Time Machine won't backup root data

As I wrote earlier, something was wrong with your Time Machine preference file. If you care to post a backup copy of the file from before you recreated it, I might be able to say more. You'd have to open the file in a text editor and anonymize any personal information it contains. Then post the contents in a reply.

Is this normal?

Yes.

bolobo wrote:

. . .

But when I start Apples Migration Assistant,it shows me, that the size of the applications that I can select for restoring, is just a couple of Mb big (see Screenshot). Normally it should be approx. 22 Gb big.

That seems to be an approximation of what would actually need to be transferred. Applications that already exist (ie, with exactly the same name and location) are not copied. Besides being unnecessary, that also prevents replacing a newer version of an app with an older one.

So in theory, you'd think it should be zero in this case. But in addition to the applications themselves, Migration Assistant transfers some support files in the top-level Library folder. So the 1.2 MB you see may be some sort of approximation of that (Apple doesn't document exactly how the calculation is done.)

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.

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.

bolobo wrote:

. . .

Then I'm just waiting for something. But after 60 minutes nothing happen. TM just stucks for example at 50 Mb of 750 Mb.

That might be a directory problem on your internal HD. Try Verifying it with Disk Utility.

Time Machine drives me nuts.

Yeah, it works fine most of the time, but sometimes when it stumbles over something, it's hard to tell just what's going on.

By the way, you might want to try the widget in #A1 of Time Machine - Troubleshooting to display the backup messages from your logs. It's somewhat easier to use than Console, but doesn't always show everything you need.

bolobo wrote:

. . .

05.01.13 19:50:30,000 kernel[0]: /SourceCache/AppleFSCompression_kexts/AppleFSCompression-49/Compressors/Datales s/compressorType5Kext.c:532: Error: post_request error for /Volumes/Time Machine/Backups.backupdb/<user>/2013-01-05-172415/Macintosh HD/.DocumentRevisions-V100/PerUID/501/1/com.apple.documentVersions/002D5961-2D5 D-4294-80AF-3F9938EAB492.numbers/Contents/PkgInfo: 35

That's entirely weird. 😟 The file in question is in your Versions database (in red) -- it's supposed to be excluded automatically, since Time Machine cannot back it up!

Unless you've edited this system file:

/System/Library/CoreServices/backupd.bundle/Contents/Resources/StdExclusions.pli st

your version of OSX seems to be damaged (which might explain what happened to the other file that was corrupted).

I'd recommend installing a fresh copy of OSX, via your Recovery HD. See Using the Recovery HD if you're not sure how to do that.

You're throwing kernel errors that point to corruption of the hidden directory that stores previous versions of files under the versioning system built into OS X. On occasion those errors may be spurious and are actually caused by "anti-virus" software, such as ESET. Have you installed anything like that? Do you have any saved versions in the Numbers application?

The file in question is in your Versions database (in red) -- it's supposed to be excluded automatically, since Time Machine cannot back it up!

Not in my copies, and I haven't changed them.

Aha! You're right -- I didn't realize that's changed in Mountain Lion (it's excluded on Lion).

But Time Machine does seem to be stumbling over whatever's wrong with it.

Bolobo: sorry about the error. 😟

I've seen this issue resolved by deleting the Versions database, and also by uninstalling ESET without deleting the database. I don't see any ESET activity in the OP's log extract, but that's not conclusive.

Since it's clearly damaged somehow, deleting it may be prudent.

Bolobo: if you don't have ESET, or can't or don't want to delete it, I see three options:

Excluding it from Time Machine manually would allow everything else to get backed-up. You'll have to check the Show invisible items box on the exclusions page to see the .DocumentRevisions-V101 folder.

If you don't have a lot of files you edit with apps that support AutoSave and Versions (TextEdit, Preview, Numbers and Pages are the common ones, but some 3rd-party apps do, too), deleting the entire database might be a good idea.

If you'd rather not do that, you might want to delete all previous versions of files made via Numbers (we can't tell which file is involved here, or whether there may be problems on other parts of the database). To do that, open each file, click the file name in the title bar and select Browse All Versions... to get to the Versions Browser. Then Option-click the title bar on the right side and select Delete Old Versions.