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]