[SOLVED]Portage/GCC broken

[phobos13013]

Hello,
Back again with another complicated problem. Upon my most recent emerge --sync and kernel upgrade, my portage has become corrupted. Most notably, when i do an emerge update on world, immediately it reports that two pkgs do not have digests. I have looked into this error but it is not clear to me how to resolve it. I tried to run an emerge world to reinstall all pkgs but it failed on gcc. Now I am getting all kinds of segfaults and errors just running emerge. I have chosen a new profile to hopefully rework this and in this phase, emerge errors that one of the files with a missing digest is corrupted. It also complains about quarantine not being an empty dir but if I try to remove the file that is lsited (under glsa) it states that the file is not there although ls reports it.....

I do not really know how to start on this. Tried to emerge glibc as a start but that freezes at random points, so does gcc when it doesnt just error out.

So I have a broken Portage and GCC, I am getting segfaults and errors left and right or out and out freezes. I have analyzed all my partitions and no issues

emerge --info

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Portage 3.0.13 (python 3.7.9-final-0, default/linux/amd64/17.1/no-multilib, gcc-9.3.0, glibc-2.32-r6, 5.4.97-gentoo x86_64)
=================================================================
System uname: Linux-5.4.97-gentoo-x86_64-AMD_A4-7300_APU_with_Radeon_HD_Graphics-with-gentoo-2.7
KiB Mem:     3202268 total,   2070148 free
KiB Swap:    2008120 total,   2008120 free
Timestamp of repository gentoo: Sat, 20 Feb 2021 00:45:01 +0000
Head commit of repository gentoo: c2fba747786131f48b94f9c8c99f3fa5552fc9d8
sh bash 5.0_p18
ld GNU ld (Gentoo 2.35.1 p2) 2.35.1
app-shells/bash:          5.0_p18::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.30.3::gentoo
dev-lang/python:          3.6.12::gentoo, 3.7.9-r2::gentoo, 3.8.7-r1::gentoo, 3.9.1-r1::gentoo
dev-util/cmake:           3.18.5::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.42.1-r1::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.2-r1::gentoo
sys-devel/binutils:       2.35.1-r1::gentoo
sys-devel/gcc:            9.3.0-r2::gentoo
sys-devel/gcc-config:     2.3.2-r1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.4-r1::gentoo (virtual/os-headers)
sys-libs/glibc:           2.32-r6::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 1
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE @FREE free-noncomm freedist linux-firmware linux-fw-redistributable MPEG-4 no-source-code"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=athlon64 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe" * Missing digest for '/usr/portage/dev-libs/xmlsec/xmlsec-1.2.31.ebuild'
 * Missing digest for '/usr/portage/dev-libs/libassuan/libassuan-2.5.3.ebuild'

GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,--as-needed"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac aalib acl alsa amd64 ape ass avi berkdb bidi bzip2 cairo cdda cddb cdio cdrom cjk cli crypt dbus divx dri dts dv dvb dvd dvdread elogind encode fame ffmpeg flac fontconfig fortran freetype gdbm glib gnutls httpd iconv imlib immqt-bc ipv6 jpeg lastfm libass libglvnd libtirpc live lua mad matroska mjpeg mmx mp3 mpeg ncurses nls nptl ogg oggvorbis opengl openmp opennmp pam pcre png pulseaudio qt4 quicktime readline seccomp split-usr sse sse2 ssl stream subtitles tcpd theora tordns truetype udev unicode v4l vcd vlm vorbis wxwindows xattr xine xinerama xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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" 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="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python2_7 python3_6 python3_7 python3_8" RUBY_TARGETS="ruby26" USERLAND="GNU" VIDEO_CARDS="radeon" 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:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

here is the beginning of emerge update world

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 * Missing digest for '/usr/portage/dev-libs/xmlsec/xmlsec-1.2.31.ebuild'
* Missing digest for '/usr/portage/dev-libs/libassuan/libassuan-2.5.3.ebuild*

here is my most recent emerge –sync output

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phobos13013@NotAnonAlready ~ $ sudo emerge --sync
>>> Syncing repository 'gentoo' into '/usr/portage'...
 * Using keys from /usr/share/openpgp-keys/gentoo-release.asc
 * Refreshing keys via WKD ...                                                                                                                                                                                                                                                                                          [ ok ]
>>> Starting rsync with rsync://[2a01:90:200:10::1a]/gentoo-portage...
>>> Checking server timestamp ...
Welcome to starling.gentoo.org / rsync.gentoo.org

Server Address : 81.91.253.252, 2a01:90:200:10::1a
Contact Name   : mirror-admin@gentoo.org
Hardware       : 2 x Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz, 3946MB RAM
Sponsor        : Qube Managed Services Limited, Zurich, Switzerland, EU

Please note: common gentoo-netiquette says you should not sync more
than once a day.  Users who abuse the rsync.gentoo.org rotation
may be added to a temporary ban list.

MOTD autogenerated by update-rsync-motd on Thu Apr  4 19:07:17 UTC 2019

receiving incremental file list
timestamp.chk

Number of files: 1 (reg: 1)
Number of created files: 0
Number of deleted files: 0
Number of regular files transferred: 1
Total file size: 32 bytes
Total transferred file size: 32 bytes
Matched data: 0 bytes
File list size: 42
File list generation time: 0.001 seconds
File list transfer time: 0.000 seconds
Total bytes sent: 104
Total bytes received: 133

sent 104 bytes  received 133 bytes  67.71 bytes/sec
total size is 32  speedup is 0.14
rm: cannot remove '/usr/portage/.tmp-unverified-download-quarantine/metadata/glsa': Directory not empty
Traceback (most recent call last):
  File "/usr/lib/python3.7/site-packages/portage/util/_async/AsyncFunction.py", line 39, in _run
    result = self.target(*(self.args or []), **(self.kwargs or {}))
  File "/usr/lib/python3.7/site-packages/portage/sync/controller.py", line 165, in sync
    taskmaster.run_tasks(tasks, func, status, options=task_opts)
  File "/usr/lib/python3.7/site-packages/portage/sync/controller.py", line 65, in run_tasks
    result = getattr(inst, func)(**kwargs)
  File "/usr/lib/python3.7/site-packages/portage/sync/syncbase.py", line 338, in sync
    return self.update()
  File "/usr/lib/python3.7/site-packages/portage/sync/modules/rsync/rsync.py", line 332, in update
    dosyncuri, timestamp, opts)
  File "/usr/lib/python3.7/site-packages/portage/sync/modules/rsync/rsync.py", line 704, in _do_rsync
    command.append(self.download_dir)
  File "/usr/lib/python3.7/site-packages/portage/sync/syncbase.py", line 130, in download_dir
    self._download_dir = self.repo_storage.init_update()
  File "/usr/lib/python3.7/site-packages/portage/util/futures/_sync_decorator.py", line 22, in wrapper
    return loop.run_until_complete(func(*args, **kwargs))
  File "/usr/lib/python3.7/site-packages/portage/util/_eventloop/asyncio_event_loop.py", line 126, in _run_until_complete
    return self._loop.run_until_complete(future)
   yield self._check_call(['rm', '-rf', update_location], loop=loop)
  File "/usr/lib/python3.7/site-packages/portage/util/futures/compat_coroutine.py", line 124, in _next
    future = self._generator.send(previous.result())
  File "/usr/lib/python3.7/site-packages/portage/repository/storage/hardlink_quarantine.py", line 53, in _check_call
    format(p.returncode, ' '.join(cmd)))
portage.repository.storage.interface.RepoStorageException: command exited with status 1: rm -rf /usr/portage/.tmp-unverified-download-quarantine

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.


Action: sync for repo: gentoo, returned code = 1

not sure what else would be useful here. Any assistance is appreciated.

[phobos13013]

Just show how complex this error is, after attempting to clear space on my machine by running eclean, I get the following error:

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Traceback (most recent call last):
  File "/usr/lib/python-exec/python3.6/eclean", line 41, in <module>
    from gentoolkit.eclean.cli import main
  File "/usr/lib64/python3.6/site-packages/gentoolkit/eclean/cli.py", line 25, in <module>
    import portage
ModuleNotFoundError: No module named 'portage'

[Buffoon]

You are using wrong python. You have 4 of them installed, why not to use a supported version? And clean out the outdated ones.

[figueroa]

Maybe "emerge-webrsync" but don't just trust me. Read about it in the forums, search the Internet, etc.

[Ionen]

python3.6 support was removed entirely (minus interpreter itself), so partial rebuilds/upgrades may possibly break things still using it as everything is force-rebuilt without support even if you have it enabled.

Once rebuild python-exec won't even be able to call 3.6 stuff anymore normally, e.g. would have to call /usr/lib/python-exec/python3.6/eclean directly to use 3.6's version

[phobos13013]

Thanks for these suggestions. I went ahead and updated python, i managed to remove pkgs to the point where I could get python, python-exec and deps to build but I am still encountering these segfaults. Most notably emerge --sync (or emerge-webrsync). I cannot seem to get past my current update and it is complaining of ghost files (which are actually reported by ls but not there with rm -rf) in tmp-unverified-download-quarantine as well as mismatched pkg sizes (likely because I am segfaulting as the tree is being downloaded.

Meanwhile, I still get errors trying to reinstall gcc or a few other specific system components such as binutils or glibc.

It is such a mess. I is there any suggestion for how to proceed now that I have a current python implmentation?

[NeddySeagoon]

phobos13013,

Are there any HDD error reports in dmesg?
Put dmesg onto a pastebin. Any error mossages will be useful.

Have any oy your filesystems gone read only due to errors?
mount will show that.

Almost everything needs glibc, so lets use that as a testbed.

Run

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emerge -1a glibc 

post any on screen error messages and put the entire build log onto a pastebin.

[phobos13013]

Oh my, I know I am in trouble if NeddySeagoon is supporting!

I have really been trying to avoid confronting the possibility of a hw issue but segfaults are always a bad sign. The only hope I have at the moment is that they appear to be specific to circumstances rather than completely random. Although I am getting occasional hangs while building as well. At any rate, I was going to fiddle with the hardware a bit tonight but I will also run the requested diagnostics and report back by the day time tomorrow (GMT). I did run badblocks on most of the partitions and got zero bad sectors. In full disclosure, I have moved and this box was exposed to some cold elements for at least a few days. The HDD itself was removed and traveled as safely with me as possible but the rest of the components were in a moving bin which I am not completely aware of its path.

Anyway, I will start looking at hardware issues at this point and report back soon.

[NeddySeagoon]

phobos13013,

If badblocks ever finds anything the drive is scrap. Drives hide bad sectors by mapping in spare sectors.
Once that process fails, the drive cannot read its own writing any more.

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smartctl -x /dev/...

is a better indicator of drive health.

While you are poking at the hardware, boot into memtest86 and run a few cycles.
Any failures at all indicates a problem. It may not be RAM though, so don't replace your RAM share the errors here first.

[phobos13013]

*FACEPALM* OK, good news. Ran smartctl, first time ever honestly so not entirely sure how to inrepret all the output but didnt see anythings screaming error or failed. Also memtest passed no problems. From there I went ahead and swapped the power and sata cbls and lo and behold no problems. Now glibc built and I am going to go ahead and rebuild system pkgs with the new python implementation just to be on the safe side, consider this one halfway solved.

That said, I am still getting the emerge sync issues. Specifically this:

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file has vanished: "/usr/portage/.tmp-unverified-download-quarantine/metadata/glsa/gmsa-200703-24.xml"
cannot delete non-empty directory: .tmp-unverified-download-quarantine/metadata/glsa
cannot delete non-empty directory: .tmp-unverified-download-quarantine/metadata
cannot delete non-empty directory: .tmp-unverified-download-quarantine/metadata
cannot delete non-empty directory: .tmp-unverified-download-quarantine

and this when running emerge update:

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 * Missing digest for '/usr/portage/dev-libs/xmlsec/xmlsec-1.2.31.ebuild
* Missing digest for '/usr/portage/dev-libs/libassuan/libassuan-2.5.3.ebuild*'

I would really prefer not to reformat if this can be saved if there was some kind of write error. But what could be causing this?

[NeddySeagoon]

phobos13013,

Can you

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rm -rf /usr/portage/.tmp-unverified-download-quarantine

Its only used bf the download and metadata check.

If it fails, what are the filenames remaining?

Boot with a liveCD and run

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fsck -f /dev/...

Do not let it change anything as it can make a bad situation worse.
Post the first error it finds, if any.

-- edit --
Missing digest .. may mean that yo hit the mirror when the mirror was updating. Mirror updates are not quite atomic.

[phobos13013]

So this is the wacky thing with the rm -rf. When I try to remove the directory it says its not empty! OK but I tried to use the force to do it! When I drill down the ONLY thing left is .../metadata/glsa/gmsa-200703-24.xml (and this after MULTIPLE syncs)

For awhile it wouldnt let me delete the file because it was reporting NO SUCH FILE OR DIRECTORY (HUH?!??! you just told me it was there!!)

Now it actually let me do the rm -rf on that file (at least without reporting an error), but when I go to delete the parent directory or any level above it, its telling me DIRECTORY NOT EMPTY and the only thing left is [see above] (HUH??!? you just performed the command with no error!!)

Meanwhile, I may have synced at a freak moment in the past, but everytime I emerge sync I get the above error and then when I go to update it tells me the digests are bad. Well I have synced like 100 times in the last five days; even having to delete timestamp.x to do it a few times (please dont ban me server!!).

I will have to see if I have a liveCD still, if so its probably veeeeeeery old and thats if I didnt toss them all in my last move as I was panicing for awhile and throwing out just about everything because I wasnt sure I was going to have a place to move to.... anyway thats just personal stuff I have landed safely at least. Anyway, if I do, I will have to do it later on in the eve (US time).

[NeddySeagoon]

phobos13013,

What are the permissions on gmsa-200703-24.xml and all the directoriep above up to and including .tmp-unverified-download-quarantine ?

Its possible that gmsa-200703-24.xml picked up the immutable bit, which means what it says. Not even root can delete it.
See

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man lsattr
man chattr

No media is needed for that.

[Hu]

When run interactively, rm should report an error for an immutable file.

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/tmp# touch immut
/tmp# chattr +i immut 
/tmp# rm immut 
rm: cannot remove 'immut': Operation not permitted
/tmp# rm -f immut 
rm: cannot remove 'immut': Operation not permitted
/tmp# rm -fr immut 
rm: cannot remove 'immut': Operation not permitted
/tmp# chattr -i immut 
/tmp# rm immut 

[phobos13013]

We are definitely getting into some quantum realm stuff to my simpleton brain. That said I do not think immutability is the issue here.

The gmsa file itself reports:

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ls: cannot access '/usr/portage/.tmp-unverified-download-quarantine/metadata/glsa/gmsa-200703-24.xml': No such file or directory

Because of course. When I just ls you told me it was there....

The parent directory looks like this:

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drwxr-xr-x 2 root root 131072 Feb 19 15:50 .
drwxr-xr-x 3 root root   4096 Feb 19 15:50 ..
-????????? ? ?    ?         ?            ? gmsa-200703-24.xml

uuuuuuuuhhhhhh

From there ls reports what you would expect. No issues with the directories.

Could I have been a victim of the keypoisining issue from a few years back? I am just aware of this reading up on converting emerge --sync to emerge webrsync in the repo.conf file.

I ask because the file that is missing the libassusaun digest is a dependency of app-crypt/pinentry and app-crypt/gnupg

If i try to install the libassusuan directly:

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phobos13013@NotAnonAlready ~ $ sudo emerge @preserved-rebuild
Calculating dependencies - * Missing digest for '/usr/portage/dev-libs/xmlsec/xmlsec-1.2.31.ebuild'
 - * Missing digest for '/usr/portage/dev-libs/libassuan/libassuan-2.5.3.ebuild'
... done!

!!! All ebuilds that could satisfy ">=dev-libs/libassuan-2.1" have been masked.
!!! One of the following masked packages is required to complete your request:
- dev-libs/libassuan-2.5.4::gentoo (masked by: ~amd64 keyword)
- dev-libs/libassuan-2.5.3::gentoo (masked by: corruption)

I can only imagine xmlsec has some kind of relation considering this gmsa file is xml. And for that matter what even is gmsa???? Why is a file from 200703 in my tmp download??

[NeddySeagoon]

phobos13013,

Can you chmod the file like

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chmod 660  gmsa-200703-24.xml

Then remove it.
You may need to

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chown root:root gmsa-200703-24.xml

I have had this happen to me and I've forgotten how I tidied up the mess.
It was losing a fight with NFS that caused my problems.

Its not related to gpg key poisoning. That only stalls gpg until you delete the affected keys.
Poisoned keys are no further use to anyone.

The backstop is to rename .tmp-unverified-download-quarantine so that portage can reuse the name.

Its still worth running a fsck to look for damage. Thats not possible on a filesystem mounted read/write.
Not all features can be used on a read only filesystem, so it really needs to happen when the filesystem is not mounted.

[phobos13013]

Any attempt to even touch the file is gives me a No such file or directory and any attempt to work above the file by directory gives me a directory not empty

I couldnt find any boot disks, I think the last one I had was like 14.1 or something at best so i figured I would toss but I am not certain my burning capability works anymore. Maybe I can try a bootable usb but I will have to fiddle with that one later.

Yeah, makes sense about bad key threats, I guess that was my paranoia talking. Almost def it was the bad sata cords.

Its gonna be a *cry* to have to spend the time to reformat and rebuild.

I tried to go ahead and rebuild gnupg with the latest libassuan accepting unstable but it wont work because of the missing libassuan-2.5.3 manifest missing for some reason.

[NeddySeagoon]

phobos13013,

Is the repo on your root filesystem?
If its on another filesystem, you may be able to unmount it to check it.

/usr/portage/ can be moved anywhere you like. The location is set in /etc/portage/repos.conf/gentoo.conf
It can be abandoned and a new location populated with a new portage snapshot.
If you have /etc/portage/distfiles and/or /etc/portage/packages, their locations are still set in make.conf.

This stackexchange may help too.
Read it all, especially the bits about backups and fsck. Although they all use rm.

The key takeaway is that the filename shown by ls may not be the actual name of the file, so file does not exist is correct.

[phobos13013]

Sorry NeddySeagoon, I kinda blew by your recommendation to move the directory. Which I did, I just moved it to /tmp/why/ but is that just a symlink move? I was able to sync but now it tells me that there is a manifest mismatch for libassuan with two different blake and sha hashes. This kinda feels like a redflag to me, am I sure there is no repo chicanery? How do I resolve this manifest issue. It seems like the last step to resolution.

[EDIT]: Nevermind looks like you might have answered this before I posted, so I will look at the stackexchange and look into moving my repo.

[NeddySeagoon]

phobos13013,

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rm -rf /usr/portage/dev-libs/libassuan

Then sync to restore it and its contents.

[phobos13013]

Yes, of course, duh. And Yes unfortunately my repos are on root, I only partition based on storage considerations not functional gentoo areas. I had tried that in the past and messed it up surprise surprise.

Ok removing the libassuan in the portage repo with resync led to a number of other Manifest issue discoveries. Then it was xmlsec. Then it was zziplib (what?!), ok then cppo, then eliom, then.... (PLEASE DO NOT BAN ME REPO SERVER!!)

Its actually still going so I am going to take a break from this embarrasing process so I really do not get banned for hitting the mirrors constantly.

I can only surmise this happened when I interrupted hanging (or perhaps what I thought was hanging) emerge --syncs... I really goofed on this one. Glad its over ...............for now.

File it under solved. Lesson learned DO NOT interrupt emerge ---sync FOR SURE!

[NeddySeagoon]

phobos13013,

You can throw away your entire repo (delete it) and untar a new snapshot in its place.
That will be clean. The get up to date with a single sync.

[pjp]

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-????????? ? ?    ?         ?            ? gmsa-200703-24.xml

I'm not sure if I've seen that type of issue, but for files otherwise inaccessible and not having xattr permissions set, sometimes you can work with them by inode.

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ls -i

and

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find /path -inum <#> -exec <do something>

If you want the contents of the file, you can try to rename it, otherwise remove it by passing rm to exec.

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$ touch t/foobar
$ ls -i t/foobar 
134876 t/foobar
$ find t/ -inum 134876 -exec ls -i {} \+
134876 t/foobar
$ find t/ -inum 134876 -exec rm -i {} \+
rm: remove regular empty file 't/foobar'? y

But I wonder if the problem is beyond even that.

[Hu]

I can only surmise this happened when I interrupted hanging (or perhaps what I thought was hanging) emerge --syncs... I really goofed on this one. Glad its over ...............for now.

File it under solved. Lesson learned DO NOT interrupt emerge ---sync FOR SURE!

Interrupting emerge --sync may result in a tree that Portage will refuse to use, but it cannot cause the issue here. This looks to me like filesystem corruption.