Rather than creating and maintaining one or more public AMIs that have RStudio Server, BioC, dada2, phyloseq installed, it might make more sense to simply post a MRE of the install code for building one. I didn't see a fix on that thread that would solve this problem from within an AMI even if we made one, because users would need to know to use that modified command to address that particular error (again, which I haven't yet encountered on AWS-builds). It sounds like the error to which you're referring is not at installation, but upon calling a particular multithreaded IO function from ShortRead package. The standard BioC installation worked fine for dada2, as did a devtools::install_local() command before the dada2 release on BioC. I don't remember the exact Linux distro I was using, but it was Ubuntu and vanilla Bioconductor installed.
The OpenMP error on the linked post is something I have never encountered. I have had a lot of experience using/building on AWS, and dada2 did not give me any unusual problems.
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