md5sum issues

Dear useRs,

I have some kind of a weird issue with md5sum() and I'm not sure where
I 
should start.

I have a repository on GitHub, with a local Git installation and 
connected with RStudio.
I am working on Windows 10 and a colleague of mine works on Linux.
We both pull the latest commits of all files, but the checksums are 
different.
Even stranger (to me at least), I get a different checksum from the 
local file (downloaded through Git via pulling) and the same file that
I 
manually download from GitHub. The checksum of the manual download from

GitHub is the same as that of my colleague on Linux.
This happens to all text-based files (Rmd, MD, CSV...) but not to 
non-editable files (PDF, XLSX...).

For example (I have shortened the paths):

library(tools)

md5sum(file.choose()) # local repo

D:\\...\\SSFAcomparisonPaper\\README.md
"e3b08fc2ab8b3c8b57e681f862a77f32"

md5sum(file.choose()) # downloaded from GitHub

C:\\Users\\...\\Downloads\\README.md
"05fab51e18b962a9f3266c7b79016ce6"

md5sum(file.choose()) # local repo

D:\\...\\SSFAcomparisonPaper\\...\\SSFA_GuineaPigs_plot.pdf
"d9b331642bfd0d192e4eff5808b2a30f"

md5sum(file.choose()) # downloaded from GitHub

C:\\Users\\...\\Downloads\\SSFA_GuineaPigs_plot.pdf
"d9b331642bfd0d192e4eff5808b2a30f"

I am not sure whether it is an issue with the algorithm of md5sum(), 
whether it's a R/RStudio/Git/GitHub/Windows issue, so I would be 
grateful if you could help me sorting it out.

Thank you in advance,
Ivan