copy is available at
- * http://www.r-project.org/Licenses/
- */
-
-#ifndef DEFN_H_
-#define DEFN_H_
-
-/* seems unused */
-#define COUNTING
-
-#define BYTECODE
-
-#define USE_CHAR_HASHING
-
-/* probably no longer needed */
-#define NEW_CONDITION_HANDLING
-
-/* To test the write barrier used by the generational collector,
- define TESTING_WRITE_BARRIER. This makes the internal structure of
- SEXPRECs visible only inside of files that explicitly define
- USE_RINTERNALS, and all uses of SEXPREC fields that do not go
- through the appropriate functions or macros will become compilation
- errors. Since this does impose a small but noticable performance
- penalty, code that includes Defn.h (or code that explicitly defines
- USE_RINTERNALS) can access a SEXPREC's fields directly. */
-
-#ifndef TESTING_WRITE_BARRIER
-# define USE_RINTERNALS
-#endif
-
-#ifdef HAVE_VISIBILITY_ATTRIBUTE
-# define attribute_visible __attribute__ ((visibility ("default")))
-# define attribute_hidden __attribute__ ((visibility ("hidden")))
-#else
-# define attribute_visible
-# define attribute_hidden
-#endif
-
-#ifdef __MAIN__
-# define extern0 attribute_hidden
-#else
-# define extern0 extern
-#endif
-
-
-#define MAXELTSIZE 8192 /* Used as a default for string buffer sizes,
- and occasionally as a limit. */
-
-#include <R_ext/Complex.h>
-void Rf_CoercionWarning(int);/* warning code */
-int Rf_LogicalFromInteger(int, int*);
-int Rf_LogicalFromReal(double, int*);
-int Rf_LogicalFromComplex(Rcomplex, int*);
-int Rf_IntegerFromLogical(int, int*);
-int Rf_IntegerFromReal(double, int*);
-int Rf_IntegerFromComplex(Rcomplex, int*);
-double Rf_RealFromLogical(int, int*);
-double Rf_RealFromInteger(int, int*);
-double Rf_RealFromComplex(Rcomplex, int*);
-Rcomplex Rf_ComplexFromLogical(int, int*);
-Rcomplex Rf_ComplexFromInteger(int, int*);
-Rcomplex Rf_ComplexFromReal(double, int*);
-
-#define CALLED_FROM_DEFN_H 1
-#include <Rinternals.h> /*-> Arith.h, Complex.h, Error.h, Memory.h
- PrtUtil.h, Utils.h */
-#undef CALLED_FROM_DEFN_H
-extern0 SEXP R_CommentSymbol; /* "comment" */
-extern0 SEXP R_DotEnvSymbol; /* ".Environment" */
-extern0 SEXP R_ExactSymbol; /* "exact" */
-extern0 SEXP R_LastvalueSymbol; /* ".Last.value" */
-extern0 SEXP R_NaRmSymbol; /* "na.rm" */
-extern0 SEXP R_RecursiveSymbol; /* "recursive" */
-extern0 SEXP R_SourceSymbol; /* "source" */
-extern0 SEXP R_SrcfileSymbol; /* "srcfile" */
-extern0 SEXP R_SrcrefSymbol; /* "srcref" */
-extern0 SEXP R_TmpvalSymbol; /* "*tmp*" */
-extern0 SEXP R_UseNamesSymbol; /* "use.names" */
-
-extern0 SEXP R_StringHash; /* Global hash of CHARSXPs */
-
-
- /* writable char access for R internal use only */
-#define CHAR_RW(x) ((char *) CHAR(x))
-
-/* CHARSXP charset bits */
-#define LATIN1_MASK (1<<2)
-#define UTF8_MASK (1<<3)
-#ifdef USE_RINTERNALS
-# define IS_LATIN1(x) ((x)->sxpinfo.gp & LATIN1_MASK)
-# define SET_LATIN1(x) (((x)->sxpinfo.gp) |= LATIN1_MASK)
-# define UNSET_LATIN1(x) (((x)->sxpinfo.gp) &= ~LATIN1_MASK)
-# define IS_UTF8(x) ((x)->sxpinfo.gp & UTF8_MASK)
-# define SET_UTF8(x) (((x)->sxpinfo.gp) |= UTF8_MASK)
-# define UNSET_UTF8(x) (((x)->sxpinfo.gp) &= ~UTF8_MASK)
-# define ENC_KNOWN(x) ((x)->sxpinfo.gp & (LATIN1_MASK | UTF8_MASK))
-#else
-/* Needed only for write-barrier testing */
-int IS_LATIN1(SEXP x);
-void SET_LATIN1(SEXP x);
-void UNSET_LATIN1(SEXP x);
-int IS_UTF8(SEXP x);
-void SET_UTF8(SEXP x);
-void UNSET_UTF8(SEXP x);
-int ENC_KNOWN(SEXP x);
-#endif
-/* macros and declarations for managing CHARSXP cache */
-#ifdef USE_CHAR_HASHING
-# define USE_ATTRIB_FIELD_FOR_CHARSXP_CACHE_CHAINS
-# ifdef USE_ATTRIB_FIELD_FOR_CHARSXP_CACHE_CHAINS
-# define CXHEAD(x) (x)
-# define CXTAIL(x) ATTRIB(x)
-SEXP (SET_CXTAIL)(SEXP x, SEXP y);
-# else
-# define CXHEAD(x) CAR(x)
-# define CXTAIL(x) CDR(x)
-# endif /* USE_ATTRIB_FIELD_FOR_CHARSXP_CACHE_CHAINS */
-#endif /* USE_CHAR_HASHING */
-
-
-#include "Internal.h" /* do_FOO */
-
-#include "Errormsg.h"
-
-#if defined(Win32) || defined(HAVE_AQUA)
-extern void R_ProcessEvents(void);
-#endif
-
-#ifdef Win32
-# include <psignal.h>
-#else
-# include <signal.h>
-# include <setjmp.h>
-#endif
-
-#ifdef Unix
-# define OSTYPE "unix"
-# define FILESEP "/"
-#endif /* Unix */
-
-#ifdef Win32
-# define OSTYPE "windows"
-# define FILESEP "/"
-#endif /* Win32 */
-
-#ifdef HAVE_F77_UNDERSCORE
-# define F77_SYMBOL(x) x ## _
-# define F77_QSYMBOL(x) #x "_"
-#else
-# define F77_SYMBOL(x) x
-# define F77_QSYMBOL(x) #x
-#endif
-
-/* Heap and Pointer Protection Stack Sizes. */
-
-/* These are for future protection: will need to be different on Win64 */
-typedef unsigned long R_ulong_t;
-typedef long R_long_t;
-
-#ifdef HAVE_INTTYPES_H
-# include <inttypes.h>
-#endif
-/* According to POSIX inttypes.h should include stdint.h, but let's be
- sure. */
-#ifdef HAVE_STDINT_H
-# include <stdint.h>
-#endif
-//#ifdef HAVE_LIMITS_H
-# include <limits.h>
-//#endif
-
-/* NB: will need a 64-bit type, ULONG64 or size_t, for Win64 */
-#if defined HAVE_DECL_SIZE_MAX && HAVE_DECL_SIZE_MAX
- typedef size_t R_size_t;
-/* final precaution in case we don't have the right headers */
-# ifdef SIZE_MAX
-# define R_SIZE_T_MAX SIZE_MAX
-# else
-# define R_SIZE_T_MAX ULONG_MAX
-# endif
-#else
- typedef unsigned long R_size_t;
-# define R_SIZE_T_MAX ULONG_MAX
-#endif
-
-/* These are optional C99 types */
-#if !defined(HAVE_INTPTR_T) && !defined(intptr_t)
- typedef long intptr_t;
-#endif
-#if !defined(HAVE_UINTPTR_T) && !defined(uintptr_t)
- typedef unsigned long uintptr_t;
-#endif
-
-
-#define Mega 1048576. /* 1 Mega Byte := 2^20 (= 1048576) Bytes */
-#define Giga 1073741824. /* 1 Giga Byte := 2^30 Bytes */
-
-/* R_PPSSIZE The pointer protection stack size */
-/* R_NSIZE The number of cons cells */
-/* R_VSIZE The vector heap size in bytes */
-/* These values are defaults and can be overridden in config.h
- The maxima and minima are in ../unix/sys-common.c */
-
-#ifndef R_PPSSIZE
-#define R_PPSSIZE 50000L
-#endif
-#ifndef R_NSIZE
-#define R_NSIZE 350000L
-#endif
-#ifndef R_VSIZE
-#define R_VSIZE 6291456L
-#endif
-
-/* some commonly needed headers */
-#include <math.h>
-#include <float.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
-
-/* declare substitutions */
-#if !defined(acosh) && defined(HAVE_DECL_ACOSH) && !HAVE_DECL_ACOSH
-extern double acosh(double x);
-#endif
-#if !defined(asinh) && defined(HAVE_DECL_ASINH) && !HAVE_DECL_ASINH
-extern double asinh(double x);
-#endif
-#if !defined(atanh) && defined(HAVE_DECL_ATANH) && !HAVE_DECL_ATANH
-extern double atanh(double x);
-#endif
-#if !defined(snprintf) && defined(HAVE_DECL_SNPRINTF) && !HAVE_DECL_SNPRINTF
-extern int snprintf (char *s, size_t n, const char *format, ...);
-#endif
-#if !defined(strdup) && defined(HAVE_DECL_STRDUP) && !HAVE_DECL_STRDUP
-extern char *strdup(const char *s1);
-#endif
-#if !defined(strncascmp) && defined(HAVE_DECL_STRNCASECMP) && !HAVE_DECL_STRNCASECMP
-extern int strncasecmp(const char *s1, const char *s2, size_t n);
-#endif
-#if !defined(vsnprintf) && defined(HAVE_DECL_VSNPRINTF) && !HAVE_DECL_VSNPRINTF
-extern int vsnprintf (char *str, size_t count, const char *fmt, va_list arg);
-#endif
-
-/* Glibc manages to not define this in -pedantic -ansi */
-#if defined(HAVE_PUTENV) && !defined(putenv) && defined(HAVE_DECL_PUTENV) && !HAVE_DECL_PUTENV
-extern int putenv(char *string);
-#endif
-
-
-/* Maximal length in bytes of an entire path name.
- POSIX has required this to be at least 255/256, and X/Open at least 1024.
- Solaris has 1024, Linux glibc has 4192.
- File names are limited to FILENAME_MAX bytes (usually the same as PATH_MAX)
- or NAME_MAX (often 255/256).
- */
-#if !defined(PATH_MAX)
-# if defined(HAVE_SYS_PARAM_H)
-# include <sys/param.h>
-# endif
-# if !defined(PATH_MAX)
-# if defined(MAXPATHLEN)
-/* Try BSD name */
-# define PATH_MAX MAXPATHLEN
-# elif defined(Win32)
-/* seems this is now defined by MinGW to be 259, whereas FILENAME_MAX
- and MAX_PATH are 260. It is not clear that this really is in bytes,
- but might be chars for the Unicode interfaces.
-*/
-# define PATH_MAX 260
-# else
-/* quite possibly unlimited, so we make this large, and test when used */
-# define PATH_MAX 5000
-# endif
-# endif
-#endif
-
-#ifdef HAVE_POSIX_SETJMP
-# define SIGJMP_BUF sigjmp_buf
-# define SIGSETJMP(x,s) sigsetjmp(x,s)
-# define SIGLONGJMP(x,i) siglongjmp(x,i)
-# define JMP_BUF sigjmp_buf
-# define SETJMP(x) sigsetjmp(x,0)
-# define LONGJMP(x,i) siglongjmp(x,i)
-#else
-# define SIGJMP_BUF jmp_buf
-# define SIGSETJMP(x,s) setjmp(x)
-# define SIGLONGJMP(x,i) longjmp(x,i)
-# define JMP_BUF jmp_buf
-# define SETJMP(x) setjmp(x)
-# define LONGJMP(x,i) longjmp(x,i)
-#endif
-
-/* Availability of timing: on Unix, we need times(2).
- On Windows and the Mac, we can do without.
-*/
-#if (defined(HAVE_TIMES) || defined(Win32))
-# define _R_HAVE_TIMING_ 1
-#endif
-
-#define HSIZE 4119 /* The size of the hash table for symbols */
-#define MAXIDSIZE 256 /* Largest symbol size possible */
-
-/* The type of the do_xxxx functions. */
-/* These are the built-in R functions. */
-typedef SEXP (*CCODE)(SEXP, SEXP, SEXP, SEXP);
-
-/* Information for Deparsing Expressions */
-typedef enum {
- PP_INVALID = 0,
- PP_ASSIGN = 1,
- PP_ASSIGN2 = 2,
- PP_BINARY = 3,
- PP_BINARY2 = 4,
- PP_BREAK = 5,
- PP_CURLY = 6,
- PP_FOR = 7,
- PP_FUNCALL = 8,
- PP_FUNCTION = 9,
- PP_IF = 10,
- PP_NEXT = 11,
- PP_PAREN = 12,
- PP_RETURN = 13,
- PP_SUBASS = 14,
- PP_SUBSET = 15,
- PP_WHILE = 16,
- PP_UNARY = 17,
- PP_DOLLAR = 18,
- PP_FOREIGN = 19,
- PP_REPEAT = 20
-} PPkind;
-
-typedef enum {
- PREC_FN = 0,
- PREC_LEFT = 1,
- PREC_EQ = 2,
- PREC_RIGHT = 3,
- PREC_TILDE = 4,
- PREC_OR = 5,
- PREC_AND = 6,
- PREC_NOT = 7,
- PREC_COMPARE = 8,
- PREC_SUM = 9,
- PREC_PROD = 10,
- PREC_PERCENT = 11,
- PREC_COLON = 12,
- PREC_SIGN = 13,
- PREC_POWER = 14,
- PREC_DOLLAR = 15,
- PREC_NS = 16,
- PREC_SUBSET = 17
-} PPprec;
-
-typedef struct {
- PPkind kind; /* deparse kind */
- PPprec precedence; /* operator precedence */
- unsigned int rightassoc; /* right associative? */
-} PPinfo;
-
-/* The type definitions for the table of built-in functions. */
-/* This table can be found in ../main/names.c */
-typedef struct {
- char *name; /* print name */
- CCODE cfun; /* c-code address */
- int code; /* offset within c-code */
- int eval; /* evaluate args? */
- int arity; /* function arity */
- PPinfo gram; /* pretty-print info */
-} FUNTAB;
-
-#ifdef USE_RINTERNALS
-/* There is much more in Rinternals.h, including function versions
- * of the Promise and Hashing groups.
- */
-
-/* Primitive Access Macros */
-#define PRIMOFFSET(x) ((x)->u.primsxp.offset)
-#define SET_PRIMOFFSET(x,v) (((x)->u.primsxp.offset)=(v))
-#define PRIMFUN(x) (R_FunTab[(x)->u.primsxp.offset].cfun)
-#define PRIMNAME(x) (R_FunTab[(x)->u.primsxp.offset].name)
-#define PRIMVAL(x) (R_FunTab[(x)->u.primsxp.offset].code)
-#define PRIMARITY(x) (R_FunTab[(x)->u.primsxp.offset].arity)
-#define PPINFO(x) (R_FunTab[(x)->u.primsxp.offset].gram)
-#define PRIMPRINT(x) (((R_FunTab[(x)->u.primsxp.offset].eval)/100)%10)
-#define PRIMINTERNAL(x) (((R_FunTab[(x)->u.primsxp.offset].eval)%100)/10)
-
-/* Promise Access Macros */
-#define PRCODE(x) ((x)->u.promsxp.expr)
-#define PRENV(x) ((x)->u.promsxp.env)
-#define PRVALUE(x) ((x)->u.promsxp.value)
-#define PRSEEN(x) ((x)->sxpinfo.gp)
-#define SET_PRSEEN(x,v) (((x)->sxpinfo.gp)=(v))
-
-/* Hashing Macros */
-#define HASHASH(x) ((x)->sxpinfo.gp)
-#define HASHVALUE(x) TRUELENGTH(x)
-#define SET_HASHASH(x,v) (((x)->sxpinfo.gp)=(v))
-#define SET_HASHVALUE(x,v) SET_TRUELENGTH(x, v)
-
-/* Vector Heap Structure */
-typedef struct {
- union {
- SEXP backpointer;
- double align;
- } u;
-} VECREC, *VECP;
-
-/* Vector Heap Macros */
-#define BACKPOINTER(v) ((v).u.backpointer)
-#define BYTE2VEC(n) (((n)>0)?(((n)-1)/sizeof(VECREC)+1):0)
-#define INT2VEC(n) (((n)>0)?(((n)*sizeof(int)-1)/sizeof(VECREC)+1):0)
-#define FLOAT2VEC(n) (((n)>0)?(((n)*sizeof(double)-1)/sizeof(VECREC)+1):0)
-#define COMPLEX2VEC(n) (((n)>0)?(((n)*sizeof(Rcomplex)-1)/sizeof(VECREC)+1):0)
-#define PTR2VEC(n) (((n)>0)?(((n)*sizeof(SEXP)-1)/sizeof(VECREC)+1):0)
-
-/* Bindings */
-/* use the same bits (15 and 14) in symbols and bindings */
-#define ACTIVE_BINDING_MASK (1<<15)
-#define BINDING_LOCK_MASK (1<<14)
-#define SPECIAL_BINDING_MASK (ACTIVE_BINDING_MASK | BINDING_LOCK_MASK)
-#define IS_ACTIVE_BINDING(b) ((b)->sxpinfo.gp & ACTIVE_BINDING_MASK)
-#define BINDING_IS_LOCKED(b) ((b)->sxpinfo.gp & BINDING_LOCK_MASK)
-#define SET_ACTIVE_BINDING_BIT(b) ((b)->sxpinfo.gp |= ACTIVE_BINDING_MASK)
-#define LOCK_BINDING(b) ((b)->sxpinfo.gp |= BINDING_LOCK_MASK)
-#define UNLOCK_BINDING(b) ((b)->sxpinfo.gp &= (~BINDING_LOCK_MASK))
-
-#else /* USE_RINTERNALS */
-
-typedef struct VECREC *VECP;
-int (PRIMOFFSET)(SEXP x);
-void (SET_PRIMOFFSET)(SEXP x, int v);
-
-#define PRIMFUN(x) (R_FunTab[PRIMOFFSET(x)].cfun)
-#define PRIMNAME(x) (R_FunTab[PRIMOFFSET(x)].name)
-#define PRIMVAL(x) (R_FunTab[PRIMOFFSET(x)].code)
-#define PRIMARITY(x) (R_FunTab[PRIMOFFSET(x)].arity)
-#define PPINFO(x) (R_FunTab[PRIMOFFSET(x)].gram)
-#define PRIMPRINT(x) (((R_FunTab[PRIMOFFSET(x)].eval)/100)%10)
-#define PRIMINTERNAL(x) (((R_FunTab[PRIMOFFSET(x)].eval)%100)/10)
-
-
-Rboolean (IS_ACTIVE_BINDING)(SEXP b);
-Rboolean (BINDING_IS_LOCKED)(SEXP b);
-void (SET_ACTIVE_BINDING_BIT)(SEXP b);
-void (LOCK_BINDING)(SEXP b);
-void (UNLOCK_BINDING)(SEXP b);
-
-#endif /* USE_RINTERNALS */
-
-#ifdef BYTECODE
-# ifdef BC_INT_STACK
-typedef union { void *p; int i; } IStackval;
-# endif
-#endif
-
-/* Stack entry for pending promises */
-typedef struct RPRSTACK {
- SEXP promise;
- struct RPRSTACK *next;
-} RPRSTACK;
-
-/* Evaluation Context Structure */
-typedef struct RCNTXT {
- struct RCNTXT *nextcontext; /* The next context up the chain */
- int callflag; /* The context "type" */
- JMP_BUF cjmpbuf; /* C stack and register information */
- int cstacktop; /* Top of the pointer protection stack */
- int evaldepth; /* evaluation depth at inception */
- SEXP promargs; /* Promises supplied to closure */
- SEXP callfun; /* The closure called */
- SEXP sysparent; /* environment the closure was called from */
- SEXP call; /* The call that effected this context*/
- SEXP cloenv; /* The environment */
- SEXP conexit; /* Interpreted "on.exit" code */
- void (*cend)(void *); /* C "on.exit" thunk */
- void *cenddata; /* data for C "on.exit" thunk */
- void *vmax; /* top of R_alloc stack */
- int intsusp; /* interrupts are suspended */
- SEXP handlerstack; /* condition handler stack */
- SEXP restartstack; /* stack of available restarts */
- struct RPRSTACK *prstack; /* stack of pending promises */
-#ifdef BYTECODE
- SEXP *nodestack;
-# ifdef BC_INT_STACK
- IStackval *intstack;
-# endif
-#endif
-} RCNTXT, *context;
-
-/* The Various Context Types.
-
- * In general the type is a bitwise OR of the values below.
- * Note that CTXT_LOOP is already the or of CTXT_NEXT and CTXT_BREAK.
- * Only functions should have the third bit turned on;
- * this allows us to move up the context stack easily
- * with either RETURN's or GENERIC's or RESTART's.
- * If you add a new context type for functions make sure
- * CTXT_NEWTYPE & CTXT_FUNCTION > 0
- */
-enum {
- CTXT_TOPLEVEL = 0,
- CTXT_NEXT = 1,
- CTXT_BREAK = 2,
- CTXT_LOOP = 3, /* break OR next target */
- CTXT_FUNCTION = 4,
- CTXT_CCODE = 8,
- CTXT_RETURN = 12,
- CTXT_BROWSER = 16,
- CTXT_GENERIC = 20,
- CTXT_RESTART = 32,
- CTXT_BUILTIN = 64 /* used in profiling */
-};
-
-/*
-TOP 0 0 0 0 0 0 = 0
-NEX 1 0 0 0 0 0 = 1
-BRE 0 1 0 0 0 0 = 2
-LOO 1 1 0 0 0 0 = 3
-FUN 0 0 1 0 0 0 = 4
-CCO 0 0 0 1 0 0 = 8
-BRO 0 0 0 0 1 0 = 16
-RET 0 0 1 1 0 0 = 12
-GEN 0 0 1 0 1 0 = 20
-RES 0 0 0 0 0 0 1 = 32
-BUI 0 0 0 0 0 0 0 1 = 64
-*/
-
-#define IS_RESTART_BIT_SET(flags) ((flags) & CTXT_RESTART)
-#define SET_RESTART_BIT_ON(flags) (flags |= CTXT_RESTART)
-#define SET_RESTART_BIT_OFF(flags) (flags &= ~CTXT_RESTART)
-
-/* Miscellaneous Definitions */
-#define streql(s, t) (!strcmp((s), (t)))
-
-/* Arithmetic and Relation Operators */
-typedef enum {
- PLUSOP = 1,
- MINUSOP,
- TIMESOP,
- DIVOP,
- POWOP,
- MODOP,
- IDIVOP
-} ARITHOP_TYPE;
-
-typedef enum {
- EQOP = 1,
- NEOP,
- LTOP,
- LEOP,
- GEOP,
- GTOP
-} RELOP_TYPE;
-
-/* File Handling */
-/*
-#define R_EOF 65535
-*/
-#define R_EOF -1
-
-
-/*--- Global Variables ---------------------------------------------------- */
-
-/* Defined and initialized in names.c (not main.c) :*/
-#ifndef __R_Names__
-extern
-#endif
-FUNTAB R_FunTab[]; /* Built in functions */
-
-
-#include <R_ext/libextern.h>
-
-#ifdef __MAIN__
-# define INI_as(v) = v
-#define extern0 attribute_hidden
-#else
-# define INI_as(v)
-#define extern0 extern
-#endif
-
-/* extern int errno; already have errno.h ! */
-extern int gc_inhibit_torture INI_as(1);
-
-LibExtern Rboolean R_interrupts_suspended INI_as(FALSE);
-LibExtern int R_interrupts_pending INI_as(0);
-
-/* R Home Directory */
-LibExtern char *R_Home; /* Root of the R tree */
-
-/* Memory Management */
-extern0 R_size_t R_NSize INI_as(R_NSIZE);/* Size of cons cell heap */
-extern0 R_size_t R_VSize INI_as(R_VSIZE);/* Size of the vector heap */
-extern0 SEXP R_NHeap; /* Start of the cons cell heap */
-extern0 SEXP R_FreeSEXP; /* Cons cell free list */
-extern0 R_size_t R_Collected; /* Number of free cons cells (after gc) */
-LibExtern int R_Is_Running; /* for Windows memory manager */
-
-/* The Pointer Protection Stack */
-extern0 int R_PPStackSize INI_as(R_PPSSIZE); /* The stack size (elements) */
-extern0 int R_PPStackTop; /* The top of the stack */
-extern0 SEXP* R_PPStack; /* The pointer protection stack */
-
-/* Evaluation Environment */
-LibExtern SEXP R_CurrentExpr; /* Currently evaluating expression */
-extern0 SEXP R_ReturnedValue; /* Slot for return-ing values */
-extern0 SEXP* R_SymbolTable; /* The symbol table */
-LibExtern RCNTXT R_Toplevel; /* Storage for the toplevel environment */
-LibExtern RCNTXT* R_ToplevelContext; /* The toplevel environment */
-LibExtern RCNTXT* R_GlobalContext; /* The global environment */
-extern0 Rboolean R_Visible; /* Value visibility flag */
-LibExtern int R_EvalDepth INI_as(0); /* Evaluation recursion depth */
-extern0 int R_BrowseLevel INI_as(0); /* how deep the browser is */
-extern0 int R_BrowseLines INI_as(0); /* lines/per call in browser */
-
-extern0 int R_Expressions INI_as(5000); /* options(expressions) */
-extern0 int R_Expressions_keep INI_as(5000); /* options(expressions) */
-extern0 Rboolean R_KeepSource INI_as(FALSE); /* options(keep.source) */
-extern0 int R_WarnLength INI_as(1000); /* Error/warning max length */
-extern uintptr_t R_CStackLimit INI_as((uintptr_t)-1); /* C stack limit */
-extern uintptr_t R_CStackStart INI_as((uintptr_t)-1); /* Initial stack address */
-extern0 int R_CStackDir INI_as(1); /* C stack direction */
-extern0 Rboolean R_WarnEscapes INI_as(TRUE); /* Warn on unrecognized escapes */
-extern0 struct RPRSTACK *R_PendingPromises INI_as(NULL); /* Pending promise stack */
-
-/* File Input/Output */
-LibExtern Rboolean R_Interactive INI_as(TRUE); /* TRUE during interactive use*/
-extern0 Rboolean R_Quiet INI_as(FALSE); /* Be as quiet as possible */
-extern Rboolean R_Slave INI_as(FALSE); /* Run as a slave process */
-extern0 Rboolean R_Verbose INI_as(FALSE); /* Be verbose */
-/* extern int R_Console; */ /* Console active flag */
-/* IoBuffer R_ConsoleIob; : --> ./IOStuff.h */
-/* R_Consolefile is used in the internet module */
-extern FILE* R_Consolefile INI_as(NULL); /* Console output file */
-extern FILE* R_Outputfile INI_as(NULL); /* Output file */
-extern0 int R_ErrorCon INI_as(2); /* Error connection */
-LibExtern char *R_TempDir INI_as(NULL); /* Name of per-session dir */
-extern0 char *Sys_TempDir INI_as(NULL); /* Name of per-session dir
- if set by R itself */
-extern0 char R_StdinEnc[31] INI_as(""); /* Encoding assumed for stdin */
-
-/* Objects Used In Parsing */
-extern0 SEXP R_CommentSxp; /* Comments accumulate here */
-extern0 int R_ParseError INI_as(0); /* Line where parse error occured */
-extern0 SEXP R_ParseErrorFile; /* Source file where parse error was seen */
-#define PARSE_ERROR_SIZE 256 /* Parse error messages saved here */
-extern0 char R_ParseErrorMsg[PARSE_ERROR_SIZE] INI_as("");
-#define PARSE_CONTEXT_SIZE 256 /* Recent parse context kept in a circular buffer */
-extern0 char R_ParseContext[PARSE_CONTEXT_SIZE] INI_as("");
-extern0 int R_ParseContextLast INI_as(0); /* last character in context buffer */
-
-/* Image Dump/Restore */
-extern int R_DirtyImage INI_as(0); /* Current image dirty */
-
-/* History */
-LibExtern char *R_HistoryFile; /* Name of the history file */
-LibExtern int R_HistorySize; /* Size of the history file */
-LibExtern int R_RestoreHistory; /* restore the history file? */
-extern void R_setupHistory(void);
-
-/* Warnings/Errors */
-extern0 int R_CollectWarnings INI_as(0); /* the number of warnings */
-extern0 SEXP R_Warnings; /* the warnings and their calls */
-extern0 int R_ShowErrorMessages INI_as(1); /* show error messages? */
-extern0 SEXP R_HandlerStack; /* Condition handler stack */
-extern0 SEXP R_RestartStack; /* Stack of available restarts */
-extern0 Rboolean R_warn_partial_match_args INI_as(FALSE);
-extern0 Rboolean R_warn_partial_match_dollar INI_as(FALSE);
-extern0 Rboolean R_warn_partial_match_attr INI_as(FALSE);
-extern0 Rboolean R_ShowWarnCalls INI_as(FALSE);
-extern0 Rboolean R_ShowErrorCalls INI_as(FALSE);
-extern0 int R_NShowCalls INI_as(50);
-
-LibExtern Rboolean utf8locale INI_as(FALSE); /* is this a UTF-8 locale? */
-LibExtern Rboolean mbcslocale INI_as(FALSE); /* is this a MBCS locale? */
-extern0 Rboolean latin1locale INI_as(FALSE); /* is this a Latin-1 locale? */
-#ifdef Win32
-LibExtern unsigned int localeCP INI_as(1252); /* the locale's codepage */
-extern0 Rboolean WinUTF8out INI_as(FALSE); /* Use UTF-8 for output */
-extern0 void WinCheckUTF8(void);
-#endif
-
-extern0 char OutDec INI_as('.'); /* decimal point used for output */
-
-/* Initialization of the R environment when it is embedded */
-extern int Rf_initEmbeddedR(int argc, char **argv);
-
-/* GUI type */
-
-extern char *R_GUIType INI_as("unknown");
-
-#ifdef BYTECODE
-#define R_BCNODESTACKSIZE 10000
-extern0 SEXP *R_BCNodeStackBase, *R_BCNodeStackTop, *R_BCNodeStackEnd;
-# ifdef BC_INT_STACK
-#define R_BCINTSTACKSIZE 10000
-extern0 IStackval *R_BCIntStackBase, *R_BCIntStackTop, *R_BCIntStackEnd;
-# endif
-#endif
-
-/* Pointer type and utilities for dispatch in the methods package */
-typedef SEXP (*R_stdGen_ptr_t)(SEXP, SEXP, SEXP); /* typedef */
-R_stdGen_ptr_t R_get_standardGeneric_ptr(void); /* get method */
-R_stdGen_ptr_t R_set_standardGeneric_ptr(R_stdGen_ptr_t, SEXP); /* set method */
-LibExtern SEXP R_MethodsNamespace;
-SEXP R_deferred_default_method(void);
-SEXP R_set_prim_method(SEXP fname, SEXP op, SEXP code_vec, SEXP fundef,
- SEXP mlist);
-SEXP do_set_prim_method(SEXP op, const char *code_string, SEXP fundef,
- SEXP mlist);
-void R_set_quick_method_check(R_stdGen_ptr_t);
-SEXP R_primitive_methods(SEXP op);
-SEXP R_primitive_generic(SEXP op);
-
-/* smallest decimal exponent, needed in format.c, set in Init_R_Machine */
-extern0 int R_dec_min_exponent INI_as(-308);
-
-/* structure for caching machine accuracy values */
-typedef struct {
- int ibeta, it, irnd, ngrd, machep, negep, iexp, minexp, maxexp;
- double eps, epsneg, xmin, xmax;
-} AccuracyInfo;
-
-LibExtern AccuracyInfo R_AccuracyInfo;
-
-extern0 unsigned int max_contour_segments INI_as(25000);
-
-extern0 Rboolean known_to_be_latin1 INI_as(FALSE);
-extern0 Rboolean known_to_be_utf8 INI_as(FALSE);
-
-
-#ifdef __MAIN__
-# undef extern
-# undef extern0
-# undef LibExtern
-#endif
-#undef INI_as
-
-#define checkArity(a,b) Rf_checkArityCall(a,b,call)
-
-/*--- FUNCTIONS ------------------------------------------------------ */
-
-# define begincontext Rf_begincontext
-# define check_stack_balance Rf_check_stack_balance
-# define CheckFormals Rf_CheckFormals
-# define CleanEd Rf_CleanEd
-# define CoercionWarning Rf_CoercionWarning
-# define ComplexFromInteger Rf_ComplexFromInteger
-# define ComplexFromLogical Rf_ComplexFromLogical
-# define ComplexFromReal Rf_ComplexFromReal
-# define ComplexFromString Rf_ComplexFromString
-# define copyListMatrix Rf_copyListMatrix
-# define copyMostAttribNoTs Rf_copyMostAttribNoTs
-# define CustomPrintValue Rf_CustomPrintValue
-# define DataFrameClass Rf_DataFrameClass
-# define ddfindVar Rf_ddfindVar
-# define deparse1 Rf_deparse1
-# define deparse1line Rf_deparse1line
-# define deparse1s Rf_deparse1s
-# define DispatchGroup Rf_DispatchGroup
-# define DispatchOrEval Rf_DispatchOrEval
-# define dynamicfindVar Rf_dynamicfindVar
-# define EncodeRaw Rf_EncodeRaw
-# define EncodeString Rf_EncodeString
-# define EnsureString Rf_EnsureString
-# define endcontext Rf_endcontext
-# define envlength Rf_envlength
-# define ErrorMessage Rf_ErrorMessage
-# define evalList Rf_evalList
-# define evalListKeepMissing Rf_evalListKeepMissing
-# define factorsConform Rf_factorsConform
-# define findcontext Rf_findcontext
-# define findVar1 Rf_findVar1
-# define FrameClassFix Rf_FrameClassFix
-# define framedepth Rf_framedepth
-# define frameSubscript Rf_frameSubscript
-# define get1index Rf_get1index
-# define getVar Rf_getVar
-# define getVarInFrame Rf_getVarInFrame
-# define InitArithmetic Rf_InitArithmetic
-# define InitColors Rf_InitColors
-# define InitConnections Rf_InitConnections
-# define InitEd Rf_InitEd
-# define InitFunctionHashing Rf_InitFunctionHashing
-# define InitBaseEnv Rf_InitBaseEnv
-# define InitGlobalEnv Rf_InitGlobalEnv
-# define InitGraphics Rf_InitGraphics
-# define InitMemory Rf_InitMemory
-# define InitNames Rf_InitNames
-# define InitOptions Rf_InitOptions
-# define InitStringHash Rf_InitStringHash
-# define InitTempDir Rf_InitTempDir
-# define initStack Rf_initStack
-# define IntegerFromComplex Rf_IntegerFromComplex
-# define IntegerFromLogical Rf_IntegerFromLogical
-# define IntegerFromReal Rf_IntegerFromReal
-# define IntegerFromString Rf_IntegerFromString
-# define internalTypeCheck Rf_internalTypeCheck
-# define isValidName Rf_isValidName
-# define ItemName Rf_ItemName
-# define jump_to_toplevel Rf_jump_to_toplevel
-# define KillAllDevices Rf_KillAllDevices
-# define levelsgets Rf_levelsgets
-# define LogicalFromComplex Rf_LogicalFromComplex
-# define LogicalFromInteger Rf_LogicalFromInteger
-# define LogicalFromReal Rf_LogicalFromReal
-# define LogicalFromString Rf_LogicalFromString
-# define mainloop Rf_mainloop
-# define makeSubscript Rf_makeSubscript
-# define markKnown Rf_markKnown
-# define mat2indsub Rf_mat2indsub
-# define matchArg Rf_matchArg
-# define matchArgExact Rf_matchArgExact
-# define matchArgs Rf_matchArgs
-# define matchPar Rf_matchPar
-# define Mbrtowc Rf_mbrtowc
-# define mbtoucs Rf_mbtoucs
-# define mkCLOSXP Rf_mkCLOSXP
-# define mkFalse Rf_mkFalse
-# define mkPROMISE Rf_mkPROMISE
-# define mkQUOTE Rf_mkQUOTE
-# define mkSYMSXP Rf_mkSYMSXP
-# define mkTrue Rf_mkTrue
-# define NewEnvironment Rf_NewEnvironment
-# define OneIndex Rf_OneIndex
-# define onintr Rf_onintr
-# define onsigusr1 Rf_onsigusr1
-# define onsigusr2 Rf_onsigusr2
-# define parse Rf_parse
-# define PrintDefaults Rf_PrintDefaults
-# define PrintGreeting Rf_PrintGreeting
-# define PrintValueEnv Rf_PrintValueEnv
-# define PrintValueRec Rf_PrintValueRec
-# define PrintVersion Rf_PrintVersion
-# define PrintVersionString Rf_PrintVersionString
-# define PrintWarnings Rf_PrintWarnings
-# define promiseArgs Rf_promiseArgs
-# define RealFromComplex Rf_RealFromComplex
-# define RealFromInteger Rf_RealFromInteger
-# define RealFromLogical Rf_RealFromLogical
-# define RealFromString Rf_RealFromString
-# define Seql Rf_Seql
-# define Scollate Rf_Scollate
-# define sortVector Rf_sortVector
-# define ssort Rf_ssort
-# define StringFromComplex Rf_StringFromComplex
-# define StringFromInteger Rf_StringFromInteger
-# define StringFromLogical Rf_StringFromLogical
-# define StringFromReal Rf_StringFromReal
-# define strIsASCII Rf_strIsASCII
-# define StrToInternal Rf_StrToInternal
-# define substituteList Rf_substituteList
-# define tsConform Rf_tsConform
-# define tspgets Rf_tspgets
-# define type2symbol Rf_type2symbol
-# define unbindVar Rf_unbindVar
-# define usemethod Rf_usemethod
-# define ucstomb Rf_ucstomb
-# define ucstoutf8 Rf_ucstoutf8
-# define utf8toucs Rf_utf8toucs
-# define utf8towcs Rf_utf8towcs
-# define vectorSubscript Rf_vectorSubscript
-# define warningcall Rf_warningcall
-# define WarningMessage Rf_WarningMessage
-# define wcstoutf8 Rf_wcstoutf8
-# define yychar Rf_yychar
-# define yylval Rf_yylval
-# define yynerrs Rf_yynerrs
-# define yyparse Rf_yyparse
-
-/* Platform Dependent Gui Hooks */
-
-#define R_CONSOLE 1
-#define R_FILE 2
-#define R_TEXT 3
-
-/* The maximum length of input line which will be asked for */
-#define CONSOLE_BUFFER_SIZE 1024
-int R_ReadConsole(const char *, unsigned char *, int, int);
-void R_WriteConsole(const char *, int); /* equivalent to R_WriteConsoleEx(a, b, 0) */
-void R_WriteConsoleEx(const char *, int, int);
-void R_ResetConsole(void);
-void R_FlushConsole(void);
-void R_ClearerrConsole(void);
-void R_Busy(int);
-int R_ShowFiles(int, const char **, const char **, const char *,
- Rboolean, const char *);
-int R_EditFiles(int, const char **, const char **, const char *);
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1509
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