I'm running 1.6.1 GENERIC on an i386 (well, 533Mhz Celeron),
and I track pkgsrc with sup.

My supfiles/coll.list:

#	$NetBSD: sup.netbsd.org,v 1.4 1999/02/16 08:22:19 abs Exp $
#
# Example supfile for sup.netbsd.org.
#

#current release=allsrc host=sup.netbsd.org hostbase=/ftp/pub \
#base=/usr prefix=/usr backup use-rel-suffix compress

#current release=doc host=sup.netbsd.org hostbase=/ftp/pub \
#base=/usr prefix=/usr backup use-rel-suffix compress

current release=pkgsrc host=sup.netbsd.org hostbase=/ftp/pub \
base=/usr prefix=/usr backup use-rel-suffix compress delete

#current release=security host=sup.netbsd.org hostbase=/ftp/pub \
#base=/usr prefix=/usr backup use-rel-suffix compress

#current release=xsrc host=sup.netbsd.org hostbase=/ftp/pub \
#base=/usr prefix=/usr backup use-rel-suffix compress


After running sup -s, lintpkgsrc -i spits out a bunch of 
stuff before reporting which pkgs need to be updated:

$ lintpkgsrc -i

Scanning pkgsrc Makefiles: Cannot open '/usr/pkgsrc/archivers/php4-bz2/../mk/autoconf.mk' (from /usr/pkgsrc/archivers/php4-bz2/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/archivers/php4-zlib/../mk/autoconf.mk' (from /usr/pkgsrc/archivers/php4-zlib/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/audio/cheesetracker/../mk/autoconf.mk' (from /usr/pkgsrc/audio/cheesetracker/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/audio/faad2/../mk/autoconf.mk' (from /usr/pkgsrc/audio/faad2/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/audio/tremor/../mk/autoconf.mk' (from /usr/pkgsrc/audio/tremor/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/audio/tremor-tools/../mk/autoconf.mk' (from /usr/pkgsrc/audio/tremor-tools/Makefile): No such file or directory
......Cannot open '/usr/pkgsrc/converters/php4-iconv/../mk/autoconf.mk' (from /usr/pkgsrc/converters/php4-iconv/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/cross/i386-netbsdpe/../../../mk/autoconf.mk' (from /usr/pkgsrc/cross/i386-netbsdpe/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/databases/php4-dba/../mk/autoconf.mk' (from /usr/pkgsrc/databases/php4-dba/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/databases/php4-dbase/../mk/autoconf.mk' (from /usr/pkgsrc/databases/php4-dbase/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/databases/php4-filepro/../mk/autoconf.mk' (from /usr/pkgsrc/databases/php4-filepro/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/databases/php4-ldap/../mk/autoconf.mk' (from /usr/pkgsrc/databases/php4-ldap/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/databases/php4-mysql/../mk/autoconf.mk' (from /usr/pkgsrc/databases/php4-mysql/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/databases/php4-odbc/../mk/autoconf.mk' (from /usr/pkgsrc/databases/php4-odbc/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/databases/php4-pgsql/../mk/autoconf.mk' (from /usr/pkgsrc/databases/php4-pgsql/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/devel/php4-gettext/../mk/autoconf.mk' (from /usr/pkgsrc/devel/php4-gettext/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/devel/php4-gmp/../mk/autoconf.mk' (from /usr/pkgsrc/devel/php4-gmp/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/devel/php4-posix/../mk/autoconf.mk' (from /usr/pkgsrc/devel/php4-posix/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/devel/php4-sysvsem/../mk/autoconf.mk' (from /usr/pkgsrc/devel/php4-sysvsem/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/devel/php4-sysvshm/../mk/autoconf.mk' (from /usr/pkgsrc/devel/php4-sysvshm/Makefile): No such file or directory
.....Cannot open '/usr/pkgsrc/games/glchess/../mk/autoconf.mk' (from /usr/pkgsrc/games/glchess/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/games/gnome-games/../mk/autoconf.mk' (from /usr/pkgsrc/games/gnome-games/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/games/xpuyopuyo/../mk/autoconf.mk' (from /usr/pkgsrc/games/xpuyopuyo/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/games/xracer/../mk/autoconf.mk' (from /usr/pkgsrc/games/xracer/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/graphics/avifile-devel/../mk/autoconf.mk' (from /usr/pkgsrc/graphics/avifile-devel/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/graphics/php4-exif/../mk/autoconf.mk' (from /usr/pkgsrc/graphics/php4-exif/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/graphics/php4-gd/../mk/autoconf.mk' (from /usr/pkgsrc/graphics/php4-gd/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/graphics/transcode/../mk/autoconf.mk' (from /usr/pkgsrc/graphics/transcode/Makefile): No such file or directory
...Cannot open '/usr/pkgsrc/lang/dylan-compiler/../mk/autoconf.mk' (from /usr/pkgsrc/lang/dylan-compiler/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/lang/dylan-interpreter/../mk/autoconf.mk' (from /usr/pkgsrc/lang/dylan-interpreter/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/mail/clamav/../mk/autoconf.mk' (from /usr/pkgsrc/mail/clamav/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/mail/php4-imap/../mk/autoconf.mk' (from /usr/pkgsrc/mail/php4-imap/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/math/php4-bcmath/../mk/autoconf.mk' (from /usr/pkgsrc/math/php4-bcmath/Makefile): No such file or directory
...Cannot open '/usr/pkgsrc/misc/php4-calendar/../mk/autoconf.mk' (from /usr/pkgsrc/misc/php4-calendar/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/misc/php4-mbstring/../mk/autoconf.mk' (from /usr/pkgsrc/misc/php4-mbstring/Makefile): No such file or directory
Cannot extract udfclient-ro1 version (/usr/pkgsrc/misc/udfclient/Makefile)
.Cannot open '/usr/pkgsrc/net/ntop2/../mk/autoconf.mk' (from /usr/pkgsrc/net/ntop2/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/net/php4-ftp/../mk/autoconf.mk' (from /usr/pkgsrc/net/php4-ftp/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/net/php4-snmp/../mk/autoconf.mk' (from /usr/pkgsrc/net/php4-snmp/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/net/php4-sockets/../mk/autoconf.mk' (from /usr/pkgsrc/net/php4-sockets/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/net/php4-yp/../mk/autoconf.mk' (from /usr/pkgsrc/net/php4-yp/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/net/quagga/../mk/autoconf.mk' (from /usr/pkgsrc/net/quagga/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/net/zebra/../mk/autoconf.mk' (from /usr/pkgsrc/net/zebra/Makefile): No such file or directory
....Cannot open '/usr/pkgsrc/print/php4-pdflib/../mk/autoconf.mk' (from /usr/pkgsrc/print/php4-pdflib/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/security/gtk-systrace/../mk/autoconf.mk' (from /usr/pkgsrc/security/gtk-systrace/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/security/php4-mcrypt/../mk/autoconf.mk' (from /usr/pkgsrc/security/php4-mcrypt/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/security/php4-mhash/../mk/autoconf.mk' (from /usr/pkgsrc/security/php4-mhash/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/security/php4-openssl/../mk/autoconf.mk' (from /usr/pkgsrc/security/php4-openssl/Makefile): No such file or directory
..Cannot open '/usr/pkgsrc/sysutils/cfengine/../mk/autoconf.mk' (from /usr/pkgsrc/sysutils/cfengine/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/textproc/php4-domxml/../mk/autoconf.mk' (from /usr/pkgsrc/textproc/php4-domxml/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/textproc/php4-wddx/../mk/autoconf.mk' (from /usr/pkgsrc/textproc/php4-wddx/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/textproc/php4-xslt/../mk/autoconf.mk' (from /usr/pkgsrc/textproc/php4-xslt/Makefile): No such file or directory
...Cannot open '/usr/pkgsrc/www/libwww/../mk/autoconf.mk' (from /usr/pkgsrc/www/libwww/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/www/php4-apc/../mk/autoconf.mk' (from /usr/pkgsrc/www/php4-apc/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/www/php4-curl/../mk/autoconf.mk' (from /usr/pkgsrc/www/php4-curl/Makefile): No such file or directory
Cannot open '/usr/pkgsrc/www/quanta/../mk/autoconf.mk' (from /usr/pkgsrc/www/quanta/Makefile): No such file or directory
.Cannot open '/usr/pkgsrc/x11/lesstif12/../mk/autoconf.mk' (from /usr/pkgsrc/x11/lesstif12/Makefile): No such file or directory                                   4088 packages

Any clues as to what's going wrong here?

-- 
Michael Parson
mparson@bl.org