Rsamtools fails to install if a message is printed from .Rprofile. (I had print("JDEnvironment loaded") in my .Rprofile)
Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.3 (2020-10-10) Installing package(s) 'Rsamtools' trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Rsamtools_2.6.0.tar.gz' Content type 'application/x-gzip' length 2906572 bytes (2.8 MB) ================================================== downloaded 2.8 MB  "JDEnvironment loaded" * installing *source* package ‘Rsamtools’ ... ** using staged installation ** libs gcc -std=c99 -I"/usr/local/Cluster-Apps/R/R.4.0.3/include" -DNDEBUG  "JDEnvironment loaded" -D_FILE_OFFSET_BITS=64 -[...] gcc: error: : No such file or directory
Obviously, this message is passed on to gcc as debug message without correct quotation. Installation works fine after removing this message.
Perhaps it is bad practice to print from .Rprofile; however, I have yet not encountered another package having difficulties being installed with this.