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12-07-2010, 06:30 PM
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#1
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Member
Registered: Jan 2010
Location: Lancashire
Distribution: Slackware Stable
Posts: 527
Rep: 
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Anacron email - Segmentation Fault - Ubuntu
My sisters machine is running ubuntu and having just logged in as root I noticed I had some emails from anacron.
These all read:
Code:
Return-Path: <root@xxx>
X-Original-To: root
Delivered-To: root@xxx
Received: by xxx (Postfix, from userid 0)
id 5B4961FF18; Wed, 1 Dec 2010 07:45:38 +0000 (GMT)
From: Anacron <root@xxx>
To: root@xxx
Subject: Anacron job 'cron.daily' on xxx
Message-Id: <20101201074538.5B4961FF18@xxx>
Date: Wed, 1 Dec 2010 07:45:38 +0000 (GMT)
/etc/cron.daily/apt:
Segmentation fault
Now, I use cron on slax with no problems at all, but I have never set up any cron jobs on the ubuntu machine so I can only assume it's some jobs which are scheduled by the default install?
Having a little dig around, here what I have so far:
/etc/anacrontab
Code:
# /etc/anacrontab: configuration file for anacron
# See anacron(8) and anacrontab(5) for details.
SHELL=/bin/sh
PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
# These replace cron's entries
1 5 cron.daily nice run-parts --report /etc/cron.daily
7 10 cron.weekly nice run-parts --report /etc/cron.weekly
@monthly 15 cron.monthly nice run-parts --report /etc/cron.monthly
/etc/cron.daily
Code:
# ls -la
total 72
drwxr-xr-x 2 root root 4096 2010-10-07 17:15 .
drwxr-xr-x 148 root root 12288 2010-12-08 00:06 ..
-rwxr-xr-x 1 root root 311 2010-06-20 09:11 0anacron
-rwxr-xr-x 1 root root 189 2010-10-01 13:17 apport
-rwxr-xr-x 1 root root 15655 2010-10-05 15:09 apt
-rwxr-xr-x 1 root root 502 2010-05-26 21:02 bsdmainutils
-rwxr-xr-x 1 root root 256 2010-09-08 10:52 dpkg
-rwxr-xr-x 1 root root 89 2010-08-05 22:04 logrotate
-rwxr-xr-x 1 root root 1335 2010-08-17 16:10 man-db
-rwxr-xr-x 1 root root 606 2010-03-24 10:16 mlocate
-rw-r--r-- 1 root root 102 2010-08-25 00:01 .placeholder
-rwxr-xr-x 1 root root 2149 2009-06-16 14:12 popularity-contest
-rwxr-xr-x 1 root root 3594 2010-08-25 00:01 standard
/etc/cron.weekly
Code:
# ls -l
total 12
-rwxr-xr-x 1 root root 312 2010-06-20 09:11 0anacron
-rwxr-xr-x 1 root root 748 2010-09-23 18:05 apt-xapian-index
-rwxr-xr-x 1 root root 895 2010-08-17 16:10 man-db
I've tried running all the jobs individually but none produce a segmentation fault problem.
The email is a daily one so looks like it's coming from cron.daily.
Any suggestions on what might be causing this?
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12-08-2010, 12:14 PM
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#2
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Member
Registered: May 2003
Location: Tengiz
Distribution: Slackware64 13.37
Posts: 669
Rep:
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What's the concents of /etc/cron.daily/apt
and do you use prelink?
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12-11-2010, 11:10 AM
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#3
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Member
Registered: Jan 2010
Location: Lancashire
Distribution: Slackware Stable
Posts: 527
Original Poster
Rep: 
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/etc/cron.daily/apt
Code:
#!/bin/sh
#set -e
#
# This file understands the following apt configuration variables:
# Values here are the default.
# Create /etc/apt/apt.conf.d/02periodic file to set your preference.
#
# Dir "/";
# - RootDir for all configuration files
#
# Dir::Cache "var/apt/cache/";
# - Set apt package cache directory
#
# Dir::Cache::Archive "archives/";
# - Set package archive directory
#
# APT::Periodic::Enable "1";
# - Enable the update/upgrade script (0=disable)
#
# APT::Periodic::BackupArchiveInterval "0";
# - Backup after n-days if archive contents changed.(0=disable)
#
# APT::Periodic::BackupLevel "3";
# - Backup level.(0=disable), 1 is invalid.
#
# Dir::Cache::Backup "backup/";
# - Set periodic package backup directory
#
# APT::Archives::MaxAge "0"; (old, deprecated)
# APT::Periodic::MaxAge "0"; (new)
# - Set maximum allowed age of a cache package file. If a cache
# package file is older it is deleted (0=disable)
#
# APT::Archives::MinAge "2"; (old, deprecated)
# APT::Periodic::MinAge "2"; (new)
# - Set minimum age of a package file. If a file is younger it
# will not be deleted (0=disable). Usefull to prevent races
# and to keep backups of the packages for emergency.
#
# APT::Archives::MaxSize "0"; (old, deprecated)
# APT::Periodic::MaxSize "0"; (new)
# - Set maximum size of the cache in MB (0=disable). If the cache
# is bigger, cached package files are deleted until the size
# requirement is met (the biggest packages will be deleted
# first).
#
# APT::Periodic::Update-Package-Lists "0";
# - Do "apt-get update" automatically every n-days (0=disable)
#
# APT::Periodic::Download-Upgradeable-Packages "0";
# - Do "apt-get upgrade --download-only" every n-days (0=disable)
#
# APT::Periodic::Download-Upgradeable-Packages-Debdelta "1";
# - Use debdelta-upgrade to download updates if available (0=disable)
#
# APT::Periodic::Unattended-Upgrade "0";
# - Run the "unattended-upgrade" security upgrade script
# every n-days (0=disabled)
# Requires the package "unattended-upgrades" and will write
# a log in /var/log/unattended-upgrades
#
# APT::Periodic::AutocleanInterval "0";
# - Do "apt-get autoclean" every n-days (0=disable)
#
# APT::Periodic::Verbose "0";
# - Send report mail to root
# 0: no report (or null string)
# 1: progress report (actually any string)
# 2: + command outputs (remove -qq, remove 2>/dev/null, add -d)
# 3: + trace on
check_stamp()
{
stamp="$1"
interval="$2"
if [ $interval -eq 0 ]; then
debug_echo "check_stamp: interval=0"
# treat as no time has passed
return 1
fi
if [ ! -f $stamp ]; then
debug_echo "check_stamp: missing time stamp file: $stamp."
# treat as enough time has passed
return 0
fi
# compare midnight today to midnight the day the stamp was updated
stamp_file="$stamp"
stamp=$(date --date=$(date -r $stamp_file --iso-8601) +%s 2>/dev/null)
if [ "$?" != "0" ]; then
# Due to some timezones returning 'invalid date' for midnight on
# certain dates (eg America/Sao_Paulo), if date returns with error
# remove the stamp file and return 0. See coreutils bug:
# http://lists.gnu.org/archive/html/bug-coreutils/2007-09/msg00176.html
rm -f "$stamp_file"
return 0
fi
now=$(date --date=$(date --iso-8601) +%s 2>/dev/null)
if [ "$?" != "0" ]; then
# As above, due to some timezones returning 'invalid date' for midnight
# on certain dates (eg America/Sao_Paulo), if date returns with error
# return 0.
return 0
fi
delta=$(($now-$stamp))
# intervall is in days, convert to sec.
interval=$(($interval*60*60*24))
debug_echo "check_stamp: interval=$interval, now=$now, stamp=$stamp, delta=$delta (sec)"
# remove timestamps a day (or more) in the future and force re-check
if [ $stamp -gt $(($now+86400)) ]; then
echo "WARNING: file $stamp_file has a timestamp in the future: $stamp"
rm -f "$stamp_file"
return 0
fi
if [ $delta -ge $interval ]; then
return 0
fi
return 1
}
update_stamp()
{
stamp="$1"
touch $stamp
}
# we check here if autoclean was enough sizewise
check_size_constraints()
{{
MaxAge=0
eval $(apt-config shell MaxAge APT::Archives::MaxAge)
eval $(apt-config shell MaxAge APT::Periodic::MaxAge)
MinAge=2
eval $(apt-config shell MinAge APT::Archives::MinAge)
eval $(apt-config shell MinAge APT::Periodic::MinAge)
MaxSize=0
eval $(apt-config shell MaxSize APT::Archives::MaxSize)
eval $(apt-config shell MaxSize APT::Periodic::MaxSize)
CacheDir="var/cache/apt/"
eval $(apt-config shell CacheDir Dir::Cache)
CacheDir=${CacheDir%/}
CacheArchive="archives/"
eval $(apt-config shell CacheArchive Dir::Cache::archives)
CacheArchive=${CacheArchive%/}
# sanity check
if [ -z "$CacheDir" -o -z "$CacheArchive" ]; then
echo "empty Dir::Cache or Dir::Cache::archives, exiting"
exit
fi
Cache="${Dir%/}/${CacheDir%/}/${CacheArchive%/}/"
# check age
if [ ! $MaxAge -eq 0 ] && [ ! $MinAge -eq 0 ]; then
debug_echo "aged: ctime <$MaxAge and mtime <$MaxAge and ctime>$MinAge and mtime>$MinAge"
find $Cache -name "*.deb" \( -mtime +$MaxAge -and -ctime +$MaxAge \) -and -not \( -mtime -$MinAge -or -ctime -$MinAge \) -print0 | xargs -r -0 rm -f
elif [ ! $MaxAge -eq 0 ]; then
debug_echo "aged: ctime <$MaxAge and mtime <$MaxAge only"
find $Cache -name "*.deb" -ctime +$MaxAge -and -mtime +$MaxAge -print0 | xargs -r -0 rm -f
else
debug_echo "skip aging since MaxAge is 0"
fi
# check size
if [ ! $MaxSize -eq 0 ]; then
# maxSize is in MB
MaxSize=$(($MaxSize*1024))
#get current time
now=$(date --date=$(date --iso-8601) +%s)
MinAge=$(($MinAge*24*60*60))
# reverse-sort by mtime
for file in $(ls -rt $Cache/*.deb 2>/dev/null); do
du=$(du -s $Cache)
size=${du%%/*}
# check if the cache is small enough
if [ $size -lt $MaxSize ]; then
debug_echo "end remove by archive size: size=$size < $MaxSize"
break
fi
# check for MinAge of the file
if [ $MinAge -ne 0 ]; then
# check both ctime and mtime
mtime=$(stat -c %Y $file)
ctime=$(stat -c %Z $file)
if [ $mtime -gt $ctime ]; then
delta=$(($now-$mtime))
else
delta=$(($now-$ctime))
fi
if [ $delta -le $MinAge ]; then
debug_echo "skip remove by archive size: $file, delta=$delta < $MinAgeSec"
break
else
# delete oldest file
debug_echo "remove by archive size: $file, delta=$delta >= $MinAgeSec (sec), size=$size >= $MaxSize"
rm -f $file
fi
fi
done
fi
}
# deal with the Apt::Periodic::BackupArchiveInterval
do_cache_backup()
{
BackupArchiveInterval="$1"
if [ $BackupArchiveInterval -eq 0 ]; then
return
fi
# Set default values and normalize
Dir="/"
eval $(apt-config shell Dir Dir)
Dir=${Dir%/}
CacheDir="var/cache/apt/"
eval $(apt-config shell CacheDir Dir::Cache)
CacheDir=${CacheDir%/}
if [ -z "$CacheDir" ]; then
debug_echo "practically empty Dir::Cache, exiting"
return 0
fi
CacheArchive="archives/"
eval $(apt-config shell CacheArchive Dir::Cache::Archives)
CacheArchive=${CacheArchive%/}
if [ -z "$CacheArchive" ]; then
debug_echo "practically empty Dir::Cache::archives, exiting"
return 0
fi
BackupLevel=3
eval $(apt-config shell BackupLevel APT::Periodic::BackupLevel)
if [ $BackupLevel -le 1 ]; then
BackupLevel=2 ;
fi
CacheBackup="backup/"
eval $(apt-config shell CacheBackup Dir::Cache::Backup)
CacheBackup=${CacheBackup%/}
if [ -z "$CacheBackup" ]; then
echo "practically empty Dir::Cache::Backup, exiting" 1>&2
return
fi
Cache="${Dir}/${CacheDir}/${CacheArchive}/"
Back="${Dir}/${CacheDir}/${CacheBackup}/"
BackX="${Back}${CacheArchive}/"
for x in $(seq 0 1 $((${BackupLevel}-1))); do
eval "Back${x}=${Back}${x}/"
done
# backup after n-days if archive contents changed.
# (This uses hardlink to save disk space)
BACKUP_ARCHIVE_STAMP=/var/lib/apt/periodic/backup-archive-stamp
if check_stamp $BACKUP_ARCHIVE_STAMP $BackupArchiveInterval; then
if [ $({(cd $Cache 2>/dev/null; find . -name "*.deb"); (cd $Back0 2>/dev/null;find . -name "*.deb") ;}| sort|uniq -u|wc -l) -ne 0 ]; then
mkdir -p $Back
rm -rf $Back$((${BackupLevel}-1))
for y in $(seq $((${BackupLevel}-1)) -1 1); do
eval BackY=${Back}$y
eval BackZ=${Back}$(($y-1))
if [ -e $BackZ ]; then
mv -f $BackZ $BackY ;
fi
done
cp -la $Cache $Back ; mv -f $BackX $Back0
update_stamp $BACKUP_ARCHIVE_STAMP
debug_echo "backup with hardlinks. (success)"
else
debug_echo "skip backup since same content."
fi
else
debug_echo "skip backup since too new."
fi
}
# sleep for a random interval of time (default 30min)
# (some code taken from cron-apt, thanks)
random_sleep()
{
RandomSleep=1800
eval $(apt-config shell RandomSleep APT::Periodic::RandomSleep)
if [ $RandomSleep -eq 0 ]; then
return
fi
if [ -z "$RANDOM" ] ; then
# A fix for shells that do not have this bash feature.
RANDOM=$(dd if=/dev/urandom count=1 2> /dev/null | cksum | cut -c"1-5")
fi
TIME=$(($RANDOM % $RandomSleep))
debug_echo "sleeping for $TIME seconds"
sleep $TIME
}
debug_echo()
{
# Display message if $VERBOSE >= 1
if [ "$VERBOSE" -ge 1 ]; then
echo $1 1>&2
fi
}
# ------------------------ main ----------------------------
# Backup the 7 last versions of APT's extended_states file
# shameless copy from dpkg cron
if cd /var/backups ; then
if ! cmp -s apt.extended_states.0 /var/lib/apt/extended_states; then
cp -p /var/lib/apt/extended_states apt.extended_states
savelog -c 7 apt.extended_states >/dev/null
fi
fi
# check apt-config exstance
if ! which apt-config >/dev/null ; then
exit 0
fi
# check if the user really wants to do something
AutoAptEnable=1 # default is yes
eval $(apt-config shell AutoAptEnable APT::Periodic::Enable)
if [ $AutoAptEnable -eq 0 ]; then
exit 0
fi
# Set VERBOSE mode from apt-config (or inherit from environment)
VERBOSE=0
eval $(apt-config shell VERBOSE APT::Periodic::Verbose)
debug_echo "verbose level $VERBOSE"
if [ "$VERBOSE" -le 2 ]; then
# quiet for 0,1,2
XSTDOUT=">/dev/null"
XSTDERR="2>/dev/null"
XAPTOPT="-qq"
XUUPOPT=""
else
XSTDOUT=""
XSTDERR=""
XAPTOPT=""
XUUPOPT="-d"
fi
if [ "$VERBOSE" -ge 3 ]; then
# trace output
set -x
fi
# laptop check, on_ac_power returns:
# 0 (true) System is on main power
# 1 (false) System is not on main power
# 255 (false) Power status could not be determined
# Desktop systems always return 255 it seems
if which on_ac_power >/dev/null; then
on_ac_power
POWER=$?
if [ $POWER -eq 1 ]; then
debug_echo "exit: system NOT on main power"
exit 0
elif [ $POWER -ne 0 ]; then
debug_echo "power status ($POWER) undetermined, continuing"
fi
debug_echo "system is on main power."
fi
# check if we can lock the cache and if the cache is clean
if which apt-get >/dev/null && ! eval apt-get check -f $XAPTOPT $XSTDERR ; then
debug_echo "error encountered in cron job with \"apt-get check\"."
exit 0
fi
# Global current time in seconds since 1970-01-01 00:00:00 UTC
now=$(date +%s)
# Support old Archive for compatibility.
# Document only Periodic for all controling parameters of this script.
UpdateInterval=0
eval $(apt-config shell UpdateInterval APT::Periodic::Update-Package-Lists)
DownloadUpgradeableInterval=0
eval $(apt-config shell DownloadUpgradeableInterval APT::Periodic::Download-Upgradeable-Packages)
UnattendedUpgradeInterval=0
eval $(apt-config shell UnattendedUpgradeInterval APT::Periodic::Unattended-Upgrade)
AutocleanInterval=0
eval $(apt-config shell AutocleanInterval APT::Periodic::AutocleanInterval)
BackupArchiveInterval=0
eval $(apt-config shell BackupArchiveInterval APT::Periodic::BackupArchiveInterval)
Debdelta=1
eval $(apt-config shell Debdelta APT::Periodic::Download-Upgradeable-Packages-Debdelta)
# check if we actually have to do anything that requires locking the cache
if [ $UpdateInterval -eq 0 ] &&
[ $DownloadUpgradeableInterval -eq 0 ] &&
[ $UnattendedUpgradeInterval -eq 0 ] &&
[ $BackupArchiveInterval -eq 0 ] &&
[ $AutocleanInterval -eq 0 ]; then
# check cache size
check_size_constraints
exit 0
fi
# deal with BackupArchiveInterval
do_cache_backup $BackupArchiveInterval
# sleep random amount of time to avoid hitting the
# mirrors at the same time
random_sleep
# include default system language so that "apt-get update" will
# fetch the right translated package descriptions
if [ -r /etc/default/locale ]; then
. /etc/default/locale
export LANG LANGUAGE LC_MESSAGES LC_ALL
fi
# update package lists
UPDATED=0
UPDATE_STAMP=/var/lib/apt/periodic/update-stamp
if check_stamp $UPDATE_STAMP $UpdateInterval; then
# check for a new archive signing key (against the master keyring)
if eval apt-key net-update $XSTDERR; then
debug_echo "apt-key net-update (success)"
else
debug_echo "apt-key net-update (failure)"
fi
# run apt-get update
if eval apt-get $XAPTOPT -y update $XSTDERR; then
debug_echo "download updated metadata (success)."
if which dbus-send >/dev/null && pidof dbus-daemon >/dev/null; then
if dbus-send --system / app.apt.dbus.updated boolean:true ; then
debug_echo "send dbus signal (success)"
else
debug_echo "send dbus signal (error)"
fi
else
debug_echo "dbus signal not send (command not available)"
fi
update_stamp $UPDATE_STAMP
UPDATED=1
# now run apt-xapian-index if it is installed to ensure the index
# is up-to-date
if [ -x /usr/sbin/update-apt-xapian-index ]; then
nice ionice -c3 update-apt-xapian-index -q
fi
else
debug_echo "download updated metadata (error)"
fi
else
debug_echo "download updated metadata (not run)."
fi
# download all upgradeable packages (if it is requested)
DOWNLOAD_UPGRADEABLE_STAMP=/var/lib/apt/periodic/download-upgradeable-stamp
if [ $UPDATED -eq 1 ] && check_stamp $DOWNLOAD_UPGRADEABLE_STAMP $DownloadUpgradeableInterval; then
if [ $Debdelta -eq 1 ]; then
debdelta-upgrade >/dev/null 2>&1 || true
fi
if eval apt-get $XAPTOPT -y -d dist-upgrade $XSTDERR; then
update_stamp $DOWNLOAD_UPGRADEABLE_STAMP
debug_echo "download upgradable (success)"
else
debug_echo "download upgradable (error)"
fi
else
debug_echo "download upgradable (not run)"
fi
# auto upgrade all upgradeable packages
UPGRADE_STAMP=/var/lib/apt/periodic/upgrade-stamp
if [ $UPDATED -eq 1 ] && which unattended-upgrade >/dev/null && check_stamp $UPGRADE_STAMP $UnattendedUpgradeInterval; then
if unattended-upgrade $XUUPOPT; then
update_stamp $UPGRADE_STAMP
debug_echo "unattended-upgrade (success)"
else
debug_echo "unattended-upgrade (error)"
fi
else
debug_echo "unattended-upgrade (not run)"
fi
# autoclean package archive
AUTOCLEAN_STAMP=/var/lib/apt/periodic/autoclean-stamp
if check_stamp $AUTOCLEAN_STAMP $AutocleanInterval; then
if eval apt-get $XAPTOPT -y autoclean $XSTDERR; then
debug_echo "autoclean (success)."
update_stamp $AUTOCLEAN_STAMP
else
debug_echo "autoclean (error)"
fi
else
debug_echo "autoclean (not run)"
fi
# check cache size
check_size_constraints
#
# vim: set sts=4 ai :
#
I don't knowingly use prelink.
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12-13-2010, 03:51 AM
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#4
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Member
Registered: May 2003
Location: Tengiz
Distribution: Slackware64 13.37
Posts: 669
Rep:
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THat's just weird now. I don't see anything would cause SEGFAULT. I don't think Ubuntu uses prelink[1] by default. My wild guess is that It's something to do with network communication. Try a manual update.
[1]Non-prelinked binaries may face SEGFAULT with prelinked libraries. I know prelinked OpenSSL Library gave me SEGFAULT while coding.
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12-13-2010, 04:51 PM
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#5
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Member
Registered: Jan 2010
Location: Lancashire
Distribution: Slackware Stable
Posts: 527
Original Poster
Rep: 
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running
Code:
apt-get update; apt-get upgrade
works fine which I believe is the Ubuntu equivalent to running "-current"?
Should I just remove it from cron and then update manually? It's not a big deal really, it just doesn't seem much point in running it if it's going to segfault! Strange how running normally it works fine though (ie, running the apt script from the shell prompt). I have removed the sleep from the file (so I don't have to wait up to half an hour lol).
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12-13-2010, 04:54 PM
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#6
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Member
Registered: Jan 2010
Location: Lancashire
Distribution: Slackware Stable
Posts: 527
Original Poster
Rep: 
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Seems I might have answered this myself (well, found someone else who has answered it!  )
http://www.tummy.com/journals/entrie...0101203_060502
I've upgraded the python package and will now see what happens on the next cron run...
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