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Bug 1677774
Summary: | dnf aborts trying to remove some packages | ||||||
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Product: | [Fedora] Fedora | Reporter: | Kevin Fenzi <kevin> | ||||
Component: | dnf | Assignee: | Lukáš Hrázký <lhrazky> | ||||
Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||
Severity: | unspecified | Docs Contact: | |||||
Priority: | medium | ||||||
Version: | 31 | CC: | jmracek, jrohel, kaveh, kevin, lhrazky, lorddarthfener, mblaha, mhatina, packaging-team-maint, pkratoch, rpm-software-management, vmukhame | ||||
Target Milestone: | --- | Keywords: | Triaged | ||||
Target Release: | --- | ||||||
Hardware: | Unspecified | ||||||
OS: | Unspecified | ||||||
Whiteboard: | |||||||
Fixed In Version: | dnf-4.2.21-1.fc31 | Doc Type: | If docs needed, set a value | ||||
Doc Text: | Story Points: | --- | |||||
Clone Of: | Environment: | ||||||
Last Closed: | 2020-04-18 00:06:59 UTC | Type: | Bug | ||||
Regression: | --- | Mount Type: | --- | ||||
Documentation: | --- | CRM: | |||||
Verified Versions: | Category: | --- | |||||
oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |||||
Cloudforms Team: | --- | Target Upstream Version: | |||||
Embargoed: | |||||||
Attachments: |
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Description
Kevin Fenzi
2019-02-15 20:33:52 UTC
Are you able to provide full traceback / coredump? And which versions of dnf/libdnf are you using? ➜ ~ rpm -q dnf python3 dnf-4.1.0-1.fc30.noarch python3-3.7.2-6.fc30.x86_64 PID: 8479 (dnf) UID: 0 (root) GID: 0 (root) Signal: 6 (ABRT) Timestamp: Mon 2019-02-18 09:22:36 PST (1min 11s ago) Command Line: /usr/bin/python3 /usr/bin/dnf remove f25-backgrounds-25.1.1-7.fc30.noarch Executable: /usr/bin/python3.7 Control Group: /user.slice/user-1000.slice/user/dbus\x2d:1.2\x2dcom.gexperts.Tilix.slice/dbus-:1.2-com.gexperts.Tilix Unit: user User Unit: dbus-:1.2-com.gexperts.Tilix Slice: user-1000.slice Owner UID: 1000 (kevin) Boot ID: 11072d611b8447159c57e65ec89f0e15 Machine ID: 54945dc7fd0a438f9f0a0a4e162d5983 Hostname: taim.scrye.com Storage: /var/lib/systemd/coredump/core.dnf.0.11072d611b8447159c57e65ec89f0e15.8479.1550510556000000.lz4 (inaccessible) Message: Process 8479 (dnf) of user 0 dumped core. Stack trace of thread 8479: #0 0x00007f50932980f5 raise (libc.so.6) #1 0x00007f5093282895 abort (libc.so.6) #2 0x00007f508511567a n/a (libstdc++.so.6) #3 0x00007f508512159c n/a (libstdc++.so.6) #4 0x00007f50851215f7 _ZSt9terminatev (libstdc++.so.6) #5 0x00007f5085121859 __cxa_throw (libstdc++.so.6) #6 0x00007f50852e44b8 n/a (libdnf.so.2) #7 0x00007f50853387c5 _ZNK6libdnf4Swdb19filterUserinstalledERNS_10PackageSetE (libdnf.so.2) #8 0x00007f508251fcf0 n/a (_hawkey.so) #9 0x00007f5093025958 _PyMethodDef_RawFastCallKeywords (libpython3.7m.so.1.0) #10 0x00007f50930641ad _PyMethodDescr_FastCallKeywords (libpython3.7m.so.1.0) #11 0x00007f509306432b n/a (libpython3.7m.so.1.0) #12 0x00007f50930aa529 _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #13 0x00007f509304d472 _PyFunction_FastCallKeywords (libpython3.7m.so.1.0) #14 0x00007f509306425f n/a (libpython3.7m.so.1.0) #15 0x00007f50930aa529 _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #16 0x00007f509304c5f0 _PyEval_EvalCodeWithName (libpython3.7m.so.1.0) #17 0x00007f509304d610 _PyFunction_FastCallKeywords (libpython3.7m.so.1.0) #18 0x00007f509306425f n/a (libpython3.7m.so.1.0) #19 0x00007f50930aa529 _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #20 0x00007f509304d472 _PyFunction_FastCallKeywords (libpython3.7m.so.1.0) #21 0x00007f509306425f n/a (libpython3.7m.so.1.0) #22 0x00007f50930aa482 _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #23 0x00007f509304d472 _PyFunction_FastCallKeywords (libpython3.7m.so.1.0) #24 0x00007f509306425f n/a (libpython3.7m.so.1.0) #25 0x00007f50930aa482 _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #26 0x00007f509304d472 _PyFunction_FastCallKeywords (libpython3.7m.so.1.0) #27 0x00007f509306425f n/a (libpython3.7m.so.1.0) #28 0x00007f50930aa482 _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #29 0x00007f509304c5f0 _PyEval_EvalCodeWithName (libpython3.7m.so.1.0) #30 0x00007f509304d610 _PyFunction_FastCallKeywords (libpython3.7m.so.1.0) #31 0x00007f509306425f n/a (libpython3.7m.so.1.0) #32 0x00007f50930aa482 _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #33 0x00007f509304c5f0 _PyEval_EvalCodeWithName (libpython3.7m.so.1.0) #34 0x00007f509304d610 _PyFunction_FastCallKeywords (libpython3.7m.so.1.0) #35 0x00007f509306425f n/a (libpython3.7m.so.1.0) #36 0x00007f50930ab31f _PyEval_EvalFrameDefault (libpython3.7m.so.1.0) #37 0x00007f509304c5f0 _PyEval_EvalCodeWithName (libpython3.7m.so.1.0) #38 0x00007f509304d349 PyEval_EvalCodeEx (libpython3.7m.so.1.0) #39 0x00007f509304d36b PyEval_EvalCode (libpython3.7m.so.1.0) #40 0x00007f5093114e23 n/a (libpython3.7m.so.1.0) #41 0x00007f50931150e7 PyRun_FileExFlags (libpython3.7m.so.1.0) #42 0x00007f509311a6e6 PyRun_SimpleFileExFlags (libpython3.7m.so.1.0) #43 0x00007f509311c39c n/a (libpython3.7m.so.1.0) #44 0x00007f509311c54c _Py_UnixMain (libpython3.7m.so.1.0) #45 0x00007f5093283f33 __libc_start_main (libc.so.6) #46 0x0000556a212d708e _start (python3.7) This happens on every 'dnf remove' I guess my history has some entry for 'dbus-libs thats causing it to blow up? Kevin, we'll work on a recovery mechanism dealing with a broken db. The question is what is the root cause. By any chance, didn't the host run out of disk space during? It seems like corrupted sqlite db because of that. Please could you reproduce the issue with the latest libdnf/dnf from our nightly repository? Just use "dnf copr enable rpmsoftwaremanagement/dnf-nightly". Sadly, I rebuilt that machine, so I no longer can debug the issue. ;( Hi, I'm having the same issue, though the package causing it is gnome-autoar and not dbus-libs on my box. I've tried rebuilding the db with `rpm --rebuilddb` but didn't help. If I manually remove gnome-autoar with `rpm -e gnome-autoar --nodeps` then `dnf remove` works, but as soon I reinstall gnome-autoar the same issue arise. $ rpm -q dnf python3 dnf-4.2.8-0.41g27b7a927.fc30.noarch python3-3.7.3-3.fc30.x86_64 $ sudo dnf remove gimp terminate called after throwing an instance of 'SQLite3::LibException' what(): 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 = 'gnome-autoar' AND i.arch = 'x86_64' ORDER BY ti.trans_id DESC LIMIT 1 Aborted And the backtrace: #0 0x00007ffff7de0e75 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50 #1 0x00007ffff7dcb895 in __GI_abort () at abort.c:79 #2 0x00007fffe9db46da in __gnu_cxx::__verbose_terminate_handler() () at ../../../../libstdc++-v3/libsupc++/vterminate.cc:95 #3 0x00007fffe9dc061c in __cxxabiv1::__terminate(void (*)()) (handler=<optimized out>) at ../../../../libstdc++-v3/libsupc++/eh_terminate.cc:47 #4 0x00007fffe9dc0677 in std::terminate() () at ../../../../libstdc++-v3/libsupc++/eh_terminate.cc:57 #5 0x00007fffe9dc08d9 in __cxxabiv1::__cxa_throw(void*, std::type_info*, void (*)(void*)) (obj=obj@entry=0x555555b1b600, tinfo=tinfo@entry=0x7fffe9bf1e40 <typeinfo for SQLite3::LibException>, dest=dest@entry=0x7fffe9b10be0 <SQLite3::LibException::~LibException()>) at ../../../../libstdc++-v3/libsupc++/eh_throw.cc:95 #6 0x00007fffe9acdd5a in SQLite3::Statement::step() (this=0x7fffffffc1f0) at /usr/include/c++/9/ext/new_allocator.h:89 #7 0x00007fffe9acdd5a in libdnf::RPMItem::resolveTransactionItemReason(std::shared_ptr<SQLite3>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long) (conn=std::shared_ptr<class SQLite3> (use count 3, weak count 0) = {...}, name="gnome-autoar", arch="x86_64", maxTransactionId=maxTransactionId@entry=-1) at /usr/src/debug/libdnf-0.35.2-0.16g5208ec9c.fc30.x86_64/libdnf/transaction/RPMItem.cpp:283 #8 0x00007fffe9b25385 in libdnf::Swdb::filterUserinstalled(libdnf::PackageSet&) const (this=0x555555b1b480, installed=...) at /usr/include/c++/9/ext/atomicity.h:96 #9 0x00007fffe7d50e50 in () at /usr/lib64/python3.7/site-packages/hawkey/_hawkey.so #10 0x00007ffff7b6b968 in _PyMethodDef_RawFastCallKeywords (method=<optimized out>, self=<_hawkey.Query at remote 0x7fffe768b1b0>, args=<optimized out>, nargs=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:690 #11 0x00007ffff7ba3e9d in _PyMethodDescr_FastCallKeywords (descrobj=<method_descriptor at remote 0x7fffe7d8a288>, args=0x7fffe76441e0, nargs=2, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/descrobject.c:288 #12 0x00007ffff7ba402b in call_function (pp_stack=0x7fffffffc5d0, oparg=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4593 #13 0x00007ffff7be1ae5 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3110 #14 0x00007ffff7b90e82 in function_code_fastcall (globals=<optimized out>, nargs=3, args=<optimized out>, co=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #15 0x00007ffff7b90e82 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=0x7fffe76bf3f8, nargs=3, kwnames=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #16 0x00007ffff7ba3f4f in call_function (pp_stack=0x7fffffffc7d0, oparg=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4616 #17 0x00007ffff7be1ae5 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3110 #18 0x00007ffff7b90000 in _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x555555adf6d0, kwcount=<optimized out>, kwstep=1, defs=0x7fffea097e60, defcount=1, kwdefs=0x0, closure=0x0, name='resolve', qualname='Base.resolve') at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3930 #19 0x00007ffff7b91022 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=0x555555adf6c0, nargs=2, kwnames=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:433 #20 0x00007ffff7ba3f4f in call_function (pp_stack=0x7fffffffcac0, oparg=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4616 #21 0x00007ffff7be1ae5 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3110 #22 0x00007ffff7b90e82 in function_code_fastcall (globals=<optimized out>, nargs=2, args=<optimized out>, co=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #23 0x00007ffff7b90e82 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=0x555555ac7de0, nargs=2, kwnames=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #24 0x00007ffff7ba3f4f in call_function (pp_stack=0x7fffffffccc8, oparg=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4616 #25 0x00007ffff7be1a40 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3124 #26 0x00007ffff7b90e82 in function_code_fastcall (globals=<optimized out>, nargs=2, args=<optimized out>, co=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #27 0x00007ffff7b90e82 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=0x5555555c7bd8, nargs=2, kwnames=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #28 0x00007ffff7ba3f4f in call_function (pp_stack=0x7fffffffcec8, oparg=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4616 #29 0x00007ffff7be1a40 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3124 #30 0x00007ffff7b90e82 in function_code_fastcall (globals=<optimized out>, nargs=4, args=<optimized out>, co=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #31 0x00007ffff7b90e82 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=0x555555599fc0, nargs=4, kwnames=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:408 #32 0x00007ffff7ba3f4f in call_function (pp_stack=0x7fffffffd0c8, oparg=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4616 #33 0x00007ffff7be1a40 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3124 #34 0x00007ffff7b90000 in _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x555555967568, kwcount=<optimized out>, kwstep=1, defs=0x7fffe7b88a38, defcount=3, kwdefs=0x0, closure=0x0, name='main', qualname='main') at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3930 #35 0x00007ffff7b91022 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=0x555555967560, nargs=1, kwnames=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:433 #36 0x00007ffff7ba3f4f in call_function (pp_stack=0x7fffffffd3b8, oparg=<optimized out>, kwnames=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4616 #37 0x00007ffff7be1a40 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3124 #38 0x00007ffff7b90000 in _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x7fffea7ec5d8, kwargs=0x7fffea926b70, kwcount=<optimized out>, kwstep=1, defs=0x7fffe7a232c8, defcount=1, kwdefs=0x0, closure=0x0, name='user_main', qualname='user_main') at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3930 #39 0x00007ffff7b91022 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=0x7fffea926b68, nargs=1, kwnames=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Objects/call.c:433 #40 0x00007ffff7ba3f4f in call_function (pp_stack=0x7fffffffd6b0, oparg=<optimized out>, kwnames=('exit_code',)) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:4616 #41 0x00007ffff7be28e9 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3139 #42 0x00007ffff7b90000 in _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x0, kwcount=<optimized out>, kwstep=2, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3930 #43 0x00007ffff7b90d59 in PyEval_EvalCodeEx (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kws=<optimized out>, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:3959 #44 0x00007ffff7b90d7b in PyEval_EvalCode (co=co@entry=<code at remote 0x7fffea7ff540>, globals=globals@entry={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='/usr/bin/dnf') at remote 0x7fffea8a9da0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7fbbc28>, '__file__': '/usr/bin/dnf', '__cached__': None, 'unicode_literals': <_Feature(optional=(2, 6, 0, 'alpha', 2), mandatory=(3, 0, 0, 'alpha', 0), compiler_flag=131072) at remote 0x7fffea7450b8>, 'sys': <module at remote 0x7ffff7fb5f98>, 'suppress_keyboard_interrupt_message': <function at remote 0x7fffea8e4268>, 'here': '/usr/bin', 'main': <module at remote 0x7fffe7bfb4a8>}, locals=locals@entry={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='/usr/bin/dnf') at remote 0x7fffea8a9da0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7fbbc28>, '__file__': '/usr/bin/dnf', '__cached__': None, 'unicode_literals': <_Feature(optional=(2, 6, 0, 'alpha', 2), mandatory=(3, 0, 0, 'alpha', 0), compiler_flag=131072) at remote 0x7fffea7450b8>, 'sys': <module at remote 0x7ffff7fb5f98>, 'suppress_keyboard_interrupt_message': <function at remote 0x7fffea8e4268>, 'here': '/usr/bin', 'main': <module at remote 0x7fffe7bfb4a8>}) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/ceval.c:524 #45 0x00007ffff7c5d093 in run_mod (mod=<optimized out>, filename=<optimized out>, globals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='/usr/bin/dnf') at remote 0x7fffea8a9da0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7fbbc28>, '__file__': '/usr/bin/dnf', '__cached__': None, 'unicode_literals': <_Feature(optional=(2, 6, 0, 'alpha', 2), mandatory=(3, 0, 0, 'alpha', 0), compiler_flag=131072) at remote 0x7fffea7450b8>, 'sys': <module at remote 0x7ffff7fb5f98>, 'suppress_keyboard_interrupt_message': <function at remote 0x7fffea8e4268>, 'here': '/usr/bin', 'main': <module at remote 0x7fffe7bfb4a8>}, locals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='/usr/bin/dnf') at remote 0x7fffea8a9da0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7fbbc28>, '__file__': '/usr/bin/dnf', '__cached__': None, 'unicode_literals': <_Feature(optional=(2, 6, 0, 'alpha', 2), mandatory=(3, 0, 0, 'alpha', 0), compiler_flag=131072) at remote 0x7fffea7450b8>, 'sys': <module at remote 0x7ffff7fb5f98>, 'suppress_keyboard_interrupt_message': <function at remote 0x7fffea8e4268>, 'here': '/usr/bin', 'main': <module at remote 0x7fffe7bfb4a8>}, flags=<optimized out>, arena=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/pythonrun.c:1035 #46 0x00007ffff7c5d3f7 in PyRun_FileExFlags (fp=0x55555559ffa0, filename_str=<optimized out>, start=<optimized out>, globals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='/usr/bin/dnf') at remote 0x7fffea8a9da0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7fbbc28>, '__file__': '/usr/bin/dnf', '__cached__': None, 'unicode_literals': <_Feature(optional=(2, 6, 0, 'alpha', 2), mandatory=(3, 0, 0, 'alpha', 0), compiler_flag=131072) at remote 0x7fffea7450b8>, 'sys': <module at remote 0x7ffff7fb5f98>, 'suppress_keyboard_interrupt_message': <function at remote 0x7fffea8e4268>, 'here': '/usr/bin', 'main': <module at remote 0x7fffe7bfb4a8>}, locals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='/usr/bin/dnf') at remote 0x7fffea8a9da0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7fbbc28>, '__file__': '/usr/bin/dnf', '__cached__': None, 'unicode_literals': <_Feature(optional=(2, 6, 0, 'alpha', 2), mandatory=(3, 0, 0, 'alpha', 0), compiler_flag=131072) at remote 0x7fffea7450b8>, 'sys': <module at remote 0x7ffff7fb5f98>, 'suppress_keyboard_interrupt_message': <function at remote 0x7fffea8e4268>, 'here': '/usr/bin', 'main': <module at remote 0x7fffe7bfb4a8>}, closeit=1, flags=0x7fffffffd990) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/pythonrun.c:988 #47 0x00007ffff7c630aa in PyRun_SimpleFileExFlags (fp=0x55555559ffa0, filename=<optimized out>, closeit=1, flags=0x7fffffffd990) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Python/pythonrun.c:429 #48 0x00007ffff7c64d9c in pymain_run_file (p_cf=0x7fffffffd990, filename=<optimized out>, fp=0x55555559ffa0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Modules/main.c:427 #49 0x00007ffff7c64d9c in pymain_run_filename (cf=0x7fffffffd990, pymain=0x7fffffffdaa0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Modules/main.c:1627 #50 0x00007ffff7c64d9c in pymain_run_python (pymain=0x7fffffffdaa0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Modules/main.c:2877 #51 0x00007ffff7c64d9c in pymain_main (pymain=0x7fffffffdaa0) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Modules/main.c:3038 #52 0x00007ffff7c64f4c in _Py_UnixMain (argc=<optimized out>, argv=<optimized out>) at /usr/src/debug/python3-3.7.3-3.fc30.x86_64/Modules/main.c:3073 #53 0x00007ffff7dccf33 in __libc_start_main (main=0x555555555050 <main>, argc=4, argv=0x7fffffffdbf8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdbe8) at ../csu/libc-start.c:308 #54 0x000055555555508e in _start () Having a look with strace seems the issue lies within the history.sqlite db. Cleaning it makes `dnf remove` working again, though I have a backup of the old one if someone needs any info. This bug appears to have been reported against 'rawhide' during the Fedora 31 development cycle. Changing version to '31'. This bug appears to have been reported against 'rawhide' during the Fedora 31 development cycle. Changing version to 31. Hello Paolo, sorry for a late response. Do you happen to still have that corrupted file? Created attachment 1644871 [details]
dnf history sqlite database
I do! Just attached it, I have a backup of the whole /var/lib/dnf folder if you need other files as well, let me know. Nice, I reproduced it. Thanks a lot! Hi, I am on fedora 29 and was trying to upgrade to 30 when I got this error. I thought it was because of vscode package ( package name code ) so I tried to uninstall that. got the same error. removed it with "rpm", and removed the microsoft repository. But I am still getting this error. here is a full copy paste of my terminal content: [root@kaveh-pc ~]# dnf update -y Adobe Systems Incorporated 9.3 kB/s | 2.9 kB 00:00 Docker CE Stable - x86_64 17 kB/s | 3.5 kB 00:00 Fedora Modular 29 - x86_64 29 kB/s | 17 kB 00:00 Fedora Modular 29 - x86_64 - Updates 63 kB/s | 16 kB 00:00 Fedora 29 - x86_64 - Updates 72 kB/s | 17 kB 00:00 Fedora 29 - x86_64 19 kB/s | 17 kB 00:00 google-chrome 11 kB/s | 1.3 kB 00:00 Google Cloud SDK 519 B/s | 454 B 00:00 MySQL 8.0 Community Server 13 kB/s | 2.5 kB 00:00 MySQL Connectors Community 14 kB/s | 2.5 kB 00:00 MySQL Tools Community 9.1 kB/s | 2.5 kB 00:00 RPM Fusion for Fedora 29 - Free - Updates 2.8 kB/s | 3.0 kB 00:01 RPM Fusion for Fedora 29 - Free 4.3 kB/s | 3.2 kB 00:00 RPM Fusion for Fedora 29 - Nonfree - Updates 4.1 kB/s | 3.0 kB 00:00 RPM Fusion for Fedora 29 - Nonfree 4.2 kB/s | 3.2 kB 00:00 Sublime Text - x86_64 - Stable 7.0 kB/s | 2.9 kB 00:00 Visual Studio Code 4.9 kB/s | 2.9 kB 00:00 Dependencies resolved. =================================================================================================================================== Package Architecture Version Repository Size =================================================================================================================================== Upgrading: google-chrome-stable x86_64 79.0.3945.88-1 google-chrome 59 M google-cloud-sdk noarch 274.0.1-1 google-cloud-sdk 37 M google-cloud-sdk-app-engine-python noarch 274.0.1-1 google-cloud-sdk 6.2 M google-cloud-sdk-datastore-emulator noarch 274.0.1-1 google-cloud-sdk 18 M google-cloud-sdk-pubsub-emulator noarch 274.0.1-1 google-cloud-sdk 35 M code x86_64 1.41.1-1576681965.el7 code 79 M Transaction Summary =================================================================================================================================== Upgrade 6 Packages Total download size: 234 M Downloading Packages: (1/6): f03ed2e0f9eadb3a46564683464d4a8fbb48a1f5a5173fe1702931dad651433a-google-cloud-sdk-app-engin 746 kB/s | 6.2 MB 00:08 (2/6): 4d2d6f2fef50ea6b4c083e933456d32d2f751c990bf41e1663ada61fa7619572-google-cloud-sdk-274.0.1-1 2.3 MB/s | 37 MB 00:16 (3/6): google-chrome-stable-79.0.3945.88-1.x86_64.rpm 2.3 MB/s | 59 MB 00:25 (4/6): 9b49a3bf890ce45c951a8962cb4c28cf32fd31629b2efffc9076807c0e61255f-google-cloud-sdk-datastore 1.0 MB/s | 18 MB 00:17 (5/6): f11084550a41a19c7edb643225f49987780370eab2cc4084a01e092bf70190b5-google-cloud-sdk-pubsub-em 2.4 MB/s | 35 MB 00:14 (6/6): code-1.41.1-1576681965.el7.x86_64.rpm 2.3 MB/s | 79 MB 00:34 ----------------------------------------------------------------------------------------------------------------------------------- Total 3.9 MB/s | 234 MB 01:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : google-cloud-sdk-274.0.1-1.noarch 1/12 Running scriptlet: google-cloud-sdk-274.0.1-1.noarch 1/12 Upgrading : google-cloud-sdk-app-engine-python-274.0.1-1.noarch 2/12 Upgrading : google-cloud-sdk-datastore-emulator-274.0.1-1.noarch 3/12 Upgrading : google-cloud-sdk-pubsub-emulator-274.0.1-1.noarch 4/12 Upgrading : code-1.41.1-1576681965.el7.x86_64 5/12 Running scriptlet: code-1.41.1-1576681965.el7.x86_64 5/12 Running scriptlet: google-chrome-stable-79.0.3945.88-1.x86_64 6/12 Upgrading : google-chrome-stable-79.0.3945.88-1.x86_64 6/12 Running scriptlet: google-chrome-stable-79.0.3945.88-1.x86_64 6/12 Redirecting to /bin/systemctl start atd.service Cleanup : google-cloud-sdk-pubsub-emulator-273.0.0-1.noarch 7/12 Cleanup : google-cloud-sdk-datastore-emulator-273.0.0-1.noarch 8/12 Cleanup : google-cloud-sdk-app-engine-python-273.0.0-1.noarch 9/12 Running scriptlet: google-cloud-sdk-273.0.0-1.noarch 10/12 Cleanup : google-cloud-sdk-273.0.0-1.noarch 10/12 Running scriptlet: google-cloud-sdk-273.0.0-1.noarch 10/12 Compiling platform/bq/third_party/yaml/lib3/__init__.py ... File "platform/bq/third_party/yaml/lib3/__init__.py", line 284 class YAMLObject(metaclass=YAMLObjectMetaclass): ^ SyntaxError: invalid syntax Running scriptlet: google-chrome-stable-79.0.3945.79-1.x86_64 11/12 Cleanup : google-chrome-stable-79.0.3945.79-1.x86_64 11/12 Running scriptlet: google-chrome-stable-79.0.3945.79-1.x86_64 11/12 Cleanup : code-1.41.0-1576089692.el7.x86_64 12/12 Running scriptlet: code-1.41.0-1576089692.el7.x86_64 12/12 Verifying : google-chrome-stable-79.0.3945.88-1.x86_64 1/12 Verifying : google-chrome-stable-79.0.3945.79-1.x86_64 2/12 Verifying : google-cloud-sdk-274.0.1-1.noarch 3/12 Verifying : google-cloud-sdk-273.0.0-1.noarch 4/12 Verifying : google-cloud-sdk-app-engine-python-274.0.1-1.noarch 5/12 Verifying : google-cloud-sdk-app-engine-python-273.0.0-1.noarch 6/12 Verifying : google-cloud-sdk-datastore-emulator-274.0.1-1.noarch 7/12 Verifying : google-cloud-sdk-datastore-emulator-273.0.0-1.noarch 8/12 Verifying : google-cloud-sdk-pubsub-emulator-274.0.1-1.noarch 9/12 Verifying : google-cloud-sdk-pubsub-emulator-273.0.0-1.noarch 10/12 Verifying : code-1.41.1-1576681965.el7.x86_64 11/12 Verifying : code-1.41.0-1576089692.el7.x86_64 12/12 Upgraded: google-chrome-stable-79.0.3945.88-1.x86_64 google-cloud-sdk-274.0.1-1.noarch google-cloud-sdk-app-engine-python-274.0.1-1.noarch google-cloud-sdk-datastore-emulator-274.0.1-1.noarch google-cloud-sdk-pubsub-emulator-274.0.1-1.noarch code-1.41.1-1576681965.el7.x86_64 Complete! [root@kaveh-pc ~]# cat /etc/os-release NAME=Fedora VERSION="29 (Twenty Nine)" ID=fedora VERSION_ID=29 VERSION_CODENAME="" PLATFORM_ID="platform:f29" PRETTY_NAME="Fedora 29 (Twenty Nine)" ANSI_COLOR="0;34" LOGO=fedora-logo-icon CPE_NAME="cpe:/o:fedoraproject:fedora:29" HOME_URL="https://fedoraproject.org/" DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f29/system-administrators-guide/" SUPPORT_URL="https://fedoraproject.org/wiki/Communicating_and_getting_help" BUG_REPORT_URL="https://bugzilla.redhat.com/" REDHAT_BUGZILLA_PRODUCT="Fedora" REDHAT_BUGZILLA_PRODUCT_VERSION=29 REDHAT_SUPPORT_PRODUCT="Fedora" REDHAT_SUPPORT_PRODUCT_VERSION=29 PRIVACY_POLICY_URL="https://fedoraproject.org/wiki/Legal:PrivacyPolicy" [root@kaveh-pc ~]# [root@kaveh-pc ~]# [root@kaveh-pc ~]# [root@kaveh-pc ~]# dnf system-upgrade download --releasever=30 Before you continue ensure that your system is fully upgraded by running "dnf --refresh upgrade". Do you want to continue [y/N]: n Error: Operation aborted. [root@kaveh-pc ~]# dnf --refresh upgrade Adobe Systems Incorporated 8.4 kB/s | 2.9 kB 00:00 Docker CE Stable - x86_64 13 kB/s | 3.5 kB 00:00 Fedora Modular 29 - x86_64 19 kB/s | 19 kB 00:00 Fedora Modular 29 - x86_64 - Updates 42 kB/s | 18 kB 00:00 Fedora 29 - x86_64 - Updates 43 kB/s | 18 kB 00:00 Fedora 29 - x86_64 46 kB/s | 19 kB 00:00 google-chrome 7.2 kB/s | 1.3 kB 00:00 Google Cloud SDK 706 B/s | 454 B 00:00 MySQL 8.0 Community Server 27 kB/s | 2.5 kB 00:00 MySQL Connectors Community 51 kB/s | 2.5 kB 00:00 MySQL Tools Community 49 kB/s | 2.5 kB 00:00 RPM Fusion for Fedora 29 - Free - Updates 2.9 kB/s | 3.0 kB 00:01 RPM Fusion for Fedora 29 - Free 4.5 kB/s | 3.2 kB 00:00 RPM Fusion for Fedora 29 - Nonfree - Updates 3.6 kB/s | 2.6 kB 00:00 RPM Fusion for Fedora 29 - Nonfree 3.7 kB/s | 2.7 kB 00:00 Sublime Text - x86_64 - Stable 6.3 kB/s | 2.9 kB 00:00 Visual Studio Code 4.3 kB/s | 2.9 kB 00:00 Dependencies resolved. Nothing to do. Complete! [root@kaveh-pc ~]# dnf system-upgrade download --releasever=30 Before you continue ensure that your system is fully upgraded by running "dnf --refresh upgrade". Do you want to continue [y/N]: y Adobe Systems Incorporated 9.6 kB/s | 2.0 kB 00:00 Docker CE Stable - x86_64 15 kB/s | 7.5 kB 00:00 Fedora Modular 30 - x86_64 689 kB/s | 1.9 MB 00:02 Fedora Modular 30 - x86_64 - Updates 662 kB/s | 3.5 MB 00:05 Fedora 30 - x86_64 - Updates 645 kB/s | 27 MB 00:42 Fedora 30 - x86_64 1.1 MB/s | 61 MB 00:54 google-chrome 21 kB/s | 3.5 kB 00:00 Google Cloud SDK 547 B/s | 454 B 00:00 Google Cloud SDK 12 kB/s | 1.8 kB 00:00 Importing GPG key 0xA7317B0F: Userid : "Google Cloud Packages Automatic Signing Key <gc-team>" Fingerprint: D0BC 747F D8CA F711 7500 D6FA 3746 C208 A731 7B0F From : https://packages.cloud.google.com/yum/doc/yum-key.gpg Is this ok [y/N]: y Importing GPG key 0xBA07F4FB: Userid : "Google Cloud Packages Automatic Signing Key <gc-team>" Fingerprint: 54A6 47F9 048D 5688 D7DA 2ABE 6A03 0B21 BA07 F4FB From : https://packages.cloud.google.com/yum/doc/yum-key.gpg Is this ok [y/N]: y Google Cloud SDK 4.3 kB/s | 975 B 00:00 Importing GPG key 0x3E1BA8D5: Userid : "Google Cloud Packages RPM Signing Key <gc-team>" Fingerprint: 3749 E1BA 95A8 6CE0 5454 6ED2 F09C 394C 3E1B A8D5 From : https://packages.cloud.google.com/yum/doc/rpm-package-key.gpg Is this ok [y/N]: y Google Cloud SDK 3.8 MB/s | 29 MB 00:07 MySQL 8.0 Community Server 2.0 MB/s | 589 kB 00:00 MySQL Connectors Community 254 kB/s | 24 kB 00:00 MySQL Tools Community 475 kB/s | 55 kB 00:00 RPM Fusion for Fedora 30 - Free - Updates 228 kB/s | 404 kB 00:01 RPM Fusion for Fedora 30 - Free 390 kB/s | 735 kB 00:01 RPM Fusion for Fedora 30 - Nonfree - Updates 61 kB/s | 77 kB 00:01 RPM Fusion for Fedora 30 - Nonfree 153 kB/s | 227 kB 00:01 Sublime Text - x86_64 - Stable 2.6 kB/s | 2.0 kB 00:00 Visual Studio Code 1.0 MB/s | 2.6 MB 00:02 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 192, 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 159, in resolving base.resolve(cli.demands.allow_erasing) File "/usr/lib/python3.7/site-packages/dnf/base.py", line 767, in resolve self._transaction = self._goal2transaction(goal) File "/usr/lib/python3.7/site-packages/dnf/base.py", line 688, in _goal2transaction ts.add_upgrade(pkg, upgraded, obs) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 272, in add_upgrade ti_new = self.new(new, libdnf.transaction.TransactionItemAction_UPGRADE) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 225, in new reason = self.get_reason(pkg) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 240, 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 = 'python3-pam' AND i.arch = 'noarch' ORDER BY ti.trans_id DESC LIMIT 1 [root@kaveh-pc ~]# rpm -qa | grep code perl-Unicode-Normalize-1.26-417.fc29.x86_64 base64coder-20101219-22.fc29.noarch unicode-ucd-12.1.0-1.fc29.noarch perl-Encode-2.98-6.fc29.x86_64 code-1.41.1-1576681965.el7.x86_64 iso-codes-3.79-2.fc29.noarch apache-commons-codec-1.11-4.fc29.noarch python3-pycodestyle-2.4.0-3.fc29.noarch ibus-rawcode-1.3.2-13.fc29.x86_64 dmidecode-3.2-1.fc29.x86_64 microcode_ctl-2.1-34.fc29.x86_64 qrencode-libs-3.4.4-6.fc29.x86_64 python3-dmidecode-3.12.2-13.fc29.x86_64 [root@kaveh-pc ~]# dnf remove code terminate called after throwing an instance of 'SQLite3::LibException' what(): 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 = 'python3-pam' AND i.arch = 'noarch' ORDER BY ti.trans_id DESC LIMIT 1 Aborted (core dumped) [root@kaveh-pc ~]# rpm -e code --nodeps [root@kaveh-pc ~]# dnf remove code No match for argument: code No packages marked for removal. Dependencies resolved. Nothing to do. Complete! [root@kaveh-pc ~]# cd /etc/yum.repos.d/ [root@kaveh-pc yum.repos.d]# ll total 84 -rw-r--r--. 1 root root 183 Jan 16 2018 adobe-linux-x86_64.repo -rw-r--r--. 1 root root 1892 Jan 16 2018 docker-ce.repo -rw-r--r--. 1 root root 705 Aug 19 10:52 fedora-cisco-openh264.repo -rw-r--r--. 1 root root 1395 Aug 19 10:52 fedora-modular.repo -rw-r--r--. 1 root root 1331 Aug 19 10:52 fedora.repo -rw-r--r--. 1 root root 1441 Aug 19 10:52 fedora-updates-modular.repo -rw-r--r--. 1 root root 1378 Aug 19 10:52 fedora-updates.repo -rw-r--r--. 1 root root 1483 Aug 19 10:52 fedora-updates-testing-modular.repo -rw-r--r--. 1 root root 1436 Aug 19 10:52 fedora-updates-testing.repo -rw-r--r--. 1 root root 173 Mar 29 2018 google-chrome.repo -rw-r--r--. 1 root root 283 Nov 26 2018 google-cloud-sdk.repo -rw-r--r--. 1 root root 1028 Jan 17 2019 mysql-community.repo -rw-r--r--. 1 root root 1081 Jan 17 2019 mysql-community-source.repo -rw-r--r--. 1 root root 1248 Oct 18 2018 rpmfusion-free.repo -rw-r--r--. 1 root root 1264 Oct 18 2018 rpmfusion-free-updates.repo -rw-r--r--. 1 root root 1324 Oct 18 2018 rpmfusion-free-updates-testing.repo -rw-r--r--. 1 root root 1312 Oct 18 2018 rpmfusion-nonfree.repo -rw-r--r--. 1 root root 1309 Oct 18 2018 rpmfusion-nonfree-updates.repo -rw-r--r--. 1 root root 1369 Oct 18 2018 rpmfusion-nonfree-updates-testing.repo -rw-r--r--. 1 root root 193 Jan 16 2018 sublime-text.repo -rw-r--r--. 1 root root 165 Dec 6 11:00 vscode.repo [root@kaveh-pc yum.repos.d]# cat vscode.repo [code] name=Visual Studio Code baseurl=https://packages.microsoft.com/yumrepos/vscode enabled=1 gpgcheck=1 gpgkey=https://packages.microsoft.com/keys/microsoft.asc [root@kaveh-pc yum.repos.d]# mv vscode.repo vscode.repo.not [root@kaveh-pc yum.repos.d]# cd [root@kaveh-pc ~]# dnf system-upgrade download --releasever=30 Before you continue ensure that your system is fully upgraded by running "dnf --refresh upgrade". Do you want to continue [y/N]: y Adobe Systems Incorporated 9.6 kB/s | 2.9 kB 00:00 Docker CE Stable - x86_64 13 kB/s | 3.5 kB 00:00 Fedora Modular 30 - x86_64 20 kB/s | 19 kB 00:00 Fedora Modular 30 - x86_64 - Updates 40 kB/s | 18 kB 00:00 Fedora 30 - x86_64 - Updates 40 kB/s | 18 kB 00:00 Fedora 30 - x86_64 43 kB/s | 19 kB 00:00 google-chrome 7.2 kB/s | 1.3 kB 00:00 Google Cloud SDK 550 B/s | 454 B 00:00 MySQL 8.0 Community Server 36 kB/s | 2.5 kB 00:00 MySQL Connectors Community 57 kB/s | 2.5 kB 00:00 MySQL Tools Community 54 kB/s | 2.5 kB 00:00 RPM Fusion for Fedora 30 - Free - Updates 3.0 kB/s | 3.2 kB 00:01 RPM Fusion for Fedora 30 - Free 4.4 kB/s | 3.2 kB 00:00 RPM Fusion for Fedora 30 - Nonfree - Updates 4.4 kB/s | 3.2 kB 00:00 RPM Fusion for Fedora 30 - Nonfree 3.8 kB/s | 2.7 kB 00:00 Sublime Text - x86_64 - Stable 6.5 kB/s | 2.9 kB 00:00 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 192, 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 159, in resolving base.resolve(cli.demands.allow_erasing) File "/usr/lib/python3.7/site-packages/dnf/base.py", line 767, in resolve self._transaction = self._goal2transaction(goal) File "/usr/lib/python3.7/site-packages/dnf/base.py", line 688, in _goal2transaction ts.add_upgrade(pkg, upgraded, obs) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 272, in add_upgrade ti_new = self.new(new, libdnf.transaction.TransactionItemAction_UPGRADE) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 225, in new reason = self.get_reason(pkg) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 240, 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 = 'python3-pam' AND i.arch = 'noarch' ORDER BY ti.trans_id DESC LIMIT 1 [root@kaveh-pc ~]# rpm --rebuilddb [root@kaveh-pc ~]# [root@kaveh-pc ~]# [root@kaveh-pc ~]# dnf system-upgrade download --releasever=30 Before you continue ensure that your system is fully upgraded by running "dnf --refresh upgrade". Do you want to continue [y/N]: y Adobe Systems Incorporated 18 kB/s | 2.9 kB 00:00 Docker CE Stable - x86_64 15 kB/s | 3.5 kB 00:00 Fedora Modular 30 - x86_64 49 kB/s | 19 kB 00:00 Fedora Modular 30 - x86_64 - Updates 84 kB/s | 18 kB 00:00 Fedora 30 - x86_64 - Updates 86 kB/s | 18 kB 00:00 Fedora 30 - x86_64 93 kB/s | 19 kB 00:00 google-chrome 19 kB/s | 1.3 kB 00:00 Google Cloud SDK 646 B/s | 454 B 00:00 MySQL 8.0 Community Server 13 kB/s | 2.5 kB 00:00 MySQL Connectors Community 46 kB/s | 2.5 kB 00:00 MySQL Tools Community 47 kB/s | 2.5 kB 00:00 RPM Fusion for Fedora 30 - Free - Updates 4.5 kB/s | 3.2 kB 00:00 RPM Fusion for Fedora 30 - Free 4.4 kB/s | 3.2 kB 00:00 RPM Fusion for Fedora 30 - Nonfree - Updates 4.5 kB/s | 3.2 kB 00:00 RPM Fusion for Fedora 30 - Nonfree 3.7 kB/s | 2.7 kB 00:00 Sublime Text - x86_64 - Stable 7.5 kB/s | 2.9 kB 00:00 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 192, 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 159, in resolving base.resolve(cli.demands.allow_erasing) File "/usr/lib/python3.7/site-packages/dnf/base.py", line 767, in resolve self._transaction = self._goal2transaction(goal) File "/usr/lib/python3.7/site-packages/dnf/base.py", line 688, in _goal2transaction ts.add_upgrade(pkg, upgraded, obs) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 272, in add_upgrade ti_new = self.new(new, libdnf.transaction.TransactionItemAction_UPGRADE) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 225, in new reason = self.get_reason(pkg) File "/usr/lib/python3.7/site-packages/dnf/db/group.py", line 240, 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 = 'python3-pam' AND i.arch = 'noarch' ORDER BY ti.trans_id DESC LIMIT 1 [root@kaveh-pc ~]# Hello kaveh, this issue is caused by corrupted SQLite database (that DNF uses to store the transaction history) at /var/lib/dnf/history.sqlite. The corruption must have occurred sometime earlier. Do you remember any power outages, hard reboots, crashes or running out of disk space? If you don't care about your transaction history, you can just remove the above mentioned file (or back it up somewhere). DNF doesn't need it to run. I've got patches for improving the error message, but unless the corruption is being caused by a bug in DNF (the number of reports we're getting hints more at random system failures), we probably can't do much more (apart from some clever logic around what to do when the DB is corrupted, which I'm not convinced we should do at all). PRs: https://github.com/rpm-software-management/libdnf/pull/866 https://github.com/rpm-software-management/dnf/pull/1558 https://github.com/rpm-software-management/ci-dnf-stack/pull/742 kaveh, I was unaware that the information which packages are user-installed (in other words, the packages you explicitly installed yourself) and also the installed groups (I think) is also stored in the history.sqlite database. So it's not just history you're losing by deleting the file. So better back it up somewhere, but since it's corrupted anyway, I don't think there's an easy way to retrieve the data from it. Sorry about the inconvenience, it's a poor design choice on the DNF side, unfortunately. Thanks. I don't remember an outages or anything like that. it could be just bit rot. Anyway I moved the history.sqlite* files to a backup folder, and now dnf seems to be happily upgrading to f30. thanks again, and happy new year ;) The error message was improved and the problem should now be reported properly to the user. FEDORA-2020-d51dbe83a9 has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2020-d51dbe83a9 FEDORA-2020-d51dbe83a9 has been pushed to the Fedora 31 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2020-d51dbe83a9` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-d51dbe83a9 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates. FEDORA-2020-d51dbe83a9 has been pushed to the Fedora 31 stable repository. If problem still persists, please make note of it in this bug report. |