Time Machine stuck in "clearing up...

Hugely appreciate any ideas how to fix this...I've tried for over a week now to get Time Machine working, but it keeps getting stuck at "clearing up", even though it seems to be only 2/3rds of the way through the back up.
I've erased the Lacie hard drive I'm using as a back up, and used it as a Time Machine back up on another computer alsewhere.
I've also reinstalled Snow Leopard, no joy.
I've reindexed the drive using Spotlight too.
Below are my Console error masaages, be grateful for any ideas - thanks in advance
Jul 8 01:07:17 rocksteady-2 com.apple.backupd-auto[8486]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 02:07:17 rocksteady-2 com.apple.backupd-auto[9296]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 03:07:17 rocksteady-2 com.apple.backupd-auto[10102]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 04:07:18 rocksteady-2 com.apple.backupd-auto[10991]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 05:07:18 rocksteady-2 com.apple.backupd-auto[11799]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 06:07:18 rocksteady-2 com.apple.backupd-auto[12604]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 07:07:18 rocksteady-2 com.apple.backupd-auto[13547]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 08:07:18 rocksteady-2 com.apple.backupd-auto[14360]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 09:07:18 rocksteady-2 com.apple.backupd-auto[15202]: Not starting scheduled Time Machine backup - time machine destination not resolvable.
Jul 8 09:09:08 rocksteady-2 com.apple.backupd[15214]: Starting standard backup
Jul 8 09:09:12 rocksteady-2 com.apple.backupd[15214]: Backing up to: /Volumes/Little Nelly/Backups.backupdb
Jul 8 09:09:17 rocksteady-2 com.apple.backupd[15214]: Backup content size: 330.3 GB excluded items size: 9.4 GB for volume Macintosh HD
Jul 8 09:09:17 rocksteady-2 com.apple.backupd[15214]: No pre-backup thinning needed: 385.08 GB requested (including padding), 465.02 GB available
Jul 8 09:09:17 rocksteady-2 com.apple.backupd[15214]: Waiting for index to be ready (101)
Jul 8 09:09:17 rocksteady-2 mds[4975]: (Normal) DiskStore: Creating index for /Volumes/Little Nelly/Backups.backupdb
Jul 8 10:09:16 rocksteady-2 com.apple.backupd[15214]: Copied 48.7 GB of 320.9 GB, 252393 of 1510480 items
Jul 8 10:33:47 rocksteady-2 com.apple.backupd[15214]: CoreEndianFlipData: error -4940 returned for rsrc type FREF (id 129, length 7, native = no)
Jul 8 10:33:47 rocksteady-2 com.apple.backupd[15214]: CoreEndianFlipData: error -4940 returned for rsrc type FREF (id 129, length 7, native = no)
Jul 8 11:09:16 rocksteady-2 com.apple.backupd[15214]: Copied 118.9 GB of 320.9 GB, 410345 of 1510480 items
Jul 8 12:09:16 rocksteady-2 com.apple.backupd[15214]: Copied 195.9 GB of 320.9 GB, 547098 of 1510480 items
Jul 8 12:25:38 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:25:38 rocksteady-2 com.apple.backupd[15214]: Error: (-36) SrcErr:NO Copying /Users/hugocurrie/Music/iTunes/iTunes Music/Keith Mansfield/Daddy Vegas 04/04 boogaloo.m4a to /Volumes/Little Nelly/Backups.backupdb/Rocksteady/2010-07-08-090915.inProgress/40F66944-A56E-40 68-B834-2A79CFBFDC93/Macintosh HD/Users/hugocurrie/Music/iTunes/iTunes Music/Keith Mansfield/Daddy Vegas 04
Jul 8 12:25:38 rocksteady-2 com.apple.backupd[15214]: Stopping backup.
Jul 8 12:26:31 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:26:31 rocksteady-2 com.apple.backupd[15214]: Error: (-8062) SrcErr:NO Copying /Users/hugocurrie/Music/iTunes/iTunes Music/Keith Mansfield/Daddy Vegas 04/04 boogaloo.m4a to /Volumes/Little Nelly/Backups.backupdb/Rocksteady/2010-07-08-090915.inProgress/40F66944-A56E-40 68-B834-2A79CFBFDC93/Macintosh HD/Users/hugocurrie/Music/iTunes/iTunes Music/Keith Mansfield/Daddy Vegas 04
Jul 8 12:36:35 rocksteady-2 mds[4975]: (Normal) DiskStore: Rebuilding index for /Volumes/Little Nelly/Backups.backupdb
Jul 8 12:40:43 rocksteady-2 mds[4975]: (Normal) DiskStore: Creating index for /Volumes/Little Nelly/Backups.backupdb
Jul 8 12:43:51 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:44:45 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:45:39 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:45:39 rocksteady-2 com.apple.backupd[15214]: Copied 548165 files (199.3 GB) from volume Macintosh HD.
Jul 8 12:46:33 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:46:33 rocksteady-2 com.apple.backupd[15214]: Copy stage failed with error:11
Jul 8 12:47:27 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:48:21 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:49:14 rocksteady-2 com.apple.backupd[15214]: Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: Input/output error
Jul 8 12:51:22 rocksteady-2 mdworker[18588]: (Normal) Import: Spotlight giving up on importing file /Volumes/Little Nelly/Backups.backupdb/Rocksteady/2010-07-08-090915.inProgress/40F66944-A56E-40 68-B834-2A79CFBFDC93/Macintosh HD after 240.001 seconds, 0 seconds of which was spent in the Spotlight importer plugin.

Thanks for the instructions - this is what the Console showed. Where there's a line break, it came from a different file, eg system.log.4.bz2 and system.log.5.bz2 etc.
Jul 26 00:48:30 rocksteady com.apple.backupd[320]: Copied 159.8 GB of 334.6 GB, 540478 of 1528593 items
Jul 26 01:48:31 rocksteady com.apple.backupd[320]: Copied 172.0 GB of 334.6 GB, 546715 of 1528593 items
Jul 26 02:48:32 rocksteady com.apple.backupd[320]: Copied 183.9 GB of 334.6 GB, 550256 of 1528593 items
Jul 26 03:48:32 rocksteady com.apple.backupd[320]: Copied 195.9 GB of 334.6 GB, 553762 of 1528593 items
Jul 26 04:48:32 rocksteady com.apple.backupd[320]: Copied 209.2 GB of 334.6 GB, 558395 of 1528593 items
Jul 26 05:48:33 rocksteady com.apple.backupd[320]: Copied 222.9 GB of 334.6 GB, 561653 of 1528593 items
Jul 26 06:48:33 rocksteady com.apple.backupd[320]: Copied 235.7 GB of 334.6 GB, 564892 of 1528593 items
Jul 26 07:48:34 rocksteady com.apple.backupd[320]: Copied 248.4 GB of 334.6 GB, 569187 of 1528593 items
Jul 26 08:48:34 rocksteady com.apple.backupd[320]: Copied 260.3 GB of 334.6 GB, 572291 of 1528593 items
Jul 26 09:48:34 rocksteady com.apple.backupd[320]: Copied 271.3 GB of 334.6 GB, 575444 of 1528593 items
Jul 26 10:48:35 rocksteady com.apple.backupd[320]: Copied 283.0 GB of 334.6 GB, 578591 of 1528593 items
Jul 26 11:45:24 rocksteady com.apple.backupd[320]: Copied 582986 files (299.1 GB) from volume Macintosh HD.
Jul 26 11:46:12 rocksteady com.apple.backupd[320]: No pre-backup thinning needed: 28.26 GB requested (including padding), 101.33 GB available
Jul 26 11:46:12 rocksteady com.apple.backupd[320]: Waiting for index to be ready (100)
Jul 26 11:47:12 rocksteady com.apple.backupd[320]: Waiting for index to be ready (100)
Jul 26 11:49:52 rocksteady com.apple.backupd[320]: Copied 12158 files (86.2 MB) from volume Macintosh HD.
Jul 26 11:50:11 rocksteady com.apple.backupd[320]: Starting post-backup thinning
Jul 26 11:50:11 rocksteady com.apple.backupd[320]: No post-back up thinning needed: no expired backups exist
Jul 26 11:50:11 rocksteady com.apple.backupd[320]: Backup completed successfully.
Jul 25 00:48:16 Rocksteady com.apple.backupd[320]: Copied 21.9 GB of 334.6 GB, 60447 of 1528593 items
Jul 25 01:48:16 Rocksteady com.apple.backupd[320]: Copied 26.7 GB of 334.6 GB, 81017 of 1528593 items
Jul 25 02:48:17 Rocksteady com.apple.backupd[320]: Copied 28.3 GB of 334.6 GB, 104365 of 1528593 items
Jul 25 03:48:17 Rocksteady com.apple.backupd[320]: Copied 30.7 GB of 334.6 GB, 119305 of 1528593 items
Jul 25 04:48:17 Rocksteady com.apple.backupd[320]: Copied 32.1 GB of 334.6 GB, 139381 of 1528593 items
Jul 25 05:48:18 Rocksteady com.apple.backupd[320]: Copied 33.5 GB of 334.6 GB, 202617 of 1528593 items
Jul 25 06:48:19 Rocksteady com.apple.backupd[320]: Copied 37.2 GB of 334.6 GB, 243417 of 1528593 items
Jul 25 07:48:20 Rocksteady com.apple.backupd[320]: Copied 46.5 GB of 334.6 GB, 251412 of 1528593 items
Jul 25 08:48:21 Rocksteady com.apple.backupd[320]: Copied 56.9 GB of 334.6 GB, 258836 of 1528593 items
Jul 25 09:48:22 Rocksteady com.apple.backupd[320]: Copied 68.8 GB of 334.6 GB, 281608 of 1528593 items
Jul 25 10:48:23 Rocksteady com.apple.backupd[320]: Copied 77.0 GB of 334.6 GB, 308346 of 1528593 items
Jul 25 11:04:37 Rocksteady com.apple.backupd[320]: CoreEndianFlipData: error -4940 returned for rsrc type FREF (id 129, length 7, native = no)
Jul 25 11:04:37 Rocksteady com.apple.backupd[320]: CoreEndianFlipData: error -4940 returned for rsrc type FREF (id 129, length 7, native = no)
Jul 25 11:48:24 Rocksteady com.apple.backupd[320]: Copied 80.2 GB of 334.6 GB, 334764 of 1528593 items
Jul 25 12:48:24 Rocksteady com.apple.backupd[320]: Copied 88.0 GB of 334.6 GB, 346337 of 1528593 items
Jul 25 13:48:25 Rocksteady com.apple.backupd[320]: Copied 103.5 GB of 334.6 GB, 348352 of 1528593 items
Jul 25 14:48:26 Rocksteady com.apple.backupd[320]: Copied 111.0 GB of 334.6 GB, 359061 of 1528593 items
Jul 25 15:48:26 Rocksteady com.apple.backupd[320]: Copied 113.2 GB of 334.6 GB, 380031 of 1528593 items
Jul 25 16:48:27 Rocksteady com.apple.backupd[320]: Copied 117.4 GB of 334.6 GB, 395142 of 1528593 items
Jul 25 17:48:27 Rocksteady com.apple.backupd[320]: Copied 125.3 GB of 334.6 GB, 417683 of 1528593 items
Jul 25 18:48:27 Rocksteady com.apple.backupd[320]: Copied 131.9 GB of 334.6 GB, 438597 of 1528593 items
Jul 25 19:48:28 Rocksteady com.apple.backupd[320]: Copied 134.6 GB of 334.6 GB, 458980 of 1528593 items
Jul 25 20:48:28 Rocksteady com.apple.backupd[320]: Copied 136.3 GB of 334.6 GB, 490606 of 1528593 items
Jul 25 21:48:28 rocksteady com.apple.backupd[320]: Copied 138.3 GB of 334.6 GB, 508152 of 1528593 items
Jul 25 22:48:29 rocksteady com.apple.backupd[320]: Copied 141.1 GB of 334.6 GB, 519798 of 1528593 items
Jul 25 23:48:30 rocksteady com.apple.backupd[320]: Copied 143.8 GB of 334.6 GB, 540256 of 1528593 items
Jul 24 20:42:25 rocksteady com.apple.backupd[239]: Starting standard backup
Jul 24 20:42:26 rocksteady com.apple.backupd[239]: Backing up to: /Volumes/Little Nelly/Backups.backupdb
Jul 24 20:42:28 rocksteady com.apple.backupd[239]: Backup content size: 344.2 GB excluded items size: 9.6 GB for volume Macintosh HD
Jul 24 20:42:28 rocksteady com.apple.backupd[239]: No pre-backup thinning needed: 401.58 GB requested (including padding), 406.22 GB available
Jul 24 20:42:28 rocksteady com.apple.backupd[239]: Waiting for index to be ready (100)
Jul 24 20:42:48 rocksteady com.apple.backupd[239]: Copied 0 files (0 bytes) from volume Macintosh HD.
Jul 24 20:42:48 rocksteady com.apple.backupd[239]: Backup canceled.
Jul 24 20:48:12 rocksteady com.apple.backupd[320]: Starting standard backup
Jul 24 20:48:13 rocksteady com.apple.backupd[320]: Backing up to: /Volumes/Little Nelly/Backups.backupdb
Jul 24 20:48:19 rocksteady com.apple.backupd[320]: Backup content size: 344.2 GB excluded items size: 9.6 GB for volume Macintosh HD
Jul 24 20:48:19 rocksteady com.apple.backupd[320]: No pre-backup thinning needed: 401.54 GB requested (including padding), 406.21 GB available
Jul 24 20:48:19 rocksteady com.apple.backupd[320]: Waiting for index to be ready (101)
Jul 24 20:48:19 rocksteady mds[42]: (Normal) DiskStore: Creating index for /Volumes/Little Nelly/Backups.backupdb
Jul 24 21:48:15 Rocksteady com.apple.backupd[320]: Copied 9.4 GB of 334.6 GB, 20141 of 1528593 items
Jul 24 22:48:15 Rocksteady com.apple.backupd[320]: Copied 16.9 GB of 334.6 GB, 20160 of 1528593 items
Jul 24 23:48:16 Rocksteady com.apple.backupd[320]: Copied 19.9 GB of 334.6 GB, 24060 of 1528593 items

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If I choose a hard drive ask my backup disk for time machine, will it clear out the data that was previously stored in my hard drive?

If I choose a hard drive ask my backup disk for time machine, will it clear out the data that was previously stored in my hard drive?

Hello edjhsu,
Unless the drive is in a format that isn't compatible with Time Machine, the files will not be overrwitten. However it is typically a better idea to keep your files and your backup separate, especially since files on the Time Machine drive will not be backed up by Time Machine.
Mac Basics: Time Machine backs up your Mac
http://support.apple.com/kb/HT1427
Cheers,
Allen

Time Machine stuck in a new and different way

Time Machine is stuck in a new way. "dtruss -e -p <pid>" shows it in a loop doing nothing but this:
   1032 __semwait_signal(0xC03, 0x0, 0x1)
= -1 Err#60
   1143 __semwait_signal(0xC03, 0x0, 0x1)
= -1 Err#60
   1155 __semwait_signal(0xC03, 0x0, 0x1)
= -1 Err#60
   1146 __semwait_signal(0xC03, 0x0, 0x1)
= -1 Err#60
   1153 __semwait_signal(0xC03, 0x0, 0x1)
= -1 Err#60
   1152 __semwait_signal(0xC03, 0x0, 0x1)
= -1 Err#60
   1138 __semwait_signal(0xC03, 0x0, 0x1)
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= -1 Err#60
   1155 __semwait_signal(0xC03, 0x0, 0x1)
= -1 Err#60
(The numbers are the elapsed times in microseconds. Err#60 is ETIMEDOUT.)
Repeated use of lsof shows that backupd has no regular files open except its log file, which ends with
+----
Processing preflight info
    Space needed for this backup: 3.83 GB (933889 blocks of size 4096)
    Preserving last snapshot /Volumes/Loki TM/Backups.backupdb/loki/2013-04-18-073658
Finished processing preflight info
Copying items from "Loki HD" (mount: '/' fsUUID: 9E4DC7A0-9DDE-3A37-827F-3BB94B19F396 eventDBUUID: AD43DC6A-C748-44F2-8A1B-494E472E3214)
+----
I killed it, trashed the .inProgress backup, and started it up again and it has been like this for two more days.
The backupd disk is a partition on a local firewire drive. Backups had been proceeding normally for a couple of months at least.
Any ideas?

If you have more than one user account, these instructions must be carried out as an administrator.
Launch the Console application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Console in the icon grid.
Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left. If you don't see that menu, select
View ▹ Show Log List
from the menu bar.
Enter the word "Starting" (without the quotes) in the String Matching text field. You should now see log messages with the words "Starting * backup," where * represents any of the words "automatic," "manual," or "standard." Note the timestamp of the last such message. Clear the text field and scroll back in the log to that time. Select the messages timestamped from then until the end of the backup, or the end of the log if that's not clear. Copy them (command-C) to the Clipboard. Paste (command-V) into a reply to this message.
If there are runs of repeated messages, post only one example of each. Don't post many repetitions of the same message.
When posting a log extract, be selective. Don't post more than is requested.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Some personal information, such as the names of your files, may be included — anonymize before posting.

Time Machine stuck in "preparing" endlessly.

I have been able to successfully back up my MacBook Pro twice in the past two months using Time Machine, but both times I had to monkey with it, and I'm not even sure what exactly I did to make it work.
Today I've tried several times to back up my machine, but it seems to get stuck "preparing" for hours.
I don't keep Time Machine plugged into my laptop because I need that USB for my printer. Rather, I periodically plug my Sea Gate FreeAgent external drive in and attempt to manually back up. But it never just works without a lot of clicking around.
What am I doing wrong??? How can I get it to work??
Thanks so much!

xtine,
Your situation is explained in the first section of the info below:
*_Time Machine May Report "Preparing..." For a Long Time_*
Consider these factors regarding an extended period of "Preparing...". Consider each topic separately and do not attempt to act on all of them at once.
*Recent Crash or Other Major System Event* (Deep Traversal)
The reasons for this process are described in an article by George Schreyer. “During the preparation step it checks the FSEvents log for consistency. If it determines that something isn't quite right it has to rescan the whole disk. This can take quite awhile. A full rescan is always triggered by a crash, an unplanned shut down event or by booting from some other bootable disk between backups…. After a crash, Time Machine must scan the whole disk to determine what it has to do because it cannot trust the information that it left behind. Connected via an Ethernet connection, this phase would typically take 20 minutes on an older PowerBook. Being connected wirelessly stretches this phase out to over 3 hours.” [http://www.girr.org/mac_stuff/backups.html]
According to the following KB article it can sometimes take a very long time if Time Machine begins this “deep traversal” and has to compare data inventories. This may apply to your situation, particularly if many Gigs of data are involved. (http://support.apple.com/kb/TS1516) Additionally, if Time Machine has not been able to perform its’ hourly backups for 24 hours or more, then it will perform a “deep traversal” once backups are renewed. This is the case for users who only backup once a week or so.
*Anti-Virus Software*
Running anti-virus software can interfere with the backup process. Either disable it altogether, or try the suggestion outlined here, “If you use third-party anti-virus scanning software and have issues, make sure your Time Machine back up folder (Backups.backupdb on the Time Machine disk) is excluded from virus scanning.” (http://support.apple.com/kb/TS1516)
*Software Updates* #
Installing new software, upgrading existing software, or updating Mac OS X system software can create major changes in the structure of your Macs directories. Time Machine will backup every file that has changed since the installation.
If you take a look at the Console logs Time Machine may be reporting that your backups need "deep traversal". That's fine. Time Machine knows what is wrong and how to fix it. If you have a great deal of data, it may take quite awhile.
After an OS update (like 10.5.5) Time Machine realizes the system no longer matches what it looked like during the previous backup. So it has determined that it's earlier catalogue of what-should-be-where is 'untrustable'. So it is going to go item-by-item comparing the before and after of your system. If you have just performed an OS Update then Time Machine knows what it's doing - let it do it!
*Spotlight Keeps Indexing Backup Drive* #
It may be that Time Machine can’t proceed or complete a backup due to a Spotlight indexing error. During this period, take a look at the Spotlight icon in the upper right corner of your screen. Is there a tiny dot pulsating in the center of the spyglass? Click on the icon. Is there a progress bar displayed? Generally, Spotlight indexing is a good thing. If it has only been a couple of hours then let the process contiune.
However, at times it may hang and never progress after many hours, preventing further backups from taking place.
Go to System Prefs --> Spotlight --> Privacy Tab.
Drag your Time Machine disk into the window. It should now be among the items to exclude from indexing.
Now quit System Prefs.
Reboot your Mac.
Reopen System Prefs and remove ("-") the Time Machine disk from the window.
Now initiate a backup.
This should clear out Spotlights cache. Naturally, Spotlight should begin indexing again (maybe even for a few hours depending on how much data there is), but it should eventually stop.
*Reboot Time Capsule* #
If, though, none of the options above have helped and it has been 12 hours or more of “Preparing…”, then the Time Capsule may need to be restarted.
Stop the backup from the Time Machine menu. (Give if a few minutes while it says “Stopping backup…”)
When the Time Machine icon stops spinning, unplug the TC from the wall outlet.
Wait 10-15 seconds.
Re-plug it in again.
After it has restarted (30-60 seconds), attempt another backup.
Time Machine will report “Preparing…” again, but it shouldn’t be lasting more than a couple of hours.
Let us know if any of the suggestions above helped in your case.
Cheers!

Time Machine Stuck on Preparing -- Solved

Info for future Internet searchers:
Thanks to the great info provided by Pondini (http://pondini.org/TM/Troubleshooting.html) I was able to solve a problem with Time Machine on a sick Macbook Pro. I may need to reload the Mac from recovery disks, but beforehand I always like to have a good backup.
First problem: Time Machine to AFP-based NAS fails. It mounts the drive, looks at the .sparsebundle file and then complains that it's already in use. This is not on an AirPort so the steps in Pondini's guide don't apply: http://pondini.org/TM/C12.html. Rebooting the NAS didn't help. I put this issue on hold for now since my goal was to get a backup by whatever means rather than trying to get the more convenient network-based backups working.
Second problem: Time Machine to a new USB drive fails. It would get stuck in "preparing to back up" with this system log message repeated for over 12 hours without change:
com.apple.backupd: Waiting for index to be ready (101)
Section D2 (http://pondini.org/TM/D2.html) had a very applicable section, "Repeated Indexing Messages." Unfortunately, removing the /Volumes/<volume name>/.Spotlight-V100 directory didn't help. However, deleting /.Spotlight-V100 from the SOURCE drive, rebooting, and letting Spotlight rebuild its index did clear up the error. Backups seem to be running to local media now.

See Pondini's TM FAQs for starters.

Time Machine stuck while copying and it ends up blocking the whole mac

I've a problem with my time machine backup. The backup drive is a partition on an external USB drive. The drive has another partition for data. Everything worked good until yesterday. It gets stuck while copying the files, e.g. 532 MB of 5.45 GB, and it doesn't move even after a couple of hours. The backupd process is constantly using 100 % of one CPU and the other applications are getting stuck as well. I also notice that the USB drive stops spinning at a certain point, as if it goes idle.
I can't cancel the backup and I have to force shut down the Mac. After the restart, the backup will stop at Zero KB. If I delete the inProgress file nothing changes.
Here's the log:
Starting manual backup
Backing up to: /Volumes/LaCie/Backups.backupdb
Event store UUIDs don't match for volume: Macintosh HD
Deep event scan at path:/ reason:must scan subdirs|new event db|
Finished scan
Found 44342 files (4.95 GB) needing backup
7.4 GB required (including padding), 11.79 GB availabe
Then nothing more.

If you have more than one user account, these instructions must be carried out as an administrator.
Launch the Console application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Console in the icon grid.
Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left. If you don't see that menu, select
View ▹ Show Log List
from the menu bar.
Enter the word "Starting" (without the quotes) in the String Matching text field. You should now see log messages with the words "Starting * backup," where * represents any of the words "automatic," "manual," or "standard." Note the timestamp of the last such message. Clear the text field and scroll back in the log to that time. Select the messages timestamped from then until the end of the backup, or the end of the log if that's not clear. Copy them (command-C) to the Clipboard. Paste (command-V) into a reply to this message.
If there are runs of repeated messages, post only one example of each. Don't post many repetitions of the same message.
When posting a log extract, be selective. Don't post more than is requested.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Some personal information, such as the names of your files, may be included — anonymize before posting.

Time Machine Stuck (Incremental backup, not Initial)

Hey...me again.
I was finally successful yesterday backing up 160GB of data with Time Machine.
However, this morning, the incremental backup is taking forever. It's been stuck at "3.6MB of 6.7MB" for over 20 minutes. It would seem to me that 6.7MB should be pretty quick to backup.
I have received these messages from TM Buddy:
Starting standard backup
Backing up to: /Volumes/Time Machine/Backups.backupdb
No pre-backup thinning needed: 100.0 MB requested (including padding), 279.56 GB available
Unable to rebuild path cache for source item. Partial source path:
Copied 305079 files (49.1 MB) from volume Macintosh HD.
No pre-backup thinning needed: 100.0 MB requested (including padding), 279.31 GB available
And Console shows this:
Aug 25 10:23:53 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd[254]: Backup requested by user
Aug 25 10:23:53 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd[254]: Starting standard backup
Aug 25 10:23:53 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd[254]: Backing up to: /Volumes/Time Machine/Backups.backupdb
Aug 25 10:26:21 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd[254]: No pre-backup thinning needed: 100.0 MB requested (including padding), 279.56 GB available
Aug 25 10:27:51 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd[254]: Unable to rebuild path cache for source item. Partial source path:
Aug 25 10:41:06 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd[254]: Copied 305079 files (49.1 MB) from volume Macintosh HD.
Aug 25 10:42:21 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd[254]: No pre-backup thinning needed: 100.0 MB requested (including padding), 279.31 GB available
Any idea on how to resolve?
Thanks,
K

kieranroy wrote:
Hey...me again
Hi again. You seem to have really angered the god of TM, haven't you!
However, this morning, the incremental backup is taking forever. It's been stuck at "3.6MB of 6.7MB" for over 20 minutes. It would seem to me that 6.7MB should be pretty quick to backup.
Unable to rebuild path cache for source item. Partial source path:
This usually doesn't cause a real problem, as long as it's occasional.
Copied 305079 files (49.1 MB) from volume Macintosh HD.
This we see on occasion -- the crazy high file count, and very slow backup.
Aug 25 10:42:21 Kieran-Roys-MacBook-Pro /System/Library/CoreServices/backupd254: No pre-backup thinning needed: 100.0 MB requested (including padding), 279.31 GB available
Normally, TM will make a second, "catch-up" pass if changes were made during it's first pass. Usually this is very quick, but since the first one way very slow, this one may be worse.
Do you have any folders, particularly email mailboxes, with a very large number of files (thousands), that are actively being added-to or changed? There was a similar situation recently where an app named SpamSieve was putting messages into a "spam" folder, and the user never cleared it out. Clearing it out helped, but excluding it from Time Machine solved the problem.
Click here to download the TimeTracker app. It shows most of the files saved by TM for each backup (excluding some hidden/system files, etc.). I think it will only show completed backups, so you may not be able to find anything. But look at what's being backed-up to see if any of the files, even if there's only one, are in extremely large folders. If so, try excluding the folder (TM Preferences > Options).

Time machine stuck in time "long ago and far away"....

Strange issue I came across today: After a reboot following a hard disc repair (Drive Genius 3) my MacPro is stuck in a time slot of several months ago. All time machine backups (even of yesterday's date stamp) just take me back even further in time. None of my app updates are there - for example, some time ago I purchased iPhoto 11 from the app store - now I can't open my iPhoto library because "it was modified using a newer version of iPhoto". The app store doesn't think I ever purchased anything, even though iPhoto was one of several (some free). Interestingly Aperture 3.0 is there (purchased when it first came out), and all my recent photos are there as well.
Anybody have a clue as to what might be going on?

I may have found the solution, although how this was created is a complete mystery to me. On the drive that was repaired by DriveGenius I found a complete "parallel universe" with all the latest files, folders, apps and everything. I can understand how it might duplicate some of the applications since I tended to keep some of them there, but how it ended up with a complete operating system, home folder, etc. essentially a clone of my root drive???? Booting into that drive got me right back to where I had been a day ago. It would almost suggest that I had been running off that drive all along, but that flies in the face of the Drive Genius repair protocol that does not allow (similar to Diskutility) repair of the drive you are booted from (somewhat obvious since it needs to be unmounted in order to be repaired).
I guess all I have to do now is clone all this back to my usual start-up drive and be done..
Thanks for your efforts! I guess this one is one for the "mark it up as experience" books....I'd still love to hear your opinion on what I might have done or ben doing that could have caused this...
Ed

Time machine tried to clear my hard drive and I chose "NO" yet hard drive is now showing no files but shows space is still used?

yesterday morning I was working and a window randomly popped up for time machine. I don't have the exact wording that was on the pop up window because I assumed it wasn't spam as it was asking me to choose a place to store my time machine backup. I've never seen this window before but just a couple week ago I was having storage problems and hae tried to fix them by clearing some files. So I assumed this window was about helping clear some space on the computer. So I chose my silver hard drive to use for the backup for time machine. 20 min later I get another pop up that is asking me if I'm sure I want to choose my silver hard drive as it will erase anything that is currently on the drive - I immediately panicked and chose "NO" for it to not use the hard drive. I assumed I was in the clear at this point. But I didn't check the drive until later yestsrday evening and now the folder is empty when I open the drive. Yet when I check the space available on the drive it shows over 400G that's taken and 600+G that's available which means the files I had on there are still there but I can't see them? Where have they gone? And was this time machine pop up window spam? I opened my time machine and it was turned off?

Choose Go to Folder from the Finder's Go menu and provide /Volumes/ as the path.
(71792)

Time machine stuck on 'calculating changes'

I have been using Time Machine backups to a 2TB Time Capsule for over a year, and one of my 4 computers has recently stopped backing up. The other 3 are still backing up fine, and I ran disk utility on the Time Capsule which stated that it was working fine as well. Backing up my MacBook Pro is now stuck in an endless (over 24 hrs) 'calculating changes'. I have tried directly connecting it via ethernet to the Time Capsule, but still have the same problem. I'd prefer not to start from scratch as the base backup is around 250GB. Any advice?

Well, I repaired the disk -- but still having the same problem. Seems to be getting stuck at the same place in the log:
Starting standard backup
Attempting to mount network destination using URL: afp://Mark%[email protected]/Data
Mounted network destination using URL: afp://Mark%[email protected]/Data
Error loading /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: dlopen(/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin, 262): no suitable image found. Did find:\n /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: mach-o, but wrong architecture
Cannot find function pointer VRPreviewCFPlugInFactory for factory 20D1C6B2-6A02-11D7-B5A6-000393D45566 in CFBundle/CFPlugIn 0x10050db60 </Library/Plug-ins/DiskImages/NUMPlugin.bundle> (bundle, not loaded)
Error loading /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: dlopen(/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin, 262): no suitable image found. Did find:\n /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: mach-o, but wrong architecture
Cannot find function pointer VRPreviewCFPlugInFactory for factory 20D1C6B2-6A02-11D7-B5A6-000393D45566 in CFBundle/CFPlugIn 0x10050db60 </Library/Plug-ins/DiskImages/NUMPlugin.bundle> (bundle, not loaded)
2010-09-12 18:23:53.015 diskimages-helper[256:2103] Error loading /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: dlopen(/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin, 262): no suitable image found. Did find:
/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: mach-o, but wrong architecture
2010-09-12 18:23:53.018 diskimages-helper[256:2103] Cannot find function pointer VRPreviewCFPlugInFactory for factory 20D1C6B2-6A02-11D7-B5A6-000393D45566 in CFBundle/CFPlugIn 0x1003193a0 </Library/Plug-ins/DiskImages/NUMPlugin.bundle> (bundle, not loaded)
2010-09-12 18:23:53.189 diskimages-helper[256:2103] Error loading /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: dlopen(/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin, 262): no suitable image found. Did find:
/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: mach-o, but wrong architecture
2010-09-12 18:23:53.190 diskimages-helper[256:2103] Cannot find function pointer VRPreviewCFPlugInFactory for factory 20D1C6B2-6A02-11D7-B5A6-000393D45566 in CFBundle/CFPlugIn 0x1003193a0 </Library/Plug-ins/DiskImages/NUMPlugin.bundle> (bundle, not loaded)
QUICKCHECK ONLY; FILESYSTEM CLEAN
2010-09-12 18:23:55.265 diskimages-helper[263:2103] Error loading /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: dlopen(/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin, 262): no suitable image found. Did find:
/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: mach-o, but wrong architecture
2010-09-12 18:23:55.267 diskimages-helper[263:2103] Cannot find function pointer VRPreviewCFPlugInFactory for factory 20D1C6B2-6A02-11D7-B5A6-000393D45566 in CFBundle/CFPlugIn 0x10051bae0 </Library/Plug-ins/DiskImages/NUMPlugin.bundle> (bundle, not loaded)
2010-09-12 18:23:55.402 diskimages-helper[263:2103] Error loading /Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPlugin: dlopen(/Library/Plug-ins/DiskImages/NUMPlugin.bundle/Contents/MacOS/NUMPl

Time machine stuck on 564bytes

Hi there.
I recently decided to backup my Mac as usual. I keep my external HD in a safe place and to my knowledge nothing has been spilled on it etc. Everything is still accesible on it. But I realised, while backing up my computer, that it was taking a really long time. I checked and I realised that only a few megabytes had been backed up. I thought nothing of it at the time but when I looked at it again a few mins later it was still at the same stage. I restarted the process and a similar thing happened this time getting stuck at the same stage (i.e actually started moving files to the external HD). I restarted a few times and the same thing happened.
Does anyone have any ideas as to what would be a good solution to the problem and maybe what's going on?
It would be greatly appreciated.
Thanks
Alex

Do you have any anti-virus installed? It can happen with them sometimes.
edit:
Time Machine buddy dashboard widget an TM Error Logger Application can help too. Try also ALT cliking the menubar icon for Time Machine and chose "verify backup" from the drop-down menu.
Hope it'll help.

Time Capsule / Time Machine stuck on 'calculating changes'

Time Machine has not backed up to my Time Capsule for the last several weeks on my MacBook Pro. It is constantly stuck on 'calculating changes' for hours. I have tried other suggestions I have found in the forum like verify and repair disc on both my internal HDD and on the time capsule drive. No errors were found on either drive. I normally backup via wifi and I have also tried plugging directly into the time capsule with an ethernet cord. It doesn't make any difference either with wifi or ethernet.
The time capsule drive is full, but I just assumed that Time Machine would erase the oldest backups and continue. I don't know if this is an issue with the problem I am having. I downloaded the time machine widget as suggested in other posts on this topic, the log is posted below. There are errors about the disc being full and an error writing to the backup log. I don't know why it can't right to the log or what could be wrong. After looking at the logs, it appears that what is shown below just continues to repeat about every two hours (time machine seems to give up after about 2 hours and starts over again with the same result).
I am thinking of erasing the time capsule disc and trying to start over, but would like to figure why this has happened before I erase the disc. I am also worried about erasing my only backups, even if they are three weeks old. Entering time machines still seems to give me all of my older backups like nothing is wrong, but I haven't restored from one so they may not work if I tried.
Any help would or insight into this would be greatly appreciated.
Starting standard backup
Attempting to mount network destination using URL: afp://Kason%[email protected]/Data
Mounted network destination using URL: afp://Kason%[email protected]/Data
QUICKCHECK ONLY; FILESYSTEM CLEAN
Disk image /Volumes/Data/MacBook Pro.sparsebundle mounted at: /Volumes/Time Machine Backups
Backing up to: /Volumes/Time Machine Backups/Backups.backupdb
Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: No space left on device
Exception writing exclusions cache. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: No space left on device
Unable to create exclusions cache data.
Failed to write exclusions cache. Continuing anyway.
Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: No space left on device
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Waiting for index to be ready (101)
Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandl

jaxx323 wrote:
The time capsule drive is full, but I just assumed that Time Machine would erase the oldest backups and continue.
Ordinarily it will. Do you have other data on the drive? If so, it appears that other data has completely filled the drive, so much so that Time Machine can't even start the hidden log it keeps there.
Error writing to backup log. NSFileHandleOperationException:* -[NSConcreteFileHandle writeData:]: No space left on device
Usually when that happens, the backup crashes.
First, cancel the backup. If it won't cancel after a few moments, see #D6 in [Time Machine - Troubleshooting|http://web.me.com/pondini/Time_Machine/Troubleshooting.html].
Then connect via an Ethernet cable if at all possible. Time Machine needs to do some intensive work, and it will be slow even via Ethernet, but 2-3 times slower via WIFI.
If there's other stuff on the drive, you could copy some of it elsewhere temporary and delete it. You only need to free up 50 MB or so.
But your best bet is to delete your oldest backup(s), then "compact" the sparse bundle they're in, to make some space. See #12 of [Time Machine - Frequently Asked Questions|http://web.me.com/pondini/Time_Machine/FAQ.html].
Since it's been several weeks, you may want to delete roughly one old backup for each of those weeks, then "compact" the sparse bundle. If you only delete one, then Time Machine will have to delete more, but it will delete one, dismount the sparse bundle, compact it, then remount it to see if there's enough room. That gets repeated over and over until there's enough space.
Once this is sorted out, if there is other stuff on your TC's internal HD, see #Q3 in [Using Time Machine with a Time Capsule|http://web.me.com/pondini/TimeMachine/TimeCapsule.html] (or use the link in *User Tips* at the top of this forum).

OS 10.7.5 time machine stuck on prepping

I am running 10.7.5 and my time machine has bee stuck on prepping for weeks.
I have seen other fixes in the support posts, but they aren't for Lion. Does anybody know if the fix is the same or is there something new?
Thanks

It's not for your system but the exerpt regarding third-party anti-virus scanning software remains applicable: Mac OS X 10.5: Time Machine may display "Preparing" for a longer time
It shoudn't take long for you to rule that out, so following that step read Apple Support Communities contributor Pondini's FAQ regarding that question: Stuck in "Preparing" or "Calculating changes"
The end of that page leads you right back where you came, so if that's how you arrived here then I'll try to rouse Mr. Pondini for you.

Time machine stuck on restore

Hi, I recently did a fresh install of Yosemite after doing a Time Machine backup on my USB drive of 10.9.2
Wanting to switch back to 10.9.2 I have booted from my a different USB drive I made for the 10.10 install, erased and partitioned the hard drive, quit disk utility, chose restore from time machine backup, selected the hard drive with the back up and the date of recent back up.
Now, it took well over 4 hours to show me the installation process but finally after it restarts I get a message saying use dick utility to fix problems, restore from time machine or continue to install OS X. I thought to myself well, I already just went through 4 hours of restoring my time machine so why choose it again and went with the option continue to install OS X.
Again, another progress bar that has been stuck on 19 minutes remaining now for well over an hour.
I hav done time machine back up restores before from lion to mavericks with no problems but can't figure out why this one is taking so long or what i have done wrong.
Any help would be greatly appreciated.
Many thanks
Kevin

The warranty entitles you to complimentary phone support for the first 90 days of ownership.

Time Machine stuck in Preparing Data Mode

In the past two days my time Machine has not made a successful back up. It seems to be stuck in "preparing data" and will stay like this all day. Even when I click the time machine preferences and stop it, it never changes. Does anyone have any solutions to this or has experienced it.Any suggestions would be greatly appreciated.
Thanks!!

Judith,
The following might contain an explanation for what you are experiencing.
*_Time Machine May Report "Preparing..." For a Long Time_*
First, it’s good to determine WHY Time Machine is "Preparing..." for an extended period of time. Examining the Console logs during this event can reveal what is actually going on behind the scenes. It may be “Preparing…” for a genuinely good reason. How long is 'too long' to wait for Time Machine to finish "Preparing..."? Some times, "Preparing..." is required to perform the normal housekeeping that Time Machine does periodically. Other times, it really is "stuck" and never proceeds after more than 24 hours.
*”Deep Traversal” (Recent Crash / Forced Restart / System Update / Extended Period Between Backups)*
According to the following KB article it can sometimes take quite a long time if Time Machine begins a “deep traversal” and has to compare data inventories. This may apply to your situation, particularly if many Gigs of data are involved. [http://support.apple.com/kb/TS1516]
You see, Time Machine *+does not+* ordinarily perform file-by-file comparisons to determine what has changed and thus determine what needs to be backed up. Rather, Time Machine relies on FSEvents notifications. This is a log that the system uses to keep track of changes to directories. Rather than scan tens of thousands of files for changes each time, Time Machine simply looks at this log and narrows its’ scan to only the directories that have experienced changes since the last backup. Otherwise, Time Machine would have to be running constantly just to catch every change on its own and thus eat up precious CPU.
Every event that FSEvents records has its’ own ID which includes a time stamp. At the end of every backup, Time Machine stores the last event ID that it processes. When the next backup is initiated, Time Machine looks at this stored ID and determines that it only needs to backup events that have occurred after the time stamp on this last event ID.
If, due to a system crash, power failure, forced restart, or some other major system event, Time Machine cannot find this last event ID in the system logs then it will consider the FSEvents log “untrustable” and it will go into what’s called “deep traversal”. The Console logs may report +“Event store UUIDs don't match”.+ In this event, Time Machine will by-pass the system log entirely and perform its’ own file-by-file comparison to determine what has changed since its’ last backup. Obviously, if tens or hundreds of Gigs are involved, then this process can take quite some time and should be allowed to proceed.
Additionally, it appears that if Time Machine has to go back too far to find the last event ID, then it will give up and simply go into “deep traversal” and do the file-by-file scan on its’ own. This can occur if Time Machine has not been able to perform its’ hourly backups for some time, as is the case for users who only backup once a week or so. This is also the case with major Mac OS system updates that change thousands of files at one time. There are simply too many events logged by the system for Time Machine to bother looking for the last known event ID.
*Consolidation / “Thinning”*
At the beginning, when Time Machine is first used, incremental backups are relatively quick events. But as time goes on, and backup files grow, Time Machine requires time to perform house-keeping on the backed up data. This maintenance is referred to in the Console logs as "thinning". The larger the backup files become, the more time Time Machine requires.
To prevent the backup drive from filling up too fast, Time Machine will periodically consolidate, or 'thin', backups to free up space for new data. After a certain period of time, each hourly backup becomes "expired". This occurs about 24-48 hours after the hourly backup took place. At that point Time Machine begins consolidating, or "thinning", all the hourly backups of a given day into one daily backup. Then, after about a month all daily backups for a given week “expire” and are consolidated into a single weekly backup.
Obviously, since the Time Machine process (backupd) does not run continuously, it has to do this "thinning" during routine backups. That is where "Preparing Backup..." and "Finishing Backup..." come in. It is during these initial and closing phases of a backup that "thinning" occurs. As a result, while not every backup will be accompanied by extended periods of "Preparing..." and "Finishing...", periodically Time Machine will require extra time to perform these space-saving consolidations.
*Anti-Virus Software*
Running anti-virus software can interfere with the backup process. Either disable it altogether, or try the suggestion outlined here, “If you use third-party anti-virus scanning software and have issues, make sure your Time Machine back up folder (Backups.backupdb on the Time Machine disk) is excluded from virus scanning.” (http://support.apple.com/kb/TS1516)
*Software Updates* #
Installing new software, upgrading existing software, or updating Mac OS X system software can create major changes in the structure of your Macs directories. Time Machine will backup every file that has changed since the installation.
After an OS update (like 10.5.5) Time Machine realizes the system no longer matches what it looked like during the previous backup. So it has determined that it's earlier catalogue of what-should-be-where is “untrustable”. So it is going to go item-by-item comparing the before and after of your system.
*Spotlight Keeps Indexing Backup Drive* #
It may be that Time Machine can’t proceed or complete a backup due to Spotlight indexing. During this period, take a look at the Spotlight icon in the upper right corner of your screen. Is there a tiny dot pulsating in the center of the spyglass? Click on the icon. Is there a progress bar displayed? Generally, Spotlight indexing is a good thing. If it has only been a couple of hours then, stop the backup, turn Time Machine OFF, and let the indexing continue.
However, at times Spotlight may hang and never progress after many hours, preventing further backups from taking place.
Go to System Preferences --> Time Machine.
Using the slider on the left, turn OFF Time Machine backups for now.
Next, click “Show All” in the toolbar.
Select the Spotlight Preferences.
Click the Privacy Tab.
First, drag your Macs’ internal hard disk from the desktop to the Privacy list.
Wait 10 seconds, then highlight the Macs’ hard disk in the list and click the tiny “-” button at the bottom to remove it from the list.
Spotlight will initiate a reindex of the hard disk. If you click on the Spotlight menu icon you may see the message:
+“Spotlight helps you quickly find things on your computer. Spotlight will be available as soon as the contents of your computer have been indexed.”+
...and a progress bar will indicate the time remaining.
Once completed, drag your Time Machine backup disk into the Privacy list of the Spotlight Preferences.
Wait 10 seconds, then highlight the Time Machine backup disk in the list and click the tiny “-” button at the bottom to remove it from the list.
Spotlight will now initiate a reindex of the hard disk.
Once completed, if you have any other hard disks attached to your Mac that are also being backed using Time Machine, then force a reindex as well using the procedure outlined above.
Then turn Time Machine back ON and initiate a backup.
*Run Away System Process*
It’s possible that Time Machine is stuck “Preparing…” because another process is monopolizing your Macs’ CPU. Launch Activity Monitor and sort the items by “CPU”. Is there a process that is at or near 100% that might be preventing the backupd process from moving forward?
One poster stated, “I took it to my local Genius Bar and they found a Syslogd daemon running, taking up 100% of my CPU….This resulted in the "Preparing..." mode running forever.” [http://discussions.apple.com/thread.jspa?threadID=1755600&tstart=15]
You may be able use Activity Monitor to “kill” the offending process. Or you may be able to resolve it simply by rebooting your Mac. Then try backing up again.
*Verify/Repair Mac Hard Disk & Permissions*
It may be that your Macs’ internal hard disk has so many file/directory issues that Time Machine simply has trouble making sense of it. Some users have had success using Disk Utility on their Macs’ hard drive.
Launch Disk Utility and click “Repair Disk Permissions”.
Once complete, attempt a backup.
If Time Machine appears to hang at “Preparing…” again, then do the following:
Insert your Macs’ original install DVD and reboot holding down the “C” key.
At the Welcome screen go up to the “Utilities” menu and select Disk Utility.
Select your Macs’ hard disk on the left and click “Verify Disk” on the right.
If problems are found click “Repair Disk”.
Reboot to your normal desktop and try backing up again.
*For Time Capsule Users* #
If, though, none of the options above have helped and it has been 12 hours or more of “Preparing…”, then the Time Capsule may need to be restarted.
Stop the backup from the Time Machine menu. (Give if a few minutes while it says “Stopping backup…”)
When the Time Machine icon stops spinning, unplug the TC from the wall outlet.
Wait 10-15 seconds.
Re-plug it in again.
After it has restarted (30-60 seconds), attempt another backup.
Time Machine will report “Preparing…” again, but it shouldn’t be lasting more than a couple of hours.
Let us know if any of the above was helpful in resolving your issue.
Cheers!

Time Machine stuck in "clearing up...

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