Security Update 2016-007 (Yosemite) and 2016-003 Supplemental (El Capitan)
On 13 December 2016, Apple released Security Update 2016-007 for OS X 10.10 Yosemite and Security Update 2016-003 for 10.11 El Capitan with patches for a number of vulnerabilities, including one that could allow an application to execute arbitrary code with kernel privileges and another that could enable a local user to cause a system denial of service.
On 17 January 2017, Apple pushed out a new version of Security Update 2016-003 to address a kernel issue that could cause a Mac running El Capitan to freeze and become unresponsive. If you applied Security Update 2016-003 before 17 January 2017, Security Update 2016-003 Supplemental will appear in Software Update. Be sure to make a backup before installing any of these updates in case of problems! (Free. For 10.10.5 Yosemite, 498.1 MB; for 10.11.6 El Capitan, 717 MB (623.9 MB for Supplemental); release notes)
The El Capitan update froze with a minute to go on my iMac. First time this has ever happened to me. Fortunately restarting worked ok.
Downloaded the security upgrade for El Capitan, the OS I'm running on my relatively new iMac. Received an error message which said it could not be installed on the "Macintosh HD" which is the internal disk for my iMac.
My El Capitan version installed with no problems. I had experienced the freezing problem; I hope the update will solve it.
Be careful adding this update to an El Capitan system without a backup. This update erased my application or rendered them unable to run (Spotlight reported each app, including Carbon Copy, as corrupt).
I was able to reboot from a Carbon Copy external drive and restore to an earlier backup. Once that completed, all applications run normally and the long freezes (even after the update) appear to be gone.
A little bird told me to do a Time Machine backup before applying the El Cap supplemental update. So I was able to restore from that when I ended up with an unstable system: Energy Saver preference pane would not open, Finder froze unpredictably, m/c failed to wake from sleep.
Perhaps I'll wait another day or two before trying again, in case Apple releases a supplement to the supplement.
Time Machine is now unusable in El Cap. It needs more than twice the space on the target drive than the system that I'm trying to back-up. It has been getting slower and slower even on a Firewire drive! How do I get back to Yosemite?
Have you considered getting a new disk and starting a TM backup from scratch? Might help.
Here's an idea. Get one quite large disk (~5 times the size of what you're trying to back up). Set aside one partition for a bootable clone, set up one other partition for TM backups. Use DiskUtility (no need for costly and/or buggy 3rd party 'solutions') to clone your Mac's main volume to the clone partition. Then use TM to back up to the other partition. That gives you a) a bootable clone you can resort to at any time and b) a backup with versioning.
In the event of catastrophe you can boot from the clone and restore your partition by copying back from the clone, or use the macOS installer to re-install and copy back from your TM backup history. You can actually even do both (as long as you do them in that order) in order to get back to exactly what you had when your last TM backup completed.
I've re-formatted my 500GB internal drive that was working fine as my main back-up drive but is now useless as it's too small!!
I have two Seagate external drives a 1TB for phots and a 4TB(1TB for photos and 3 for Time Machine) however their power supplies are blowing up and I'm on my last one:(
So I'm going to buy a Toshiba 4TB and use it as you suggest, thanks.
Wish Seagate would resurrect their excellent Customer Service where they replaced the blown power supply but they've gone the way of most CS and are useless!
I had some trouble with external disks too.
At some point I simply gave up on buying complete units. Instead I bought an external dock (USB3) and from then on just kept buying regular 3.5" HDDs intended for installation in desktops. If a HDD dies (sometimes that does happen after a few years) I just throw it out and buy a new disk, plop it into the dock, and presto. The docks (I have three different ones at my various work places) have never died on me so far. The solution is inexpensive and reliable. Plus, since it's modular, even when something does fail you usually recover quickly and without much hassle.
I'm not aware of any real changes in Time Machine between Yosemite and El Capitan, or even Sierra. It's not perfect, but starting a new backup would likely fix your issues. Simon's suggestion above for a bootable duplicate plus a Time Machine backup on a new big disk is a good one.