I did several searches on this forum and on the internet but didn't find anything to resolve my issue.  I am running FreeBSD 11.2-Stable inside of a Jail.  I first noticed this issue in 11.0-RELEASE.
	
	
	
		
	
	
	
		
/var/db/pkg/local.sqlite reports
	
	
	
		
	
	
	
		
Then I again ran
So I ran
	
	
	
		
after which 
Since my phpmyadmin installation was dated, I tried removing that package and installing the latest version using pkg, but it reports that as orphaned as well. Any ideas how to fix this?[/code]
				
			 pkg version -v reports
		Code:
	
	44bsd-csh-20001106_5               ?   orphaned: shells/44bsd-csh
GeoIP-1.6.12                       ?   orphaned: net/GeoIP
ap24-mod_evasive-1.10.1_1          ?   orphaned: www/mod_evasive
ap24-mod_geoip2-1.2.10             ?   orphaned: www/mod_geoip2
ap24-mod_security-2.9.2_2          ?   orphaned: www/mod_security
apache24-2.4.37                    ?   orphaned: www/apache24
apg-2.3.0b_5                       ?   orphaned: security/apg
apr-1.6.5.1.6.1                    ?   orphaned: devel/apr1
ca_root_nss-3.40                   ?   orphaned: security/ca_root_nss
chkrootkit-0.52                    ?   orphaned: security/chkrootkit
curl-7.62.0                        ?   orphaned: ftp/curl
cvsps-2.1_2                        ?   orphaned: devel/cvsps
cyrus-sasl-2.1.26_13               ?   orphaned: security/cyrus-sasl2
db5-5.3.28_7                       ?   orphaned: databases/db5
diffutils-3.6                      ?   orphaned: textproc/diffutils
expat-2.2.6_1                      ?   orphaned: textproc/expat2
freetype2-2.9.1                    ?   orphaned: print/freetype2
gdbm-1.13_1                        ?   orphaned: databases/gdbm
geoipupdate-3.1.1                  ?   orphaned: net/geoipupdate
gettext-runtime-0.19.8.1_1         ?   orphaned: devel/gettext-runtime
git-2.19.1                         ?   orphaned: devel/git
icu-63.1,1                         ?   orphaned: devel/icu
indexinfo-0.3.1                    ?   orphaned: print/indexinfo
jpeg-turbo-2.0.0                   ?   orphaned: graphics/jpeg-turbo
libICE-1.0.9_3,1                   ?   orphaned: x11/libICE
libSM-1.2.3,1                      ?   orphaned: x11/libSM
libX11-1.6.6_1,1                   ?   orphaned: x11/libX11
libXau-1.0.8_5                     ?   orphaned: x11/libXau
libXaw-1.0.13_2,2                  ?   orphaned: x11-toolkits/libXaw
libXdmcp-1.1.2_2                   ?   orphaned: x11/libXdmcp
libXext-1.3.3_3,1                  ?   orphaned: x11/libXext
libXmu-1.1.2_5,1                   ?   orphaned: x11-toolkits/libXmu
libXp-1.0.3_2,1                    ?   orphaned: x11/libXp
libXpm-3.5.12_2                    ?   orphaned: x11/libXpm
libXt-1.1.5_2,1                    ?   orphaned: x11-toolkits/libXt
libedit-3.1.20170329_2,1           ?   orphaned: devel/libedit
libevent-2.1.8_2                   ?   orphaned: devel/libevent
libffi-3.2.1_2                     ?   orphaned: devel/libffi
libiconv-1.14_11                   ?   orphaned: converters/libiconv
libltdl-2.4.6                      ?   orphaned: devel/libltdl
liblz4-1.8.3,1                     ?   orphaned: archivers/liblz4
libmcrypt-2.5.8_3                  ?   orphaned: security/libmcrypt
libnghttp2-1.34.0                  ?   orphaned: www/libnghttp2
libpthread-stubs-0.4               ?   orphaned: devel/libpthread-stubs
libsigsegv-2.12                    ?   orphaned: devel/libsigsegv
libxcb-1.13.1                      ?   orphaned: x11/libxcb
libxml2-2.9.7                      ?   orphaned: textproc/libxml2
libzip-1.5.1                       ?   orphaned: archivers/libzip
logrotate-3.13.0_1                 ?   orphaned: sysutils/logrotate
lsof-4.92.b_1,8                    ?   orphaned: sysutils/lsof
lynis-2.7.0                        ?   orphaned: security/lynis
mod_php56-5.6.38                   ?   orphaned: www/mod_php56
mysql57-client-5.7.24              ?   orphaned: databases/mysql57-client
mysql57-server-5.7.24              ?   orphaned: databases/mysql57-server
oniguruma-6.9.0                    ?   orphaned: devel/oniguruma
openssl-unsafe-1.0.2.20170706      ?   orphaned: security/openssl-unsafe
p5-Authen-Htpasswd-0.171_1         ?   orphaned: security/p5-Authen-Htpasswd
p5-Authen-SASL-2.16_1              ?   orphaned: security/p5-Authen-SASL
p5-CGI-4.40                        ?   orphaned: www/p5-CGI
p5-Class-Accessor-0.51             ?   orphaned: devel/p5-Class-Accessor
p5-Crypt-PasswdMD5-1.40            ?   orphaned: security/p5-Crypt-PasswdMD5
p5-Digest-HMAC-1.03_1              ?   orphaned: security/p5-Digest-HMAC
p5-Digest-SHA1-2.13_1              ?   orphaned: security/p5-Digest-SHA1
p5-Error-0.17027                   ?   orphaned: lang/p5-Error
p5-File-Tail-1.3                   ?   orphaned: devel/p5-File-Tail
p5-GSSAPI-0.28_1                   ?   orphaned: security/p5-GSSAPI
p5-HTML-Parser-3.72                ?   orphaned: www/p5-HTML-Parser
p5-HTML-Tagset-3.20_1              ?   orphaned: www/p5-HTML-Tagset
p5-IO-LockedFile-0.23_1            ?   orphaned: devel/p5-IO-LockedFile
p5-IO-Socket-INET6-2.72_1          ?   orphaned: net/p5-IO-Socket-INET6
p5-IO-Socket-SSL-2.060             ?   orphaned: security/p5-IO-Socket-SSL
p5-Mozilla-CA-20180117             ?   orphaned: www/p5-Mozilla-CA
p5-Net-SSLeay-1.85                 ?   orphaned: security/p5-Net-SSLeay
p5-Socket6-0.29                    ?   orphaned: net/p5-Socket6
pcre-8.42                          ?   orphaned: devel/pcre
pecl-APCu4-4.0.11_1                ?   orphaned: devel/pecl-APCu4
perl5-5.26.2_1                     ?   orphaned: lang/perl5.26
php-suhosin-0.9.38_3               ?   orphaned: security/php-suhosin
php56-5.6.38                       ?   orphaned: lang/php56
php56-bcmath-5.6.38                ?   orphaned: math/php56-bcmath
php56-bz2-5.6.38                   ?   orphaned: archivers/php56-bz2
php56-ctype-5.6.38                 ?   orphaned: textproc/php56-ctype
php56-curl-5.6.38                  ?   orphaned: ftp/php56-curl
php56-dom-5.6.38                   ?   orphaned: textproc/php56-dom
php56-exif-5.6.38                  ?   orphaned: graphics/php56-exif
php56-filter-5.6.38                ?   orphaned: security/php56-filter
php56-gd-5.6.38                    ?   orphaned: graphics/php56-gd
php56-gettext-5.6.38               ?   orphaned: devel/php56-gettext
php56-hash-5.6.38                  ?   orphaned: security/php56-hash
php56-iconv-5.6.38                 ?   orphaned: converters/php56-iconv
php56-json-5.6.38                  ?   orphaned: devel/php56-json
php56-mbstring-5.6.38              ?   orphaned: converters/php56-mbstring
php56-mcrypt-5.6.38                ?   orphaned: security/php56-mcrypt
php56-mysql-5.6.38                 ?   orphaned: databases/php56-mysql
php56-mysqli-5.6.38                ?   orphaned: databases/php56-mysqli
php56-opcache-5.6.38               ?   orphaned: www/php56-opcache
php56-openssl-5.6.38_1             ?   orphaned: security/php56-openssl
php56-pecl-intl-3.0.0_16           ?   orphaned: devel/pecl-intl
php56-readline-5.6.38              ?   orphaned: devel/php56-readline
php56-session-5.6.38               ?   orphaned: www/php56-session
php56-sockets-5.6.38               ?   orphaned: net/php56-sockets
php56-xml-5.6.38                   ?   orphaned: textproc/php56-xml
php56-xmlreader-5.6.38             ?   orphaned: textproc/php56-xmlreader
php56-zip-5.6.38                   ?   orphaned: archivers/php56-zip
php56-zlib-5.6.38                  ?   orphaned: archivers/php56-zlib
phpMyAdmin-php56-4.8.3             ?   orphaned: databases/phpmyadmin
pkg-1.10.5_5                       ?   orphaned: ports-mgmt/pkg
png-1.6.35                         ?   orphaned: graphics/png
popt-1.16_2                        ?   orphaned: devel/popt
protobuf-3.5.2_1,1                 ?   orphaned: devel/protobuf
py27-setuptools-40.4.3             ?   orphaned: devel/py-setuptools
py27-sqlite3-2.7.15_7              ?   orphaned: databases/py-sqlite3
pydio-8.0.2                        ?   orphaned: www/pydio
python27-2.7.15                    ?   orphaned: lang/python27
readline-7.0.3_1                   ?   orphaned: devel/readline
serf-1.3.9_3                       ?   orphaned: www/serf
sqlite3-3.25.1_1                   ?   orphaned: databases/sqlite3
sshblock-1.0_1                     ?   orphaned: security/sshblock
sslscan-1.11.11.16                 ?   orphaned: security/sslscan
subversion-1.11.0                  ?   orphaned: devel/subversion
sudo-1.8.25p1                      ?   orphaned: security/sudo
t1lib-5.1.2_4,1                    ?   orphaned: devel/t1lib
utf8proc-2.1.0                     ?   orphaned: textproc/utf8proc
xorgproto-2018.4                   ?   orphaned: x11/xorgproto
yajl-2.1.0                         ?   orphaned: devel/yajl pkg -vv reports
		Code:
	
	Version                 : 1.10.5
PKG_DBDIR = "/var/db/pkg";
PKG_CACHEDIR = "/var/cache/pkg";
PORTSDIR = "/usr/ports";
INDEXDIR = "";
INDEXFILE = "INDEX-11";
HANDLE_RC_SCRIPTS = false;
DEFAULT_ALWAYS_YES = false;
ASSUME_ALWAYS_YES = false;
REPOS_DIR [
    "/etc/pkg/",
    "/usr/local/etc/pkg/repos/",
]
PLIST_KEYWORDS_DIR = "";
SYSLOG = true;
ABI = "FreeBSD:11:amd64";
ALTABI = "freebsd:11:x86:64";
DEVELOPER_MODE = false;
VULNXML_SITE = "http://vuxml.freebsd.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 = "";
HTTP_USER_AGENT = "pkg/1.10.5";
EVENT_PIPE = "";
FETCH_TIMEOUT = 30;
UNSET_TIMESTAMP = false;
SSH_RESTRICT_DIR = "";
PKG_ENV {
}
PKG_SSH_ARGS = "";
DEBUG_LEVEL = 0;
ALIAS {
    all-depends = "query %dn-%dv";
    annotations = "info -A";
    build-depends = "info -qd";
    cinfo = "info -Cx";
    comment = "query -i \"%c\"";
    csearch = "search -Cx";
    desc = "query -i \"%e\"";
    download = "fetch";
    iinfo = "info -ix";
    isearch = "search -ix";
    prime-list = "query -e '%a = 0' '%n'";
    prime-origins = "query -e '%a = 0' '%o'";
    leaf = "query -e '%#r == 0' '%n-%v'";
    list = "info -ql";
    noauto = "query -e '%a == 0' '%n-%v'";
    options = "query -i \"%n - %Ok: %Ov\"";
    origin = "info -qo";
    provided-depends = "info -qb";
    raw = "info -R";
    required-depends = "info -qr";
    roptions = "rquery -i \"%n - %Ok: %Ov\"";
    shared-depends = "info -qB";
    show = "info -f -k";
    size = "info -sq";
}
CUDF_SOLVER = "";
SAT_SOLVER = "";
RUN_SCRIPTS = true;
CASE_SENSITIVE_MATCH = false;
LOCK_WAIT = 1;
LOCK_RETRIES = 5;
SQLITE_PROFILE = false;
WORKERS_COUNT = 0;
READ_LOCK = false;
PLIST_ACCEPT_DIRECTORIES = false;
IP_VERSION = 0;
AUTOMERGE = true;
VERSION_SOURCE = "";
CONSERVATIVE_UPGRADE = true;
PKG_CREATE_VERBOSE = false;
AUTOCLEAN = false;
DOT_FILE = "";
REPOSITORIES {
}
VALID_URL_SCHEME [
    "pkg+http",
    "pkg+https",
    "https",
    "http",
    "file",
    "ssh",
    "ftp",
    "ftps",
    "pkg+ssh",
    "pkg+ftp",
    "pkg+ftps",
]
ALLOW_BASE_SHLIBS = false;
WARN_SIZE_LIMIT = 1048576;
METALOG = "";
OSVERSION = 1102000;
IGNORE_OSVERSION = false;
Repositories:
  FreeBSD: {
    url             : "pkg+http://pkg.FreeBSD.org/freebsd:11:x86:64/latest",
    enabled         : yes,
    priority        : 0,
    mirror_type     : "SRV",
    signature_type  : "FINGERPRINTS",
    fingerprints    : "/usr/share/keys/pkg"
  }/var/db/pkg/local.sqlite reports
		Code:
	
	sqlite> .mode column
sqlite> .headers on
sqlite> select id, origin, name, automatic, lockec d, datetime(" tiome   me, 'unipo  xeph och; '), pkg_format_version from packages where automatic - = 0;
id          origin                name         automatic   locked      datetime(time, 'unixepoch')  pkg_format_version
----------  --------------------  -----------  ----------  ----------  ---------------------------  ------------------
101         security/php-suhosin  php-suhosin  0           0           2017-07-20 16:07:27                           
184         devel/pecl-APCu4      pecl-APCu4   0           0           2017-09-28 12:28:52                           
240         www/pydio             pydio        0           0           2018-01-06 02:37:08                           
413         lang/php56            php56        0           0           2018-11-15 07:24:16                           
448         sysutils/lsof         lsof         0           0           2018-11-15 07:24:22                           
458         www/apache24          apache24     0           0           2018-11-15 07:24:25                           
460         ports-mgmt/pkg        pkg          0           0           2018-11-15 07:24:26                           
461         security/sudo         sudo         0           0           2018-11-15 07:24:27                           
462         devel/subversion      subversion   0           0           2018-11-15 07:24:27                           
463         security/sslscan      sslscan      0           0           2018-11-15 07:24:27                           
464         security/sshblock     sshblock     0           0           2018-11-15 07:24:27                           
466         archivers/php56-zlib  php56-zlib   0           0           2018-11-15 07:24:28                           
467         archivers/php56-zip   php56-zip    0           0           2018-11-15 07:24:28                           
468         textproc/php56-xmlre  php56-xmlre  0           0           2018-11-15 07:24:28                           
470         net/php56-sockets     php56-socke  0           0           2018-11-15 07:24:28                           
471         www/php56-session     php56-sessi  0           0           2018-11-15 07:24:28                           
472         devel/php56-readline  php56-readl  0           0           2018-11-15 07:24:28                           
473         devel/pecl-intl       php56-pecl-  0           0           2018-11-15 07:24:28                           
474         security/php56-opens  php56-opens  0           0           2018-11-15 07:24:28                           
475         www/php56-opcache     php56-opcac  0           0           2018-11-15 07:24:28                           
476         databases/php56-mysq  php56-mysql  0           0           2018-11-15 07:24:28                           
477         databases/php56-mysq  php56-mysql  0           0           2018-11-15 07:24:28                           
478         security/php56-mcryp  php56-mcryp  0           0           2018-11-15 07:24:29                           
479         converters/php56-mbs  php56-mbstr  0           0           2018-11-15 07:24:29                           
480         devel/php56-json      php56-json   0           0           2018-11-15 07:24:29                           
481         converters/php56-ico  php56-iconv  0           0           2018-11-15 07:24:30                           
482         security/php56-hash   php56-hash   0           0           2018-11-15 07:24:30                           
483         devel/php56-gettext   php56-gette  0           0           2018-11-15 07:24:30                           
484         graphics/php56-gd     php56-gd     0           0           2018-11-15 07:24:30                           
486         graphics/php56-exif   php56-exif   0           0           2018-11-15 07:24:30                           
487         ftp/php56-curl        php56-curl   0           0           2018-11-15 07:24:30                           
488         textproc/php56-ctype  php56-ctype  0           0           2018-11-15 07:24:30                           
489         archivers/php56-bz2   php56-bz2    0           0           2018-11-15 07:24:30                           
490         math/php56-bcmath     php56-bcmat  0           0           2018-11-15 07:24:30                           
491         security/p5-Authen-H  p5-Authen-H  0           0           2018-11-15 07:24:30                           
492         databases/mysql57-se  mysql57-ser  0           0           2018-11-15 07:24:30                           
493         www/mod_php56         mod_php56    0           0           2018-11-15 07:24:32                           
494         security/lynis        lynis        0           0           2018-11-15 07:24:32                           
495         sysutils/logrotate    logrotate    0           0           2018-11-15 07:24:33                           
496         devel/git             git          0           0           2018-11-15 07:24:33                           
497         net/geoipupdate       geoipupdate  0           0           2018-11-15 07:24:34                           
498         textproc/diffutils    diffutils    0           0           2018-11-15 07:24:34                           
499         security/chkrootkit   chkrootkit   0           0           2018-11-15 07:24:34                           
500         security/apg          apg          0           0           2018-11-15 07:24:34                           
501         www/mod_security      ap24-mod_se  0           0           2018-11-15 07:24:34                           
502         www/mod_geoip2        ap24-mod_ge  0           0           2018-11-15 07:24:34                           
503         www/mod_evasive       ap24-mod_ev  0           0           2018-11-15 07:24:34                           
504         databases/phpmyadmin  phpMyAdmin-  0           0           2018-11-15 07:27:29                           
505         shells/44bsd-csh      44bsd-csh    0           0           2018-11-15 07:44:29 pkg update -f reports
		Code:
	
	Updating FreeBSD repository catalogue...
[REDACTED] Fetching meta.txz:   0%
...
[REDACTED] Fetching meta.txz: 100%    944 B   0.9kB/s    00:01   
[REDACTED] Fetching packagesite.txz:   0%
...
[REDACTED] Fetching packagesite.txz: 100%    6 MiB 850.5kB/s    00:08   
Processing entries:   0%
...
Processing entries: 100%
FreeBSD repository update completed. 33415 packages processed.
All repositories are up to date.Then I again ran
 pkg version -v with the same list where all packages were orphaned.So I ran
 pkg upgrade -f and it reported
		Code:
	
	Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
Checking for upgrades (125 candidates):   0%
...
Checking for upgrades (125 candidates): 100%
Processing candidates (125 candidates):   0%
...
Processing candidates (125 candidates): 100%
Checking integrity... done (0 conflicting)
The following 122 package(s) will be affected (of 0 checked):
Installed packages to be REINSTALLED:
    pkg-1.10.5_5
    yajl-2.1.0
    xorgproto-2018.4
    utf8proc-2.1.0
    t1lib-5.1.2_4,1
    sudo-1.8.25p1
    subversion-1.11.0
    sslscan-1.11.11.16
    sshblock-1.0_1
    sqlite3-3.25.1_1
    serf-1.3.9_3
    readline-7.0.3_1
    python27-2.7.15
    py27-sqlite3-2.7.15_7
    py27-setuptools-40.4.3
    protobuf-3.5.2_1,1
    popt-1.16_2
    png-1.6.35
    phpMyAdmin-php56-4.8.3
    php56-zlib-5.6.38
    php56-zip-5.6.38
    php56-xmlreader-5.6.38
    php56-xml-5.6.38
    php56-sockets-5.6.38
    php56-session-5.6.38
    php56-readline-5.6.38
    php56-pecl-intl-3.0.0_16
    php56-openssl-5.6.38_1
    php56-opcache-5.6.38
    php56-mysqli-5.6.38
    php56-mysql-5.6.38
    php56-mcrypt-5.6.38
    php56-mbstring-5.6.38
    php56-json-5.6.38
    php56-iconv-5.6.38
    php56-hash-5.6.38
    php56-gettext-5.6.38
    php56-gd-5.6.38
    php56-filter-5.6.38
    php56-exif-5.6.38
    php56-dom-5.6.38
    php56-curl-5.6.38
    php56-ctype-5.6.38
    php56-bz2-5.6.38
    php56-bcmath-5.6.38
    php56-5.6.38
    perl5-5.26.2_1
    pcre-8.42
    p5-Socket6-0.29
    p5-Net-SSLeay-1.85
    p5-Mozilla-CA-20180117
    p5-IO-Socket-SSL-2.060
    p5-IO-Socket-INET6-2.72_1
    p5-IO-LockedFile-0.23_1
    p5-HTML-Tagset-3.20_1
    p5-HTML-Parser-3.72
    p5-GSSAPI-0.28_1
    p5-File-Tail-1.3
    p5-Error-0.17027
    p5-Digest-SHA1-2.13_1
    p5-Digest-HMAC-1.03_1
    p5-Crypt-PasswdMD5-1.40
    p5-Class-Accessor-0.51
    p5-CGI-4.40
    p5-Authen-SASL-2.16_1
    p5-Authen-Htpasswd-0.171_1
    openssl-unsafe-1.0.2.20170706
    oniguruma-6.9.0
    mysql57-server-5.7.24
    mysql57-client-5.7.24
    mod_php56-5.6.38
    lynis-2.7.0
    lsof-4.92.b_1,8
    logrotate-3.13.0_1
    libzip-1.5.1
    libxml2-2.9.7
    libxcb-1.13.1
    libsigsegv-2.12
    libpthread-stubs-0.4
    libnghttp2-1.34.0
    libmcrypt-2.5.8_3
    liblz4-1.8.3,1
    libltdl-2.4.6
    libiconv-1.14_11
    libffi-3.2.1_2
    libevent-2.1.8_2
    libedit-3.1.20170329_2,1
    libXt-1.1.5_2,1
    libXpm-3.5.12_2
    libXp-1.0.3_2,1
    libXmu-1.1.2_5,1
    libXext-1.3.3_3,1
    libXdmcp-1.1.2_2
    libXaw-1.0.13_2,2
    libXau-1.0.8_5
    libX11-1.6.6_1,1
    libSM-1.2.3,1
    libICE-1.0.9_3,1
    jpeg-turbo-2.0.0
    indexinfo-0.3.1
    icu-63.1,1
    git-2.19.1
    gettext-runtime-0.19.8.1_1
    geoipupdate-3.1.1
    gdbm-1.13_1
    freetype2-2.9.1
    expat-2.2.6_1
    diffutils-3.6
    db5-5.3.28_7
    cyrus-sasl-2.1.26_13
    cvsps-2.1_2
    curl-7.62.0
    chkrootkit-0.52
    ca_root_nss-3.40
    apr-1.6.5.1.6.1
    apg-2.3.0b_5
    apache24-2.4.37
    ap24-mod_security-2.9.2_2
    ap24-mod_geoip2-1.2.10
    ap24-mod_evasive-1.10.1_1
    GeoIP-1.6.12
    44bsd-csh-20001106_5
Number of packages to be reinstalled: 122
Proceed with this action? [y/N]: y pkg version -v reports the exact same thing as above... everything orphaned.Since my phpmyadmin installation was dated, I tried removing that package and installing the latest version using pkg, but it reports that as orphaned as well. Any ideas how to fix this?[/code]
 
			     
 
		 
 
		