Hi Olivia,
Our team recently made a patch fix 2-3 weeks ago that removed the dependency on log4r. I'm not sure why you're still not able to install MSstats though.
Given the fix was in the MSstatsConvert package (which MSstats depends on), could you try installing MSstatsConvert first with Bioconductor and confirm the version number is 1.22.1? And then install MSstats afterwards.
Let me know if you run into any issues.
Thanks,
Tony