On a fresh system, I can not install GenomicRanges, because biocLite tries do download 1.28.1 while 1.28.2 is the one available.

> BiocInstaller::biocLite("GenomicRanges")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘GenomicRanges’
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz': HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘GenomicRanges’ failed

$ wget https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz
--2017-05-17 10:33:45--  https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz
Resolving bioconductor.org (bioconductor.org)... 52.222.205.48, 52.222.205.68, 52.222.205.109, ...
Connecting to bioconductor.org (bioconductor.org)|52.222.205.48|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2017-05-17 10:33:45 ERROR 404: Not Found.

$ wget https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.2.tar.gz
--2017-05-17 10:33:50--  https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.2.tar.gz
Resolving bioconductor.org (bioconductor.org)... 52.222.205.162, 52.222.205.41, 52.222.205.52, ...
Connecting to bioconductor.org (bioconductor.org)|52.222.205.162|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1010076 (986K) [application/x-gzip]
Saving to: ‘GenomicRanges_1.28.2.tar.gz’

GenomicRanges_1.28.2.tar.gz     100%[=====================================================>] 986.40K   883KB/s    in 1.1s    

2017-05-17 10:33:52 (883 KB/s) - ‘GenomicRanges_1.28.2.tar.gz’ saved [1010076/1010076]

The problem is that R uses a 'cache' to remember packages that are available for installation, and your cache is stale -- try installing the package from a new session (start R, preferably from the command line and with the --vanilla option), rather than from a long-running session.

But you say 'fresh system', and maybe you are already doing that?