makoto@ubuntu12-ja-emacs24:/usr/pkgsrc/bootstrap$ \
  time sudo ./bootstrap --prefix=/usr/pkg --pkgdbdir=/var/db/pkgdb
ERROR: Your shell's echo command is not BSD-compatible.
ERROR: Please select another shell by setting the environment
ERROR: variable SH.

real 0m0.197s
user 0m0.008s
sys 0m0.156s

export SH=/bin/bash

=> Full dependency bootstrap-mk-files-[0-9]*: found bootstrap-mk-files-20140314
 find_best:5: no such file or directory:
  /usr/pkgsrc/bootstrap/work/sbin/pkg_info -K /var/db/pkgdb
ERROR: [resolve-dependencies] A package matching ``bootstrap-mk-files-[0-9]*'' should
ERROR:     be installed, but one cannot be found.  Perhaps there is a
ERROR:     stale work directory for ../../pkgtools/bootstrap-mk-files?
*** Error code 1

ubuntu12-ja-emacs24@root 02:17:28/140319(..pkgsrc/bootstrap)% grep -r find_best ../mk
../mk/pkgformat/pkg/resolve-dependencies:find_best() {
../mk/pkgformat/pkg/resolve-dependencies:  pkg=`find_best "$type" "$pattern"`

    32 find_best() {
    33  case $1 in
    34  bootstrap|tool)
    35   ${HOST_PKG_INFO} -E "$2" || ${TRUE};;
    36  build|full)
    37   ${PKG_INFO} -E "$2" || ${TRUE};;
    38  esac
    39 }

=> Registering installation for bootstrap-mk-files-20140314
===> running: (cd /usr/pkgsrc/devel/bmake &&
  /usr/pkgsrc/bootstrap/work/bin/bmake USE_DESTDIR=no
  -DPKG_PRESERVE MAKECONF=/usr/pkgsrc/bootstrap/work/mk.conf
  install)
===> Installing dependencies for bmake-20140314
=> Full dependency bootstrap-mk-files-[0-9]*: found
 bootstrap-mk-files-20140314 find_best:5:
 no such file or directory:
  /usr/pkgsrc/bootstrap/work/sbin/pkg_info -K /var/db/pkgdb
ERROR: [reduce-resolved-depends.awk] invalid dependency line
  full bootstrap-mk-files-[0-9]*
  /usr/pkgsrc/bootstrap/work/sbin/pkg_info -K /var/db/pkgdb
*** Error code 1

Stop.
bmake: stopped in /usr/pkgsrc/devel/bmake
===> exited with status 1
aborted.
ubuntu12-ja-emacs24@root 08:30:51/140319(..pkgsrc/bootstrap)

ubuntu12-ja-emacs24@root 09:35:37/140319(..pkgsrc/bootstrap)% \
cat -n ../mk/pkgformat/pkg/depends.mk | sed -n 45,51p

    45
    46 _REDUCE_RESOLVED_DEPENDS_CMD=${PKGSRC_SETENV} CAT=${CAT:Q}   \
    47     PKG_INFO=${PKG_INFO:Q}    \
    48     HOST_PKG_INFO=${HOST_PKG_INFO:Q}   \
    49    ${AWK} -f ${PKGSRCDIR}/mk/pkgformat/pkg/reduce-resolved-depends.awk \
    50     < ${_RDEPENDS_FILE}
    51

実は何とか手で bootstrap して、何とか使い始めたのですが、

=> Returning to build of libtool-base-2.4.2nb6

ERROR: [reduce-resolved-depends.awk] invalid dependency line
 bootstrap digest>=20010302 /usr/pkg/sbin/pkg_info -K /var/db/pkg
*** Error code 1

どうも bootstrap と full が逆になっているのではないかという気も
(そんなことがあるはずもないですが)
root@ubuntu12-ja-emacs24:/usr/pkgsrc/security/sudo# \ cat -n ../../mk/pkgformat/pkg/reduce-resolved-depends.awk | sed -n 90,144p

    90
    91  for (i = 0; i < lines; ++i) {
    92   if (type[i] == "bootstrap" && checked_bootstrap[pkg[i]] != 1) {
    93    checked_bootstrap[pkg[i]] = 1
    94    found = 0
    95    if (PKG_INFO == HOST_PKG_INFO) {
    96     cmd = PKG_INFO " -qr " pkg[i]
    97     while (cmd | getline dpkg) {
    98       if (checked_full[dpkg] == 1)
    99        found = 1
   100     }
   101     close(cmd)
   102    }
   103    if (found == 0)
   104     print_line[i] = 1
   105   }
   106  }
   107
   108  for (i = 0; i < lines; ++i) {
   109   if (type[i] == "tool" && checked_tool[pkg[i]] != 1) {
   110    checked_tool[pkg[i]] = 1
   111    if (checked_bootstrap[pkg[i]] == 1)
   112     continue
   113    found = 0
   114    if (PKG_INFO == HOST_PKG_INFO) {
   115     cmd = PKG_INFO " -qr " pkg[i]
   116     while (cmd | getline dpkg) {
   117       if (checked_full[dpkg] == 1)
   118        found = 1
   119     }
   120     close(cmd)
   121    }
   122    if (found == 0)
   123     print_line[i] = 1
   124   }
   125  }
   126
   127  for (i = 0; i < lines; ++i) {
   128   if (type[i] == "build" && checked_build[pkg[i]] != 1) {
   129    checked_build[pkg[i]] = 1
   130    if (PKG_INFO == HOST_PKG_INFO)
   131     if (checked_bootstrap[pkg[i]] == 1)
   132       continue
   133    found = 0
   134    cmd = PKG_INFO " -qr " pkg[i]
   135    while (cmd | getline dpkg) {
   136     if (checked_full[dpkg] == 1)
   137       found = 1
   138    }
   139    close(cmd)
   140    if (found == 0)
   141     print_line[i] = 1
   142   }
   143  }
   144
root@ubuntu12-ja-emacs24:/usr/pkgsrc/security/sudo# 

 53 BEGIN {
 54         CAT = ENVIRON["CAT"] ? ENVIRON["CAT"] : "cat"
 55         PKG_INFO = ENVIRON["PKG_INFO"] ? ENVIRON["PKG_INFO"] : "pkg_info"
 56         HOST_PKG_INFO = ENVIRON["HOST_PKG_INFO"] ? ENVIRON["HOST_PKG_INFO"] : "pkg_info"
 57 
 58         PROGNAME = "reduce-resolved-depends.awk"
 59         ERRCAT = CAT " 1>&2"
 60 
 61         while (getline == 1) {
 62                 if (NF != 3) {
 63                         print "ERROR: [" PROGNAME "] (1) invalid dependency line " $0 | ERRCAT
 64                         exit 1
 65                 }
 66                 if ($1 != "full" &&
 67                     $1 != "build" &&
 68                     $1 != "tool" &&
 69                     $1 != "bootstrap") {
 70                         print "ERROR: [" PROGNAME "] (2) invalid dependency line " $0 | ERRCAT
 71                         exit 1
 72                 }
 73                 type[NR] = $1
 74                 pattern[NR] = $2
 75                 pkg[NR] = $3
 76         }
 77         lines = NR + 1
 78 

(同じ行があると、どちらか分らないが、この場合は (1) の方で出ている。(次の行の) Number of Field が違うと (?)

 bootstrap digest>=20010302 /usr/pkg/sbin/pkg_info -K /var/db/pkg

確かに三つではない。

root@ubuntu12-ja-emacs24:/usr/pkgsrc/devel/libtool-base# \
head `/usr/pkg/bin/bmake show-var VARNAME=_RDEPENDS_FILE`
bootstrap digest>=20010302     /usr/pkg/sbin/pkg_info -K /var/db/pkg
digest-20121220
tool nbpatch-[0-9]* /usr/pkg/sbin/pkg_info -K /var/db/pkg
nbpatch-20100124

この上の行から来ているらしい。ここに限って言えば -K /var/db/pkg は不要の気がする。
もしかして /var/db/pkg と /var/db/pkgdb を僕が混用しているのかな