database disk image is malformed with dnf on Fedora 29
Clash Royale CLAN TAG#URR8PPP
2
I have cross-posted this on ask.fedora.org as I am still uncertain whether this or the other side has the larger Fedora userbase.
For a few days now I could not install updates due to this error:
# env LC_ALL=C dnf update
Last metadata expiration check: 0:18:57 ago on Wed Jan 23 16:16:14 2019.
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 681, in _goal2transaction
ts.add_upgrade(pkg, upgraded, obs)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 269, in add_upgrade
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_UPGRADE)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 222, in new
reason = self.get_reason(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: database disk image is malformed in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'python2-rpkg'
AND i.arch = 'noarch'
ORDER BY
ti.trans_id DESC
LIMIT 1
I found that one shall do these commands in order to fix it, and I tried, but it has not resolved the problem.
dnf clean alldnf makecacherpm --buildddb
On Ask Fedora somebody suggested that dnf is not able to recover from that and that one has to repair the SQLite database manually.
I have tried to run the command given,
sqlite3 history-<date>.sqlite ".dump" | sqlite3 history-<new date>.db && rm history-<date>.sqlite
Doing it on /var/lib/dnf/history/history-2015-10-25.sqlite had no effect. Doing it on /var/lib/dnf/history.sqlite resulted in a new error:
# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 1:22:29 am Mi 23 Jan 2019 16:39:44 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 657, in _goal2transaction
ts.add_install(pkg, obs, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 256, in add_install
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_INSTALL, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 219, in new
rpm_item = self._pkg_to_swdb_rpm_item(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 210, in _pkg_to_swdb_rpm_item
rpm_item = self.history.swdb.createRPMItem()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 472, in close
self._finalize_base()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 455, in _finalize_base
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
Looking further into the sqlite3 .dump thing, I see this:
/var/lib/dnf# sqlite3 history.sqlite .dump
PRAGMA foreign_keys=OFF;
BEGIN TRANSACTION;
/**** ERROR: (10) disk I/O error *****/
ROLLBACK; -- due to errors
However, when I copy this history.sqlite into /tmp and execute that .dump there, I get a sensibly looking database. Also opening it with the GUI sqliteman works fine. It seems that the database itself is okay.
Dumping the database into a new file somewhere else and copying it back then gives me this:
/v/l/dnf# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 0:30:51 am Sa 26 Jan 2019 13:21:13 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 650, in _goal2transaction
reason_obsolete = ts.get_reason(obsolete)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: disk I/O error in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'libmodulemd'
AND i.arch = 'x86_64'
ORDER BY
ti.trans_id DESC
LIMIT 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 473, in close
self.reset(sack=True, repos=True, goal=True)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 504, in reset
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: disk I/O error
Exception ignored in: <function SwdbInterface.__del__ at 0x7f28b02e4510>
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 262, in __del__
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
RuntimeError: Exec failed: disk I/O error
I also restored the SELinux labels, but that did not change anything, it is
-rw-r--r--. 1 root root unconfined_u:object_r:rpm_var_lib_t:s0 29M 26. Jan 13:52 history.sqlite
Root can also read the file:
/v/l/dnf# head -c 1000 history.sqlite
SQLite format 3@ ,�,.,P��⏎
How is this on Fedora 29, can I recover from this?
fedora dnf
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
|
show 2 more comments
2
I have cross-posted this on ask.fedora.org as I am still uncertain whether this or the other side has the larger Fedora userbase.
For a few days now I could not install updates due to this error:
# env LC_ALL=C dnf update
Last metadata expiration check: 0:18:57 ago on Wed Jan 23 16:16:14 2019.
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 681, in _goal2transaction
ts.add_upgrade(pkg, upgraded, obs)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 269, in add_upgrade
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_UPGRADE)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 222, in new
reason = self.get_reason(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: database disk image is malformed in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'python2-rpkg'
AND i.arch = 'noarch'
ORDER BY
ti.trans_id DESC
LIMIT 1
I found that one shall do these commands in order to fix it, and I tried, but it has not resolved the problem.
dnf clean alldnf makecacherpm --buildddb
On Ask Fedora somebody suggested that dnf is not able to recover from that and that one has to repair the SQLite database manually.
I have tried to run the command given,
sqlite3 history-<date>.sqlite ".dump" | sqlite3 history-<new date>.db && rm history-<date>.sqlite
Doing it on /var/lib/dnf/history/history-2015-10-25.sqlite had no effect. Doing it on /var/lib/dnf/history.sqlite resulted in a new error:
# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 1:22:29 am Mi 23 Jan 2019 16:39:44 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 657, in _goal2transaction
ts.add_install(pkg, obs, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 256, in add_install
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_INSTALL, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 219, in new
rpm_item = self._pkg_to_swdb_rpm_item(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 210, in _pkg_to_swdb_rpm_item
rpm_item = self.history.swdb.createRPMItem()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 472, in close
self._finalize_base()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 455, in _finalize_base
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
Looking further into the sqlite3 .dump thing, I see this:
/var/lib/dnf# sqlite3 history.sqlite .dump
PRAGMA foreign_keys=OFF;
BEGIN TRANSACTION;
/**** ERROR: (10) disk I/O error *****/
ROLLBACK; -- due to errors
However, when I copy this history.sqlite into /tmp and execute that .dump there, I get a sensibly looking database. Also opening it with the GUI sqliteman works fine. It seems that the database itself is okay.
Dumping the database into a new file somewhere else and copying it back then gives me this:
/v/l/dnf# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 0:30:51 am Sa 26 Jan 2019 13:21:13 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 650, in _goal2transaction
reason_obsolete = ts.get_reason(obsolete)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: disk I/O error in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'libmodulemd'
AND i.arch = 'x86_64'
ORDER BY
ti.trans_id DESC
LIMIT 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 473, in close
self.reset(sack=True, repos=True, goal=True)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 504, in reset
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: disk I/O error
Exception ignored in: <function SwdbInterface.__del__ at 0x7f28b02e4510>
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 262, in __del__
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
RuntimeError: Exec failed: disk I/O error
I also restored the SELinux labels, but that did not change anything, it is
-rw-r--r--. 1 root root unconfined_u:object_r:rpm_var_lib_t:s0 29M 26. Jan 13:52 history.sqlite
Root can also read the file:
/v/l/dnf# head -c 1000 history.sqlite
SQLite format 3@ ,�,.,P��⏎
How is this on Fedora 29, can I recover from this?
fedora dnf
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
Have you trieddnf clean dbcache?
– maulinglawns
Jan 23 at 16:54
The question from ask fedora you refer to has a solution as th first answer. Did you run those commands?
– Panther
Jan 23 at 16:54
I did, but it did not help. The question is updated accordingly.
– Martin Ueding
Jan 23 at 17:04
@maulinglawns: I did, but it turned out to be already included indnf clean all.
– Martin Ueding
Jan 23 at 17:04
Ah, I see. Not a Fedora user myself. I have usedyum clean dbcachewith success on CentOS.
– maulinglawns
Jan 23 at 17:11
|
show 2 more comments
2
2
2
I have cross-posted this on ask.fedora.org as I am still uncertain whether this or the other side has the larger Fedora userbase.
For a few days now I could not install updates due to this error:
# env LC_ALL=C dnf update
Last metadata expiration check: 0:18:57 ago on Wed Jan 23 16:16:14 2019.
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 681, in _goal2transaction
ts.add_upgrade(pkg, upgraded, obs)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 269, in add_upgrade
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_UPGRADE)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 222, in new
reason = self.get_reason(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: database disk image is malformed in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'python2-rpkg'
AND i.arch = 'noarch'
ORDER BY
ti.trans_id DESC
LIMIT 1
I found that one shall do these commands in order to fix it, and I tried, but it has not resolved the problem.
dnf clean alldnf makecacherpm --buildddb
On Ask Fedora somebody suggested that dnf is not able to recover from that and that one has to repair the SQLite database manually.
I have tried to run the command given,
sqlite3 history-<date>.sqlite ".dump" | sqlite3 history-<new date>.db && rm history-<date>.sqlite
Doing it on /var/lib/dnf/history/history-2015-10-25.sqlite had no effect. Doing it on /var/lib/dnf/history.sqlite resulted in a new error:
# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 1:22:29 am Mi 23 Jan 2019 16:39:44 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 657, in _goal2transaction
ts.add_install(pkg, obs, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 256, in add_install
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_INSTALL, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 219, in new
rpm_item = self._pkg_to_swdb_rpm_item(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 210, in _pkg_to_swdb_rpm_item
rpm_item = self.history.swdb.createRPMItem()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 472, in close
self._finalize_base()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 455, in _finalize_base
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
Looking further into the sqlite3 .dump thing, I see this:
/var/lib/dnf# sqlite3 history.sqlite .dump
PRAGMA foreign_keys=OFF;
BEGIN TRANSACTION;
/**** ERROR: (10) disk I/O error *****/
ROLLBACK; -- due to errors
However, when I copy this history.sqlite into /tmp and execute that .dump there, I get a sensibly looking database. Also opening it with the GUI sqliteman works fine. It seems that the database itself is okay.
Dumping the database into a new file somewhere else and copying it back then gives me this:
/v/l/dnf# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 0:30:51 am Sa 26 Jan 2019 13:21:13 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 650, in _goal2transaction
reason_obsolete = ts.get_reason(obsolete)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: disk I/O error in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'libmodulemd'
AND i.arch = 'x86_64'
ORDER BY
ti.trans_id DESC
LIMIT 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 473, in close
self.reset(sack=True, repos=True, goal=True)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 504, in reset
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: disk I/O error
Exception ignored in: <function SwdbInterface.__del__ at 0x7f28b02e4510>
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 262, in __del__
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
RuntimeError: Exec failed: disk I/O error
I also restored the SELinux labels, but that did not change anything, it is
-rw-r--r--. 1 root root unconfined_u:object_r:rpm_var_lib_t:s0 29M 26. Jan 13:52 history.sqlite
Root can also read the file:
/v/l/dnf# head -c 1000 history.sqlite
SQLite format 3@ ,�,.,P��⏎
How is this on Fedora 29, can I recover from this?
fedora dnf
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
I have cross-posted this on ask.fedora.org as I am still uncertain whether this or the other side has the larger Fedora userbase.
For a few days now I could not install updates due to this error:
# env LC_ALL=C dnf update
Last metadata expiration check: 0:18:57 ago on Wed Jan 23 16:16:14 2019.
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 681, in _goal2transaction
ts.add_upgrade(pkg, upgraded, obs)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 269, in add_upgrade
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_UPGRADE)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 222, in new
reason = self.get_reason(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: database disk image is malformed in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'python2-rpkg'
AND i.arch = 'noarch'
ORDER BY
ti.trans_id DESC
LIMIT 1
I found that one shall do these commands in order to fix it, and I tried, but it has not resolved the problem.
dnf clean alldnf makecacherpm --buildddb
On Ask Fedora somebody suggested that dnf is not able to recover from that and that one has to repair the SQLite database manually.
I have tried to run the command given,
sqlite3 history-<date>.sqlite ".dump" | sqlite3 history-<new date>.db && rm history-<date>.sqlite
Doing it on /var/lib/dnf/history/history-2015-10-25.sqlite had no effect. Doing it on /var/lib/dnf/history.sqlite resulted in a new error:
# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 1:22:29 am Mi 23 Jan 2019 16:39:44 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 657, in _goal2transaction
ts.add_install(pkg, obs, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 256, in add_install
ti_new = self.new(new, libdnf.transaction.TransactionItemAction_INSTALL, reason)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 219, in new
rpm_item = self._pkg_to_swdb_rpm_item(pkg)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 210, in _pkg_to_swdb_rpm_item
rpm_item = self.history.swdb.createRPMItem()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 472, in close
self._finalize_base()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 455, in _finalize_base
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: malformed database schema (1467577792)
Looking further into the sqlite3 .dump thing, I see this:
/var/lib/dnf# sqlite3 history.sqlite .dump
PRAGMA foreign_keys=OFF;
BEGIN TRANSACTION;
/**** ERROR: (10) disk I/O error *****/
ROLLBACK; -- due to errors
However, when I copy this history.sqlite into /tmp and execute that .dump there, I get a sensibly looking database. Also opening it with the GUI sqliteman works fine. It seems that the database itself is okay.
Dumping the database into a new file somewhere else and copying it back then gives me this:
/v/l/dnf# dnf update
Letzte Prüfung auf abgelaufene Metadaten: vor 0:30:51 am Sa 26 Jan 2019 13:21:13 CET.
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 99, in _main
return cli_run(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 123, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 146, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 760, in resolve
self._transaction = self._goal2transaction(goal)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 650, in _goal2transaction
reason_obsolete = ts.get_reason(obsolete)
File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 237, in get_reason
return self.history.swdb.resolveRPMTransactionItemReason(pkg.name, pkg.arch, -1)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 788, in resolveRPMTransactionItemReason
return _transaction.Swdb_resolveRPMTransactionItemReason(self, name, arch, maxTransactionId)
RuntimeError: Step: disk I/O error in
SELECT
ti.action as action,
ti.reason as reason
FROM
trans_item ti
JOIN
trans t ON ti.trans_id = t.id
JOIN
rpm i USING (item_id)
WHERE
t.state = 1
/* see comment in TransactionItem.hpp - TransactionItemAction */
AND ti.action not in (3, 5, 7, 10)
AND i.name = 'libmodulemd'
AND i.arch = 'x86_64'
ORDER BY
ti.trans_id DESC
LIMIT 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/dnf", line 58, in <module>
main.user_main(sys.argv[1:], exit_code=True)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 179, in user_main
errcode = main(args)
File "/usr/lib/python3.7/site-packages/dnf/cli/main.py", line 64, in main
return _main(base, args, cli_class, option_parser_class)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 121, in __exit__
self.close()
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 473, in close
self.reset(sack=True, repos=True, goal=True)
File "/usr/lib/python3.7/site-packages/dnf/base.py", line 504, in reset
self.history.close()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
self.swdb.closeTransaction()
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
self._swdb = libdnf.transaction.Swdb(self.dbpath)
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
this = _transaction.new_Swdb(*args)
RuntimeError: Exec failed: disk I/O error
Exception ignored in: <function SwdbInterface.__del__ at 0x7f28b02e4510>
Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 262, in __del__
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 305, in close
File "/usr/lib/python3.7/site-packages/dnf/db/history.py", line 291, in swdb
File "/usr/lib64/python3.7/site-packages/libdnf/transaction.py", line 729, in __init__
RuntimeError: Exec failed: disk I/O error
I also restored the SELinux labels, but that did not change anything, it is
-rw-r--r--. 1 root root unconfined_u:object_r:rpm_var_lib_t:s0 29M 26. Jan 13:52 history.sqlite
Root can also read the file:
/v/l/dnf# head -c 1000 history.sqlite
SQLite format 3@ ,�,.,P��⏎
How is this on Fedora 29, can I recover from this?
fedora dnf
fedora dnf
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
edited Jan 26 at 12:58
Martin Ueding
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
asked Jan 23 at 15:44
Martin UedingMartin Ueding
1,31511228
1,31511228
Have you trieddnf clean dbcache?
– maulinglawns
Jan 23 at 16:54
The question from ask fedora you refer to has a solution as th first answer. Did you run those commands?
– Panther
Jan 23 at 16:54
I did, but it did not help. The question is updated accordingly.
– Martin Ueding
Jan 23 at 17:04
@maulinglawns: I did, but it turned out to be already included indnf clean all.
– Martin Ueding
Jan 23 at 17:04
Ah, I see. Not a Fedora user myself. I have usedyum clean dbcachewith success on CentOS.
– maulinglawns
Jan 23 at 17:11
|
show 2 more comments
Have you trieddnf clean dbcache?
– maulinglawns
Jan 23 at 16:54
The question from ask fedora you refer to has a solution as th first answer. Did you run those commands?
– Panther
Jan 23 at 16:54
I did, but it did not help. The question is updated accordingly.
– Martin Ueding
Jan 23 at 17:04
@maulinglawns: I did, but it turned out to be already included indnf clean all.
– Martin Ueding
Jan 23 at 17:04
Ah, I see. Not a Fedora user myself. I have usedyum clean dbcachewith success on CentOS.
– maulinglawns
Jan 23 at 17:11
Have you tried
dnf clean dbcache?– maulinglawns
Jan 23 at 16:54
Have you tried
dnf clean dbcache?– maulinglawns
Jan 23 at 16:54
The question from ask fedora you refer to has a solution as th first answer. Did you run those commands?
– Panther
Jan 23 at 16:54
The question from ask fedora you refer to has a solution as th first answer. Did you run those commands?
– Panther
Jan 23 at 16:54
I did, but it did not help. The question is updated accordingly.
– Martin Ueding
Jan 23 at 17:04
I did, but it did not help. The question is updated accordingly.
– Martin Ueding
Jan 23 at 17:04
@maulinglawns: I did, but it turned out to be already included in
dnf clean all.– Martin Ueding
Jan 23 at 17:04
@maulinglawns: I did, but it turned out to be already included in
dnf clean all.– Martin Ueding
Jan 23 at 17:04
Ah, I see. Not a Fedora user myself. I have used
yum clean dbcache with success on CentOS.– maulinglawns
Jan 23 at 17:11
Ah, I see. Not a Fedora user myself. I have used
yum clean dbcache with success on CentOS.– maulinglawns
Jan 23 at 17:11
|
show 2 more comments
1 Answer
1
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I have tried this dump again after restarting the system. Perhaps the restoration of SELinux labels needed to be adjusted. Now the updates seem to work again.
answered Jan 27 at 8:14
Martin UedingMartin Ueding
1,31511228
add a comment |
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I have tried this dump again after restarting the system. Perhaps the restoration of SELinux labels needed to be adjusted. Now the updates seem to work again.
answered Jan 27 at 8:14
Martin UedingMartin Ueding
1,31511228
add a comment |
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I have tried this dump again after restarting the system. Perhaps the restoration of SELinux labels needed to be adjusted. Now the updates seem to work again.
answered Jan 27 at 8:14
Martin UedingMartin Ueding
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I have tried this dump again after restarting the system. Perhaps the restoration of SELinux labels needed to be adjusted. Now the updates seem to work again.
answered Jan 27 at 8:14
Martin UedingMartin Ueding
1,31511228
I have tried this dump again after restarting the system. Perhaps the restoration of SELinux labels needed to be adjusted. Now the updates seem to work again.
answered Jan 27 at 8:14
Martin UedingMartin Ueding
1,31511228
answered Jan 27 at 8:14
Martin UedingMartin Ueding
1,31511228
answered Jan 27 at 8:14
Martin UedingMartin Ueding
1,31511228
answered Jan 27 at 8:14
Martin UedingMartin Ueding
1,31511228
1,31511228
add a comment |
add a comment |
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Have you tried
dnf clean dbcache?– maulinglawns
Jan 23 at 16:54
The question from ask fedora you refer to has a solution as th first answer. Did you run those commands?
– Panther
Jan 23 at 16:54
I did, but it did not help. The question is updated accordingly.
– Martin Ueding
Jan 23 at 17:04
@maulinglawns: I did, but it turned out to be already included in
dnf clean all.– Martin Ueding
Jan 23 at 17:04
Ah, I see. Not a Fedora user myself. I have used
yum clean dbcachewith success on CentOS.– maulinglawns
Jan 23 at 17:11