Since the new pkg 1.3.x I am unable to upgrade pkg itself from our own repository. Repository has been built using poudriere-devel 3.0.99.20140626 # pkg version -vR | grep pkg pkg-1.2.7_3 ? orphaned: ports-mgmt/pkg But it's available. root@log2:~ # pkg -vv Version : 1.2.7_3 PACKAGESITE : PKG_DBDIR : /var/db/pkg PKG_CACHEDIR : /var/cache/pkg PORTSDIR : /usr/ports PUBKEY : HANDLE_RC_SCRIPTS : no ASSUME_ALWAYS_YES : no REPOS_DIR : [ /etc/pkg/, /usr/local/etc/pkg/repos/, ] PLIST_KEYWORDS_DIR : SYSLOG : yes AUTODEPS : yes ABI : freebsd:9:x86:64 DEVELOPER_MODE : no PORTAUDIT_SITE : http://portaudit.FreeBSD.org/auditfile.tbz VULNXML_SITE : http://www.vuxml.org/freebsd/vuln.xml.bz2 MIRROR_TYPE : SRV FETCH_RETRY : 3 PKG_PLUGINS_DIR : /usr/local/lib/pkg/ PKG_ENABLE_PLUGINS : yes PLUGINS : [ ] DEBUG_SCRIPTS : no PLUGINS_CONF_DIR : /usr/local/etc/pkg/ PERMISSIVE : no REPO_AUTOUPDATE : yes NAMESERVER : EVENT_PIPE : FETCH_TIMEOUT : 30 UNSET_TIMESTAMP : no SSH_RESTRICT_DIR : PKG_SSH_ARGS : PKG_ENV : { } DISABLE_MTREE : no DEBUG_LEVEL : 0 ALIAS : { } Repositories: FreeBSD: { url : "pkg+http://pkg.FreeBSD.org/freebsd:9:x86:64/latest", enabled : no, mirror_type : "SRV", signature_type : "FINGERPRINTS", fingerprints : "/usr/share/keys/pkg" } rc-repo: { url : "http://our-repo.example.com/packages/TC92-RELEASE-default/", enabled : yes } root@log2:~ # fetch http://our-repo.example.com/packages/TC92-RELEASE-default/All/pkg-1.3.2.txz pkg-1.3.2.txz 100% of 1937 kB 90 MBps 00m00s root@log2:~ # tar -zxvf pkg-1.3.2.txz x +COMPACT_MANIFEST x +MANIFEST x +MTREE_DIRS tar: Removing leading '/' from member names x usr/local/share/licenses/pkg-1.3.2/catalog.mk x usr/local/share/licenses/pkg-1.3.2/LICENSE x usr/local/share/licenses/pkg-1.3.2/BSD2CLAUSE x usr/local/etc/bash_completion.d/_pkg.bash x usr/local/etc/periodic/daily/411.pkg-backup x usr/local/etc/periodic/daily/490.status-pkg-changes x usr/local/etc/periodic/security/410.pkg-audit x usr/local/etc/periodic/security/460.pkg-checksum x usr/local/etc/periodic/weekly/400.status-pkg x usr/local/etc/pkg.conf.sample x usr/local/include/pkg.h x usr/local/lib/libpkg.a x usr/local/lib/libpkg.so x usr/local/lib/libpkg.so.3 x usr/local/lib/libpkg.so.3.0.0 x usr/local/libdata/pkgconfig/pkg.pc x usr/local/man/man3/pkg_printf.3.gz x usr/local/man/man3/pkg_repos.3.gz x usr/local/man/man5/pkg-repository.5.gz x usr/local/man/man5/pkg.conf.5.gz x usr/local/man/man8/pkg-add.8.gz x usr/local/man/man8/pkg-annotate.8.gz x usr/local/man/man8/pkg-audit.8.gz x usr/local/man/man8/pkg-autoremove.8.gz x usr/local/man/man8/pkg-backup.8.gz x usr/local/man/man8/pkg-check.8.gz x usr/local/man/man8/pkg-clean.8.gz x usr/local/man/man8/pkg-config.8.gz x usr/local/man/man8/pkg-convert.8.gz x usr/local/man/man8/pkg-create.8.gz x usr/local/man/man8/pkg-delete.8.gz x usr/local/man/man8/pkg-fetch.8.gz x usr/local/man/man8/pkg-info.8.gz x usr/local/man/man8/pkg-install.8.gz x usr/local/man/man8/pkg-lock.8.gz x usr/local/man/man8/pkg-query.8.gz x usr/local/man/man8/pkg-register.8.gz x usr/local/man/man8/pkg-remove.8.gz x usr/local/man/man8/pkg-repo.8.gz x usr/local/man/man8/pkg-rquery.8.gz x usr/local/man/man8/pkg-search.8.gz x usr/local/man/man8/pkg-set.8.gz x usr/local/man/man8/pkg-shell.8.gz x usr/local/man/man8/pkg-shlib.8.gz x usr/local/man/man8/pkg-ssh.8.gz x usr/local/man/man8/pkg-static.8.gz x usr/local/man/man8/pkg-stats.8.gz x usr/local/man/man8/pkg-unlock.8.gz x usr/local/man/man8/pkg-update.8.gz x usr/local/man/man8/pkg-updating.8.gz x usr/local/man/man8/pkg-upgrade.8.gz x usr/local/man/man8/pkg-version.8.gz x usr/local/man/man8/pkg-which.8.gz x usr/local/man/man8/pkg.8.gz x usr/local/sbin/pkg x usr/local/sbin/pkg-static x usr/local/sbin/pkg2ng x usr/local/share/zsh/site-functions/_pkg x usr/local/etc/bash_completion.d/ x usr/local/etc/periodic/daily/ x usr/local/etc/periodic/security/ x usr/local/etc/periodic/weekly/ x usr/local/etc/periodic/ x usr/local/share/zsh/site-functions/ x usr/local/share/zsh/ x usr/local/share/licenses/pkg-1.3.2/ x usr/local/share/licenses/ root@log2:~ # usr/local/sbin/pkg-static add pkg-1.3.2.txz the most recent version of pkg-1.2.7_3 is already installed Failed to install the following 1 package(s): pkg-1.3.2.txz root@log2:~ # pkg delete -f pkg pkg: warning: database version 27 is newer than libpkg(3) version 21, but still compatible Deinstallation has been requested for the following 1 packages: pkg-1.2.7_3 The deinstallation will free 7 MB Proceed with deinstalling packages [y/N]: y [1/1] Deleting pkg-1.2.7_3... done root@log2:~ # usr/local/sbin/pkg-static add pkg-1.3.2.txz Installing pkg-1.3.2: 100% Message for pkg-1.3.2: If you are upgrading from the old package format, first run: # pkg2ng root@log2:~ # pkg version -vR | grep pkg pkg: Repo "rc-repo" upgrade schema 2006 to 2007: Add conflicts and provides pkg: Repo "rc-repo" upgrade schema 2007 to 2008: Add FTS index pkg: Repo "rc-repo" upgrade schema 2008 to 2009: Optimize indicies pkg: Repo "rc-repo" upgrade schema 2009 to 2010: Add legacy digest field pkg-1.3.2 ? orphaned: ports-mgmt/pkg root@log2:~ # pkg version -vR | grep pkg pkg-1.3.2 ? orphaned: ports-mgmt/pkg root@log2:~ # root@log2:~ # pkg -vv Version : 1.3.2 PKG_DBDIR = "/var/db/pkg"; PKG_CACHEDIR = "/var/cache/pkg"; PORTSDIR = "/usr/ports"; INDEXDIR = ""; INDEXFILE = "INDEX-9"; HANDLE_RC_SCRIPTS = false; ASSUME_ALWAYS_YES = false; REPOS_DIR [ "/etc/pkg/", "/usr/local/etc/pkg/repos/", ] PLIST_KEYWORDS_DIR = ""; SYSLOG = true; ABI = "freebsd:9:x86:64"; DEVELOPER_MODE = false; VULNXML_SITE = "http://www.vuxml.org/freebsd/vuln.xml.bz2"; FETCH_RETRY = 3; PKG_PLUGINS_DIR = "/usr/local/lib/pkg/"; PKG_ENABLE_PLUGINS = true; PLUGINS [ ] DEBUG_SCRIPTS = false; PLUGINS_CONF_DIR = "/usr/local/etc/pkg/"; PERMISSIVE = false; REPO_AUTOUPDATE = true; NAMESERVER = ""; EVENT_PIPE = ""; FETCH_TIMEOUT = 30; UNSET_TIMESTAMP = false; SSH_RESTRICT_DIR = ""; PKG_ENV { } DISABLE_MTREE = false; PKG_SSH_ARGS = ""; DEBUG_LEVEL = 0; ALIAS { } CUDF_SOLVER = ""; SAT_SOLVER = ""; RUN_SCRIPTS = true; CASE_SENSITIVE_MATCH = false; LOCK_WAIT = 1; LOCK_RETRIES = 5; SQLITE_PROFILE = false; WORKERS_COUNT = 0; Repositories: rc-repo: { url : "http://our-repo.example.com/packages/TC92-RELEASE-default/", enabled : yes } Running 'pkg repo -L' on the repository helped with a few older clients. Everything is updated except pkg itself. Forcing installation doesn't work either. root@log2:~ # pkg install -f pkg Updating repository catalogue rc-repo repository is up-to-date All repositories are up-to-date Updating database digests format: 100% pkg: No packages available to install matching 'pkg' have been found in the repositories It looks like the pkg entry is simply missing from the packagesite/digest/meta database. This happens on 9.2-RELEASE-p7 and 9.3-RELEASE machines. I haven't tested 10.0-RELEASE or 10-STABLE yet.
Over to maintainer
I just submitted a similar bug (192243). I wonder if you delete the custom repo's sqlite file from /var/db/pkg and re-run pkg upgrade if it works.
one need to pkg update -f first This has been fixed since