* guix pull error: symlink
@ 2018-12-14 12:03 Giovanni Biscuolo
2018-12-16 4:31 ` Chris Marusich
0 siblings, 1 reply; 4+ messages in thread
From: Giovanni Biscuolo @ 2018-12-14 12:03 UTC (permalink / raw)
To: help-guix
[-- Attachment #1: Type: text/plain, Size: 781 bytes --]
Hi,
don't know how but I someway, sometime, messed up permissions in my
normal user home and some files/dirs were owned by root [1]
now I changed the owner of my entire $HOME but "guix pull" still gives
me this error:
--8<---------------cut here---------------start------------->8---
gbiscuolo@guixsdtest:~$ guix pull
Migrating profile generations to '/var/guix/profiles/per-user/gbiscuolo'...
guix pull: error: symlink: File exists: "/var/guix/profiles/per-user/gbiscuolo/current-guix-1-link"
--8<---------------cut here---------------end--------------->8---
please how can I fix this?
thanks!
Giovanni
[1] maybe I mede some error using "sudo guix..." instead of the recommended "sudo -E guix..."
--
Giovanni Biscuolo
Xelera IT Infrastructures
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 832 bytes --]
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: guix pull error: symlink
2018-12-14 12:03 guix pull error: symlink Giovanni Biscuolo
@ 2018-12-16 4:31 ` Chris Marusich
2018-12-17 12:02 ` Giovanni Biscuolo
0 siblings, 1 reply; 4+ messages in thread
From: Chris Marusich @ 2018-12-16 4:31 UTC (permalink / raw)
To: Giovanni Biscuolo; +Cc: help-guix
[-- Attachment #1: Type: text/plain, Size: 1578 bytes --]
Giovanni Biscuolo <g@xelera.eu> writes:
> gbiscuolo@guixsdtest:~$ guix pull
> Migrating profile generations to '/var/guix/profiles/per-user/gbiscuolo'...
> guix pull: error: symlink: File exists: "/var/guix/profiles/per-user/gbiscuolo/current-guix-1-link"
>
> please how can I fix this?
The failure message seems to indicate Guix failed while executing the
migrate-generations procedure (defined in guix/scripts/pull.scm).
Do symlinks like the following still exist on your system?
~/.config/guix/current-1-link
~/.config/guix/current-2-link
~/.config/guix/current-3-link
...
If so, you may be able to simply delete the following symlinks and then
run "guix pull" again:
/var/guix/profiles/per-user/gbiscuolo/current-guix-1-link
/var/guix/profiles/per-user/gbiscuolo/current-guix-2-link
/var/guix/profiles/per-user/gbiscuolo/current-guix-3-link
...
/var/guix/profiles/per-user/gbiscuolo/current
Of course, before deleting anything, please be sure to record each of
the symlinks, their permissions, and their targets so that you can undo
the deletion if necessary. Please be careful when deleting.
If all goes well, when you run "guix pull", Guix should automatically
migrate your profile generations successfully into the
/var/guix/profiles/per-user/gbiscuolo directory. After that, you won't
have to worry about it again (for the gbiscuolo user, at least).
> [1] maybe I mede some error using "sudo guix..." instead of the recommended "sudo -E guix..."
That could be. Hopefully my suggestion will help!
--
Chris
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 832 bytes --]
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: guix pull error: symlink
2018-12-16 4:31 ` Chris Marusich
@ 2018-12-17 12:02 ` Giovanni Biscuolo
2018-12-17 15:44 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Giovanni Biscuolo @ 2018-12-17 12:02 UTC (permalink / raw)
To: Chris Marusich; +Cc: help-guix
[-- Attachment #1: Type: text/plain, Size: 14824 bytes --]
Hi Chris,
your suggestion worked, thank you!
unfortunately "guix pull" failed since it started building
gcc-cross-boot-0-5.5.0.drv and was killed by OOM
note that on subsequent test I made "guix pull --dry-run" but the pull
always triggers a build:
--8<---------------cut here---------------start------------->8---
Building from this channel:
guix https://git.savannah.gnu.org/git/guix.git 1e2ebf7
Computing Guix derivation for 'x86_64-linux'... /@ build-started /gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv - x86_64-linux /var/log/guix/drvs/aw//mnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv.bz2 29475/@ build-log 29475 39
--8<---------------cut here---------------end--------------->8---
(note that meanwhile threre was a new commit in guix.git)
I'm using a QEMU VM with 1GB RAM form my testing purposes, that
configuration is definitely not suitable to build, it needs subsitutes
(using the default channel with a specific previous commit should help
me)
below the details of my test
thanks!
Giovanni
P.S.: later I realized that the swap space (2GB) on the test VM was off,
now I'm starting again with "guix pull" with swap on
Chris Marusich <cmmarusich@gmail.com> writes:
[...]
> If so, you may be able to simply delete the following symlinks and then
> run "guix pull" again:
>
> /var/guix/profiles/per-user/gbiscuolo/current-guix-1-link
> /var/guix/profiles/per-user/gbiscuolo/current-guix-2-link
> /var/guix/profiles/per-user/gbiscuolo/current-guix-3-link
> ...
> /var/guix/profiles/per-user/gbiscuolo/current
>
> Of course, before deleting anything, please be sure to record each of
> the symlinks, their permissions, and their targets so that you can undo
> the deletion if necessary. Please be careful when deleting.
>
> If all goes well, when you run "guix pull", Guix should automatically
> migrate your profile generations successfully into the
> /var/guix/profiles/per-user/gbiscuolo directory. After that, you won't
> have to worry about it again (for the gbiscuolo user, at least).
oh yes, your suggestion worked: "git pull" started upgrading again
unfortunately it also started building derivations (sorry I do not have
a list), e.g.:
--8<---------------cut here---------------start------------->8---
Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.org/git/guix.git'...
Building from this channel:
guix https://git.savannah.gnu.org/git/guix.git 6845fdc
building /gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv...
[...]
gcc-5.5.0/zlib/zutil.c
gcc-5.5.0/zlib/zutil.h
phase `unpack' succeeded after 1180.6 seconds
starting phase `unpack-gmp&co'
gmp-6.0.0/
gmp-6.0.0/.gdbinit
gmp-6.0.0/AUTHORS
gmp-6.0.0/COPYING
[...]
--8<---------------cut here---------------end--------------->8---
finally failing for OOM
--8<---------------cut here---------------start------------->8---
build/genautomata ../../gcc-5.5.0/gcc/common.md ../../gcc-5.5.0/gcc/config/i386/i386.md \
insn-conditions.md > tmp-automata.c
make[2]: *** [Makefile:2156: s-attrtab] Killed
make[2]: *** Waiting for unfinished jobs....
/gnu/store/8z9avbgm73nzrbkhscps68gcpfipgllc-bootstrap-binaries-0/bin/bash ../../gcc-5.5.0/gcc/../move-if-change tmp-automata.c insn-automata.c
echo timestamp > s-automata
make[2]: Leaving directory '/tmp/guix-build-gcc-cross-boot0-5.5.0.drv-0/build/gcc'
make[1]: *** [Makefile:4105: all-gcc] Error 2
make[1]: Leaving directory '/tmp/guix-build-gcc-cross-boot0-5.5.0.drv-0/build'
make: *** [Makefile:859: all] Error 2
Backtrace:
In ice-9/boot-9.scm:
157: 12 [catch #t #<catch-closure c92c80> ...]
In unknown file:
?: 11 [apply-smob/1 #<catch-closure c92c80>]
In ice-9/boot-9.scm:
63: 10 [call-with-prompt prompt0 ...]
In ice-9/eval.scm:
432: 9 [eval # #]
In ice-9/boot-9.scm:
2320: 8 [save-module-excursion #<procedure cc0b80 at ice-9/boot-9.scm:3961:3 ()>]
3966: 7 [#<procedure cc0b80 at ice-9/boot-9.scm:3961:3 ()>]
1645: 6 [%start-stack load-stack #<procedure cc1dc0 at ice-9/boot-9.scm:3957:10 ()>]
1650: 5 [#<procedure cc2060 ()>]
In unknown file:
?: 4 [primitive-load "/gnu/store/1ybknnj20hqz1mnzi3my0hpd3mj7gpjz-gcc-cross-boot0-5.5.0-guile-builder"]
In ice-9/eval.scm:
387: 3 [eval # ()]
In srfi/srfi-1.scm:
830: 2 [every1 #<procedure e62a00 at /gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/gnu-build-system.scm:795:9 (expr)> ...]
In /gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/gnu-build-system.scm:
799: 1 [#<procedure e62a00 at /gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/gnu-build-system.scm:795:9 (expr)> #]
In /gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/utils.scm:
616: 0 [invoke "make" "-j" ...]
/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/utils.scm:616:6: In procedure invoke:
/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/utils.scm:616:6: Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "make" arguments: ("-j" "2" "LDFLAGS=-Wl,-rpath=/gnu/store/8zqhf670igizfl895hnhhmx9vz6zyzsj-glibc-bootstrap-0/lib -Wl,-dynamic-linker -Wl,/gnu/store/8zqhf670igizfl895hnhhmx9vz6zyzsj-glibc-bootstrap-0/lib/ld-linux-x86-64.so.2" "BOOT_CFLAGS=-O2 -g0") exit-status: 2 term-signal: #f stop-signal: #f] 3e46180>)'.
builder for `/gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv' failed with exit code 1
build of /gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv failed
View build log at '/var/log/guix/drvs/aw/mnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv.bz2'.
cannot build derivation `/gnu/store/qhwr5smc6nsr0j8nh3hfa0h73xydc9ck-gcc-cross-boot0-wrapped-5.5.0.drv': 1 dependencies couldn't be built
cannot build derivation `/gnu/store/1wp0jy2sdxgyn0mxvds75jan2c0az0q0-glibc-2.28.drv': 1 dependencies couldn't be built
building /gnu/store/8qsid2pqlav3454pzw783j6zy2n0j2l6-perl-boot0-5.28.0.drv...
cannot build derivation `/gnu/store/cz4sr5whzf3qhp8c47bzlfzcxxwl485i-python2-2.7.15.drv': 1 dependencies couldn't be built
guix pull: error: build failed: build of `/gnu/store/cz4sr5whzf3qhp8c47bzlfzcxxwl485i-python2-2.7.15.drv' failed
--8<---------------cut here---------------end--------------->8---
OOM from dmesg:
--8<---------------cut here---------------start------------->8---
[263725.076217] genautomata invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), nodemask=(null), order=0, oom_score_adj=0
[263725.232974] genautomata cpuset=/ mems_allowed=0
[263725.234315] CPU: 1 PID: 29391 Comm: genautomata Not tainted 4.19.8-gnu #1
[263725.235668] Hardware name: QEMU Standard PC (i440FX + PIIX, 1996), BIOS 1.10.2-1 04/01/2014
[263725.237169] Call Trace:
[263725.238684] dump_stack+0x63/0x85
[263725.240130] dump_header+0x6e/0x295
[263725.241559] oom_kill_process+0x25d/0x280
[263725.243365] out_of_memory+0x2af/0x4d0
[263725.244842] __alloc_pages_slowpath+0xa6a/0xdf0
[263725.246305] __alloc_pages_nodemask+0x298/0x2c0
[263725.248053] alloc_pages_vma+0x88/0x1f0
[263725.249539] __handle_mm_fault+0x8b8/0x12b0
[263725.250986] handle_mm_fault+0xe3/0x220
[263725.252468] __do_page_fault+0x250/0x4d0
[263725.253923] do_page_fault+0x2d/0xf0
[263725.255372] ? async_page_fault+0x8/0x30
[263725.256947] do_async_page_fault+0x51/0x80
[263725.258413] async_page_fault+0x1e/0x30
[263725.259878] RIP: 0033:0x7ffff77b1257
[263725.261367] Code: Bad RIP value.
[263725.262852] RSP: 002b:00007fffffffb500 EFLAGS: 00010206
[263725.264605] RAX: 0000000000000261 RBX: 00007ffff0000020 RCX: 0000000000000004
[263725.266123] RDX: 00007ffff00afdb0 RSI: 00007ffff00b0da0 RDI: 00007ffff00b0000
[263725.267639] RBP: 0000000000000ff5 R08: 0000000000000000 R09: 00000000000b0000
[263725.269229] R10: 0000000000000250 R11: 0000000000000206 R12: 0000000000000fe0
[263725.270877] R13: 00007ffff00afdc0 R14: 00007ffff0000078 R15: 00007ffff00afdb0
[263725.272538] Mem-Info:
[263725.274199] active_anon:234404 inactive_anon:0 isolated_anon:0
active_file:9 inactive_file:28 isolated_file:0
unevictable:4 dirty:0 writeback:0 unstable:0
slab_reclaimable:3540 slab_unreclaimable:4393
mapped:2 shmem:0 pagetables:865 bounce:0
free:5708 free_pcp:67 free_cma:0
[263725.283600] Node 0 active_anon:937616kB inactive_anon:0kB active_file:36kB inactive_file:112kB unevictable:16kB isolated(anon):0kB isolated(file):0kB mapped:8kB dirty:0kB writeback:0kB shmem:0kB shmem_thp: 0kB shmem_pmdmapped: 0kB anon_thp: 163840kB writeback_tmp:0kB unstable:0kB all_unreclaimable? yes
[263725.288764] Node 0 DMA32 free:22832kB min:22528kB low:28160kB high:33792kB active_anon:937616kB inactive_anon:0kB active_file:116kB inactive_file:200kB unevictable:16kB writepending:0kB present:1048056kB managed:1010468kB mlocked:16kB kernel_stack:1952kB pagetables:3460kB bounce:0kB free_pcp:268kB local_pcp:188kB free_cma:0kB
[263725.294467] lowmem_reserve[]: 0 0 0 0
[263725.296640] Node 0 DMA32: 370*4kB (UME) 287*8kB (UEH) 261*16kB (UMEH) 119*32kB (UMEH) 73*64kB (MEH) 22*128kB (ME) 8*256kB (MEH) 1*512kB (H) 1*1024kB (H) 0*2048kB 0*4096kB = 22832kB
[263725.300795] Node 0 hugepages_total=0 hugepages_free=0 hugepages_surp=0 hugepages_size=2048kB
[263725.302843] 53 total pagecache pages
[263725.305140] 0 pages in swap cache
[263725.307263] Swap cache stats: add 0, delete 0, find 0/0
[263725.309295] Free swap = 0kB
[263725.311150] Total swap = 0kB
[263725.313094] 262014 pages RAM
[263725.314903] 0 pages HighMem/MovableOnly
[263725.316780] 9397 pages reserved
[263725.318546] 0 pages cma reserved
[263725.320431] 0 pages hwpoisoned
[263725.322295] Tasks state (memory values in pages):
[263725.324261] [ pid ] uid tgid total_vm rss pgtables_bytes swapents oom_score_adj name
[263725.326090] [ 166] 0 166 1191 360 49152 0 0 udevd
[263725.327924] [ 220] 0 220 135344 67 106496 0 0 nscd
[263725.329888] [ 228] 0 228 3009 132 61440 0 0 guix-daemon
[263725.331747] [ 231] 0 231 717 62 40960 0 0 syslogd
[263725.333713] [ 232] 0 232 591 12 40960 0 0 mingetty
[263725.335586] [ 233] 0 233 591 12 40960 0 0 mingetty
[263725.337535] [ 234] 0 234 591 13 45056 0 0 mingetty
[263725.339370] [ 235] 0 235 591 12 40960 0 0 mingetty
[263725.341293] [ 236] 0 236 591 13 49152 0 0 mingetty
[263725.343096] [ 252] 0 252 1556 287 49152 0 0 dhclient
[263725.344999] [ 264] 0 264 745 54 45056 0 0 login
[263725.346824] [ 265] 1000 265 2122 460 53248 0 0 bash
[263725.348736] [ 1177] 0 1177 1960 135 57344 0 -1000 sshd
[263725.350537] [ 1178] 0 1178 1998 147 61440 0 0 sshd
[263725.352427] [ 1180] 1000 1180 2032 161 61440 0 0 sshd
[263725.354194] [ 1181] 1000 1181 2106 438 57344 0 0 bash
[263725.355944] [ 1182] 1000 1182 1653 89 49152 0 0 screen
[263725.357850] [ 1183] 1000 1183 1719 165 49152 0 0 screen
[263725.359593] [ 1184] 1000 1184 2172 516 57344 0 0 bash
[263725.361426] [ 1318] 0 1318 1764 117 53248 0 0 sudo
[263725.363139] [ 1319] 0 1319 1507 95 49152 0 0 su
[263725.364933] [ 1320] 0 1320 2128 462 57344 0 0 bash
[263725.366619] [ 1388] 1000 1388 2120 444 49152 0 0 bash
[263725.368394] [ 1389] 0 1389 1764 116 53248 0 0 sudo
[263725.370061] [ 1390] 0 1390 1507 96 49152 0 0 su
[263725.371712] [ 1391] 0 1391 2324 653 53248 0 0 bash
[263725.373425] [ 1422] 1000 1422 2146 486 57344 0 0 bash
[263725.374971] [ 16084] 0 16084 1998 147 53248 0 0 sshd
[263725.376563] [ 16086] 1000 16086 2028 161 53248 0 0 sshd
[263725.377986] [ 16087] 1000 16087 1894 235 49152 0 0 sh
[263725.379345] [ 16210] 1000 16210 88537 36125 589824 0 0 .guix-real
[263725.380765] [ 16223] 0 16223 5627 2518 77824 0 0 guix-daemon
[263725.382061] [ 16225] 0 16225 34080 3805 151552 0 0 guix substitute
[263725.383302] [ 16229] 0 16229 17328 2969 139264 0 0 guix offload
[263725.384592] [ 16234] 30001 16234 34623 11738 163840 0 0 .guile-real
[263725.385753] [ 17821] 30001 17821 1983 396 45056 0 0 make
[263725.386881] [ 17823] 30001 17823 431 51 32768 0 0 bash
[263725.388080] [ 17836] 30001 17836 2017 450 45056 0 0 make
[263725.389231] [ 26453] 30001 26453 466 71 32768 0 0 bash
[263725.390339] [ 26461] 30001 26461 466 83 32768 0 0 bash
[263725.391445] [ 26484] 30001 26484 4074 2448 61440 0 0 make
[263725.392666] [ 29382] 30001 29382 134420 117369 983040 0 0 genattrtab
[263725.393797] [ 29390] 30001 29390 431 22 32768 0 0 bash
[263725.394925] [ 29391] 30001 29391 63890 45834 409600 0 0 genautomata
[263725.396159] Out of memory: Kill process 29382 (genattrtab) score 465 or sacrifice child
[263725.397352] Killed process 29382 (genattrtab) total-vm:537680kB, anon-rss:469476kB, file-rss:0kB, shmem-rss:0kB
[263725.509294] oom_reaper: reaped process 29382 (genattrtab), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
--8<---------------cut here---------------end--------------->8---
>> [1] maybe I mede some error using "sudo guix..." instead of the recommended "sudo -E guix..."
>
> That could be. Hopefully my suggestion will help!
>
> --
> Chris
--
Giovanni Biscuolo
Xelera IT Infrastructures
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 832 bytes --]
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: guix pull error: symlink
2018-12-17 12:02 ` Giovanni Biscuolo
@ 2018-12-17 15:44 ` Ricardo Wurmus
0 siblings, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2018-12-17 15:44 UTC (permalink / raw)
To: Giovanni Biscuolo; +Cc: help-guix
Giovanni Biscuolo <g@xelera.eu> writes:
> unfortunately "guix pull" failed since it started building
> gcc-cross-boot-0-5.5.0.drv and was killed by OOM
>
> note that on subsequent test I made "guix pull --dry-run" but the pull
> always triggers a build:
Try also “--no-grafts”. Together with “--dry-run” it should show you
what work will be done. (The current implementation of grafts does not
allow us to print the work that is supposed to be performed right away.)
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2018-12-17 15:45 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2018-12-14 12:03 guix pull error: symlink Giovanni Biscuolo
2018-12-16 4:31 ` Chris Marusich
2018-12-17 12:02 ` Giovanni Biscuolo
2018-12-17 15:44 ` Ricardo Wurmus
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).