The changes for R are all to do with portability:

__inline__ is not portable.
fdopen is POSIX but not C89
Solaris' cc objects to inlining functions with names starting with 'main'.
C character strings are limited for ca 500 chars.

diff -u ./blocksort.c /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/blocksort.c
--- ./blocksort.c	2005-02-15 16:19:38.000000000 +0000
+++ /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/blocksort.c	2006-09-04 15:41:36.488779000 +0100
@@ -75,7 +75,7 @@
 
 /*---------------------------------------------*/
 static 
-__inline__
+R_INLINE
 void fallbackSimpleSort ( UInt32* fmap, 
                           UInt32* eclass, 
                           Int32   lo, 
@@ -389,9 +389,10 @@
 /*---------------------------------------------*/
 
 /*---------------------------------------------*/
+/* Solaris cc objects to inlining functions whose names start with `main' */
 static
-__inline__
-Bool mainGtU ( UInt32  i1, 
+R_INLINE
+Bool BZmainGtU ( UInt32  i1, 
                UInt32  i2,
                UChar*  block, 
                UInt16* quadrant,
@@ -402,7 +403,7 @@
    UChar  c1, c2;
    UInt16 s1, s2;
 
-   AssertD ( i1 != i2, "mainGtU" );
+   AssertD ( i1 != i2, "BZmainGtU" );
    /* 1 */
    c1 = block[i1]; c2 = block[i2];
    if (c1 != c2) return (c1 > c2);
@@ -558,7 +559,7 @@
          if (i > hi) break;
          v = ptr[i];
          j = i;
-         while ( mainGtU ( 
+         while ( BZmainGtU ( 
                     ptr[j-h]+d, v+d, block, quadrant, nblock, budget 
                  ) ) {
             ptr[j] = ptr[j-h];
@@ -572,7 +573,7 @@
          if (i > hi) break;
          v = ptr[i];
          j = i;
-         while ( mainGtU ( 
+         while ( BZmainGtU ( 
                     ptr[j-h]+d, v+d, block, quadrant, nblock, budget 
                  ) ) {
             ptr[j] = ptr[j-h];
@@ -586,7 +587,7 @@
          if (i > hi) break;
          v = ptr[i];
          j = i;
-         while ( mainGtU ( 
+         while ( BZmainGtU ( 
                     ptr[j-h]+d, v+d, block, quadrant, nblock, budget 
                  ) ) {
             ptr[j] = ptr[j-h];
@@ -626,7 +627,7 @@
 }
 
 static 
-__inline__
+R_INLINE
 UChar mmed3 ( UChar a, UChar b, UChar c )
 {
    UChar t;
diff -u ./bzlib.c /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/bzlib.c
--- ./bzlib.c	2005-02-15 16:24:58.000000000 +0000
+++ /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/bzlib.c	2006-09-04 15:41:36.538746000 +0100
@@ -98,8 +98,9 @@
       BZ2_bzlibVersion()
    );
 
+   /* split up over-long message */
    if (errcode == 1007) {
-   fprintf(stderr,
+       fprintf(stderr, "%s%s%s",
       "\n*** A special note about internal error number 1007 ***\n"
       "\n"
       "Experience suggests that a common cause of i.e. 1007\n"
@@ -107,7 +108,7 @@
       "just happens to cross-check the results of huge numbers of\n"
       "memory reads/writes, and so acts (unintendedly) as a stress\n"
       "test of your memory system.\n"
-      "\n"
+       "\n",
       "I suggest the following: try compressing the file again,\n"
       "possibly monitoring progress in detail with the -vv flag.\n"
       "\n"
@@ -117,7 +118,7 @@
       "  (www.memtest86.com).  At the time of writing it is free (GPLd).\n"
       "  Memtest86 tests memory much more thorougly than your BIOSs\n"
       "  power-on test, and may find failures that the BIOS doesn't.\n"
-      "\n"
+      "\n",
       "* If the error can be repeatably reproduced, this is a bug in\n"
       "  bzip2, and I would very much like to hear about it.  Please\n"
       "  let me know, and, ideally, save a copy of the file causing the\n"
@@ -728,7 +729,7 @@
 
 
 /*---------------------------------------------------*/
-__inline__ Int32 BZ2_indexIntoF ( Int32 indx, Int32 *cftab )
+R_INLINE Int32 BZ2_indexIntoF ( Int32 indx, Int32 *cftab )
 {
    Int32 nb, na, mid;
    nb = 0;
@@ -1424,6 +1425,11 @@
 #else
 #   define SET_BINARY_MODE(file)
 #endif
+
+#if !defined(fdopen) && defined(HAVE_FDOPEN)
+  FILE *fdopen(int fildes, const char *mode);
+#endif
+
 static
 BZFILE * bzopen_or_bzdopen
                ( const char *path,   /* no use when bzdopen */
@@ -1470,7 +1476,7 @@
         fp = fopen(path,mode2);
       }
    } else {
-#ifdef BZ_STRICT_ANSI
+#ifndef HAVE_FDOPEN
       fp = NULL;
 #else
       fp = fdopen(fd,mode2);
diff -u ./bzlib_private.h /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/bzlib_private.h
--- ./bzlib_private.h	2005-02-15 16:24:27.000000000 +0000
+++ /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/bzlib_private.h	2006-09-04 15:41:36.438748000 +0100
@@ -62,6 +62,7 @@
 #ifndef _BZLIB_PRIVATE_H
 #define _BZLIB_PRIVATE_H
 
+#include <config.h> /* for R_INLINE */
 #include <stdlib.h>
 
 #ifndef BZ_NO_STDIO
Only in .: bzmore
Only in .: bzmore.1
diff -u ./compress.c /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/compress.c
--- ./compress.c	2005-02-15 16:23:23.000000000 +0000
+++ /data/gannet/ripley/R/svn/R-patched/src/extra/bzip2/compress.c	2006-09-04 15:41:36.768745000 +0100
@@ -113,7 +113,7 @@
 
 /*---------------------------------------------------*/
 static
-__inline__
+R_INLINE
 void bsW ( EState* s, Int32 n, UInt32 v )
 {
    bsNEEDW ( n );