Fedora 29 の dnf でデータベースディスクイメージが不正な形式になる

2024-6-10 • tag-icon

Fedora 29 の dnf でデータベースディスクイメージが不正な形式になる

私はこれをクロスポストしましたフェドラなぜなら、こちら側と向こう側のどちらに Fedora ユーザーベースが大きいのかまだ不明だからです。

ここ数日間、次のエラーのためアップデートをインストールできませんでした:

# 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

この問題を解決するにはこれらのコマンドを実行する必要があることがわかり、試してみましたが、問題は解決しませんでした。

dnf clean all
dnf makecache
rpm --buildddb

の上誰かが提案したFedoraに聞いてみようdnf では回復できず、SQLite データベースを手動で修復する必要があります。

与えられたコマンドを実行しようとしましたが、

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

で実行しても/var/lib/dnf/history/history-2015-10-25.sqlite効果はありませんでした。で実行すると、/var/lib/dnf/history.sqlite新しいエラーが発生しました:

# 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)

さらに詳しく調べてみるとsqlite3 .dump、次のことがわかります。

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

しかし、これをコピーhistory.sqliteして/tmp実行すると.dump、見栄えの良いデータベースが作成されます。また、GUI で開いてもsqliteman問題なく動作します。データベース自体は問題ないようです。

データベースを別の場所の新しいファイルにダンプし、それをコピーし直すと、次のようになります。

/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

SELinuxラベルも復元しましたが、何も変わりませんでした。

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

ルートは次のファイルも読み取ることができます:

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

Fedora 29 ではどうなっているのでしょうか、回復できますか?

答え1

システムを再起動した後に、このダンプを再度試しました。おそらく、SELinux ラベルの復元を調整する必要があったのでしょう。これで、更新は再び機能するようになったようです。

答え2

Centos のような OS の Docker イメージを開発しているのですが、このエラーが発生しました。私のイメージを使って試してみてください:

docker run --rm -it pasaopasen/redos7.3:2023-12-07_22-19 bash

実行してみてください:

dnf update -y
dnf install nginx -y

同じエラーが表示されます。

この問題を解決するのに役立つものはありませんでした。これは、のグローバル更新がうまくいかなかったことなどが原因であるようですrpm。python3古いVMインスタンスのバックアップからのグローバル更新だけで解決しました。

答え1

答え2

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