When installing VariantAnnotation from source in windows, I get the following error:

Makevars.win:4: C:/Users/Simon: No such file or directory
Makevars.win:4: Coetzee/Documents/R/win-library/3.4/Rsamtools/usretc/i386/Rsamtools.mk: No such file or directory

It seems to have an issue with spaces in the path names, if I modify the Makevars.win to point to the path thusly:

C:/Users/Simon\ Coetzee/Documents/R/win-library/3.4/Rsamtools/usretc/x64/Rsamtools.mk

note the backslash between my names, All is compiled fine. I don't know how to make

system.file()

or

file.path()

produce the escape sequence to make this a universal solution.

Thanks; on windows I think the output of system.file() can be passed to shortPathName(). I'll update VariantAnnotation (and the instructions in Rsamtools).