Corrupt/missing store items

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From: Jack Hill <jackhill@jackhill.us>
To: help-guix@gnu.org
Subject: Corrupt/missing store items
Date: Mon, 21 Jun 2021 14:30:20 -0400 (EDT)	[thread overview]
Message-ID: <alpine.DEB.2.21.2106211418560.2109@marsh.hcoop.net> (raw)

Hi Guix,

I could use some help figuring out what's happened to my store and how to 
recover.

I first noticed the problem when trying to check if a package build 
reproducably. Unfortunately, I did not capture the output from that, but 
did capture subsequent commands. It seems as if the metadata has gotten 
out of sync with the store:

jackhill@kalessin ~$ guix gc --verify
reading the store...
checking path existence...
path `/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16' disappeared, but it still has valid referrers!

jackhill@kalessin ~$ guix build /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv
The following graft will be made:
    /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv
applying 1 graft for /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv ...
grafting '/gnu/store/199npi1hcv7zn0r19vl29np6ccshii4p-gnutls-3.6.16-debug' -> '/gnu/store/2vjql2vd6srqxhr0r9xnhclqgc5kxlh1-gnutls-3.6.16-debug'...
grafting '/gnu/store/8ixa3p7hwb26warjinffcrvzl064wbcg-gnutls-3.6.16-doc' -> '/gnu/store/ads39f4czri8s1k43qd0qpxi6dr3w0zn-gnutls-3.6.16-doc'...
grafting '/gnu/store/akc7l65z459pnifrr6bcm97cjvmpvp9k-gnutls-3.6.16' -> '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16'...
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/certtool'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/gnutls-cli'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/gnutls-cli-debug'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/gnutls-serv'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/ocsptool'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/psktool'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/srptool'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/guile/3.0/extensions/guile-gnutls-v-2.so.0.0.0'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/guile/3.0/site-ccache/gnutls.go'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/guile/3.0/site-ccache/gnutls/extra.go'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/libgnutls.so.30.28.2'
updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/libgnutlsxx.so.28.1.0'
successfully built /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv
/gnu/store/2vjql2vd6srqxhr0r9xnhclqgc5kxlh1-gnutls-3.6.16-debug
/gnu/store/ads39f4czri8s1k43qd0qpxi6dr3w0zn-gnutls-3.6.16-doc
/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16
jackhill@kalessin ~$ guix gc --verify                                                      reading the store...
checking path existence...
path `/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16' disappeared, but it still has valid referrers!
jackhill@kalessin ~$ ls -l /gnu/store/^C
^C^C
jackhill@kalessin ~$ ls -l /gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16
ls: cannot access '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16': No such file or directory

Then, I ran `guix gc` to collect all the garbage. Trying to rebuild the gnutls derivation results in:

jackhill@kalessin ~$ guix build /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv
18.6 MB will be downloaded:
    /gnu/store/2wrp7x9aclqsapm58dz5i654qds8nbb8-guile-2.0.14
    /gnu/store/mz5fvdfks10rmwxf29n95bp9bim6wq7g-nettle-3.5.1
    /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31
    /gnu/store/s3dcqzwqaakv1yx37by9chksdbkgih17-glibc-2.31-static
    /gnu/store/199npi1hcv7zn0r19vl29np6ccshii4p-gnutls-3.6.16-debug
    /gnu/store/8ixa3p7hwb26warjinffcrvzl064wbcg-gnutls-3.6.16-doc
    /gnu/store/akc7l65z459pnifrr6bcm97cjvmpvp9k-gnutls-3.6.16
The following graft will be made:
    /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv
substituting /gnu/store/2wrp7x9aclqsapm58dz5i654qds8nbb8-guile-2.0.14...
Backtrace:
In ice-9/boot-9.scm:
   1752:10 19 (with-exception-handler _ _ #:unwind? _ # _)
   1752:10 18 (with-exception-handler _ _ #:unwind? _ # _)
In guix/scripts/substitute.scm:
    771:15 17 (_)
In ice-9/exceptions.scm:
    406:15 16 (process-substitution #<output: file 4> _ "/gnu/store/…" …)
In ice-9/boot-9.scm:
   1752:10 15 (with-exception-handler _ _ #:unwind? _ # _)
In guix/scripts/substitute.scm:
     479:9 14 (_)
In ice-9/boot-9.scm:
   1747:15 13 (with-exception-handler #<procedure 7fb7171635a0 at ic…> …)
In guix/scripts/substitute.scm:
    408:14 12 (_)
    382:28 11 (_ #<<uri> scheme: https userinfo: #f host: "ci.guix.g…> …)
In guix/build/download.scm:
     453:4 10 (open-connection-for-uri _ #:timeout _ # _)
     251:2  9 (tls-wrap #<input-output: socket 14> "ci.guix.gnu.org" # …)
    164:15  8 (load-gnutls)
In ice-9/boot-9.scm:
    3329:6  7 (resolve-interface (gnutls) #:select _ #:hide _ #:prefix …)
   1685:16  6 (raise-exception _ #:continuable? _)
   1683:16  5 (raise-exception _ #:continuable? _)
   1685:16  4 (raise-exception _ #:continuable? _)
   1780:13  3 (_ #<&compound-exception components: (#<&error> #<&orig…>)
   1685:16  2 (raise-exception _ #:continuable? _)
   1683:16  1 (raise-exception _ #:continuable? _)
   1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
no code for module (gnutls)
substitution of /gnu/store/2wrp7x9aclqsapm58dz5i654qds8nbb8-guile-2.0.14 failed
guix build: error: corrupt input while restoring archive from #<closed: file 7f6110e16150>

Both /gnu and /var/guix are on the same btrfs filesystem. I ran a btrfs 
scrub, and that did not turn up any errors. The other "interesting" thing 
about this system, is that it once had deduplication turned off, but that 
has since been turned back on because of bug 47115 [0].

[0] https://issues.guix.gnu.org/47115

Best,
Jack

next             reply	other threads:[~2021-06-21 18:36 UTC|newest]

Thread overview: 7+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-06-21 18:30 Jack Hill [this message]
2021-06-21 20:28 ` Corrupt/missing store items Jack Hill
2021-06-22  8:20   ` Christopher Baines
2021-06-22 13:21     ` Jack Hill
2021-06-22 13:45       ` Jack Hill
2021-06-22 18:46   ` Ricardo Wurmus
2021-06-22 19:29     ` Jack Hill

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