bug#34006: Guix gc killed live roots - broke git

bug#34006: Guix gc killed live roots - broke git

[swedebugia]

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Hi

Yesterday I hacked on guix. Everything was fine. Store was 43G.
I ran guix gc to clean up.

Afterwards git broke:

$ git pull swedebugia 
fatal: unable to fork

Stracing it reveals that it is missing something (see full attached):
execve("/home/sdb/.guix-profile/bin/git", ["git", "pull", "swedebugia"],
0x7ffe05bad790 /* 66 vars */) = 0
brk(NULL)                               = 0xbfe000
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0)
= 0x7f61627a1000
access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or
directory)
...

$ which git
/home/sdb/.guix-profile/bin/git
$ guix --version
guix (GNU Guix) 0.16.0 <- vanilla 0.16 initted from the installer

$ guix package -l|grep -5 git
Generation 1	Dec 24 2018 07:36:14
 
emacs-paredit	24	out	/gnu/store/1zha5anxg029qfl7r569aap5lfyrb66a-emacs-paredit-24
 
emacs-no-x	26.1	out	/gnu/store/9v7m3c83rm1rgi99ph5xdkpnnd0c62x4-emacs-no-x-26.1
 
setxkbmap	1.3.1	out	/gnu/store/3px1119mhx9q7xzmi5jlg5wylhkx84cr-setxkbmap-1.3.1
  git	2.19.2	out	/gnu/store/iffgahfxnk13narndlaqf9xm0yhyhyyv-git-2.19.2

Is this a bug?

If yes I think it is serious.

-- 
Cheers 
Swedebugia

[-- Attachment #2: strace-git.txt --]
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execve("/home/sdb/.guix-profile/bin/git", ["git", "pull", "swedebugia", "2"], 0x7ffecfa0cf88 /* 66 vars */) = 0
brk(NULL)                               = 0x239e000
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f15df169000
access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls/x86_64/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls/x86_64/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/tls", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/x86_64/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/x86_64/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib", {st_mode=S_IFDIR|0555, st_size=4096, ...}) = 0
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls/x86_64/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls/x86_64/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/tls", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/x86_64/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/x86_64/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib", {st_mode=S_IFDIR|0555, st_size=4096, ...}) = 0
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls/x86_64/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls/x86_64/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/tls", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/x86_64/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/x86_64/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/x86_64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/x86_64", 0x7ffc20998c80) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib/libz.so.1", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\3602\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0555, st_size=125128, ...}) = 0
mmap(NULL, 119168, PROT_READ, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f15df14b000
mprotect(0x7f15df14e000, 102400, PROT_NONE) = 0
mmap(0x7f15df14e000, 73728, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x3000) = 0x7f15df14e000
mmap(0x7f15df160000, 24576, PROT_READ, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x15000) = 0x7f15df160000
mmap(0x7f15df167000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1b000) = 0x7f15df167000
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/librt.so.1", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\260#\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0555, st_size=46544, ...}) = 0
mmap(NULL, 39904, PROT_READ, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f15df141000
mmap(0x7f15df143000, 16384, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x2000) = 0x7f15df143000
mmap(0x7f15df147000, 8192, PROT_READ, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x6000) = 0x7f15df147000
mmap(0x7f15df149000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x7000) = 0x7f15df149000
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/libgcc_s.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/libgcc_s.so.1", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\3402\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0444, st_size=107408, ...}) = 0
mmap(NULL, 99360, PROT_READ, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f15df128000
mmap(0x7f15df12b000, 69632, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x3000) = 0x7f15df12b000
mmap(0x7f15df13c000, 12288, PROT_READ, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x14000) = 0x7f15df13c000
mmap(0x7f15df13f000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x16000) = 0x7f15df13f000
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/libpthread.so.0", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\300l\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0555, st_size=147192, ...}) = 0
mmap(NULL, 132256, PROT_READ, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f15df107000
mmap(0x7f15df10d000, 61440, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x6000) = 0x7f15df10d000
mmap(0x7f15df11c000, 24576, PROT_READ, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x15000) = 0x7f15df11c000
mmap(0x7f15df122000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1a000) = 0x7f15df122000
mmap(0x7f15df124000, 13472, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f15df124000
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0`,\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0555, st_size=2029832, ...}) = 0
mmap(NULL, 1804288, PROT_READ, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f15def4e000
mprotect(0x7f15def70000, 1626112, PROT_NONE) = 0
mmap(0x7f15def70000, 1306624, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x22000) = 0x7f15def70000
mmap(0x7f15df0af000, 315392, PROT_READ, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x161000) = 0x7f15df0af000
mmap(0x7f15df0fd000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1ae000) = 0x7f15df0fd000
mmap(0x7f15df103000, 14336, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f15df103000
close(3)                                = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f15def4c000
arch_prctl(ARCH_SET_FS, 0x7f15def4d540) = 0
mprotect(0x7f15df0fd000, 16384, PROT_READ) = 0
mprotect(0x7f15df122000, 4096, PROT_READ) = 0
mprotect(0x7f15df13f000, 4096, PROT_READ) = 0
mprotect(0x7f15df149000, 4096, PROT_READ) = 0
mprotect(0x7f15df167000, 4096, PROT_READ) = 0
mprotect(0x632000, 4096, PROT_READ)     = 0
mprotect(0x7f15df192000, 4096, PROT_READ) = 0
set_tid_address(0x7f15def4d810)         = 19245
set_robust_list(0x7f15def4d820, 24)     = 0
rt_sigaction(SIGRTMIN, {sa_handler=0x7f15df10d720, sa_mask=[], sa_flags=SA_RESTORER|SA_SIGINFO, sa_restorer=0x7f15df119750}, NULL, 8) = 0
rt_sigaction(SIGRT_1, {sa_handler=0x7f15df10d7b0, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART|SA_SIGINFO, sa_restorer=0x7f15df119750}, NULL, 8) = 0
rt_sigprocmask(SIG_UNBLOCK, [RTMIN RT_1], NULL, 8) = 0
prlimit64(0, RLIMIT_STACK, NULL, {rlim_cur=8192*1024, rlim_max=RLIM64_INFINITY}) = 0
openat(AT_FDCWD, "/dev/null", O_RDWR)   = 3
close(3)                                = 0
brk(NULL)                               = 0x239e000
brk(0x23bf000)                          = 0x23bf000
stat("/gnu/store/iffgahfxnk13narndlaqf9xm0yhyhyyv-git-2.19.2/share/locale", {st_mode=S_IFDIR|0555, st_size=4096, ...}) = 0
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0444, st_size=2997, ...}) = 0
read(3, "# Locale name alias data base.\n#"..., 4096) = 2997
read(3, "", 4096)                       = 0
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/lib/locale/2.28/en_US.utf8/LC_MESSAGES", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFDIR|0555, st_size=4096, ...}) = 0
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/lib/locale/2.28/en_US.utf8/LC_MESSAGES/SYS_LC_MESSAGES", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0444, st_size=57, ...}) = 0
mmap(NULL, 57, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f15def4b000
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/gconv/gconv-modules.cache", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib/gconv/gconv-modules", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0444, st_size=56352, ...}) = 0
read(3, "# GNU libc iconv configuration.\n"..., 4096) = 4096
read(3, "1002//\tJUS_I.B1.002//\nmodule\tJUS"..., 4096) = 4096
read(3, "ISO-IR-110//\t\tISO-8859-4//\nalias"..., 4096) = 4096
read(3, "\t\tISO-8859-14//\nalias\tISO_8859-1"..., 4096) = 4096
read(3, "IC-ES//\nalias\tEBCDICES//\t\tEBCDIC"..., 4096) = 4096
read(3, "DIC-CP-ES//\t\tIBM284//\nalias\tCSIB"..., 4096) = 4096
read(3, "\tIBM863//\nalias\tOSF1002035F//\t\tI"..., 4096) = 4096
read(3, "37//\t\tIBM937//\nmodule\tIBM937//\t\t"..., 4096) = 4096
read(3, "JIS//\t\t\tEUC-JP//\nmodule\tEUC-JP//"..., 4096) = 4096
read(3, "ias\tISO2022CN//\t\tISO-2022-CN//\nm"..., 4096) = 4096
read(3, "_5427-EXT//\nalias\tISO_5427EXT//\t"..., 4096) = 4096
brk(0x23e0000)                          = 0x23e0000
read(3, "st\nmodule\tMAC-SAMI//\t\tINTERNAL\t\t"..., 4096) = 4096
read(3, "12//\t\tINTERNAL\t\tIBM1112\t\t1\nmodul"..., 4096) = 4096
read(3, "\tCP9448//\t\tIBM9448//\nalias\tCSIBM"..., 4096) = 3104
read(3, "", 4096)                       = 0
close(3)                                = 0
futex(0x7f15df102a08, FUTEX_WAKE_PRIVATE, 2147483647) = 0
openat(AT_FDCWD, "/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/lib/locale/2.28/en_US.utf8/LC_TIME", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0444, st_size=3316, ...}) = 0
mmap(NULL, 3316, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f15def4a000
close(3)                                = 0
openat(AT_FDCWD, "/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/lib/locale/2.28/en_US.utf8/LC_CTYPE", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0444, st_size=337024, ...}) = 0
mmap(NULL, 337024, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f15deef7000
close(3)                                = 0
rt_sigprocmask(SIG_UNBLOCK, [PIPE], NULL, 8) = 0
rt_sigaction(SIGPIPE, {sa_handler=SIG_DFL, sa_mask=[PIPE], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7f15def83b80}, {sa_handler=SIG_IGN, sa_mask=[], sa_flags=0}, 8) = 0
getcwd("/home/sdb/src/guix-npm", 129)   = 23
stat("/home/sdb/src/guix-npm", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
stat("/home/sdb/src/guix-npm/.git", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat("/home/sdb/src/guix-npm/.git/HEAD", {st_mode=S_IFREG|0644, st_size=21, ...}) = 0
openat(AT_FDCWD, "/home/sdb/src/guix-npm/.git/HEAD", O_RDONLY) = 3
read(3, "ref: refs/heads/npm2\n", 255)  = 21
read(3, "", 234)                        = 0
close(3)                                = 0
lstat("/home/sdb/src/guix-npm/.git/commondir", 0x7ffc209994f0) = -1 ENOENT (No such file or directory)
access("/home/sdb/src/guix-npm/.git/objects", X_OK) = 0
access("/home/sdb/src/guix-npm/.git/refs", X_OK) = 0
lstat(".git/commondir", 0x7ffc209995d0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, ".git/config", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=842, ...}) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=842, ...}) = 0
read(3, "[core]\n\trepositoryformatversion "..., 4096) = 842
read(3, "", 4096)                       = 0
close(3)                                = 0
getcwd("/home/sdb/src/guix-npm", 129)   = 23
stat(".git", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat(".git/commondir", 0x7ffc20999550) = -1 ENOENT (No such file or directory)
access("/gnu/store/iffgahfxnk13narndlaqf9xm0yhyhyyv-git-2.19.2/etc/gitconfig", R_OK) = -1 ENOENT (No such file or directory)
access("/home/sdb/.config/git/config", R_OK) = -1 ENOENT (No such file or directory)
access("/home/sdb/.gitconfig", R_OK)    = 0
openat(AT_FDCWD, "/home/sdb/.gitconfig", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=57, ...}) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=57, ...}) = 0
read(3, "[user]\n\temail = swedebugia@riseu"..., 4096) = 57
read(3, "", 4096)                       = 0
close(3)                                = 0
access(".git/config", R_OK)             = 0
openat(AT_FDCWD, ".git/config", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=842, ...}) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=842, ...}) = 0
read(3, "[core]\n\trepositoryformatversion "..., 4096) = 842
read(3, "", 4096)                       = 0
close(3)                                = 0
getcwd("/home/sdb/src/guix-npm", 129)   = 23
chdir("/home/sdb/src/guix-npm")         = 0
access("/gnu/store/iffgahfxnk13narndlaqf9xm0yhyhyyv-git-2.19.2/etc/gitconfig", R_OK) = -1 ENOENT (No such file or directory)
access("/home/sdb/.config/git/config", R_OK) = -1 ENOENT (No such file or directory)
access("/home/sdb/.gitconfig", R_OK)    = 0
openat(AT_FDCWD, "/home/sdb/.gitconfig", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=57, ...}) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=57, ...}) = 0
read(3, "[user]\n\temail = swedebugia@riseu"..., 4096) = 57
read(3, "", 4096)                       = 0
close(3)                                = 0
access(".git/config", R_OK)             = 0
openat(AT_FDCWD, ".git/config", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=842, ...}) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=842, ...}) = 0
read(3, "[core]\n\trepositoryformatversion "..., 4096) = 842
read(3, "", 4096)                       = 0
close(3)                                = 0
lstat(".git/commondir", 0x7ffc20999440) = -1 ENOENT (No such file or directory)
lstat(".git/HEAD", {st_mode=S_IFREG|0644, st_size=21, ...}) = 0
openat(AT_FDCWD, ".git/HEAD", O_RDONLY) = 3
read(3, "ref: refs/heads/npm2\n", 256)  = 21
read(3, "", 235)                        = 0
close(3)                                = 0
lstat(".git/refs/heads/npm2", {st_mode=S_IFREG|0644, st_size=41, ...}) = 0
openat(AT_FDCWD, ".git/refs/heads/npm2", O_RDONLY) = 3
read(3, "ca5bfd0260d214c2dce4f52af339eacb"..., 256) = 41
read(3, "", 215)                        = 0
close(3)                                = 0
gettimeofday({tv_sec=1546855336, tv_usec=432620}, NULL) = 0
clock_gettime(CLOCK_MONOTONIC, {tv_sec=19670, tv_nsec=171929444}) = 0
openat(AT_FDCWD, ".git/index", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=176304, ...}) = 0
mmap(NULL, 176304, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f15deecb000
close(3)                                = 0
mmap(NULL, 245760, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f15dee8f000
munmap(0x7f15deecb000, 176304)          = 0
lstat(".git/MERGE_HEAD", 0x7ffc209995e0) = -1 ENOENT (No such file or directory)
lstat(".git/HEAD", {st_mode=S_IFREG|0644, st_size=21, ...}) = 0
openat(AT_FDCWD, ".git/HEAD", O_RDONLY) = 3
read(3, "ref: refs/heads/npm2\n", 256)  = 21
read(3, "", 235)                        = 0
close(3)                                = 0
lstat(".git/refs/heads/npm2", {st_mode=S_IFREG|0644, st_size=41, ...}) = 0
openat(AT_FDCWD, ".git/refs/heads/npm2", O_RDONLY) = 3
read(3, "ca5bfd0260d214c2dce4f52af339eacb"..., 256) = 41
read(3, "", 215)                        = 0
close(3)                                = 0
lstat(".git/refs/HEAD", 0x7ffc209992c0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, ".git/packed-refs", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=5457, ...}) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=5457, ...}) = 0
read(3, "# pack-refs with: peeled fully-p"..., 5457) = 5457
close(3)                                = 0
lstat(".git/refs/tags/HEAD", 0x7ffc209992c0) = -1 ENOENT (No such file or directory)
stat(".git/packed-refs", {st_mode=S_IFREG|0644, st_size=5457, ...}) = 0
lstat(".git/refs/heads/HEAD", 0x7ffc209992c0) = -1 ENOENT (No such file or directory)
stat(".git/packed-refs", {st_mode=S_IFREG|0644, st_size=5457, ...}) = 0
lstat(".git/refs/remotes/HEAD", 0x7ffc209992c0) = -1 ENOENT (No such file or directory)
stat(".git/packed-refs", {st_mode=S_IFREG|0644, st_size=5457, ...}) = 0
lstat(".git/refs/remotes/HEAD/HEAD", 0x7ffc209992c0) = -1 ENOENT (No such file or directory)
stat(".git/packed-refs", {st_mode=S_IFREG|0644, st_size=5457, ...}) = 0
stat("/home/sdb/.guix-profile/libexec/git-core/git", {st_mode=S_IFREG|0555, st_size=2637416, ...}) = 0
pipe([3, 4])                            = 0
rt_sigprocmask(SIG_SETMASK, ~[RTMIN RT_1], [], 8) = 0
clone(child_stack=NULL, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x7f15def4d810) = 19246
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
close(4)                                = 0
read(3, "", 8)                          = 0
close(3)                                = 0
wait4(19246, fatal: unable to fork
[{WIFEXITED(s) && WEXITSTATUS(s) == 128}], 0, NULL) = 19246
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=19246, si_uid=1000, si_status=128, si_utime=0, si_stime=0} ---
exit_group(1)                           = ?
+++ exited with 1 +++

bug#34006: Guix gc killed live roots - broke git

[Ricardo Wurmus]

Hi swedebugia,

> $ git pull swedebugia 
> fatal: unable to fork
>
> Stracing it reveals that it is missing something (see full attached):

Where do you see that?

-- 
Ricardo

bug#34006: Guix gc killed live roots - broke git

[swedebugia]

On 2019-01-07 12:31, Ricardo Wurmus wrote:
> 
> Hi swedebugia,
> 
>> $ git pull swedebugia
>> fatal: unable to fork
>>
>> Stracing it reveals that it is missing something (see full attached):
> 
> Where do you see that?

Ah, sorry the full command was:
strace git pull swedebugia

I tried installing git again with guix package -i git, but it seems no 
substitutes are available anymore to my surprise (0.16 is not even 2 
months old).

-- 
Cheers Swedebugia

bug#34006: Guix gc killed live roots - broke git

[Ricardo Wurmus]

swedebugia <swedebugia@riseup.net> writes:

> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>
>> Hi swedebugia,
>>
>>> $ git pull swedebugia
>>> fatal: unable to fork
>>>
>>> Stracing it reveals that it is missing something (see full attached):
>>
>> Where do you see that?
>
> Ah, sorry the full command was:
> strace git pull swedebugia

What I meant is that the excerpt you showed does not reveal that
“missing something” is the cause of the error.  Having a bunch of things
not found is pretty normal given that search paths are used.

> I tried installing git again with guix package -i git, but it seems no
> substitutes are available anymore to my surprise (0.16 is not even 2
> months old).

Substitutes from berlin / ci.guix.info?

-- 
Ricardo

bug#34006: Guix gc killed live roots - broke git

[Mark H Weaver]

Hi,

swedebugia <swedebugia@riseup.net> writes:

> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>
>>> $ git pull swedebugia
>>> fatal: unable to fork
>>>
>>> Stracing it reveals that it is missing something (see full attached):
>>
>> Where do you see that?
>
> Ah, sorry the full command was:
> strace git pull swedebugia

I looked at the strace output you provided, and didn't find any evidence
of a missing file, which I doubt would lead to the error message "unable
to fork" anyway.  The short excerpt that you quoted in your earlier mail
showed the failure to find "/etc/ld.so.preload", but that's expected,
and does not indicate a problem.  The problem might be happening in the
child process (/home/sdb/.guix-profile/libexec/git-core/git), so adding
the -f option to strace, i.e. "strace -f git pull swedebugia", might
yield more useful information.

If I'm not mistaken, "unable to fork" more likely indicates a lack of
available resources, possibly due to configured resource limits (see
ulimit(3) and the 'ulimit' bash builtin, e.g. try "ulimit -a").
Otherwise, I guess it could be due to restrictions imposed by the use of
a security framework.

       Mark

bug#34006: Guix gc killed live roots - broke git

[swedebugia]

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Mark H Weaver <mhw@netris.org> skrev: (8 januari 2019 08:50:53 CET)
>Hi,
>
>swedebugia <swedebugia@riseup.net> writes:
>
>> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>>
>>>> $ git pull swedebugia
>>>> fatal: unable to fork
>>>>
>>>> Stracing it reveals that it is missing something (see full
>attached):
>>>
>>> Where do you see that?
>>
>> Ah, sorry the full command was:
>> strace git pull swedebugia
>
>I looked at the strace output you provided, and didn't find any
>evidence
>of a missing file, which I doubt would lead to the error message
>"unable
>to fork" anyway.  The short excerpt that you quoted in your earlier
>mail
>showed the failure to find "/etc/ld.so.preload", but that's expected,
>and does not indicate a problem.  The problem might be happening in the
>child process (/home/sdb/.guix-profile/libexec/git-core/git), so adding
>the -f option to strace, i.e. "strace -f git pull swedebugia", might
>yield more useful information.
>
>If I'm not mistaken, "unable to fork" more likely indicates a lack of
>available resources, possibly due to configured resource limits (see
>ulimit(3) and the 'ulimit' bash builtin, e.g. try "ulimit -a").
>Otherwise, I guess it could be due to restrictions imposed by the use
>of
>a security framework.
>
>       Mark

Thanks for the -f tip. I thought the errors were significant, but now I understood they are not.
I will reply to the thread with more information if upgrading does not solve it. 
It is a vanilla 0.16 with a few packages installed, no security framework. 
I will share the whole environment also.
Git has been upgraded so I will try installing the newer version next.
-- 
Sent from my p≡p for Android.

[-- Attachment #2: pEpkey.asc --]
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bug#34006: Guix gc killed live roots - broke git

[swedebugia]

On 2019-01-08 07:50, Mark H Weaver wrote:
> Hi,
> 
> swedebugia <swedebugia@riseup.net> writes:
> 
>> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>>
>>>> $ git pull swedebugia
>>>> fatal: unable to fork
>>>>
>>>> Stracing it reveals that it is missing something (see full attached):
>>>
>>> Where do you see that?
>>
>> Ah, sorry the full command was:
>> strace git pull swedebugia
> 
> I looked at the strace output you provided, and didn't find any evidence
> of a missing file, which I doubt would lead to the error message "unable
> to fork" anyway.  The short excerpt that you quoted in your earlier mail
> showed the failure to find "/etc/ld.so.preload", but that's expected,
> and does not indicate a problem.  The problem might be happening in the
> child process (/home/sdb/.guix-profile/libexec/git-core/git), so adding
> the -f option to strace, i.e. "strace -f git pull swedebugia", might
> yield more useful information.
> 
> If I'm not mistaken, "unable to fork" more likely indicates a lack of
> available resources, possibly due to configured resource limits (see
> ulimit(3) and the 'ulimit' bash builtin, e.g. try "ulimit -a").
> Otherwise, I guess it could be due to restrictions imposed by the use of
> a security framework.

Tried again with "strace -f" and got this:

stat("/home/sdb/.guix-profile/libexec/git-core/ssh", 0x7ffe26617620) =
-1 ENOENT (No such file or directory)
stat("/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/bin/ssh",
0x7ffe26617620) = -1 ENOENT (No such file or directory)
stat("/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/sbin/ssh",
0x7ffe26617620) = -1 ENOENT (No such file or directory)
stat("/home/sdb/.local/bin;/home/sdb/.guix-profile/bin/ssh",
0x7ffe26617620) = -1 ENOENT (No such file or directory)
stat("/home/sdb/.guix-profile/sbin/ssh", 0x7ffe26617620) = -1 ENOENT (No
such file or directory)
stat("/run/setuid-programs/ssh", 0x7ffe26617620) = -1 ENOENT (No such
file or directory)
stat("/home/sdb/.config/guix/current/bin/ssh", 0x7ffe26617620) = -1
ENOENT (No such file or directory)
stat("/home/sdb/.guix-profile/bin/ssh", 0x7ffe26617620) = -1 ENOENT (No
such file or directory)
stat("/home/sdb/.guix-profile/sbin/ssh", 0x7ffe26617620) = -1 ENOENT (No
such file or directory)
stat("/run/current-system/profile/bin/ssh", 0x7ffe26617620) = -1 ENOENT
(No such file or directory)
stat("/run/current-system/profile/sbin/ssh", 0x7ffe26617620) = -1 ENOENT
(No such file or directory)
close(14)                               = 0

So installing ssh might be a good idea >D

Solved! :D

-- 
Cheers 
Swedebugia