Quoting Marc Espie <es...@nerim.net>:

On Tue, Feb 27, 2018 at 10:14:51PM +0000, Zsolt Kantor wrote:
What exactly does the pkg_check -F option? If I use it, it does some filesystem check, and some "Locating unknown files".

At the end I get: "Locating unknown files: ok", "Locating unknown directories: ok", and a long list of "not found" directories and files, like below.
Not found:
        /boot
        /bsd
        /bsd.rd
        /bsd.sp
        /bsd.syspatch61
        /etc/X11/xenodm/authdir
. . . .

Those are objects that are expected on a normal system, but that are not
there, see the locate(8) dbs under /usr/lib/locate/src.db and
/usr/X11R6/lib/locate/xorg.db

Not having /bsd and /bsd.rd   seems really strange.

I am using 6.2 -current from

builder.ftlcloud.ca$ sysctl kern.version
kern.version=OpenBSD 6.2-current (GENERIC.MP) #6: Sun Feb 18 20:12:24 CST 2018
    vi...@builder.ftlcloud.ca:/usr/src/sys/arch/amd64/compile/GENERIC.MP

and ran pkg_check -F

Not much going on on the package build system

builder.ftlcloud.ca$ w
 6:53AM  up 9 days, 10:40, 3 users, load averages: 0.49, 0.26, 0.11
USER    TTY FROM              LOGIN@  IDLE WHAT
vijay p0 10.0.0.154 6:49AM 0 /usr/bin/perl /usr/sbin/pkg_check -F vijay p1 10.72.3.61 Tue01PM 17:16 /usr/bin/ftp -V -m -C -o /usr/ports/
vijay    p2 10.0.0.154        6:52AM     0 w

There were no "errors" when pkg_check was run using the root account but it gave detailed information that helped me understand what was wrong with everything I am doing :) Thank you very much for pkg_check.

When running pkg_check using the user account that I use to build ports, I did get the type of errors the OP mentioned.

DETAILS BELOW AS ROOT

builder.ftlcloud.ca# pkg_check -F
Packing-list sanity: ok
Direct dependencies: ok
Reverse dependencies: ok
Files from packages: ok
--- e2fsprogs-1.42.12p4 -------------------
/usr/local/include/et/com_err.h doesn't link to /usr/local/include/com_err.h
/usr/local/man/man3/uuid_generate_random.3 doesn't link to /usr/local/man/man3/uuid_generate.3 /usr/local/man/man3/uuid_generate_time.3 doesn't link to /usr/local/man/man3/uuid_generate.3
/usr/local/man/man5/ext3.5 doesn't link to /usr/local/man/man5/ext2.5
/usr/local/man/man5/ext4.5 doesn't link to /usr/local/man/man5/ext2.5
/usr/local/man/man8/fsck.ext2.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/fsck.ext3.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/fsck.ext4.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/fsck.ext4dev.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/mkfs.ext2.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/man/man8/mkfs.ext3.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/man/man8/mkfs.ext4.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/man/man8/mkfs.ext4dev.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/sbin/findfs doesn't link to /usr/local/sbin/e2label
/usr/local/sbin/fsck.ext2 doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/fsck.ext3 doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/fsck.ext4 doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/fsck.ext4dev doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/mkfs.ext2 doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/mkfs.ext3 doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/mkfs.ext4 doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/mkfs.ext4dev doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/tune2fs doesn't link to /usr/local/sbin/e2label
--- g95-4.9.4p7 -------------------
/usr/local/bin/x86_64-unknown-openbsd6.2-egfortran doesn't link to /usr/local/bin/egfortran
--- gawk-4.2.0 -------------------
/usr/local/bin/gawk-4.2.0 doesn't link to /usr/local/bin/gawk
--- gcc-4.9.4p7 -------------------
/usr/local/bin/x86_64-unknown-openbsd6.2-egcc doesn't link to /usr/local/bin/egcc /usr/local/bin/x86_64-unknown-openbsd6.2-egcc-ar doesn't link to /usr/local/bin/egcc-ar /usr/local/bin/x86_64-unknown-openbsd6.2-egcc-nm doesn't link to /usr/local/bin/egcc-nm /usr/local/bin/x86_64-unknown-openbsd6.2-egcc-ranlib doesn't link to /usr/local/bin/egcc-ranlib /usr/local/bin/x86_64-unknown-openbsd6.2-gcc-4.9.4 doesn't link to /usr/local/bin/egcc
--- iodbc-3.52.12 -------------------
/usr/local/man/man1/iodbctestw.1 doesn't link to /usr/local/man/man1/iodbctest.1
--- libexecinfo-0.3p0v0 -------------------
/usr/local/man/man3/backtrace_symbols.3 doesn't link to /usr/local/man/man3/backtrace.3 /usr/local/man/man3/backtrace_symbols_fd.3 doesn't link to /usr/local/man/man3/backtrace.3
--- python-3.6.4 -------------------
/usr/local/bin/python3.6m doesn't link to /usr/local/bin/python3.6
.
.
.

In dbus-1.12.2p0v0:x11/dbus,-main:
        /etc/machine-id
In isc-dhcp-server-4.3.6p0:net/isc-dhcp,-main:
        /var/db/dhcpd.leases
In libxml-2.9.7:textproc/libxml,-main:
        /var/db/xmlcatalog
In lighttpd-1.4.48p0-ldap-mysql:www/lighttpd,ldap,mysql:
        /var/www/logs/access.log
        /var/www/logs/error.log
Locating unknown directories: ok


When it was run as a regular user account, I did see the type of issues the OP mentioned.

DETAILS BELOW WITH USER ACCOUNT

builder.ftlcloud.ca$ pkg_check -F
Packing-list sanity: ok
Direct dependencies: ok
Reverse dependencies: ok
Files from packages: ok
--- apache-httpd-common-2.4.29 -------------------
can't read /var/www/cgi-bin/printenv
can't read /var/www/cgi-bin/test-cgi
--- cups-2.2.6p3 -------------------
can't read /usr/local/libexec/cups/backend/dnssd
can't read /usr/local/libexec/cups/backend/ipp
can't read /usr/local/libexec/cups/backend/lpd
can't read /usr/local/sbin/cupsd
can't read /usr/local/share/examples/cups/cups-files.conf
can't read /usr/local/share/examples/cups/cups-files.conf.default
can't read /usr/local/share/examples/cups/cupsd.conf
can't read /usr/local/share/examples/cups/cupsd.conf.default
can't read /usr/local/share/examples/cups/snmp.conf
can't read /usr/local/share/examples/cups/snmp.conf.default
--- dbus-daemon-launch-helper-1.12.2 -------------------
can't read /usr/local/libexec/dbus-daemon-launch-helper
--- e2fsprogs-1.42.12p4 -------------------
/usr/local/include/et/com_err.h doesn't link to /usr/local/include/com_err.h
/usr/local/man/man3/uuid_generate_random.3 doesn't link to /usr/local/man/man3/uuid_generate.3 /usr/local/man/man3/uuid_generate_time.3 doesn't link to /usr/local/man/man3/uuid_generate.3
/usr/local/man/man5/ext3.5 doesn't link to /usr/local/man/man5/ext2.5
/usr/local/man/man5/ext4.5 doesn't link to /usr/local/man/man5/ext2.5
/usr/local/man/man8/fsck.ext2.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/fsck.ext3.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/fsck.ext4.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/fsck.ext4dev.8 doesn't link to /usr/local/man/man8/e2fsck.8
/usr/local/man/man8/mkfs.ext2.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/man/man8/mkfs.ext3.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/man/man8/mkfs.ext4.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/man/man8/mkfs.ext4dev.8 doesn't link to /usr/local/man/man8/mke2fs.8
/usr/local/sbin/findfs doesn't link to /usr/local/sbin/e2label
/usr/local/sbin/fsck.ext2 doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/fsck.ext3 doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/fsck.ext4 doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/fsck.ext4dev doesn't link to /usr/local/sbin/e2fsck
/usr/local/sbin/mkfs.ext2 doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/mkfs.ext3 doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/mkfs.ext4 doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/mkfs.ext4dev doesn't link to /usr/local/sbin/mke2fs
/usr/local/sbin/tune2fs doesn't link to /usr/local/sbin/e2label
--- g95-4.9.4p7 -------------------
/usr/local/bin/x86_64-unknown-openbsd6.2-egfortran doesn't link to /usr/local/bin/egfortran
--- gawk-4.2.0 -------------------
/usr/local/bin/gawk-4.2.0 doesn't link to /usr/local/bin/gawk
--- gcc-4.9.4p7 -------------------
/usr/local/bin/x86_64-unknown-openbsd6.2-egcc doesn't link to /usr/local/bin/egcc /usr/local/bin/x86_64-unknown-openbsd6.2-egcc-ar doesn't link to /usr/local/bin/egcc-ar /usr/local/bin/x86_64-unknown-openbsd6.2-egcc-nm doesn't link to /usr/local/bin/egcc-nm /usr/local/bin/x86_64-unknown-openbsd6.2-egcc-ranlib doesn't link to /usr/local/bin/egcc-ranlib /usr/local/bin/x86_64-unknown-openbsd6.2-gcc-4.9.4 doesn't link to /usr/local/bin/egcc
--- gdm-3.26.2.1p3 -------------------
/usr/local/share/examples/gdm/var/db/gdm/.pulse/client.conf should exist
/usr/local/share/examples/gdm/var/db/gdm/.pulse/client.conf is not a file
can't read /usr/local/share/examples/gdm/var/db/gdm/.pulse/client.conf
--- gnome-control-center-3.26.2 -------------------
/usr/local/share/polkit-1/rules.d/gnome-control-center.rules should exist
/usr/local/share/polkit-1/rules.d/gnome-control-center.rules is not a file
can't read /usr/local/share/polkit-1/rules.d/gnome-control-center.rules
--- iodbc-3.52.12 -------------------
/usr/local/man/man1/iodbctestw.1 doesn't link to /usr/local/man/man1/iodbctest.1
--- libexecinfo-0.3p0v0 -------------------
/usr/local/man/man3/backtrace_symbols.3 doesn't link to /usr/local/man/man3/backtrace.3 /usr/local/man/man3/backtrace_symbols_fd.3 doesn't link to /usr/local/man/man3/backtrace.3
--- polkit-0.113p5 -------------------
/usr/local/share/examples/polkit/polkit-1/rules.d/50-default.rules should exist /usr/local/share/examples/polkit/polkit-1/rules.d/50-default.rules is not a file
can't read /usr/local/share/examples/polkit/polkit-1/rules.d/50-default.rules
--- python-3.6.4 -------------------
/usr/local/bin/python3.6m doesn't link to /usr/local/bin/python3.6
can't enter /usr/local/share/examples/gdm/var/db/gdm/.pulse
can't enter /usr/local/share/examples/polkit/polkit-1/rules.d
can't enter /usr/local/share/polkit-1/rules.d
Checking file system||Can't cd to (/usr/libexec/) auth: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
                     /Can't cd to (/var/) authpf: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/var/db/) ldap: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/var/db/) yubikey: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
can't enter /var/db/gdm
can't enter /var/db/rrd
Checking file system|/Can't cd to (/var/games/hackdir/) save: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/var/nsd/) etc: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/var/nsd/run/) xfr: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/var/) quotas: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't opendir(/var/spool/ftp/bin): Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't opendir(/var/spool/ftp/etc): Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't opendir(/var/spool/ftp/hidden): Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't opendir(/var/spool/smtpd): Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/var/) sysmerge: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/var/www/) cache: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
can't enter /var/www/tmp
can't enter /var/samba/private
can't enter /var/kdm
can't enter /builds
Checking file system|-Can't cd to (/etc/) acme: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/etc/iked/) private: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/etc/isakmpd/) private: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/etc/ldap/) certs: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/etc/skel/) .ssh: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Can't cd to (/etc/ssl/) private: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
can't enter /etc/cups/ssl
can't enter /etc/polkit-1/rules.d
Checking file system|\Can't cd to (/) root: Permission denied
 at /usr/libdata/perl5/OpenBSD/PkgCheck.pm line 889.
Unknown file system entries.

etc.
--
Vijay Sankar, M.Eng., P.Eng.
ForeTell Technologies Limited
vsan...@foretell.ca

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