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detroy
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Joined: 29 Apr 2013
Posts: 6
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 Posted: Mon Apr 29, 2013 12:22 am Post subject: [SOLVED]Cannot upgrade sys-apps/usbutils. |
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snapshot-20130427
Just doing "emerge --update --deep --newuse --with-bdeps=y world"
while installing usbutils with portage 2.1.11.62, I got the following output that Google Can't answer. 
| Code: |
……
make[2]: Leaving directory `/var/tmp/portage/sys-apps/usbutils-006-r1/work/usbutils-006'
make[1]: Leaving directory `/var/tmp/portage/sys-apps/usbutils-006-r1/work/usbutils-006'
>>> Completed installing usbutils-006-r1 into /var/tmp/portage/sys-apps/usbutils-006-r1/image/
strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment -R .GCC.command.line -R .note.gnu.gold-version
usr/bin/usbhid-dump
usr/bin/lsusb
ecompressdir: bzip2 -9 /usr/share/doc
ecompressdir: bzip2 -9 /usr/share/man
>>> Installing (1 of 1) sys-apps/usbutils-006-r1
Traceback (most recent call last):
File "/usr/lib64/portage/pym/portage/dbapi/_MergeProcess.py", line 230, in _spawn
prev_mtimes=self.prev_mtimes, counter=counter)
File "/usr/lib64/portage/pym/portage/dbapi/vartree.py", line 4794, in merge
counter=counter)
File "/usr/lib64/portage/pym/portage/dbapi/vartree.py", line 3611, in treewalk
retval = self._security_check(others_in_slot)
File "/usr/lib64/portage/pym/portage/dbapi/vartree.py", line 3384, in _security_check
s = os.lstat(path)
File "/usr/lib64/portage/pym/portage/__init__.py", line 246, in __call__
rval = self._func(*wrapped_args, **wrapped_kwargs)
OSError: [Errno 22] Invalid argument: '/usr/share/doc/usbutils-006/ChangeLog.bz2'
>>> Failed to install sys-apps/usbutils-006-r1, Log file:
>>> '/var/tmp/portage/sys-apps/usbutils-006-r1/temp/build.log'
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Tried to unmerge usbutils, no success...I had to mask usbutils-006-r1 to do world updating.
Anyone please tell how to fix this? 
==================================================
After running python-updater && revdep-rebuild, the problem happens still the same.
emerge --info =sys-apps/usbutils-006-r1
| Code: | Portage 2.1.11.62 (default/linux/amd64/13.0/desktop/kde, gcc-4.6.3, glibc-2.15-r3, 3.7.9-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-3.7.9-gentoo-x86_64-Intel-R-_Core-TM-_i7-2630QM_CPU_@_2.00GHz-with-gentoo-2.2
KiB Mem: 16380268 total, 1681812 free
KiB Swap: 2097148 total, 2097044 free
Timestamp of tree: Sun, 28 Apr 2013 00:45:01 +0000
ld GNU ld (GNU Binutils) 2.22
app-shells/bash: 4.2_p37
dev-lang/python: 2.7.3-r3, 3.2.3-r2
dev-util/cmake: 2.8.10.2-r2
dev-util/pkgconfig: 0.28
sys-apps/baselayout: 2.2
sys-apps/openrc: 0.11.8
sys-apps/sandbox: 2.5
sys-devel/autoconf: 2.13, 2.69
sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6
sys-devel/binutils: 2.22-r1
sys-devel/gcc: 4.6.3
sys-devel/gcc-config: 1.7.3
sys-devel/libtool: 2.4-r1
sys-devel/make: 3.82-r4
sys-kernel/linux-headers: 3.7 (virtual/os-headers)
sys-libs/glibc: 2.15-r3
Repositories: gentoo sunrise
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -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 webrsync-gpg"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="gentoo.aditsu.net:8000"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j6"
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="/var/lib/layman/sunrise"
SYNC=""
USE="X a52 aac acl acpi alsa amd64 avx berkdb branding bzip2 cairo cdda cdr cjk cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif gpm gtk iconv ipv6 jpeg kde kipi lame lcms ldap libnotify lm_sensors mad mmx mmxext mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds pulseaudio qt3support qt4 readline sdl semantic-desktop session spell sqlite sse sse2 sse4_1 sse4_2 ssl ssse3 startup-notification svg symlink tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci 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 author" 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" LINGUAS="en en_GB en_US zh_CN" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="x86_64 i386" QEMU_USER_TARGETS="x86_64 i386" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="intel nvidia" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON |
Last edited by detroy on Mon Apr 29, 2013 10:45 am; edited 2 times in total |
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Navar
Guru
Joined: 20 Aug 2012
Posts: 353
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| Posted: Mon Apr 29, 2013 3:41 am Post subject: |
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Hi, detroy
An unemerge probably won't work because the build errored out of the install portion. There is likely nothing to remove.
Please provide output for the following:
In a separate post (or edit into your first) your original emerge with --tree option.
Then,
| Code: | | emerge --info =sys-apps/usbutils-006-r1 |
Or just emerge --info if the above didn't work.
| Code: | | eselect python list |
| Code: | | eselect python list --python3 |
| Code: | | eselect profile list |
Your profile output should show, but is this hardened Gentoo with selinux?
Just as a clarification due to your snapshot reference, this is a new install? If not, when did you last run python-updater?
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detroy
n00b
Joined: 29 Apr 2013
Posts: 6
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| Posted: Mon Apr 29, 2013 5:47 am Post subject: |
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Thanks for the tips, the profile is
| Code: | [5] default/linux/amd64/13.0/desktop/kde *
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Python set to
emerge --info =sys-apps/usbutils-006-r1
| Code: | ... done!
[ebuild U ] sys-apps/usbutils-006-r1 [006] USE="zlib -python" PYTHON_SINGLE_TARGET="python2_7%*" PYTHON_TARGETS="python2_7%*" 0 kB
Total: 1 package (1 upgrade), Size of downloads: 0 kB
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About one and a half month ago, I did a full system update, may be there is new python update in snapshot-20130427 ? 
I'll try python-updater after my computer completing the current emerge task, then post the results. Still 75 packages left for compiling... |
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Navar
Guru
Joined: 20 Aug 2012
Posts: 353
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| Posted: Mon Apr 29, 2013 7:25 am Post subject: |
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| detroy wrote: | emerge --info =sys-apps/usbutils-006-r1
| Code: | ... done!
[ebuild U ] sys-apps/usbutils-006-r1 [006] USE="zlib -python" PYTHON_SINGLE_TARGET="python2_7%*" PYTHON_TARGETS="python2_7%*" 0 kB
Total: 1 package (1 upgrade), Size of downloads: 0 kB
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If python-updater doesn't resolve the problem, your output there appears to have been missing the --info option when actually ran. It should have looked something like:
| Quote: |
$ emerge --info =sys-apps/usbutils-006-r1
Portage 2.1.11.62 (default/linux/amd64/13.0, gcc-4.6.3, glibc-2.15-r3, 3.7.10-gentoo-r1 x86_64)
=================================================================
System Settings
=================================================================
/\ [...snip... lots of details here we want to see...]
||
\/
=================================================================
Package Settings
=================================================================
sys-apps/usbutils-006-r1 was built with the following:
USE="zlib -python" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7"
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If you don't get that, then just try an emerge --info by itself to post the output of.
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detroy
n00b
Joined: 29 Apr 2013
Posts: 6
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| Posted: Mon Apr 29, 2013 7:39 am Post subject: |
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Updated.
Still same problem, repost emerge --info sys-apps/usbutils information. |
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Navar
Guru
Joined: 20 Aug 2012
Posts: 353
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| Posted: Mon Apr 29, 2013 9:06 am Post subject: Re: Cannot upgrade sys-apps/usbutils. |
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| detroy wrote: | snapshot-20130427
>>> Installing (1 of 1) sys-apps/usbutils-006-r1
Traceback (most recent call last):
File "/usr/lib64/portage/pym/portage/dbapi/_MergeProcess.py", line 230, in _spawn
prev_mtimes=self.prev_mtimes, counter=counter)
File "/usr/lib64/portage/pym/portage/dbapi/vartree.py", line 4794, in merge
counter=counter)
File "/usr/lib64/portage/pym/portage/dbapi/vartree.py", line 3611, in treewalk
retval = self._security_check(others_in_slot)
File "/usr/lib64/portage/pym/portage/dbapi/vartree.py", line 3384, in _security_check
s = os.lstat(path)
File "/usr/lib64/portage/pym/portage/__init__.py", line 246, in __call__
rval = self._func(*wrapped_args, **wrapped_kwargs)
OSError: [Errno 22] Invalid argument: '/usr/share/doc/usbutils-006/ChangeLog.bz2'
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Something isn't adding up to me here.
ls -ald /usr/share/doc/usb* shows what? The argument above for the path shows older usbutils-006 instead of /usr/share/doc/usbutils-006-r1/ChangeLog.bz2.
You have no rsync server set. So you do not emerge --sync to update your copy of the portage tree? You picked an interesting date, a lot of changes happened on 4/27, newer portage, baselayout, icu, e2fsprogs, tar, kbuild, libxml and of course usbutils.
_________________
Ph'nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn.
Last edited by Navar on Mon Apr 29, 2013 9:25 am; edited 1 time in total |
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detroy
n00b
Joined: 29 Apr 2013
Posts: 6
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| Posted: Mon Apr 29, 2013 9:13 am Post subject: |
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That bothers Me too.
ls -ald /usr/share/doc/usb*
| Code: | | drwxr-xr-x 2 root root 103 Feb 23 19:25 /usr/share/doc/usbutils-006 |
That is my old 006 usbutils directory.
Why it is not usbutils-006-r1? No clue... I 'm a networker, not developer tho. 
And yes I have no rsync server set, I prefer gpg-verified snapshots, emerge-webrsync it is.
All other upgrading thing done and rebooted, going all well, guess I'll just wait for new updates of usbutils. |
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Navar
Guru
Joined: 20 Aug 2012
Posts: 353
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| Posted: Mon Apr 29, 2013 9:38 am Post subject: |
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| detroy wrote: | | drwxr-xr-x 2 root root 103 Feb 23 19:25 /usr/share/doc/usbutils-006 |
 Dunno what filesystem (reiser?) you're using, but that definitely doesn't look right to me. Default is usually a size of 4096 (4k) for directory inodes for ext fs types if I recall correctly.
For giggles if and only if this is an ext2/3/4 file system /usr is mounted on (and e2fsprogs-libs was updated...), please humor me by touch /forcefsck, then sync, reboot, pray and check the ls -ald output from /usr/share/doc/usb* again which hopefully will be corrected and lstat will act sane along with your emerge.
Otherwise, failing that, I think someone more knowledgeable, like Ssuominen, may need to jump in.
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detroy
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Joined: 29 Apr 2013
Posts: 6
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| Posted: Mon Apr 29, 2013 9:57 am Post subject: |
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XFS file system. 
Directory seems fine, I can access it from both CLI and KDE.
Wait, While I check the usbutils-006 dir under CLI, there is an red flashy file.
| Code: |
?????????? ? ? ? ? ? ChangeLog.bz2
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Could that be the problem?
How does that Happen?
Since that file can't be deleted, I'll try remove the whole usbutils-006 directory and fix it.
=====
Edited for typos...
Last edited by detroy on Mon Apr 29, 2013 10:35 am; edited 1 time in total |
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Navar
Guru
Joined: 20 Aug 2012
Posts: 353
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| Posted: Mon Apr 29, 2013 10:13 am Post subject: |
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http://xfs.org/index.php/XFS_FAQ makes mention of:
Q: Why some files of my filesystem shows as "?????????? ? ? ? ? ? filename" ?
followed by,
ls: cannot access /pathtodir/file1: Invalid argument or
failed to stat /pathtodir/file1 (sound familiar?)
| Quote: | It is very probable your filesystem must be mounted with inode64
# mount -oremount,inode64 /dev/diskpart /mnt/xfs
should make it work ok again. If it works, add the option to fstab. |
If this resolves things for you, please mark this thread [solved] in the title so I can scrub my brain cells free of XFS details. 
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detroy
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Joined: 29 Apr 2013
Posts: 6
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| Posted: Mon Apr 29, 2013 10:44 am Post subject: |
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Oh No!
I don't have a disk with 100TB, I wish though.
The problem is not inode64, since I only have ONE 750GB Harddrive.
Here's how I fix it.
1. Pull out my long-trusty system-rescue-cd, set the bios.
2. No luck, cause that cd has a long fissure I didn't see for the first time...
3. Then I find out another liveCD(linux mint), then boot...
4. Run xfs_repair /dev/rootpartition, then it told me that the wrong index entry of changelog.bz2 has been fixed.
reboot
emerge-webrsync ----->snapshots-20130428
emerge --update --newuse --deep --with-bdeps=y world
Voila, usbutils-006-r1 had just been installed successfully.
====================================
Now, it is solved, totally irrelevant with python or portage or profile... |
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Navar
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Joined: 20 Aug 2012
Posts: 353
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| Posted: Mon Apr 29, 2013 11:57 am Post subject: |
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| Quote: | | Now, it is solved, totally irrelevant with python or portage or profile |
Uh, you're welcome I think... Problem is that error was possible with either of the 3 (hint--google OSError: [Errno 22] Invalid argument), except when the underlying base layer they depend upon was broken.  Just had to dig with magnifying glass and some luck to find.
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