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.

Similar Messages

Time Machine stuck while backing up

Time machine has worked fine since I set it up, but now it has not finished a backup since 4/16. Time Machine just sits there and says Backing Up: 4KB of 9.1GB. I have left it on for days and it never gets past this point. I have done some of the suggestions here. Turned off spotlight on the backup disk, ran disk Utility (with no issues), Repaired Permissions, I deselected my backup disk and then reselected it in Time Machine, and I do not have set the HD to go to sleep. I have download the Time Machine Buddy widget and this is what is says currently:
Starting standard backup
Mounted network destination using URL: afp://David%[email protected]/Backup
Backup destination mounted at path: /Volumes/Backup-1
Disk image /Volumes/Backup-1/David Grayson’s iMac_001ec214f4f7.sparsebundle mounted at: /Volumes/Backup of David Grayson’s iMac
Backing up to: /Volumes/Backup of David Grayson’s iMac/Backups.backupdb
Event store UUIDs don't match for volume: Macintosh HD
Waiting for index to be ready (905 > 0)
Waiting for index to be ready (905 > 0)
Waiting for index to be ready (905 > 0)
Node requires deep traversal:/ reason:kFSEDBEventFlagMustScanSubDirs|kFSEDBEventFlagReasonEventDBUntrustable|
No pre-backup thinning needed: 12.40 GB requested (including padding), 58.98 GB available
Several previous messages say:
Starting standard backup
Backup destination alias resolved to path: /Volumes/Backup
Disk image /Volumes/Backup/David Grayson’s iMac_001ec214f4f7.sparsebundle mounted at: /Volumes/Backup of David Grayson’s iMac
Backing up to: /Volumes/Backup of David Grayson’s iMac/Backups.backupdb
No pre-backup thinning needed: 12.36 GB requested (including padding), 59.31 GB available
Stopping backupd to allow ejection of backup destination disk!
I think the last line is there when I shutdown the computer.
Any help would be greatly appreciated.
Thank you
David

Well I am not sure what I did (one log from Time Machine Buddy did mention having problems with a Logitech app, so I deleted it) but the backup worked last night. FYI, I did not run Disk Utility on the Backup Disk.
Thanks anyway.
David

Time Machine Erroroccured while copying files to the backup volume.

Time Machine Error
Unable to complete backup. An error

While I am glad this worked for you, I tried this multiple times and my problem remains.
I think the concept of the timer machine is great, but backup methods that aren't reliable don't do much for me. I have a folder called "Precious" that I drag stuff into and I keep a copy of that folder on an external mirrored drive attached via firewire 800. I am sad to have to manage my files this way in 2009 but being responsible for your own data is and always has been the bottom line.
My Mac Book Pro just died after I updated to 10.5.6. It no longer boots, and AppleCare has asked me to fedex my notebook to them. They have warned me that they may wipe or replace my drive. Because of the failure of time machine, all the critical notes on my desktop are not backed up, and I have lost data I really needed.
You would think by 2009 there would be some kind of usable backup technology to help us safeguard our day to day data. Please Apple, do something about this.
Even with time machine, it is not clear to me how to restore a working operating system if something goes terribly wrong with Leopard. In the DOS days, programs and their data were stored in a directory and if you backed up that directory, you had your software and your data for later, minus of cource config.sys and autoexec.bat mods. These days with the software and data splattered all over in various directories, it is difficult (for me impossible) to assure you have everything you need to get back to where you were should something happen. I am tired of losing my data periodically when the OS tanks and I have to reload. Files I have created or downloaded I can do something about, but software is troublesome. I have multiple application programs that enforce install counts and will not reload more than two times. I am tired of begging vendors to reset my counts, and in the case of WordSearch (bible software), they refused and I lost significant time and money.

How do I move just my iPhoto files from Time Machine into my new Macbook Pro system without loading the whole former identity?

I don't wan to load my entire former user ID onto my new system. iPhoto keeps saying "The iPhoto library is a Time Machine Backup, and so cannot be used as the main library. Reopen iPhoto with the Option key held down to choose another library."
The only option is to close that window then and relaunch iPhoto as suggested with Option held down... that still will not allow me to put the pics in, however. Any suggestions? Thanks!

OS X Yosemite- Restore items backed up with Time Machine
Please visit Pondini's Time Machine FAQ for help with all things Time Machine.

I am having trouble uploading photos to facebook. I saw a block tab on the upload button, I clicked it and a mozilla window opened. I didn't understand it and then ended up blocking the facebook loader. How do I undo this?

When I tried to load picture to facebook it wouldn't load. Then in the upload pop-up I noticed a block tab over the upload button. I clicked it and a Mozilla window opened with all kinds of selections I didn't understand. In an attempt to get out of it I blocked the uploader now in FB and can't figure out how to make Mozilla unblock it.

That was probably an Adblock Plus "block tab" that you clicked.
Open ABP prefs and look at the top section of the Filter Rule section > My Ad Blocking Rules = right-click the rule that you just set and use '''Delete'''.

My Time Machine keeps backing up and won't stop.

My Time Machine keeps backing up and won't stop. The problem started when it said I was out if space. It is supposed to delete the oldest backup. Now I cannot even backup at all. It just keep going and never stops, although it really does not work at all. I have used the disk utilities and iI have Zeroed out. The TC is a 1 TB and is about 13 months old. Right now it says "79.9 MB of 104.9 MB" and "backing up 961,837 items". I do not have the check mark in "Notify after old backups are deleted." It will stay stuck like this for hours and hours. The TC is plugged into a U-verse router and the 27" MAC is plugged into the TC.

So you already wiped the old backup and started again??
If that is the case it did a fresh full backup ok?
How much free space is on the TC now?
Do you happen to have multiple network links? Meaning do you have TC bridged to the U-verse router.. with both ethernet and wireless working at the same time. I discovered this one all by my loansome.. having multiple paths does not seem to worry most things on the computer.. but it totally kills TM.
I had the same sort of thing happening in testing a TC I am fixing. So I have multiple ethernet and wireless. The incremental backups became extremely slow.. by turning off wireless and one ethernet so there is only one route to the TC.. it flys again.

I bought an external hard drive and now use it as time machine. I copied my photos to it. Can I now delete my iphotos?

My photo library is full. I bought an external hard drive and am using it as time machine. I copied my photo library to the external hard drive and burned all of my pictures onto DVD's. If I delete my photos from my computer, will the photos still be on the external hard drive and saved in time machine? I am parinoid about losing my photos (memories).

I think you mean Your Hard Disc is Full as opposed to iPhoto.
agrech21 wrote:
My photo library is full.
With regard to your iPhoto Library... you can Move it to another External Drive and use it from there and then you can use TM to Backup that Drive as well as as your Mac.
1) Move iPhoto Library to External Drive
See > iPhoto: How to move the Library to an EHD
First... Make sure the EHD is Formatted Mac OS Extended (journaled)...
Format, Erase, or Reformat a drive
Quit iPhoto if open.
Open your Pictures folder and select the iPhoto Library.
Drag the iPhoto Library to the External Hard Drive.
To Use iPhoto on an External Drive...
Hold down the Option key on the keyboard and open iPhoto. Keep the Option key held down until you are prompted to create or choose an iPhoto Library.
Click Choose Library.
Locate and select the iPhoto Library in its new location.
And also make sure that all is working to your Satisfaction before Deleting anything.

I try to backup my Macbook with Time machine, it goes fine and at the end it says that it could not be completed because "/Volumes/Data-2/ MacBook.sparsebundle is already in use".. What is that?!

I try to backup my Macbook with Time machine, it goes fine and at the end it says that it could not be completed because "/Volumes/Data-2/ MacBook.sparsebundle is already in use".. What is that?!

See #C12 in Time Machine - Troubleshooting

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!

Errors with Time Machine (not completing backup, and needing to erase the ".inProgress" package)

I have in a previous discussion been talking about errors with my Time Machine backup. The errors were with a problem with Indexing a file, it fails and stops the whole backup. Each time it attemps another backup, it fills my ".inProgress" package with a (nearly) whole backup, filling my Time Machine hard drive, and thus errasing my previous good backups. The error occurs after about 95% completion.
In my last post of a similar disscussion, the problem was indexing the Preference Pane files and this caused the whole backup to fail. This was my last post there: (below in some additional info of my situation)
I did exclude the MobileMe.prefPane. And I got:
12/16/11 9:24:50.468 PM com.apple.backupd: Starting standard backup
12/16/11 9:24:50.556 PM com.apple.backupd: Backing up to: /Volumes/3 TB GoFlex Drive/Backups.backupdb
12/16/11 9:25:14.418 PM com.apple.backupd: Waiting for index to be ready (101)
12/16/11 9:27:02.366 PM com.apple.backupd: Deep event scan at path:/ reason:must scan subdirs|
12/16/11 9:27:02.366 PM com.apple.backupd: Finished scan
12/16/11 9:33:37.119 PM com.apple.backupd: Deep event scan at path:/Volumes/Mac OS Lion GM reason:must scan subdirs|
12/16/11 9:33:37.119 PM com.apple.backupd: Finished scan
12/16/11 9:36:15.650 PM com.apple.backupd: 758.92 GB required (including padding), 830.32 GB available
12/16/11 10:25:14.873 PM com.apple.backupd: Copied 22.8 GB of 630.5 GB, 782749 of 2357620 items
12/16/11 11:25:15.335 PM com.apple.backupd: Copied 86.6 GB of 630.5 GB, 1167675 of 2357620 items
12/17/11 12:25:16.227 AM com.apple.backupd: Copied 152.2 GB of 630.5 GB, 1393795 of 2357620 items
Dec 17 01:25:16 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Copied 305.2 GB of 630.5 GB, 1413946 of 2357620 items
Dec 17 02:25:16 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Copied 457.1 GB of 630.5 GB, 1419190 of 2357620 items
Dec 17 03:19:07 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Copied 1736865 files (568.3 GB) from volume Macintosh HD.
Dec 17 03:25:16 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Copied 572.1 GB of 630.5 GB, 1848939 of 2357620 items
Dec 17 03:40:33 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Indexing a file failed. Returned 200 for: /Volumes/Mac OS Lion GM/System/Library/PreferencePanes/Mouse.prefPane, /Volumes/3 TB GoFlex Drive/Backups.backupdb/Tom iMac/2011-12-14-171406.inProgress/7DB524DD-EFB9-42A6-8A21-0A2A312EDA6D/Mac OS Lion GM/System/Library/PreferencePanes/Mouse.prefPane
Dec 17 03:40:33 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Aborting backup because indexing a file failed.
Dec 17 03:40:33 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Stopping backup.
Dec 17 03:40:33 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Copied 2164998 files (581.1 GB) from volume Mac OS Lion GM.
Dec 17 03:40:33 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Copy stage failed with error:11
Dec 17 03:40:50 Thomas-P-Kellys-iMac com.apple.backupd[99858]: Backup failed with error: 11
This time it was the Mouse.prefPane that caused the error. I'd like to exclude the entire PreferencePanes directory.
This was my error message this time:
I just realized this was on my small Developers partition. Perhaps there is an error with the build, OR an error with the initial restore. I'd like to perhaps exclude the entire /Volumes/Mac OS Lion GM. I expect that Time Machine is working fine with my main partition and the error happens when it's almost done with the Mac OS Lion GM partition.
The problem now is that I only have 265 GB of 3 TB available on my Time Machine HDD. If attempt another backup, it'll surely erase about 410 GB of my past saved backups. I've already lost 6 months, and I only have two months left of backups. I need to erase the ".inProgress" package again. That'll take time, and it's impossible to do from this main partition, even at root access. This ".inProgress" has a total of two (nearly) full backups; it didn't cleanup the first full backup attempt while starting the second,perhaps it would have had it finished. But I fear even if I exclude the whole "Mac OS Lion GM" partition, It'll create a third full backup before cleanup and erase ~400 GB of previous good backups. Then, I'll have a total of 4 (nearly) full backups! 3 TB is just enough without any past backups.
Maybe I'll just copy my documentations of my 'errasing the ".inProgress" package' last time (from the Mac OS Lion GM partition) and do a full restore of just that partition. Thus erasing the errors all together. If it doesn't fix the errors then this could be a bug in the build that doesn't allow Time Machine to work. I've always included this partition in Time Machine before, even with other Lion builds, so I suspect that it was an error in the initial restore. (I may be answering my own questions, and that the inital restore (of the small partition) is the problem, and I just need to re-restore the small partition)
Again, I'm going to have to erase the ".inProgress" file to regain 1.53 TB of space before proceeding.
Also, I gave myself permission to read the ".Backup.345781513.887697.log", the log that was created last night when I first started Time Machine this last time. It was interesting, but didn't show the error I could see from the console.
Right now, mds and mdworker appear to be going crazy even after I just now turned off Time Machine. I think I'll let it go for the rest of the night. Then I'll work on erasing the ".inProgress" package from the other partition boot up.
That was my entire last post. To add some information, I have two OS X partitons, both Mac OS X Lion. One is my large main partition, the other is one I don't mind testing with. I recently replaced my internal hard drive in my iMac and restored from Time Machine both partitions. This appeared to go smoothly. But I have yet to create a single successful Time Machine backup since. At first it was doing a Full Backup, which I didn't like, but now it just aborts around 95% completion. Each, time, it tries it fills the Time Machine hard drive with duplicate (nearly) full backups errasing my older good backups. I would like to erase the ".inProgress" file to save space.
My main question in this new discussion is does anyone know of a good way of erasing the ".inProgress" file? This is so I can preseerve my previous backups. ACLs and other permissions seem to make it impossible to erase from this startup partition, the one I'm running Time Machine from. Even at root level, if I give myself permission to change permissions or delete a file, it'll say Operation not Permitted instead of Permission Denied. I have been able to delete this ".inProgress" package before when booting from the other partition, but with great difficulty. I have had much help from another Member in this Support Community when it comes to solving my Time Machine problems. I think I have found the problem (indexing files in my small OS X partition), as stated in my copy& pasted post above, but I really need to delete this inProgress package first to save space before continuing!

Pondini wrote:
Gator TPK wrote:
Now I'll have to fix the small partition? How's the best way to do this? There could be thousands of files that won't index fine.
See if there's anything you haven't done, that applies, in the pink box of #C3 in Time Machine - Troubleshooting
Otherwise, since most (or all?) of the indexing errors are in OSX, you might want to just reinstall it. Something may have gone wrong sometime, that damaged those files.
I reviewed #C3 in Time Machine - Troubleshooting and I have already done most of those things. I have just learned something new though:
When I included my Main OS X partition again, I got an indexing error for the first time for that partition. I might be interesting to note that the _spotlight process was running, and it's running again (the magnifying glass has a dot and it generically says "Indexing Tom's iMac"). mdworker, mds and backupd processes really are working hard, one moment they used over 500% of my CPU. It's nice to know for once quad core is good for something other than video encoding. (Now if they could just get the Finder to do more than 100.1%, only 1 thread is doing 100%, I'd like to see file size calculations 8 times quicker!)
I never got an indexing error once in the past 2 weeks for that large Mac OS X v10.7.2 main volume, and it had appeared to finish that partition backup before running into problems with my smaller test partition. Also, I had just updated the smaller test partition with a later build of Mac OS X. But It appears that the beta builds are clearly not the problem. I thought I could just restore again (from the December 4th backup) the small partition and both would be fine.
I'll finish reviewing all the suggestions on Time Machine - Troubleshooting and go from there. Hopefully, the _spotlight indexing simutaniously was the only problem. It's strange that the indexing hasn't happened since the original restore last week untill I finally got a good clean complete partial Time Machine backup. Why would the first Time Machine backup trigger indexing again?
For now, I'm going to exclude the Main Partition again, and let another good backup run. And try your suggestions. (And wait till mds, mdworker, etc. to finish!)
I have the logs of the first two sucsessful backups and the last two failed backups from the last 3 hours, if that would help.?

Time Machine Restore Mangles Permissions and Groups

Circumstance:
My Macbook Pro running 10.5.5 gave a gray spinner after a restart last week. The restart was to clear out a couple of system processes eating up CPU when I had left it alone for a few hours.
Action:
After Disk Utility, zapping PRAM, and the probably some other standard trouble-shooting actions didn't fix the stuck start-up problem, I decided to try a full system restore from my Time Machine backups. I had previously successfully restored individual folders and files. Time Machine backs up wireless to a USB hard drive connected to my AirPort Extreme. To speed up the restore, I ran an Ethernet cable to the MBP from the Airport. The restore completed successfully. All the folders & files are correct, looks the same, etc. I restarted using the restored boot drive.
Problem:
The MBP is like a museum now--I can look but I can't touch. I first noticed something was wrong after logging in the first time because I couldn't move a file into a folder via drag-n-drop. Then Terminal went into a spinning beach ball when I opened it. Spotlight was not running. Then I noticed that my entire boot disk was read-only. I got info on the boot disk, and the Users & Groups list was strange--everyone was read-only, "wheel" had read-write and was the owner, and staff had read-write. Basically, it's like me, the Finder, an all applications have lost all their write/execute permissions on the entire drive.
*Unsuccessful Steps Taken:*
Ran Disk Utilities' Repair Permissions from Leopard dvd. Ran fsck -fy after mount / -uw from Leopard dvd Terminal and from single-user boot mode. Time Machine restore direct from TM disk via USB. Joined my user to wheel group. Changed my user password from Leopard dvd (which repairs home folder permissions). Played with chown to make all wheel-owned items staff-owned.
*Open Theories:*
Airport Time Machine restores strips ACLs and Permissions. I have to restore over wireless, not ethernet or usb. My TM backup is screwed up somehow.
Whew. This has been going on for a while, so I'm ready to give up and do an Archive & Install and begin manual migration from the backups, but my MPB is a fine-tuned machine and I hate to lose that, especially since it taunts me by being so close to normal (I can see everything! My desktop background and apps are there!).
Any help much appreciated!

The "full restore" from Time Machine is only for OSX drives.
For data-only drives, use the Time Machine browser (the "Star Wars" display). See Time Machine - Frequently Asked Question #15.
Depending on your setup, you may also want to review Transferring Home Folders not on a Startup volume.

TimeMachine not backing up, as hard drive is full. Can the time machine clear old backups and replace them with new?

Time Macine not backing up.
As the harddrive is full, Can the time machine clear old backups, and override them with new backups. For example 5 - 6 days +++ old. Backups were proformed dayly
Any help much appreciated
Many thanks,

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.

Does Time Machine replace changed files and delete old files?

I haven't upgraded to Leopard yet, but my son is a NEW CONVERT to the Mac; has uses Dells for years. He has a new Macbook Pro with Leopard. I use SuperDuper! with my Tiger Mini Mac.
I don't understand what Time Machine does. Does it continually update files on the target device, and if so how does it handle deleted and renamed files on the source device.
Thanks.

Time Machine takes a snapshot of the drive it is backing up every hour. If a file is new, renamed or modified since its last backup, Time Machine will make a physical copy of that file. To conserve drive space Time Machine will only make hard links back to its previously backed up files for files that exist on its source drive which remain unchanged. Hard links work in a somewhat similar fashion as aliases. If a file has been deleted Time Machine won't make a copy or hard link. You can read about how hard links work in Time Machine in this Ars Technica review.
http://arstechnica.com/reviews/os/mac-os-x-10-5.ars/14
If a file is not on the hard drive for over an hour and is deleted before Time Machine makes its hourly backup that file will not be in any of Time Machine's backups.
Time Machine only retains the first hourly backup of the day as its daily backup. The other hourly backups get deleted in the course of the day. That means that to be retained in the daily backups a file must be on the hard drive for over a day or be physically present on the source drive for the first backup of the day.
After a month, Time Machine retains the daily backup made on the same day of the week as the initial backup as its weekly backup. If a file is on the source drive for less than a week and is not in the daily backup retained as the weekly it will end up being deleted when Time Machine thins its daily backups.
When the Time Machine volume fills up, Time Machine will start deleting its earliest backups to make room for new ones.

MacPro wont back up to Time Machine or Carbon Copy Cloner?

I am running 10.6.8 on my 2 x 3 Ghz Intel Mac Pro with 10 Gb of Ram. I have been backing up my two internal drives to an external 2 Tb WD for over a year using time machine and it would lose the drive every once in a while but I could get it back. Now after multiple erasures and reformats I can't get Time Machine or Carbon Copy Cloner (not at the same time : ) ) to run any faster than 1Gb/13min. Just my big ol' music drive will take 6 days at that speed!
I know there is something wrong for these speeds to be this slow. Does anyone have any suggestions of ways to speed up transfer and get the data flowing freely like it should or even theories about what's going on? I am using USB 2.0 from the drive to the tower. Cheers.

First what interface did you use? USB2? can't and expect any decent backup performance and forget zeroing a drive. FW800? on some WD MyBook, yes.
I would if possible move it into a FW800/400/eSATA drive case from OWC.
Add a PCIe SATA + USB3 CalDigit card and use that.
Move the drive inside an option? some WD MyBook can't, were built around the external drive case.
Your profile is out of date 10.4.11 is way old and didn't include TimeMachine (10.5 Oct 2007)
Lion and ML are better at Disk Utility and managing disk drives.
I use WD Green, very inexpensive, but no MyBook (yet, maybe USB3 NAS some day).
Why keep your data on one drive that has been beaten to death and not try a WD Black or couple other drives - or do you have those just not listed? Clone your system, clone your data, and even a spare TimeMachine... but I would go with two system backup drives. That is safe, and covers anyone's important system and media and digital library needs.

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 while copying and it ends up blocking the whole mac

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