Persistence when running update.packages in R - r

Question

If I open up an R console and send the command
update.packages(repos = "https://cran.cnr.Berkeley.edu/",ask=FALSE,checkBuilt=TRUE)`
It starts updating a small collection of packages, a somewhat representative output might include
Warning: package 'mgcv' in library 'C:/Program Files/R/R-3.4.2/library' will not be updated
There is a binary version available but the source version is later:
binary source needs_compilation
rlang 0.1.2 0.1.4 TRUE
Binaries will be installed
trying URL 'https://cran.cnr.Berkeley.edu/bin/windows/contrib/3.4/rlang_0.1.2.zip'
Content type 'application/zip' length 466520 bytes (455 KB)
downloaded 455 KB
package 'rlang' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\me\AppData\Local\Temp\RtmpYFaFCR\downloaded_packages
update.packages(repos = "https://cran.cnr.Berkeley.edu/",ask=FALSE,checkBuilt=TRUE)
Warning: package 'mgcv' in library 'C:/Program Files/R/R-3.4.2/library' will not be updated
There is a binary version available but the source version is later:
binary source needs_compilation
rlang 0.1.2 0.1.4 TRUE
Binaries will be installed
trying URL 'https://cran.cnr.Berkeley.edu/bin/windows/contrib/3.4/rlang_0.1.2.zip'
Content type 'application/zip' length 466520 bytes (455 KB)
downloaded 455 KB
package 'rlang' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\me\AppData\Local\Temp\RtmpYFaFCR\downloaded_packages
Unfortunately, if I turn around and run this again, I get the same report. This strikes me as not quite right, as these packages (with the exception of the ones explicitly tagged as "Will not be updated") should have been updated. Why are they still out of date?
The example above is small because I'm starting from a relatively new install, but as the months go by, this list will get longer and longer and it bogs down my script.
Hopefully this will be easily reproducible.