cannot access to pkgdb: Bad file descriptor

["Christer Sjöholm" <"h..."@furuvik.net>]

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Hi, got a problem I can't get my head around.

After a update and reboot a while ago (March 7), all xbps commands that try 
to read the pkgdb exits with:

ERROR: cannot access to pkgdb: Bad file descriptor

I have both swiched filesystem, var was on a f2fs partition, and moved the 
pkgdb to another void machine but the error persists. So it looks like it 
is corrupted some way that causes the problem.
Looking inside it at least the begining and end looks like correct XML.

Has anyone else has this problem, or know what it can be?
If not, any ideas about how to go about recreating the pkgdb?


My pkgdb can be seen here:     
https://gist.githubusercontent.com/christer/25f40aa5c546c7742a68/raw/pkgdb-0.38.plist


And here is the end of an strace of xbps-query -l

access("/etc/xbps.d/xbps.conf", R_OK)   = -1 ENOENT (No such file or 
directory)
open("/usr/share/xbps.d/xbps.conf", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=3194, ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 
0x7f8b54bc0000
read(3, "# Configuration file for XBPS.\n#"..., 4096) = 3194
read(3, "", 4096)                       = 0
close(3)                                = 0
munmap(0x7f8b54bc0000, 4096)            = 0
chdir("/home/hcs/temp/strace-4.9_1.x86_64/usr/bin") = 0
open("/var/db/xbps/pkgdb-0.38.plist", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=1613824, ...}) = 0
mmap(NULL, 1617920, PROT_READ, MAP_SHARED, 3, 0) = 0x7f8b54a20000
close(3)                                = 0
madvise(0x7f8b54a20000, 1613824, MADV_SEQUENTIAL) = 0
mmap(0x7f8b54baa000, 4096, PROT_READ, MAP_PRIVATE|MAP_FIXED, -1, 0) = -1 
EBADF (Bad file descriptor)
munmap(0x7f8b54a20000, 1613824)         = 0
write(2, "ERROR: ", 7ERROR: )                  = 7
write(2, "cannot access to pkgdb: Bad file"..., 44cannot access to pkgdb: 
Bad file descriptor
) = 44
ioctl(1, TIOCGWINSZ, {ws_row=69, ws_col=255, ws_xpixel=0, ws_ypixel=0}) = 0
exit_group(9)                           = ?
+++ exited with 9 +++


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