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naviehuynh
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Joined: 20 Dec 2012
Posts: 15

PostPosted: Sun Dec 30, 2012 2:30 pm    Post subject: [Solved] Emerge error: "Unable to read COUNTER file&quo Reply with quote

Hi,
Im trying to run emerge --update --deep --newuse world and got the following error. I tried to search but there seems to be no similar problem. Can someone help me solve it?

Code:
>>> Installing (1 of 47) app-admin/eselect-qtgraphicssystem-1.1.1
!!! Unable to read COUNTER file: '/var/cache/edb/counter'
!!! [Errno 5] Input/output error: '/var/cache/edb/counter'
Traceback (most recent call last):
  File "/usr/bin/emerge", line 48, in <module>
    retval = emerge_main()
  File "/usr/lib/portage/pym/_emerge/main.py", line 1044, in emerge_main
    gc_locals=locals().clear)
  File "/usr/lib/portage/pym/_emerge/actions.py", line 3885, in run_action
    myopts, myaction, myfiles, spinner)
  File "/usr/lib/portage/pym/_emerge/actions.py", line 464, in action_build
    retval = mergetask.merge()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1011, in merge
    rval = self._merge()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1396, in _merge
    self._main_loop()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1367, in _main_loop
    self._event_loop.iteration()
  File "/usr/lib/portage/pym/portage/util/_eventloop/EventLoop.py", line 191, in iteration
    if not x.callback(f, event, *x.args):
  File "/usr/lib/portage/pym/portage/util/_async/PipeLogger.py", line 119, in _output_handler
    self._unregister_if_appropriate(event)
  File "/usr/lib/portage/pym/_emerge/AbstractPollTask.py", line 129, in _unregister_if_appropriate
    self.wait()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 57, in wait
    self._wait_hook()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 161, in _wait_hook
    self._exit_listener_stack.pop()(self)
  File "/usr/lib/portage/pym/_emerge/SpawnProcess.py", line 142, in _pipe_logger_exit
    self.wait()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 57, in wait
    self._wait_hook()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 161, in _wait_hook
    self._exit_listener_stack.pop()(self)
  File "/usr/lib/portage/pym/_emerge/EbuildPhase.py", line 287, in _post_phase_exit
    self.wait()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 57, in wait
    self._wait_hook()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 161, in _wait_hook
    self._exit_listener_stack.pop()(self)
  File "/usr/lib/portage/pym/_emerge/TaskSequence.py", line 43, in _task_exit_handler
    self.wait()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 57, in wait
    self._wait_hook()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 161, in _wait_hook
    self._exit_listener_stack.pop()(self)
  File "/usr/lib/portage/pym/_emerge/CompositeTask.py", line 134, in _default_final_exit
    return self.wait()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 57, in wait
    self._wait_hook()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 161, in _wait_hook
    self._exit_listener_stack.pop()(self)
  File "/usr/lib/portage/pym/_emerge/EbuildBuild.py", line 294, in _build_exit
    self.wait()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 57, in wait
    self._wait_hook()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 161, in _wait_hook
    self._exit_listener_stack.pop()(self)
  File "/usr/lib/portage/pym/_emerge/CompositeTask.py", line 134, in _default_final_exit
    return self.wait()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 57, in wait
    self._wait_hook()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 161, in _wait_hook
    self._exit_listener_stack.pop()(self)
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1318, in _build_exit
    self._task_queues.merge.add(merge)
  File "/usr/lib/portage/pym/_emerge/SequentialTaskQueue.py", line 23, in add
    self.schedule()
  File "/usr/lib/portage/pym/_emerge/SequentialTaskQueue.py", line 45, in schedule
    task.start()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 30, in start
    self._start()
  File "/usr/lib/portage/pym/_emerge/PackageMerge.py", line 43, in _start
    self._start_task(task, self._default_final_exit)
  File "/usr/lib/portage/pym/_emerge/CompositeTask.py", line 151, in _start_task
    task.start()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 30, in start
    self._start()
  File "/usr/lib/portage/pym/_emerge/EbuildMerge.py", line 34, in _start
    self._start_task(merge_task, self._merge_exit)
  File "/usr/lib/portage/pym/_emerge/CompositeTask.py", line 151, in _start_task
    task.start()
  File "/usr/lib/portage/pym/_emerge/AsynchronousTask.py", line 30, in start
    self._start()
  File "/usr/lib/portage/pym/portage/dbapi/_MergeProcess.py", line 55, in _start
    super(MergeProcess, self)._start()
  File "/usr/lib/portage/pym/_emerge/SpawnProcess.py", line 89, in _start
    retval = self._spawn(self.args, **kwargs)
  File "/usr/lib/portage/pym/portage/dbapi/_MergeProcess.py", line 139, in _spawn
    counter = self.vartree.dbapi.counter_tick()
  File "/usr/lib/portage/pym/portage/dbapi/vartree.py", line 870, in counter_tick
    return self.counter_tick_core(incrementing=1, mycpv=mycpv)
  File "/usr/lib/portage/pym/portage/dbapi/vartree.py", line 966, in counter_tick_core
    write_atomic(self._counter_path, str(counter))
  File "/usr/lib/portage/pym/portage/util/__init__.py", line 1258, in write_atomic
    f.close()
  File "/usr/lib/portage/pym/portage/util/__init__.py", line 1211, in close
    apply_stat_permissions(f.name, os.stat(real_name))
  File "/usr/lib/portage/pym/portage/__init__.py", line 224, in __call__
    rval = self._func(*wrapped_args, **wrapped_kwargs)
OSError: [Errno 5] Input/output error: '/var/cache/edb/counter'


Last edited by naviehuynh on Mon Dec 31, 2012 11:00 am; edited 1 time in total
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gabrielg
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Joined: 16 Nov 2012
Posts: 87

PostPosted: Sun Dec 30, 2012 2:53 pm    Post subject: Reply with quote

Can you access /var at all? Try
Code:

echo test > /var/cache/edb/foo ; cat /var/cache/edb/foo

and post the output.

I'm assuming that you checked that you haven't run out of space or inodes (where applicable). Test with df -k and df -i respectively.
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naviehuynh
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Joined: 20 Dec 2012
Posts: 15

PostPosted: Sun Dec 30, 2012 3:43 pm    Post subject: Reply with quote

gabrielg wrote:
Can you access /var at all? Try
Code:

echo test > /var/cache/edb/foo ; cat /var/cache/edb/foo

and post the output.

I'm assuming that you checked that you haven't run out of space or inodes (where applicable). Test with df -k and df -i respectively.


Hi,
I have checked the inodes and space usage, they're 56% and 55% respectively.
I can access the foo file as you suggested too:

Code:
test
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BillWho
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Posts: 1600
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PostPosted: Sun Dec 30, 2012 5:19 pm    Post subject: Reply with quote

naviehuynh,

Try eix-sync && emerge portage. If you don't have eix installed then emerge --sync && emerge portage.

Then check the permissions of counter
Code:
xen edb # stat /var/cache/edb/counter
  File: '/var/cache/edb/counter'
  Size: 4            Blocks: 8          IO Block: 4096   regular file
Device: 805h/2053d   Inode: 297728      Links: 1
Access: (0644/-rw-r--r--)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2012-12-30 08:23:39.000000000 -0500
Modify: 2012-12-30 08:23:39.000000000 -0500
Change: 2012-12-30 08:23:39.000000000 -0500
 Birth: -
xen edb #

_________________
Good luck :wink:

Since installing gentoo, my life has become one long emerge :)
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naviehuynh
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PostPosted: Sun Dec 30, 2012 6:01 pm    Post subject: Reply with quote

Hi BillWho,
It fixed the problem, but I think I got another issue :P

Code:
 * Package:    dev-libs/gobject-introspection-1.34.2-r1
 * Repository: gentoo
 * Maintainer: gnome@gentoo.org
 * USE:        elibc_glibc kernel_linux python_single_target_python2_7 python_targets_python2_7 userland_GNU x86
 * FEATURES:   sandbox
>>> Unpacking source...
>>> Unpacking gobject-introspection-1.34.2.tar.xz to /var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work
>>> Source unpacked in /var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work
>>> Preparing source in /var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work/gobject-introspection-1.34.2 ...
 * Applying gobject-introspection-1.34.2-better-traceback.patch ...
 [ ok ]
 * Fixing OMF Makefiles ...
 [ ok ]
 * Disabling deprecation warnings ...
 [ ok ]
 * Running elibtoolize in: gobject-introspection-1.34.2/build-aux/
 *   Applying portage/1.2.0 patch ...
 *   Applying sed/1.5.6 patch ...
 *   Applying as-needed/2.4.2 patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work/gobject-introspection-1.34.2 ...
 * econf: updating gobject-introspection-1.34.2/build-aux/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating gobject-introspection-1.34.2/build-aux/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-silent-rules --disable-dependency-tracking --disable-static YACC=/usr/bin/yacc --disable-doctool --disable-tests --disable-gtk-doc --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make supports nested variables... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether i686-pc-linux-gnu-gcc accepts -g... yes
checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of i686-pc-linux-gnu-gcc... none
checking whether i686-pc-linux-gnu-gcc and cc understand -c and -o together... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld
checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r
checking for i686-pc-linux-gnu-objdump... i686-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for i686-pc-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar
checking for archiver @FILE support... @
checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip
checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib
checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok
checking for sysroot... no
checking for i686-pc-linux-gnu-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if i686-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if i686-pc-linux-gnu-gcc static flag -static works... yes
checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if i686-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for i686-pc-linux-gnu-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for bison... /usr/bin/yacc
checking for dlopen in -ldl... yes
checking for the suffix of shared libraries... .so
checking for GLIB... yes
checking for GOBJECT... yes
checking for GMODULE... yes
checking for GIO... yes
checking for GIO_UNIX... yes
checking for SCANNER... yes
checking for FFI... yes
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of long... 4
checking for GIREPO... yes
checking for gtkdoc-check... no
checking for gtkdoc-rebase... /usr/bin/gtkdoc-rebase
checking for gtkdoc-mkpdf... no
checking whether to build gtk-doc documentation... no
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for working strtod... yes
checking for memchr... yes
checking for strchr... yes
checking for strspn... yes
checking for strstr... yes
checking for strtol... yes
checking for strtoull... yes
checking for backtrace... yes
checking for backtrace_symbols... yes
checking whether /usr/bin/python2.7 version >= 2.5... yes
checking for /usr/bin/python2.7 version... 2.7
checking for /usr/bin/python2.7 platform... linux2
checking for /usr/bin/python2.7 script directory... ${prefix}/lib/python2.7/site-packages
checking for /usr/bin/python2.7 extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for headers required to compile python extensions... not found
configure: error: Python headers not found

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work/gobject-introspection-1.34.2/config.log
 * ERROR: dev-libs/gobject-introspection-1.34.2-r1 failed (configure phase):
 *   econf failed
 *
 * Call stack:
 *          ebuild.sh, line   93:  Called src_configure
 *        environment, line 3299:  Called gnome2_src_configure
 *        environment, line 2333:  Called econf '--disable-static' 'YACC=/usr/bin/yacc' '--disable-doctool' '--disable-tests' '--disable-gtk-doc' '--disable-maintainer-mode'
 *   phase-helpers.sh, line  505:  Called die
 * The specific snippet of code:
 *            die "econf failed"
 *
 * If you need support, post the output of `emerge --info '=dev-libs/gobject-introspection-1.34.2-r1'`,
 * the complete build log and the output of `emerge -pqv '=dev-libs/gobject-introspection-1.34.2-r1'`.
 * The complete build log is located at '/var/log/portage/logs/dev-libs:gobject-introspection-1.34.2-r1:20121230-174206.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work/gobject-introspection-1.34.2'
 * S: '/var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work/gobject-introspection-1.34.2'


you can check the file /var/tmp/portage/dev-libs/gobject-introspection-1.34.2-r1/work/gobject-introspection-1.34.2/config.log at
http://pastebin.com/u3dA0nm4


Last edited by naviehuynh on Sun Dec 30, 2012 6:13 pm; edited 2 times in total
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BillWho
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PostPosted: Sun Dec 30, 2012 6:08 pm    Post subject: Reply with quote

naviehuynh,

It looks like a misssng version of python :?

See if emerge -av =dev-lang/python-2.7.3-r2 takes care of it :wink:
_________________
Good luck :wink:

Since installing gentoo, my life has become one long emerge :)
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naviehuynh
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PostPosted: Sun Dec 30, 2012 6:17 pm    Post subject: Reply with quote

BillWho, you are just awesome!
but how did you figure out it was python?
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BillWho
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PostPosted: Sun Dec 30, 2012 6:22 pm    Post subject: Reply with quote

naviehuynh wrote:
BillWho, you are just awesome!
but how did you figure out it was python?


Look at the messages just before the failure
Code:
checking for /usr/bin/python2.7 script directory... ${prefix}/lib/python2.7/site-packages
checking for /usr/bin/python2.7 extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for headers required to compile python extensions... not found
configure: error: Python headers not found

Not found provides the crucial clue :wink:
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Since installing gentoo, my life has become one long emerge :)
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naviehuynh
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PostPosted: Sun Dec 30, 2012 6:40 pm    Post subject: Reply with quote

ok, I looked into the error messages more carefully this time but still cant find any useful clue(yet another problem found :D ) :

Code:
navieh-ThinkPad-T410 modules # emerge --update --deep --newuse world
Calculating dependencies... done!
>>> Verifying ebuild manifests
>>> Running pre-merge checks for x11-base/xorg-server-1.13.1
>>> Running pre-merge checks for kde-base/kdelibs-4.9.4-r1
>>> Starting parallel fetch
>>> Emerging (1 of 47) app-admin/eselect-qtgraphicssystem-1.1.1
>>> Jobs: 0 of 47 complete, 1 running               Load avg: 0.38, 0.62, 0.69
Traceback (most recent call last):
  File "/usr/bin/emerge", line 48, in <module>
    retval = emerge_main()
  File "/usr/lib/portage/pym/_emerge/main.py", line 1044, in emerge_main
    gc_locals=locals().clear)
  File "/usr/lib/portage/pym/_emerge/actions.py", line 3885, in run_action
    myopts, myaction, myfiles, spinner)
  File "/usr/lib/portage/pym/_emerge/actions.py", line 464, in action_build
    retval = mergetask.merge()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1011, in merge
    rval = self._merge()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1396, in _merge
    self._main_loop()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1363, in _main_loop
    self._schedule()
  File "/usr/lib/portage/pym/_emerge/PollScheduler.py", line 125, in _schedule
    self._schedule_tasks()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1564, in _schedule_tasks
    if self._schedule_tasks_imp():
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1642, in _schedule_tasks_imp
    task = self._task(pkg)
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1682, in _task
    operation="uninstall")
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1949, in _pkg
    metadata = zip(db_keys, db.aux_get(cpv, db_keys, myrepo=myrepo))
  File "/usr/lib/portage/pym/portage/dbapi/vartree.py", line 702, in aux_get
    mydata.update(self._aux_get(mycpv, aux_keys, st=mydir_stat))
  File "/usr/lib/portage/pym/portage/dbapi/vartree.py", line 734, in _aux_get
    raise KeyError(mycpv)
KeyError: 'app-admin/eselect-pinentry-0.3'
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BillWho
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PostPosted: Sun Dec 30, 2012 6:50 pm    Post subject: Reply with quote

naviehuynh,

Since I've never encountered so many errors with an emerge update I suspect something else is awry here.

Did you set your profile to desktop or desktop/gnome etc. :?: Not having the necessary use flags set will cause unusual errors. If you haven't set it, please do so now.

I also see a check for x11-base/xorg-server-1.13.1 when x11-base/xorg-server-1.13.0-r1 is the latest stable version. Did you add packages to package.accept_keywords or change ACCEPT_KEYWORDS in make.conf :?:

Mixing repos can cause errors if you're not careful :wink:

Paste back emerge --info to get a better idea of how your setup is configured.
_________________
Good luck :wink:

Since installing gentoo, my life has become one long emerge :)
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naviehuynh
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PostPosted: Sun Dec 30, 2012 7:02 pm    Post subject: Reply with quote

hmm, I guess you still remember this thread (http://forums.gentoo.org/viewtopic-t-946314.html).

I needed to install KDE (Stable version or not, whatever is ok, I just need to get Gentoo work first and learn further later).
So I added this line to package.use

Code:
dev-python/PyQt4 webkit declarative sql script


and created accept_keywords file with following content:
Code:
sys-fs/udev
sys-apps/kmod
sys-apps/hwids
sys-fs/udev-init-scripts
virtual/udev

In addition, I added
Code:
ACCEPT_KEYWORDS="~x86"

to the make.conf file
I wonder if I should add the line ACCEPT_KEYWORDS="~x86", I was lazy back then, so I think something global might slow down my gentoo but at least could run =|

And then more issues appear as you see in this thread. What should I do now?
btw, here is the emerge --info you asked for:

Code:

Portage 2.1.11.38 (default/linux/x86/10.0/desktop, gcc-4.5.4, glibc-2.16.0, 3.5.0-17-generic i686)
=================================================================
System uname: Linux-3.5.0-17-generic-i686-Intel-R-_Core-TM-_i7_CPU_M_620_@_2.67GHz-with-gentoo-2.2
Timestamp of tree: Sun, 30 Dec 2012 17:30:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p39-r1
dev-lang/python:          2.7.3-r3, 3.2.3-r2
dev-util/pkgconfig:       0.27.1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.12.6
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.5.4, 4.6.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.7 (virtual/os-headers)
sys-libs/glibc:           2.16.0
Repositories: gentoo
ACCEPT_KEYWORDS="x86 ~x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=i686 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -march=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="-j5"
FCFLAGS="-O2 -march=i686 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -march=i686 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif gpm iconv ipv6 jpeg kde lcms ldap libnotify mad mng modules mp3 mp4 mpeg mudflap ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pppd qt3support qt4 readline sdl session spell ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 x86 xcb xml xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="EVDEV SYNAPTICS" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
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BillWho
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PostPosted: Sun Dec 30, 2012 7:19 pm    Post subject: Reply with quote

naviehuynh,

Yep, those changes introduced a myriad of inconsistencies :?

The accept_keywords file should look something like this:
Code:
#required by git-sources (argument)
sys-kernel/git-sources  ~amd64
#required by sci-geosciences/googleearth-6.0.3.2197, required by =sci-geosciences/googleearth-6.0.3.2197 (argument)
=dev-util/patchelf-0.6 ~amd64
#required by =sci-geosciences/googleearth-6.0.3.2197 (argument)
=sci-geosciences/googleearth-6.0.3.2197 ~amd64

I don't see any 'keywords' in yours :?

ACCEPT_KEYWORDS="~x86" really did you in - now you're in the testing (unstable) repos which is probably not what you expected or wanted for that matter.

I suspect though that you might be pulling udev, kmod and udev-init-scripts from the x86 repo since you're not specifying any in package.accept_keywords.

To see if things improve, remove all the entries in package.accept_keywords, cross your fingers and try emerge -uavDN @world
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Since installing gentoo, my life has become one long emerge :)
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naviehuynh
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Posts: 15

PostPosted: Sun Dec 30, 2012 7:41 pm    Post subject: Reply with quote

Hi BillWho,
emerge -uavDN @world returns the same error:
Code:

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] app-admin/eselect-qtgraphicssystem-1.1.1  USE="(-X%*) (-ipv6%*) (-nls%*) (-selinux%)" 0 kB
[ebuild  N     ] app-admin/eselect-pinentry-0.3  0 kB
[ebuild   R    ] app-portage/layman-2.0.0  USE="git%* -bazaar% -cvs% -darcs% -mercurial% -subversion% {-test%}" 0 kB
[ebuild  N     ] net-print/foomatic-filters-4.0.17  USE="cups dbus" 0 kB
[ebuild  N     ] media-plugins/gst-plugins-mpeg2dec-0.10.19:0.10  0 kB
[ebuild  N     ] media-plugins/gst-plugins-meta-0.10-r7:0.10  USE="X a52 aac alsa dts dvd flac mp3 mpeg ogg vorbis xv -dv -dvb -ffmpeg -http -lame -libvisual -mms -musepack -oss -pulseaudio -taglib -theora -v4l -vcd -vpx -wavpack" 0 kB
[ebuild     U  ] sys-fs/e2fsprogs-1.42.6 [1.42] USE="nls -static-libs" 0 kB
[ebuild  N     ] app-arch/libarchive-3.0.4-r1  USE="acl bzip2 e2fsprogs iconv lzma zlib -expat -nettle -static-libs -xattr" 0 kB
[ebuild  N     ] dev-util/cmake-2.8.10.2  USE="ncurses qt4 -emacs {-test} -vim-syntax" 0 kB
[ebuild  N     ] app-text/poppler-0.20.5  USE="cairo cxx introspection jpeg lcms png qt4 tiff utils -cjk -curl -debug -doc -jpeg2k" 0 kB
[ebuild  N     ] net-print/cups-filters-1.0.25  USE="jpeg png tiff -perl -static-libs" 0 kB
[ebuild  N     ] kde-base/oxygen-icons-4.9.4:4  USE="bindist (-aqua)" 0 kB
[ebuild  N     ] media-libs/qimageblitz-0.0.6-r1  USE="-3dnow (-altivec) -debug -mmx -sse -sse2" 0 kB
[ebuild  N     ] dev-libs/libattica-0.4.1  USE="-debug {-test}" 0 kB
[ebuild  N     ] dev-libs/libdbusmenu-qt-0.9.2  USE="-debug -doc {-test}" 0 kB
[ebuild  N     ] app-misc/strigi-0.7.7-r2  USE="dbus exif fam qt4 -clucene -debug -ffmpeg -hyperestraier -inotify (-log) {-test}" 0 kB
[ebuild  N     ] dev-util/automoc-0.9.88  0 kB
[ebuild  N    *] media-libs/phonon-9999  USE="gstreamer (-aqua) -debug -pulseaudio -vlc (-zeitgeist)" 0 kB
[ebuild  N     ] sys-power/pm-utils-1.4.1-r2  USE="alsa -debug -ntp" VIDEO_CARDS="-intel -radeon" 0 kB
[ebuild  N     ] sys-auth/polkit-0.109-r1  USE="introspection kde nls pam -examples -gtk (-selinux) (-systemd)" 0 kB
[ebuild  N     ] sys-auth/polkit-qt-0.103.0  USE="-debug -examples" 0 kB
[ebuild     U  ] virtual/udev-196 [171] USE="gudev* hwdb* introspection* keymap* (-selinux) -static-libs (-acl%*)" 0 kB
[ebuild  N     ] sys-fs/udev-init-scripts-18  0 kB
[ebuild     U  ] sys-fs/udev-196-r1 [171-r9] USE="acl%* gudev* hwdb* introspection* keymap* kmod%* openrc%* -doc% (-selinux) -static-libs% (-action_modeswitch%) (-build%) (-debug%) (-edd%) (-extras%) (-floppy%) (-rule_generator%*) (-test%)" 0 kB
[blocks b      ] <sys-fs/udev-186 ("<sys-fs/udev-186" is blocking sys-fs/udev-init-scripts-18)
[ebuild  N     ] sys-auth/consolekit-0.4.5_p20120320-r1  USE="acl pam policykit -debug -doc (-selinux) {-test}" 0 kB
[ebuild     U  ] sys-apps/util-linux-2.22.2 [2.21.2] USE="cramfs crypt ncurses nls udev* unicode -ddate -old-linux -perl (-selinux) -slang -static-libs (-uclibc%)" 0 kB
[ebuild  N     ] app-misc/media-player-info-17  0 kB
[ebuild  N     ] sys-power/upower-0.9.18  USE="introspection -debug -doc -ios (-systemd)" 0 kB
[ebuild  N     ] dev-libs/libatasmart-0.19  USE="-static-libs" 0 kB
[ebuild  N     ] sys-fs/lvm2-2.02.97-r1  USE="lvm1 readline thin udev -clvm (-cman) (-selinux) -static -static-libs" 0 kB
[ebuild  N     ] virtual/eject-0  0 kB
[ebuild  N     ] sys-fs/udisks-1.0.4-r4  USE="nls -debug -remote-access (-selinux)" 0 kB
[ebuild     U  ] x11-base/xorg-server-1.13.1 [1.13.0-r1] USE="ipv6 nptl suid udev xorg -dmx -doc -kdrive -minimal (-selinux) -static-libs -tslib -xnest -xvfb" 0 kB
[ebuild  N     ] kde-base/kdelibs-4.9.4-r1:4  USE="acl alsa bzip2 fam handbook nls opengl policykit spell ssl udev udisks upower -3dnow (-altivec) (-aqua) -debug -doc -jpeg2k -kerberos -lzma -mmx -openexr -semantic-desktop -sse -sse2 {-test} (-udisks2) (-upnp) -zeroconf" 0 kB
[ebuild  N     ] sys-auth/polkit-kde-agent-0.99.0:4  USE="(-aqua) -debug" LINGUAS="-ca -ca@valencia -cs -da -de -en_GB -eo -es -et -fi -fr -ga -gl -hr -hu -is -it -ja -km -lt -mai -ms -nb -nds -nl -pa -pt -pt_BR -ro -ru -sk -sr -sr@ijekavian -sr@ijekavianlatin -sr@latin -sv -th -tr -uk -zh_TW" 0 kB
[ebuild  N     ] kde-base/katepart-4.9.4:4  USE="handbook (-aqua) -debug" 0 kB
[ebuild  N     ] kde-misc/polkit-kde-kcmodules-0.98_pre20120917-r1:4  USE="(-aqua) -debug" 0 kB
[ebuild  N     ] kde-base/kdesu-4.9.4:4  USE="handbook (-aqua) -debug" 0 kB
[ebuild  N     ] kde-base/khelpcenter-4.9.4:4  USE="(-aqua) -debug" 0 kB
[ebuild  N     ] net-libs/libproxy-0.4.10-r1  USE="kde -gnome -mono -networkmanager -perl -python -spidermonkey {-test} -webkit" 0 kB
[ebuild  N     ] net-libs/glib-networking-2.34.2  USE="libproxy ssl -gnome -smartcard {-test}" 0 kB
[ebuild  N     ] net-libs/libsoup-2.40.2:2.4  USE="introspection ssl -debug -samba {-test}" 0 kB
[ebuild  N     ] media-plugins/gst-plugins-soup-0.10.31:0.10  0 kB
[ebuild  N    *] media-libs/phonon-gstreamer-9999  USE="alsa network -debug" 0 kB
[ebuild     U  ] sys-auth/pambase-20120417-r1 [20101024-r2] USE="consolekit* cracklib sha512 -debug -gnome-keyring -minimal -mktemp -pam_krb5 -pam_ssh -passwdqc (-selinux) -systemd%" 0 kB
[ebuild     U  ] sys-apps/shadow-4.1.5.1-r1 [4.1.4.3] USE="acl%* cracklib nls pam -audit (-selinux) -skey -xattr%" 0 kB
[blocks b      ] <sys-apps/shadow-4.1.5-r1 ("<sys-apps/shadow-4.1.5-r1" is blocking sys-auth/pambase-20120417-r1)
[ebuild     U  ] net-misc/openssh-6.1_p1 [5.9_p1-r4] USE="X* bindist hpn ldap* pam tcpd -X509 -kerberos -libedit (-selinux) -skey -static" 0 kB

Total: 47 packages (8 upgrades, 37 new, 2 reinstalls), Size of downloads: 0 kB
Conflict: 2 blocks

Would you like to merge these packages? [Yes/No] Yes
>>> Verifying ebuild manifests
>>> Running pre-merge checks for x11-base/xorg-server-1.13.1
>>> Running pre-merge checks for kde-base/kdelibs-4.9.4-r1
>>> Starting parallel fetch
>>> Emerging (1 of 47) app-admin/eselect-qtgraphicssystem-1.1.1
>>> Jobs: 0 of 47 complete, 1 running               Load avg: 0.53, 0.19, 0.17
Traceback (most recent call last):
  File "/usr/bin/emerge", line 48, in <module>
    retval = emerge_main()
  File "/usr/lib/portage/pym/_emerge/main.py", line 1044, in emerge_main
    gc_locals=locals().clear)
  File "/usr/lib/portage/pym/_emerge/actions.py", line 3885, in run_action
    myopts, myaction, myfiles, spinner)
  File "/usr/lib/portage/pym/_emerge/actions.py", line 464, in action_build
    retval = mergetask.merge()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1011, in merge
    rval = self._merge()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1396, in _merge
    self._main_loop()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1363, in _main_loop
    self._schedule()
  File "/usr/lib/portage/pym/_emerge/PollScheduler.py", line 125, in _schedule
    self._schedule_tasks()
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1564, in _schedule_tasks
    if self._schedule_tasks_imp():
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1642, in _schedule_tasks_imp
    task = self._task(pkg)
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1682, in _task
    operation="uninstall")
  File "/usr/lib/portage/pym/_emerge/Scheduler.py", line 1949, in _pkg
    metadata = zip(db_keys, db.aux_get(cpv, db_keys, myrepo=myrepo))
  File "/usr/lib/portage/pym/portage/dbapi/vartree.py", line 702, in aux_get
    mydata.update(self._aux_get(mycpv, aux_keys, st=mydir_stat))
  File "/usr/lib/portage/pym/portage/dbapi/vartree.py", line 734, in _aux_get
    raise KeyError(mycpv)
KeyError: 'app-admin/eselect-pinentry-0.3'


Yeah, I didn't really understand keywords back then, so I made a "stupid" package.accept_keywords file :@)
So, just to confirm I dont mistake anything, x86 and ~x86 are different: x86 is the stable trunk while ~x86 is the testing branch
I was in the x86 branch in the first place, since I chose to install KDE "emerge -av kde-meta", it asked for some packages in ~x86. So I just need to declare some keywords for those packages
However, what I did was to add ~x86 to the ACCEPT_KEYWORDS in make.conf file and I was like switching to the ~x86 branch. Is it also the reason why emerge --update takes such long time to finish (several hours with 320+ packages)?
What should I do now? Is it possible to switch back to either x86 or ~x86? Or is it to late to rescue things and I have to re-install Gentoo from beginning :O
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BillWho
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PostPosted: Sun Dec 30, 2012 8:49 pm    Post subject: Reply with quote

naviehuynh wrote:
So, just to confirm I dont mistake anything, x86 and ~x86 are different: x86 is the stable trunk while ~x86 is the testing branch
I was in the x86 branch in the first place, since I chose to install KDE "emerge -av kde-meta", it asked for some packages in ~x86. So I just need to declare some keywords for those packages
However, what I did was to add ~x86 to the ACCEPT_KEYWORDS in make.conf file and I was like switching to the ~x86 branch. Is it also the reason why emerge --update takes such long time to finish (several hours with 320+ packages)?

I couldn't have explained it better myself :D I think it's best to stay in ~x86 at this point.

All your current errors appear to be python related so try this first:
Code:
xen portage # eselect python list
Available Python interpreters:
  [1]   python2.7 *
  [2]   python3.2


Set it to 2.7 with eselect python set 1 as it would be #1 in the example above.

If you made any USE changes in make.conf, undo them and make sure the accept.keywords file is empty.

Then run python-updater

If that works then emerge portage again

If the above doesn't pan out there's always unpacking the stage3 and portage tarballs, but we're trying to avoid that at this point :wink:
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Since installing gentoo, my life has become one long emerge :)
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naviehuynh
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PostPosted: Mon Dec 31, 2012 6:17 am    Post subject: Reply with quote

BillWho,
Python update stops when adding the "file" packages.
Recently I ran into another problem with my root partition. It says something is corrupted while mounting /dev/sda8 and repairing with e2fsck can temporarily solve the problem, but it just randomly happens over and over again. I guess I should start over, from re-formatting the partition properly. I know it's a bad habit to re-install everything to solve a problem, but I messed up with the keywords anyway, even when I can find a workaround this time, there will be likely many other problems in the future.

I just wanna say thank you very much! I will certainly have more issues later with the new Gentoo installation; I hope I can receive your help in other threads, see ya :D
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dol-sen
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PostPosted: Mon Dec 31, 2012 4:00 pm    Post subject: Reply with quote

Code:
  File "/usr/lib/portage/pym/portage/dbapi/vartree.py", line 734, in _aux_get
    raise KeyError(mycpv)
KeyError: 'app-admin/eselect-pinentry-0.3'


It looks like there was more filesystem corruption. The above error indicates it did not find eselect-pinentry in the installed db.

It would be in /var/db/pkg/app-admin/eselect-pinentry-0.3. There should be a number of files in that directory. You should have a look through that whole installed /var/db/pkg subdir system. Look for more unusual/bad files, etc..
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