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Question

Martin Ueding

Asked: 2019-01-24 07:44:51 +0800 CST2019-01-24 07:44:51 +0800 CST 2019-01-24 07:44:51 +0800 CST

Fedora 29 上的 dnf 数据库磁盘映像格式错误

772

我已经在ask.fedora.org上交叉发布了这个，因为我仍然不确定这方或另一方是否拥有更大的 Fedora 用户群。

几天以来，由于此错误，我无法安装更新：

# 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

我发现应该执行这些命令来修复它，我尝试了，但它没有解决问题。

dnf clean all
dnf makecache
rpm --buildddb

在Ask Fedora 上，有人建议dnf 无法从中恢复，必须手动修复 SQLite 数据库。

我试图运行给定的命令，

sqlite3 history-<date>.sqlite ".dump" | sqlite3 history-<new date>.db && rm history-<date>.sqlite

这样做/var/lib/dnf/history/history-2015-10-25.sqlite没有效果。这样做会/var/lib/dnf/history.sqlite导致一个新的错误：

# 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)

进一步研究这sqlite3 .dump件事，我看到了这一点：

/var/lib/dnf# sqlite3 history.sqlite .dump 
PRAGMA foreign_keys=OFF;
BEGIN TRANSACTION;
/**** ERROR: (10) disk I/O error *****/
ROLLBACK; -- due to errors

但是，当我将它复制history.sqlite到那里/tmp并在那里执行.dump时，我得到了一个看起来很合理的数据库。使用 GUI 打开它也sqliteman可以正常工作。看来数据库本身没问题。

将数据库转储到其他地方的新文件中并将其复制回来然后给我这个：

/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

我还恢复了 SELinux 标签，但这并没有改变任何东西，它是

-rw-r--r--. 1 root root unconfined_u:object_r:rpm_var_lib_t:s0 29M 26. Jan 13:52 history.sqlite

root 也可以读取文件：

/v/l/dnf# head -c 1000 history.sqlite 
SQLite format 3@  ,�,.,P��⏎

Fedora 29 上的情况如何，我可以从中恢复吗？

1 个回答

Voted

Martin Ueding · Answer 1 · 2019-01-28T00:14:03+08:00

Best Answer

Martin Ueding

2019-01-28T00:14:03+08:002019-01-28T00:14:03+08:00

重新启动系统后，我再次尝试了此转储。也许需要调整 SELinux 标签的恢复。现在更新似乎再次起作用。

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