How to update ConfigMgr 2012 R2 to SP1

***Edit: So it turns out that I really didn't need the SC2012_R2_SP1_Configmgr.exe package because that is only needed if you are upgrading from 2012 SP1, not if you are already at R2.  Just ignore those parts below.  Everything else looks like it worked correctly.

If you are currently at ConfigMgr 2012 R2, all you need is the SC2012_SP2_Configmgr_SCEP.exe file to update.  If you are at ConfigMgr 2012 SP1, you will first run the SC2012_SP2_Configmgr_SCEP.exe file and then run the SC2012_R2_SP1_Configmgr.exe file to enable the R2 features.***

How I updated my ConfigMgr 2012 R2 lab to SP1:

Here are some helpful links on Planning for the update and what's new.
https://technet.microsoft.com/en-us/library/464a3ce6-3bbf-45d8-aeaa-0040f64214c5#BKMK_UpgradeVersions
https://technet.microsoft.com/library/mt131422.aspx

System Center Configuration Manager 2012 R2 Service Pack 1 comes with Configuration Manager 2012 Service Pack 2.

SC2012_R2_SP1_Configmgr.exe

SC2012_SP2_Configmgr_SCEP.exe

When you extract these to their default locations, which is a folder on the C: drive with the same name as the file, you will need at least 1.2GBs free just for the files.

If you try to run the C:\SC2012_R2_SP1_Configmgr\SMSSETUP\X64\Configmgr2012R2SP1.msi, you get an error saying "You must have local Administrator permissions to install this software."

It seems a little odd, but to install R2 SP1, you have to run the installer for non-R2 SP2, which is the second file that you downloaded.  Open C:\SC2012_SP2_Configmgr_SCEP\SMSSETUP\BIN\X64 and run Setup.exe.  The setup will create multiple logfiles in the root of the C: drive.  The main log will be C:\ConfigMgrSetup.lo_ and ConfigMgrSetup.log.  At the bottom of the installer will be a button for View Log.  If you have CMTrace installed on your server, (why would you not have it?) you can watch the log as everything happens.

At the beginning of the installer it asks to download the latest update files or use an existing set.  I tried to point it to the SP1 folder as an existing set, but it didn't like that.  So I used the option to download files to a new location and picked a new, empty folder.

Two of the first couple of lines tell me that the installer was at least looking toward the SP1 folder. And no, there was no manifest file there but there is one in the new folder where I had the latest updates go to.  So I wonder if I was supposed to tell the installer to download the latest files to the SP1 folder.  Too late now because an uninstall of SP1 is not supported.  I will have to try that in another environment.

INFO: Downloading files to C:\SC2012_R2_SP1_Configmgr

ERROR: Manifest file C:\SC2012_R2_SP1_Configmgr\ConfigMgr.Manifest.cab not found. Verification failed.

My test lab is small with a database about 5.0GB.  The database update part took the longest by far, about 40 minutes.  The total update took about 58 minutes and was very easy and smooth.  Once it was all done I quickly scanned through the logfile to see if there were any errors to be concerned with.  I didn't see anything too concerning but I did see the following warning that you should know about.

WARN: Setup does not upgrade customized boot image package. Please update it manually.

Configuration Manager Client Package gets automatically updated.

Open the Configuration Manger console and in the About you can see the new Console and Site version numbers, which matches the Full Version and Full UI Version in the registry at HKLM\Software\Microsoft\SMS.  5.0.8239.1000

The new Client installer version in the \\ConfigMgrSrv\SMS_Site\Client folder says version 5.0.8239.1001.

But the Client on the endpoint machines show the same as the new server version, 5.0.8239.1000.

So it looks like my update was successful.  Happy installing!