pkgsrc/databases/shared-mime-info/work/.buildlink/lib/libxml2.so: 
	undefined reference to `gzopen64'
pkgsrc/databases/shared-mime-info/work/.buildlink/lib/libxml2.so: 
	undefined reference to `gzdirect@ZLIB_1.2.2.3'

こういうのがいくつも出る ?

This is because we have following part in /usr/include

cat -n /usr/include/zlib.h

1372:#if defined(_LARGEFILE64_SOURCE) || _FILE_OFFSET_BITS == 64
1373-   ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
...
1380-#if _FILE_OFFSET_BITS == 64
1381:#  define gzopen gzopen64

By renaming some file not to use, and let pkgsrc zlib.h include files be effective, These problem may be skipped. (or passing -D_LARGEFILE64SOURCE=1 in CFLAG to gcc when compiling all related src, libxml2, xmlto etc (?))

ubuntu@makoto 23:18:37/100523(~)% ls -l /usr/include/*-dist     
-rw-r--r-- 1 root root 12217 2009-11-10 00:25 /usr/include/zconf.h-dist
-rw-r--r-- 1 root root 68287 2009-11-10 00:25 /usr/include/zlib.h-dist

textproc/xmlto is good small candidate to check.